Changeset 6280

trunk/ARBDB/ad_prot.h

r6270	r6280
239	239	long GB_read_usr_private P_((GBDATA *gbd));
240	240	GB_ERROR GB_write_usr_private P_((GBDATA *gbd, long ref));
241		~~GB_ERROR~~ GB_write_flag P_((GBDATA *gbd, long flag));
	241	void GB_write_flag P_((GBDATA *gbd, long flag));
242	242	int GB_read_flag P_((GBDATA *gbd));
243	243	void GB_touch P_((GBDATA *gbd));

trunk/ARBDB/aditem.c

r6100	r6280
38	38	else {
39	39	error = GBT_write_string(gb_item, id_field, id); // write item identifier
40		if (!error && markCreated) ~~error =~~ GB_write_flag(gb_item, 1); // mark generated item
	40	if (!error && markCreated) GB_write_flag(gb_item, 1); // mark generated item
41	41	}
42	42	}
…	…
294	294	mark and unmark species
295	295	********************************************************************************************/
296		void GBT_mark_all(GBDATA *gb_main, int flag)
297		{
	296	void GBT_mark_all(GBDATA *gb_main, int flag) {
	297	// flag == 0 -> unmark
	298	// flag == 1 -> mark
	299	// flag == 2 -> invert
	300
298	301	GBDATA *gb_species;
299	302	GB_push_transaction(gb_main);

trunk/ARBDB/adseqcompr.c

r6197	r6280
18	18
19	19	typedef struct gb_seq_compr_tree {
20		#ifdef FAKE_VTAB_PTR
21		virtualTable dummy_virtual; / simulate pointer to virtual-table used in AP_tree */
22		#endif
23		GBT_TREE_ELEMENTS(struct gb_seq_compr_tree);
	20	GBT_VTAB_AND_TREE_ELEMENTS(struct gb_seq_compr_tree);
24	21
25	22	int index; /* master(inner nodes) or sequence(leaf nodes) index */

trunk/ARBDB/arbdb.c

r6262	r6280
2489	2489	********************************************************************************************/
2490	2490
2491		~~GB_ERROR~~ GB_write_flag(GBDATA *gbd,long flag)
	2491	void GB_write_flag(GBDATA *gbd,long flag)
2492	2492	{
2493	2493	GBCONTAINER gbc = (GBCONTAINER )gbd;
…	…
2510	2510	GB_DO_CALLBACKS(gbd);
2511	2511	}
2512		~~return 0;~~
2513	2512	}
2514	2513

trunk/ARBDB/arbdbt.h

r6127	r6280
45	45	#ifdef FAKE_VTAB_PTR
46	46	/* if defined, FAKE_VTAB_PTR contains 'char' */
47		typedef FAKE_VTAB_PTR virtualTable;
	47	typedef FAKE_VTAB_PTR virtualTable;
	48	#define GBT_VTAB_AND_TREE_ELEMENTS(type) \
	49	virtualTable *dummy_virtual; \
	50	GBT_TREE_ELEMENTS(type)
	51	#else
	52	#define GBT_VTAB_AND_TREE_ELEMENTS(type) GBT_TREE_ELEMENTS(type)
48	53	#endif
49	54
50	55	typedef struct gbt_tree_struct {
51		#ifdef FAKE_VTAB_PTR
52		virtualTable dummy_virtual; / simulate pointer to virtual-table used in AP_tree */
53		#endif
54		GBT_TREE_ELEMENTS(struct gbt_tree_struct);
	56	GBT_VTAB_AND_TREE_ELEMENTS(struct gbt_tree_struct);
55	57	} GBT_TREE;
56	58

trunk/ARB_GDE/GDE.cxx

r6069	r6280
1		~~#include <cstdio>~~
2		~~#include <cstdlib>~~
3		~~#include <cstring>~~
4		~~#include <cmath>~~
5
6		~~#include <arbdb.h>~~
7		~~#include <arbdbt.h>~~
8		~~// #include <malloc.h>~~
9		~~#include <aw_root.hxx>~~
10		~~#include <aw_device.hxx>~~
11		~~#include <aw_window.hxx>~~
12		~~#include <awt.hxx>~~
13		~~#include <awt_sel_boxes.hxx>~~
14
15		~~#include "gde.hxx"~~
16		~~#include "GDE_menu.h"~~
17		~~#include "GDE_def.h"~~
18	1	#include "GDE_extglob.h"
19	2	#include "GDE_awars.h"
	3
	4	#include <awt_sel_boxes.hxx>
	5	#include <awt_filter.hxx>
	6	#include <aw_window.hxx>
	7
	8	/AISC_MKPT_PROMOTE:#ifndef GDE_MENU_H/
	9	/AISC_MKPT_PROMOTE:#include "GDE_menu.h"/
	10	/AISC_MKPT_PROMOTE:#endif/
20	11
21	12	adfiltercbstruct *agde_filtercd = 0;

trunk/ARB_GDE/GDE_FileIO.cxx

r5901	r6280
1		#include <stdio.h>
2		#include <stdlib.h>
3		// #include <malloc.h>
4		#include <string.h>
5
6		#include <arbdb.h>
7		#include <arbdbt.h>
8		#include <aw_root.hxx>
9		#include <aw_device.hxx>
10		#include <aw_window.hxx>
11		#include <awt.hxx>
12
13		#include "gde.hxx"
14		#include "GDE_def.h"
15		#include "GDE_menu.h"
16		#include "GDE_extglob.h"
	1	#include "GDE_proto.h"
17	2
18	3	int MAX(int a,int b)

trunk/ARB_GDE/GDE_Genbank.cxx

r5695	r6280
1		#include <sys/time.h>
2		#include <stdio.h>
3		// #include <malloc.h>
4		#include <string.h>
	1	#include "GDE_extglob.h"
5	2	#include <time.h>
6
7		~~//#include <xview/xview.h>~~
8		~~//#include <xview/panel.h>~~
9
10		~~#include <arbdb.h>~~
11		~~#include <aw_root.hxx>~~
12		~~#include <aw_device.hxx>~~
13		~~#include <aw_window.hxx>~~
14		~~#include <awt.hxx>~~
15
16		~~#include "gde.hxx"~~
17		~~#include "GDE_menu.h"~~
18		~~#include "GDE_def.h"~~
19		~~#include "GDE_extglob.h"~~
20	3
21	4	/*

trunk/ARB_GDE/GDE_HGLfile.cxx

r5695	r6280
1		#include <sys/time.h>
2		#include <stdio.h>
3		#include <stdlib.h>
4		// #include <malloc.h>
5		#include <string.h>
	1	#include "GDE_extglob.h"
6	2	#include <time.h>
7
8		~~//#include <xview/xview.h>~~
9		~~//#include <xview/panel.h>~~
10
11		~~#include <arbdb.h>~~
12		~~#include <aw_root.hxx>~~
13		~~#include <aw_device.hxx>~~
14		~~#include <aw_window.hxx>~~
15		~~#include <awt.hxx>~~
16
17		~~#include "gde.hxx"~~
18		~~#include "GDE_menu.h"~~
19		~~#include "GDE_def.h"~~
20		~~#include "GDE_extglob.h"~~
21	3
22	4	/*

trunk/ARB_GDE/GDE_ParseMenu.cxx

r6141	r6280
1		#include <stdio.h>
2		#include <stdlib.h>
3		#include <string.h>
4		// #include <malloc.h>
	1	#include "GDE_extglob.h"
5	2	#include <ctype.h>
6		~~#include <assert.h>~~
7
8		~~#include <arbdb.h>~~
9		~~#include <aw_root.hxx>~~
10		~~#include <aw_device.hxx>~~
11		~~#include <aw_window.hxx>~~
12		~~#include <awt.hxx>~~
13
14		~~#include "gde.hxx"~~
15		~~#include "GDE_menu.h"~~
16		~~#include "GDE_def.h"~~
17		~~#include "GDE_global.h"~~
18		~~#include "GDE_extglob.h"~~
19	3
20	4	static int getline(FILE file,char string)
…	…
468	452	}
469	453
470		assert(num_menus>0); // if this fails, the file ARB_GDEmenus contained no menus (maybe file has zero size)
	454	gde_assert(num_menus>0); // if this fails, the file ARB_GDEmenus contained no menus (maybe file has zero size)
471	455
472	456	return;

trunk/ARB_GDE/GDE_arbdb_io.cxx

r6141	r6280
1		#include <stdio.h>
2		#include <stdlib.h>
3		#include <string.h>
4		#include <memory.h>
5
6		#include <arbdb.h>
7		#include <arbdbt.h>
8		#include <aw_root.hxx>
9		#include <aw_device.hxx>
10		#include <aw_window.hxx>
11		#include <awt.hxx>
	1	#include "GDE_def.h"
	2	#include "GDE_proto.h"
	3
	4	#include <AW_rename.hxx>
	5	#include <AP_filter.hxx>
12	6	#include <aw_awars.hxx>
13		#include <awt_tree.hxx>
14
15		#include "gde.hxx"
16		#include "GDE_def.h"
17		#include "GDE_menu.h"
18		#include "GDE_extglob.h"
19		#include "AW_rename.hxx"
	7
	8	/AISC_MKPT_PROMOTE:#ifndef GDE_EXTGLOB_H/
	9	/AISC_MKPT_PROMOTE:#include "GDE_extglob.h"/
	10	/AISC_MKPT_PROMOTE:#endif/
20	11
21	12	typedef unsigned int UINT;
…	…
41	32	static int InsertDatainGDE(NA_Alignment dataset,GBDATA the_species,unsigned char *the_names,
42	33	unsigned char **the_sequences, unsigned long numberspecies,
43		unsigned long maxalignlen, AP_filter *filter, GapCompression compress,
	34	unsigned long maxalignlen, const AP_filter *filter, GapCompression compress,
44	35	bool cutoff_stop_codon)
45	36	{
…	…
47	38	GBDATA *gb_species;
48	39	GBDATA *gbd;
49		~~int newfiltercreated = 0;~~
50	40	NA_Sequence *this_elem;
	41	AP_filter *allocatedFilter = 0;
51	42
52	43	gde_assert((the_species==0) != (the_names==0));
53	44
54	45	if (filter==0) {
55		filter = new AP_filter;
56		filter->init(maxalignlen);
57		newfiltercreated=1;
	46	allocatedFilter = new AP_filter(maxalignlen);
	47	filter = allocatedFilter;
58	48	}
59	49	else {
60		size_t fl = filter->~~filter_len~~;
	50	size_t fl = filter->get_length();
61	51	if (fl < maxalignlen) {
62	52	aw_message("Warning: Your filter is shorter than the alignment len");
…	…
91	81
92	82	if (compress==COMPRESS_ALL) { // compress all gaps and filter positions
93		long len = filter->~~real_len~~;
	83	long len = filter->get_filtered_length();
94	84	unsigned long i;
95	85
…	…
100	90	char c = the_sequences[i][col];
101	91	if (!c) break;
102		if ((filter->~~filter_mask[col]~~) && (c!='-') && (c!='.')) {
	92	if ((filter->use_position(col)) && (c!='-') && (c!='.')) {
103	93	sequfilt[i][newcount++] = c;
104	94	}
…	…
134	124	}
135	125
	126	bool modified = false;
	127	char *filterString = filter->to_string();
	128
136	129	for (i=0; i<maxalignlen; i++) {
137		if (filter->~~filter_mask[i]~~) {
	130	if (filter->use_position(i)) {
138	131	bool wantColumn = false;
139	132
…	…
147	140	}
148	141	if (!wantColumn) {
149		filter~~->filter_mask[i] = 0~~;
150		~~filter->real_len--~~;
	142	filterString[i] = '0';
	143	modified = true;
151	144	}
152	145	}
153	146	}
154		}
155
156		long len = filter->real_len;
	147
	148	if (modified) {
	149	size_t len = filter->get_length();
	150
	151	delete allocatedFilter;
	152	filter = allocatedFilter = new AP_filter(filterString, NULL, len);
	153	}
	154
	155	free(filterString);
	156	}
	157
	158	long len = filter->get_filtered_length();
157	159	size_t i;
158	160
…	…
165	167	memset(sequfilt[i],'.',len); // Generate empty sequences
166	168
167		~~size_t col~~;
168		for (col=0; (col<maxalignlen) && (c=the_sequences[i][col]); col++) {
169		if (filter->~~filter_mask[col]~~) {
170		sequfilt[i][newcount++] = ~~filter->~~simplify[c];
	169	const uchar *simplify = filter->get_simplify_table();
	170	for (size_t col=0; (col<maxalignlen) && (c=the_sequences[i][col]); col++) {
	171	if (filter->use_position(col)) {
	172	sequfilt[i][newcount++] = simplify[c];
171	173	}
172	174	}
…	…
303	305	free(sequfilt);
304	306	}
305		~~if (newfiltercreated) delete f~~ilter;
	307	delete allocatedFilter;
306	308	return 0;
307	309	}

trunk/ARB_GDE/GDE_def.h

r5078	r6280
	1	#ifndef GDE_DEF_H
	2	#define GDE_DEF_H
	3
	4	#ifndef ARBDBT_H
	5	#include <arbdbt.h>
	6	#endif
	7
1	8	/*
2	9
…	…
236	243	extern NA_Alignment *DataSet;
237	244
238
239	245	#define getcmask(a,b) (b < ((a)->offset))?0:((a)->cmask[(b-(a)->offset)])
240	246
	247	#else
	248	#error GDE_def.h included twice
	249	#endif // GDE_DEF_H

trunk/ARB_GDE/GDE_event.cxx

r6141	r6280
1		~~#include <unistd.h>~~
2		~~#include <netdb.h>~~
3		~~#include <sys/time.h>~~
4		~~#include <sys/types.h>~~
5		~~#include <sys/stat.h>~~
6		~~#include <stdio.h>~~
7		~~#include <stdlib.h>~~
8		~~#include <string.h>~~
9		~~//#include <xview/xview.h>~~
10		~~//#include <xview/panel.h>~~
11		~~#include <arbdb.h>~~
12		~~#include <arbdbt.h>~~
13		~~// #include <malloc.h>~~
14		~~#include <aw_root.hxx>~~
15		~~#include <aw_device.hxx>~~
16		~~#include <aw_window.hxx>~~
17		~~#include <awt.hxx>~~
18		~~#include <awt_tree.hxx>~~
19		~~#include <awt_sel_boxes.hxx>~~
20		~~#include <gde.hxx>~~
21		~~#include "GDE_menu.h"~~
22		~~#include "GDE_def.h"~~
23	1	#include "GDE_extglob.h"
24	2	#include "GDE_awars.h"
25	3
	4	#include <awt_filter.hxx>
	5	#include <aw_window.hxx>
	6	#include <AP_filter.hxx>
	7
	8	#include <set>
26	9	#include <string>
27		~~#include <set>~~
28	10
29	11	using namespace std;

trunk/ARB_GDE/GDE_menu.h

r6141	r6280
	1	// =============================================================== //
	2	// //
	3	// File : GDE_menu.h //
	4	// Purpose : //
	5	// //
	6	// =============================================================== //
	7
	8	#ifndef GDE_MENU_H
	9	#define GDE_MENU_H
	10
	11	#ifndef GDE_HXX
	12	#include "gde.hxx"
	13	#endif
	14	#ifndef GDE_DEF_H
	15	#include "GDE_def.h"
	16	#endif
1	17
2	18	#ifndef ARB_ASSERT_H
3	19	#include <arb_assert.h>
4	20	#endif
	21
5	22	#define gde_assert(bed) arb_assert(bed)
6	23
…	…
43	60	} GfileFormat;
44	61
	62	class AW_window;
	63
45	64	typedef struct GmenuItemtype
46	65	{
…	…
73	92	} Gmenu;
74	93
75		// typedef unsigned char uchar;
	94	typedef unsigned char uchar;
76	95
77	96	extern struct choose_get_sequence_struct {
…	…
81	100	} gde_cgss;
82	101
	102
	103	#else
	104	#error GDE_menu.h included twice
	105	#endif // GDE_MENU_H

trunk/ARB_GDE/GDE_proto.h

r5968	r6280
14	14
15	15
16		/* GDE_ParseMenu.cxx */
17		void ParseMenu(void);
18		int Find(const char target, const char key);
19		int Find2(const char target, const char key);
20		void Error(const char *msg) __ATTR__NORETURN;
21		void crop(char input, char head, char *tail);
	16	/* GDE.cxx */
22	17
23		/* GDE.cxx */
	18	#ifndef GDE_MENU_H
	19	#include "GDE_menu.h"
	20	#endif
	21
24	22	char GDE_makeawarname(GmenuItem gmenuitem, long i);
25	23	void GDE_load_menu(AW_window awm, AW_active mask, const char menulabel, const char *menuitemlabel);
26	24	void create_gde_var(AW_root aw_root, AW_default aw_def, char (get_sequences )(void THIS, GBDATA &the_species, uchar &the_names, uchar *&the_sequences, long &numberspecies, long &maxalignlen ), gde_cgss_window_type wt, void THIS);
27
28		~~/* GDE_event.cxx */~~
29		~~void GDE_startaction_cb(AW_window aw, GmenuItem gmenuitem, AW_CL cd);~~
30
31		~~/* GDE_arbdb_io.cxx */~~
32		~~void ReadArbdb_plain(char filename, NA_Alignment dataset, int type);~~
33		~~int ReadArbdb2(NA_Alignment dataset, AP_filter filter, GapCompression compress, bool cutoff_stop_codon);~~
34		~~int ReadArbdb(NA_Alignment dataset, bool marked, AP_filter filter, GapCompression compress, bool cutoff_stop_codon);~~
35		~~int getelem(NA_Sequence *a, int b);~~
36		~~void putelem(NA_Sequence *a, int b, NA_Base c);~~
37
38		~~/* GDE_HGLfile.cxx */~~
39		~~void ReadGDE(char filename, NA_Alignment dataset, int type);~~
40		~~int WriteGDE(NA_Alignment aln, char filename, int method, int maskable);~~
41		~~void SeqNorm(NA_Sequence *seq);~~
42		~~char *uniqueID(void);~~
43
44		~~/* GDE_Genbank.cxx */~~
45		~~void ReadGen(char filename, NA_Alignment dataset, int type);~~
46		~~int WriteGen(NA_Alignment aln, char filename, int method, int maskable);~~
47		~~void SetTime(void *b);~~
48	25
49	26	/* GDE_FileIO.cxx */
…	…
67	44	int WriteCMask(NA_Alignment aln, char filename, int method, int maskable);
68	45
	46	/* GDE_Genbank.cxx */
	47	void ReadGen(char filename, NA_Alignment dataset, int type);
	48	int WriteGen(NA_Alignment aln, char filename, int method, int maskable);
	49	void SetTime(void *b);
	50
	51	/* GDE_HGLfile.cxx */
	52	void ReadGDE(char filename, NA_Alignment dataset, int type);
	53	int WriteGDE(NA_Alignment aln, char filename, int method, int maskable);
	54	void SeqNorm(NA_Sequence *seq);
	55	char *uniqueID(void);
	56
	57	/* GDE_ParseMenu.cxx */
	58	void ParseMenu(void);
	59	int Find(const char target, const char key);
	60	int Find2(const char target, const char key);
	61	void Error(const char *msg) __ATTR__NORETURN;
	62	void crop(char input, char head, char *tail);
	63
	64	/* GDE_arbdb_io.cxx */
	65
	66	#ifndef GDE_EXTGLOB_H
	67	#include "GDE_extglob.h"
	68	#endif
	69
	70	void ReadArbdb_plain(char filename, NA_Alignment dataset, int type);
	71	int ReadArbdb2(NA_Alignment dataset, AP_filter filter, GapCompression compress, bool cutoff_stop_codon);
	72	int ReadArbdb(NA_Alignment dataset, bool marked, AP_filter filter, GapCompression compress, bool cutoff_stop_codon);
	73	int getelem(NA_Sequence *a, int b);
	74	void putelem(NA_Sequence *a, int b, NA_Base c);
	75
	76	/* GDE_event.cxx */
	77	void GDE_startaction_cb(AW_window aw, GmenuItem gmenuitem, AW_CL cd);
	78
69	79	#else
70	80	#error GDE_proto.h included twice

trunk/ARB_GDE/Makefile

r6277	r6280
2	2	.SUFFIXES: .o .cxx .depend
3	3
4		CPP_OBJECTS = GDE_ParseMenu.o GDE.o GDE_event.o \
5		GDE_arbdb_io.o GDE_HGLfile.o\
6		GDE_Genbank.o GDE_FileIO.o
	4	CPP_OBJECTS = \
	5	GDE.o \
	6	GDE_FileIO.o \
	7	GDE_Genbank.o \
	8	GDE_HGLfile.o \
	9	GDE_ParseMenu.o \
	10	GDE_arbdb_io.o \
	11	GDE_event.o \
	12	GDE_global.o \
7	13
8	14	CPP_FILES=$(CPP_OBJECTS:.o=.cxx)
…	…
13	19	$(CPP) $(cflags) -c $< $(CPPINCLUDES)
14	20
15		~~proto: GDE_proto.h~~
16
17	21	GDE_proto.h: $(CPP_FILES) Makefile
18		../MAKEBIN/aisc_mkpt -G -A -E -w GDE_proto.h $(CPP_FILES) > GDE_proto.h.tmp
	22	$(MAKE) proto
	23
	24	proto:
	25	../MAKEBIN/aisc_mkpt -P -G -A -E -w GDE_proto.h $(CPP_FILES) > GDE_proto.h.tmp
19	26	../SOURCE_TOOLS/mv_if_diff GDE_proto.h.tmp GDE_proto.h
20	27
…	…
60	67	GDE.o: $(ARBHOME)/INCLUDE/aw_root.hxx
61	68	GDE.o: $(ARBHOME)/INCLUDE/aw_window.hxx
62		GDE.o: $(ARBHOME)/INCLUDE/awt.hxx
	69	GDE.o: $(ARBHOME)/INCLUDE/awt_filter.hxx
63	70	GDE.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx
64	71	GDE.o: $(ARBHOME)/INCLUDE/smartptr.h
…	…
72	79	GDE_arbdb_io.o: $(ARBHOME)/INCLUDE/ad_prot.h
73	80	GDE_arbdb_io.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
	81	GDE_arbdb_io.o: $(ARBHOME)/INCLUDE/AP_filter.hxx
74	82	GDE_arbdb_io.o: $(ARBHOME)/INCLUDE/arb_assert.h
75	83	GDE_arbdb_io.o: $(ARBHOME)/INCLUDE/arb_error.h
…	…
80	88	GDE_arbdb_io.o: $(ARBHOME)/INCLUDE/attributes.h
81	89	GDE_arbdb_io.o: $(ARBHOME)/INCLUDE/aw_awars.hxx
82		~~GDE_arbdb_io.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx~~
83		~~GDE_arbdb_io.o: $(ARBHOME)/INCLUDE/aw_device.hxx~~
84		~~GDE_arbdb_io.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx~~
85		~~GDE_arbdb_io.o: $(ARBHOME)/INCLUDE/aw_position.hxx~~
86	90	GDE_arbdb_io.o: $(ARBHOME)/INCLUDE/AW_rename.hxx
87	91	GDE_arbdb_io.o: $(ARBHOME)/INCLUDE/aw_root.hxx
88		~~GDE_arbdb_io.o: $(ARBHOME)/INCLUDE/aw_window.hxx~~
89		~~GDE_arbdb_io.o: $(ARBHOME)/INCLUDE/awt.hxx~~
90		~~GDE_arbdb_io.o: $(ARBHOME)/INCLUDE/awt_pro_a_nucs.hxx~~
91		~~GDE_arbdb_io.o: $(ARBHOME)/INCLUDE/awt_tree.hxx~~
92	92	GDE_arbdb_io.o: $(ARBHOME)/INCLUDE/smartptr.h
93	93
…	…
101	101	GDE_event.o: $(ARBHOME)/INCLUDE/ad_prot.h
102	102	GDE_event.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
	103	GDE_event.o: $(ARBHOME)/INCLUDE/AP_filter.hxx
103	104	GDE_event.o: $(ARBHOME)/INCLUDE/arb_assert.h
104	105	GDE_event.o: $(ARBHOME)/INCLUDE/arb_error.h
…	…
108	109	GDE_event.o: $(ARBHOME)/INCLUDE/arbtools.h
109	110	GDE_event.o: $(ARBHOME)/INCLUDE/attributes.h
110		~~GDE_event.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx~~
111	111	GDE_event.o: $(ARBHOME)/INCLUDE/aw_device.hxx
112	112	GDE_event.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
…	…
114	114	GDE_event.o: $(ARBHOME)/INCLUDE/aw_root.hxx
115	115	GDE_event.o: $(ARBHOME)/INCLUDE/aw_window.hxx
116		GDE_event.o: $(ARBHOME)/INCLUDE/awt.hxx
117		GDE_event.o: $(ARBHOME)/INCLUDE/awt_pro_a_nucs.hxx
118		GDE_event.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx
119		GDE_event.o: $(ARBHOME)/INCLUDE/awt_tree.hxx
	116	GDE_event.o: $(ARBHOME)/INCLUDE/awt_filter.hxx
120	117	GDE_event.o: $(ARBHOME)/INCLUDE/smartptr.h
121	118
…	…
135	132	GDE_FileIO.o: $(ARBHOME)/INCLUDE/arbtools.h
136	133	GDE_FileIO.o: $(ARBHOME)/INCLUDE/attributes.h
137		~~GDE_FileIO.o: $(ARBHOME)/INCLUDE/aw_device.hxx~~
138		~~GDE_FileIO.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx~~
139		~~GDE_FileIO.o: $(ARBHOME)/INCLUDE/aw_position.hxx~~
140	134	GDE_FileIO.o: $(ARBHOME)/INCLUDE/aw_root.hxx
141		~~GDE_FileIO.o: $(ARBHOME)/INCLUDE/aw_window.hxx~~
142		~~GDE_FileIO.o: $(ARBHOME)/INCLUDE/awt.hxx~~
143	135	GDE_FileIO.o: $(ARBHOME)/INCLUDE/smartptr.h
144	136
…	…
150	142	GDE_Genbank.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
151	143	GDE_Genbank.o: $(ARBHOME)/INCLUDE/ad_prot.h
	144	GDE_Genbank.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
152	145	GDE_Genbank.o: $(ARBHOME)/INCLUDE/arb_assert.h
153	146	GDE_Genbank.o: $(ARBHOME)/INCLUDE/arb_error.h
154	147	GDE_Genbank.o: $(ARBHOME)/INCLUDE/arbdb.h
155	148	GDE_Genbank.o: $(ARBHOME)/INCLUDE/arbdb_base.h
	149	GDE_Genbank.o: $(ARBHOME)/INCLUDE/arbdbt.h
156	150	GDE_Genbank.o: $(ARBHOME)/INCLUDE/arbtools.h
157	151	GDE_Genbank.o: $(ARBHOME)/INCLUDE/attributes.h
158		~~GDE_Genbank.o: $(ARBHOME)/INCLUDE/aw_device.hxx~~
159		~~GDE_Genbank.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx~~
160		~~GDE_Genbank.o: $(ARBHOME)/INCLUDE/aw_position.hxx~~
161	152	GDE_Genbank.o: $(ARBHOME)/INCLUDE/aw_root.hxx
162		~~GDE_Genbank.o: $(ARBHOME)/INCLUDE/aw_window.hxx~~
163		~~GDE_Genbank.o: $(ARBHOME)/INCLUDE/awt.hxx~~
164	153	GDE_Genbank.o: $(ARBHOME)/INCLUDE/smartptr.h
	154
	155	GDE_global.o: gde.hxx
	156	GDE_global.o: GDE_def.h
	157	GDE_global.o: GDE_extglob.h
	158	GDE_global.o: GDE_menu.h
	159	GDE_global.o: GDE_proto.h
	160	GDE_global.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
	161	GDE_global.o: $(ARBHOME)/INCLUDE/ad_prot.h
	162	GDE_global.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
	163	GDE_global.o: $(ARBHOME)/INCLUDE/arb_assert.h
	164	GDE_global.o: $(ARBHOME)/INCLUDE/arb_error.h
	165	GDE_global.o: $(ARBHOME)/INCLUDE/arbdb.h
	166	GDE_global.o: $(ARBHOME)/INCLUDE/arbdb_base.h
	167	GDE_global.o: $(ARBHOME)/INCLUDE/arbdbt.h
	168	GDE_global.o: $(ARBHOME)/INCLUDE/arbtools.h
	169	GDE_global.o: $(ARBHOME)/INCLUDE/attributes.h
	170	GDE_global.o: $(ARBHOME)/INCLUDE/aw_root.hxx
	171	GDE_global.o: $(ARBHOME)/INCLUDE/smartptr.h
165	172
166	173	GDE_HGLfile.o: gde.hxx
…	…
171	178	GDE_HGLfile.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
172	179	GDE_HGLfile.o: $(ARBHOME)/INCLUDE/ad_prot.h
	180	GDE_HGLfile.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
173	181	GDE_HGLfile.o: $(ARBHOME)/INCLUDE/arb_assert.h
174	182	GDE_HGLfile.o: $(ARBHOME)/INCLUDE/arb_error.h
175	183	GDE_HGLfile.o: $(ARBHOME)/INCLUDE/arbdb.h
176	184	GDE_HGLfile.o: $(ARBHOME)/INCLUDE/arbdb_base.h
	185	GDE_HGLfile.o: $(ARBHOME)/INCLUDE/arbdbt.h
177	186	GDE_HGLfile.o: $(ARBHOME)/INCLUDE/arbtools.h
178	187	GDE_HGLfile.o: $(ARBHOME)/INCLUDE/attributes.h
179		~~GDE_HGLfile.o: $(ARBHOME)/INCLUDE/aw_device.hxx~~
180		~~GDE_HGLfile.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx~~
181		~~GDE_HGLfile.o: $(ARBHOME)/INCLUDE/aw_position.hxx~~
182	188	GDE_HGLfile.o: $(ARBHOME)/INCLUDE/aw_root.hxx
183		~~GDE_HGLfile.o: $(ARBHOME)/INCLUDE/aw_window.hxx~~
184		~~GDE_HGLfile.o: $(ARBHOME)/INCLUDE/awt.hxx~~
185	189	GDE_HGLfile.o: $(ARBHOME)/INCLUDE/smartptr.h
186	190
…	…
188	192	GDE_ParseMenu.o: GDE_def.h
189	193	GDE_ParseMenu.o: GDE_extglob.h
190		~~GDE_ParseMenu.o: GDE_global.h~~
191	194	GDE_ParseMenu.o: GDE_menu.h
192	195	GDE_ParseMenu.o: GDE_proto.h
193	196	GDE_ParseMenu.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
194	197	GDE_ParseMenu.o: $(ARBHOME)/INCLUDE/ad_prot.h
	198	GDE_ParseMenu.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
195	199	GDE_ParseMenu.o: $(ARBHOME)/INCLUDE/arb_assert.h
196	200	GDE_ParseMenu.o: $(ARBHOME)/INCLUDE/arb_error.h
197	201	GDE_ParseMenu.o: $(ARBHOME)/INCLUDE/arbdb.h
198	202	GDE_ParseMenu.o: $(ARBHOME)/INCLUDE/arbdb_base.h
	203	GDE_ParseMenu.o: $(ARBHOME)/INCLUDE/arbdbt.h
199	204	GDE_ParseMenu.o: $(ARBHOME)/INCLUDE/arbtools.h
200	205	GDE_ParseMenu.o: $(ARBHOME)/INCLUDE/attributes.h
201		~~GDE_ParseMenu.o: $(ARBHOME)/INCLUDE/aw_device.hxx~~
202		~~GDE_ParseMenu.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx~~
203		~~GDE_ParseMenu.o: $(ARBHOME)/INCLUDE/aw_position.hxx~~
204	206	GDE_ParseMenu.o: $(ARBHOME)/INCLUDE/aw_root.hxx
205		~~GDE_ParseMenu.o: $(ARBHOME)/INCLUDE/aw_window.hxx~~
206		~~GDE_ParseMenu.o: $(ARBHOME)/INCLUDE/awt.hxx~~
207	207	GDE_ParseMenu.o: $(ARBHOME)/INCLUDE/smartptr.h

trunk/ARB_GDE/gde.hxx

r5834	r6280
11	11	#ifndef GDE_HXX
12	12	#define GDE_HXX
	13
	14	#ifndef AW_ROOT_HXX
	15	#include <aw_root.hxx>
	16	#endif
13	17
14	18	typedef unsigned char uchar;

trunk/AWT

Property svn:ignore

old	new
5	5	libAWT.so
6	6	Makefile.bak
	7	Makefile.old

trunk/AWT/AWT_db_browser.cxx

r6277	r6280
13	13
14	14	#include "awt.hxx"
15		#include "awt_tree.hxx"
	15
	16	#include <arbdbt.h>
16	17	#include <inline.h>
	18	#include <AP_Tree.hxx>
17	19
18	20	#include <string>

trunk/AWT/AWT_query_and_functions.cxx

r6187	r6280
1743	1743
1744	1744	// @@@ awt_mark_colored is obsolete! (will be replaced by dynamic coloring in the future)
1745		static void awt_mark_colored(AW_window *aww, AW_CL cl_cmd, AW_CL cl_mode)
1746		{
	1745	static void awt_mark_colored(AW_window *aww, AW_CL cl_cmd, AW_CL cl_mode) {
1747	1746	const color_mark_data cmd = (struct color_mark_data )cl_cmd;
1748	1747	const ad_item_selector *sel = cmd->sel;
1749	1748	int mode = int(cl_mode); // 0 = unmark 1 = mark 2 = invert
1750		~~GB_ERROR error = 0;~~
1751	1749	AW_root *aw_root = aww->get_root();
1752	1750	int color_group = aw_root->awar(AWAR_COLORIZE)->read_int();
…	…
1756	1754
1757	1755	for (GBDATA *gb_item_container = sel->get_first_item_container(cmd->gb_main, aw_root, range);
1758		~~!error &&~~ gb_item_container;
	1756	gb_item_container;
1759	1757	gb_item_container = sel->get_next_item_container(gb_item_container, range))
	1758	{
	1759	for (GBDATA *gb_item = sel->get_first_item(gb_item_container);
	1760	gb_item;
	1761	gb_item = sel->get_next_item(gb_item))
1760	1762	{
1761		for (GBDATA *gb_item = sel->get_first_item(gb_item_container);
1762		!error && gb_item;
1763		gb_item = sel->get_next_item(gb_item))
1764		{
1765		long my_color = AW_find_color_group(gb_item, true);
1766		if (my_color == color_group) {
1767		bool marked = GB_read_flag(gb_item);
1768
1769		switch (mode) {
1770		case 0: marked = 0; break;
1771		case 1: marked = 1; break;
1772		case 2: marked = !marked; break;
1773		default : awt_assert(0); break;
1774		}
1775
1776		error = GB_write_flag(gb_item, marked);
1777		}
1778		}
1779		}
1780
1781		if (error) GB_export_error(error);
	1763	long my_color = AW_find_color_group(gb_item, true);
	1764	if (my_color == color_group) {
	1765	bool marked = GB_read_flag(gb_item);
	1766
	1767	switch (mode) {
	1768	case 0: marked = 0; break;
	1769	case 1: marked = 1; break;
	1770	case 2: marked = !marked; break;
	1771	default : awt_assert(0); break;
	1772	}
	1773
	1774	GB_write_flag(gb_item, marked);
	1775	}
	1776	}
	1777	}
	1778
1782	1779	}
1783	1780

trunk/AWT/Makefile

r6277	r6280
4	4
5	5	OBJECTS = \
6		AWT_input_mask.o AWT_hotkeys.o \
7		AWT_www.o AWT_tables.o AWT_irstree.o \
8		AWT_asciiprint.o AWT_map_key.o AWT_tree_cmp.o AWT_seq_colors.o \
9		AWT_pro_a_nucs.o AWT_csp.o AWT_canvas.o AWT_dtree.o AWT_tree.o AWT_tree_cb.o AWT_nei.o \
10		AWT_filter.o AWT_sel_boxes.o AWT_canio.o AWT_nds.o \
11		AWT_query_and_functions.o AWT_file_selection.o \
12		AWT_preset.o AWT_seq_dna.o AWT_seq_protein.o AWT_seq_simple_pro.o \
13		AWT_codon_table.o AWT_iupac.o AWT_config_manager.o AWT_advice.o AWT_db_browser.o \
14		AWT_attributes.o AWT_changekey.o AWT_item_sel_list.o AWT_macro.o AWT_translate.o
	6	AWT_advice.o \
	7	AWT_asciiprint.o \
	8	AWT_attributes.o \
	9	AWT_canio.o \
	10	AWT_canvas.o \
	11	AWT_changekey.o \
	12	AWT_config_manager.o \
	13	AWT_db_browser.o \
	14	AWT_file_selection.o \
	15	AWT_hotkeys.o \
	16	AWT_input_mask.o \
	17	AWT_item_sel_list.o \
	18	AWT_iupac.o \
	19	AWT_macro.o \
	20	AWT_map_key.o \
	21	AWT_nds.o \
	22	AWT_preset.o \
	23	AWT_query_and_functions.o \
	24	AWT_sel_boxes.o \
	25	AWT_seq_colors.o \
	26	AWT_tables.o \
	27	AWT_www.o \
15	28
16	29	$(MAIN): $(OBJECTS)
…	…
22	35
23	36	# $(CPPLIB) $(cflags) -c -D_USE_AW_WINDOW $< $(CPPINCLUDES)
24
25		~~awt_tree_cb.hxx: AWT_tree_cb.cxx~~
26		~~rm -f $@~~
27		~~../MAKEBIN/aisc_mkpt -w $@ -C $? >$@~~
28	37
29	38	clean:
…	…
152	161	AWT_changekey.o: $(ARBHOME)/INCLUDE/smartptr.h
153	162
154		~~AWT_codon_table.o: awt.hxx~~
155		~~AWT_codon_table.o: awt_codon_table.hxx~~
156		~~AWT_codon_table.o: awt_iupac.hxx~~
157		~~AWT_codon_table.o: $(ARBHOME)/INCLUDE/ad_k_prot.h~~
158		~~AWT_codon_table.o: $(ARBHOME)/INCLUDE/ad_prot.h~~
159		~~AWT_codon_table.o: $(ARBHOME)/INCLUDE/arb_assert.h~~
160		~~AWT_codon_table.o: $(ARBHOME)/INCLUDE/arb_error.h~~
161		~~AWT_codon_table.o: $(ARBHOME)/INCLUDE/arbdb.h~~
162		~~AWT_codon_table.o: $(ARBHOME)/INCLUDE/arbdb_base.h~~
163		~~AWT_codon_table.o: $(ARBHOME)/INCLUDE/arbtools.h~~
164		~~AWT_codon_table.o: $(ARBHOME)/INCLUDE/attributes.h~~
165		~~AWT_codon_table.o: $(ARBHOME)/INCLUDE/aw_device.hxx~~
166		~~AWT_codon_table.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx~~
167		~~AWT_codon_table.o: $(ARBHOME)/INCLUDE/aw_position.hxx~~
168		~~AWT_codon_table.o: $(ARBHOME)/INCLUDE/aw_root.hxx~~
169		~~AWT_codon_table.o: $(ARBHOME)/INCLUDE/aw_window.hxx~~
170		~~AWT_codon_table.o: $(ARBHOME)/INCLUDE/smartptr.h~~
171
172	163	AWT_config_manager.o: awt.hxx
173	164	AWT_config_manager.o: awt_config_manager.hxx
…	…
187	178	AWT_config_manager.o: $(ARBHOME)/INCLUDE/smartptr.h
188	179
189		~~AWT_csp.o: awt.hxx~~
190		~~AWT_csp.o: awt_csp.hxx~~
191		~~AWT_csp.o: awt_pro_a_nucs.hxx~~
192		~~AWT_csp.o: awt_sel_boxes.hxx~~
193		~~AWT_csp.o: awt_tree.hxx~~
194		~~AWT_csp.o: $(ARBHOME)/INCLUDE/ad_k_prot.h~~
195		~~AWT_csp.o: $(ARBHOME)/INCLUDE/ad_prot.h~~
196		~~AWT_csp.o: $(ARBHOME)/INCLUDE/ad_t_prot.h~~
197		~~AWT_csp.o: $(ARBHOME)/INCLUDE/arb_assert.h~~
198		~~AWT_csp.o: $(ARBHOME)/INCLUDE/arb_error.h~~
199		~~AWT_csp.o: $(ARBHOME)/INCLUDE/arbdb.h~~
200		~~AWT_csp.o: $(ARBHOME)/INCLUDE/arbdb_base.h~~
201		~~AWT_csp.o: $(ARBHOME)/INCLUDE/arbdbt.h~~
202		~~AWT_csp.o: $(ARBHOME)/INCLUDE/arbtools.h~~
203		~~AWT_csp.o: $(ARBHOME)/INCLUDE/attributes.h~~
204		~~AWT_csp.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx~~
205		~~AWT_csp.o: $(ARBHOME)/INCLUDE/aw_device.hxx~~
206		~~AWT_csp.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx~~
207		~~AWT_csp.o: $(ARBHOME)/INCLUDE/aw_position.hxx~~
208		~~AWT_csp.o: $(ARBHOME)/INCLUDE/aw_root.hxx~~
209		~~AWT_csp.o: $(ARBHOME)/INCLUDE/aw_window.hxx~~
210		~~AWT_csp.o: $(ARBHOME)/INCLUDE/BI_helix.hxx~~
211		~~AWT_csp.o: $(ARBHOME)/INCLUDE/smartptr.h~~
212
213	180	AWT_db_browser.o: awt.hxx
214		~~AWT_db_browser.o: awt_pro_a_nucs.hxx~~
215		~~AWT_db_browser.o: awt_tree.hxx~~
216	181	AWT_db_browser.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
217	182	AWT_db_browser.o: $(ARBHOME)/INCLUDE/ad_prot.h
218	183	AWT_db_browser.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
	184	AWT_db_browser.o: $(ARBHOME)/INCLUDE/AliView.hxx
	185	AWT_db_browser.o: $(ARBHOME)/INCLUDE/AP_sequence.hxx
	186	AWT_db_browser.o: $(ARBHOME)/INCLUDE/AP_Tree.hxx
219	187	AWT_db_browser.o: $(ARBHOME)/INCLUDE/arb_assert.h
220	188	AWT_db_browser.o: $(ARBHOME)/INCLUDE/arb_error.h
	189	AWT_db_browser.o: $(ARBHOME)/INCLUDE/ARB_Tree.hxx
221	190	AWT_db_browser.o: $(ARBHOME)/INCLUDE/arbdb.h
222	191	AWT_db_browser.o: $(ARBHOME)/INCLUDE/arbdb_base.h
…	…
230	199	AWT_db_browser.o: $(ARBHOME)/INCLUDE/aw_root.hxx
231	200	AWT_db_browser.o: $(ARBHOME)/INCLUDE/aw_window.hxx
	201	AWT_db_browser.o: $(ARBHOME)/INCLUDE/downcast.h
232	202	AWT_db_browser.o: $(ARBHOME)/INCLUDE/inline.h
233	203	AWT_db_browser.o: $(ARBHOME)/INCLUDE/smartptr.h
234
235		~~AWT_dtree.o: awt.hxx~~
236		~~AWT_dtree.o: awt_attributes.hxx~~
237		~~AWT_dtree.o: awt_canvas.hxx~~
238		~~AWT_dtree.o: awt_dtree.hxx~~
239		~~AWT_dtree.o: awt_nds.hxx~~
240		~~AWT_dtree.o: awt_pro_a_nucs.hxx~~
241		~~AWT_dtree.o: awt_tree.hxx~~
242		~~AWT_dtree.o: $(ARBHOME)/INCLUDE/ad_k_prot.h~~
243		~~AWT_dtree.o: $(ARBHOME)/INCLUDE/ad_prot.h~~
244		~~AWT_dtree.o: $(ARBHOME)/INCLUDE/ad_t_prot.h~~
245		~~AWT_dtree.o: $(ARBHOME)/INCLUDE/arb_assert.h~~
246		~~AWT_dtree.o: $(ARBHOME)/INCLUDE/arb_error.h~~
247		~~AWT_dtree.o: $(ARBHOME)/INCLUDE/arbdb.h~~
248		~~AWT_dtree.o: $(ARBHOME)/INCLUDE/arbdb_base.h~~
249		~~AWT_dtree.o: $(ARBHOME)/INCLUDE/arbdbt.h~~
250		~~AWT_dtree.o: $(ARBHOME)/INCLUDE/arbtools.h~~
251		~~AWT_dtree.o: $(ARBHOME)/INCLUDE/attributes.h~~
252		~~AWT_dtree.o: $(ARBHOME)/INCLUDE/aw_awars.hxx~~
253		~~AWT_dtree.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx~~
254		~~AWT_dtree.o: $(ARBHOME)/INCLUDE/aw_device.hxx~~
255		~~AWT_dtree.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx~~
256		~~AWT_dtree.o: $(ARBHOME)/INCLUDE/aw_position.hxx~~
257		~~AWT_dtree.o: $(ARBHOME)/INCLUDE/aw_preset.hxx~~
258		~~AWT_dtree.o: $(ARBHOME)/INCLUDE/aw_root.hxx~~
259		~~AWT_dtree.o: $(ARBHOME)/INCLUDE/aw_window.hxx~~
260		~~AWT_dtree.o: $(ARBHOME)/INCLUDE/smartptr.h~~
261	204
262	205	AWT_file_selection.o: awt.hxx
…	…
279	222	AWT_file_selection.o: $(ARBHOME)/INCLUDE/aw_window.hxx
280	223	AWT_file_selection.o: $(ARBHOME)/INCLUDE/smartptr.h
281
282		~~AWT_filter.o: awt.hxx~~
283		~~AWT_filter.o: awt_pro_a_nucs.hxx~~
284		~~AWT_filter.o: awt_sel_boxes.hxx~~
285		~~AWT_filter.o: awt_tree.hxx~~
286		~~AWT_filter.o: awtfilter.hxx~~
287		~~AWT_filter.o: $(ARBHOME)/INCLUDE/ad_k_prot.h~~
288		~~AWT_filter.o: $(ARBHOME)/INCLUDE/ad_prot.h~~
289		~~AWT_filter.o: $(ARBHOME)/INCLUDE/ad_t_prot.h~~
290		~~AWT_filter.o: $(ARBHOME)/INCLUDE/arb_assert.h~~
291		~~AWT_filter.o: $(ARBHOME)/INCLUDE/arb_error.h~~
292		~~AWT_filter.o: $(ARBHOME)/INCLUDE/arbdb.h~~
293		~~AWT_filter.o: $(ARBHOME)/INCLUDE/arbdb_base.h~~
294		~~AWT_filter.o: $(ARBHOME)/INCLUDE/arbdbt.h~~
295		~~AWT_filter.o: $(ARBHOME)/INCLUDE/arbtools.h~~
296		~~AWT_filter.o: $(ARBHOME)/INCLUDE/attributes.h~~
297		~~AWT_filter.o: $(ARBHOME)/INCLUDE/aw_awars.hxx~~
298		~~AWT_filter.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx~~
299		~~AWT_filter.o: $(ARBHOME)/INCLUDE/aw_device.hxx~~
300		~~AWT_filter.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx~~
301		~~AWT_filter.o: $(ARBHOME)/INCLUDE/aw_position.hxx~~
302		~~AWT_filter.o: $(ARBHOME)/INCLUDE/aw_root.hxx~~
303		~~AWT_filter.o: $(ARBHOME)/INCLUDE/aw_window.hxx~~
304		~~AWT_filter.o: $(ARBHOME)/INCLUDE/smartptr.h~~
305	224
306	225	AWT_hotkeys.o: awt_hotkeys.hxx
…	…
328	247	AWT_input_mask.o: $(ARBHOME)/INCLUDE/smartptr.h
329	248
330		~~AWT_irstree.o: awt_canvas.hxx~~
331		~~AWT_irstree.o: awt_dtree.hxx~~
332		~~AWT_irstree.o: awt_nds.hxx~~
333		~~AWT_irstree.o: awt_pro_a_nucs.hxx~~
334		~~AWT_irstree.o: awt_tree.hxx~~
335		~~AWT_irstree.o: $(ARBHOME)/INCLUDE/ad_k_prot.h~~
336		~~AWT_irstree.o: $(ARBHOME)/INCLUDE/ad_prot.h~~
337		~~AWT_irstree.o: $(ARBHOME)/INCLUDE/ad_t_prot.h~~
338		~~AWT_irstree.o: $(ARBHOME)/INCLUDE/arb_assert.h~~
339		~~AWT_irstree.o: $(ARBHOME)/INCLUDE/arb_error.h~~
340		~~AWT_irstree.o: $(ARBHOME)/INCLUDE/arbdb.h~~
341		~~AWT_irstree.o: $(ARBHOME)/INCLUDE/arbdb_base.h~~
342		~~AWT_irstree.o: $(ARBHOME)/INCLUDE/arbdbt.h~~
343		~~AWT_irstree.o: $(ARBHOME)/INCLUDE/arbtools.h~~
344		~~AWT_irstree.o: $(ARBHOME)/INCLUDE/attributes.h~~
345		~~AWT_irstree.o: $(ARBHOME)/INCLUDE/aw_awars.hxx~~
346		~~AWT_irstree.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx~~
347		~~AWT_irstree.o: $(ARBHOME)/INCLUDE/aw_device.hxx~~
348		~~AWT_irstree.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx~~
349		~~AWT_irstree.o: $(ARBHOME)/INCLUDE/aw_position.hxx~~
350		~~AWT_irstree.o: $(ARBHOME)/INCLUDE/aw_root.hxx~~
351		~~AWT_irstree.o: $(ARBHOME)/INCLUDE/aw_window.hxx~~
352		~~AWT_irstree.o: $(ARBHOME)/INCLUDE/smartptr.h~~
353
354	249	AWT_item_sel_list.o: awt.hxx
355	250	AWT_item_sel_list.o: awt_item_sel_list.hxx
…	…
434	329	AWT_nds.o: $(ARBHOME)/INCLUDE/aw_window.hxx
435	330	AWT_nds.o: $(ARBHOME)/INCLUDE/smartptr.h
436
437		~~AWT_nei.o: awt_nei.hxx~~
438		~~AWT_nei.o: awt_pro_a_nucs.hxx~~
439		~~AWT_nei.o: awt_tree.hxx~~
440		~~AWT_nei.o: $(ARBHOME)/INCLUDE/ad_k_prot.h~~
441		~~AWT_nei.o: $(ARBHOME)/INCLUDE/ad_prot.h~~
442		~~AWT_nei.o: $(ARBHOME)/INCLUDE/ad_t_prot.h~~
443		~~AWT_nei.o: $(ARBHOME)/INCLUDE/arb_assert.h~~
444		~~AWT_nei.o: $(ARBHOME)/INCLUDE/arb_error.h~~
445		~~AWT_nei.o: $(ARBHOME)/INCLUDE/arbdb.h~~
446		~~AWT_nei.o: $(ARBHOME)/INCLUDE/arbdb_base.h~~
447		~~AWT_nei.o: $(ARBHOME)/INCLUDE/arbdbt.h~~
448		~~AWT_nei.o: $(ARBHOME)/INCLUDE/arbtools.h~~
449		~~AWT_nei.o: $(ARBHOME)/INCLUDE/attributes.h~~
450		~~AWT_nei.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx~~
451		~~AWT_nei.o: $(ARBHOME)/INCLUDE/aw_root.hxx~~
452		~~AWT_nei.o: $(ARBHOME)/INCLUDE/smartptr.h~~
453	331
454	332	AWT_preset.o: aw_def.hxx
…	…
474	352	AWT_preset.o: $(ARBHOME)/INCLUDE/aw_window.hxx
475	353	AWT_preset.o: $(ARBHOME)/INCLUDE/smartptr.h
476
477		~~AWT_pro_a_nucs.o: awt.hxx~~
478		~~AWT_pro_a_nucs.o: awt_codon_table.hxx~~
479		~~AWT_pro_a_nucs.o: awt_pro_a_nucs.hxx~~
480		~~AWT_pro_a_nucs.o: $(ARBHOME)/INCLUDE/ad_k_prot.h~~
481		~~AWT_pro_a_nucs.o: $(ARBHOME)/INCLUDE/ad_prot.h~~
482		~~AWT_pro_a_nucs.o: $(ARBHOME)/INCLUDE/ad_t_prot.h~~
483		~~AWT_pro_a_nucs.o: $(ARBHOME)/INCLUDE/arb_assert.h~~
484		~~AWT_pro_a_nucs.o: $(ARBHOME)/INCLUDE/arb_error.h~~
485		~~AWT_pro_a_nucs.o: $(ARBHOME)/INCLUDE/arbdb.h~~
486		~~AWT_pro_a_nucs.o: $(ARBHOME)/INCLUDE/arbdb_base.h~~
487		~~AWT_pro_a_nucs.o: $(ARBHOME)/INCLUDE/arbdbt.h~~
488		~~AWT_pro_a_nucs.o: $(ARBHOME)/INCLUDE/arbtools.h~~
489		~~AWT_pro_a_nucs.o: $(ARBHOME)/INCLUDE/attributes.h~~
490		~~AWT_pro_a_nucs.o: $(ARBHOME)/INCLUDE/aw_device.hxx~~
491		~~AWT_pro_a_nucs.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx~~
492		~~AWT_pro_a_nucs.o: $(ARBHOME)/INCLUDE/aw_position.hxx~~
493		~~AWT_pro_a_nucs.o: $(ARBHOME)/INCLUDE/aw_root.hxx~~
494		~~AWT_pro_a_nucs.o: $(ARBHOME)/INCLUDE/aw_window.hxx~~
495		~~AWT_pro_a_nucs.o: $(ARBHOME)/INCLUDE/inline.h~~
496		~~AWT_pro_a_nucs.o: $(ARBHOME)/INCLUDE/smartptr.h~~
497	354
498	355	AWT_query_and_functions.o: awt.hxx
…	…
567	424	AWT_seq_colors.o: $(ARBHOME)/INCLUDE/smartptr.h
568	425
569		~~AWT_seq_dna.o: awt_parsimony_defaults.hxx~~
570		~~AWT_seq_dna.o: awt_pro_a_nucs.hxx~~
571		~~AWT_seq_dna.o: awt_seq_dna.hxx~~
572		~~AWT_seq_dna.o: awt_tree.hxx~~
573		~~AWT_seq_dna.o: $(ARBHOME)/INCLUDE/ad_k_prot.h~~
574		~~AWT_seq_dna.o: $(ARBHOME)/INCLUDE/ad_prot.h~~
575		~~AWT_seq_dna.o: $(ARBHOME)/INCLUDE/ad_t_prot.h~~
576		~~AWT_seq_dna.o: $(ARBHOME)/INCLUDE/arb_assert.h~~
577		~~AWT_seq_dna.o: $(ARBHOME)/INCLUDE/arb_error.h~~
578		~~AWT_seq_dna.o: $(ARBHOME)/INCLUDE/arbdb.h~~
579		~~AWT_seq_dna.o: $(ARBHOME)/INCLUDE/arbdb_base.h~~
580		~~AWT_seq_dna.o: $(ARBHOME)/INCLUDE/arbdbt.h~~
581		~~AWT_seq_dna.o: $(ARBHOME)/INCLUDE/arbtools.h~~
582		~~AWT_seq_dna.o: $(ARBHOME)/INCLUDE/attributes.h~~
583		~~AWT_seq_dna.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx~~
584		~~AWT_seq_dna.o: $(ARBHOME)/INCLUDE/aw_root.hxx~~
585		~~AWT_seq_dna.o: $(ARBHOME)/INCLUDE/smartptr.h~~
586
587		~~AWT_seq_protein.o: awt_parsimony_defaults.hxx~~
588		~~AWT_seq_protein.o: awt_pro_a_nucs.hxx~~
589		~~AWT_seq_protein.o: awt_seq_protein.hxx~~
590		~~AWT_seq_protein.o: awt_tree.hxx~~
591		~~AWT_seq_protein.o: $(ARBHOME)/INCLUDE/ad_k_prot.h~~
592		~~AWT_seq_protein.o: $(ARBHOME)/INCLUDE/ad_prot.h~~
593		~~AWT_seq_protein.o: $(ARBHOME)/INCLUDE/ad_t_prot.h~~
594		~~AWT_seq_protein.o: $(ARBHOME)/INCLUDE/arb_assert.h~~
595		~~AWT_seq_protein.o: $(ARBHOME)/INCLUDE/arb_error.h~~
596		~~AWT_seq_protein.o: $(ARBHOME)/INCLUDE/arbdb.h~~
597		~~AWT_seq_protein.o: $(ARBHOME)/INCLUDE/arbdb_base.h~~
598		~~AWT_seq_protein.o: $(ARBHOME)/INCLUDE/arbdbt.h~~
599		~~AWT_seq_protein.o: $(ARBHOME)/INCLUDE/arbtools.h~~
600		~~AWT_seq_protein.o: $(ARBHOME)/INCLUDE/attributes.h~~
601		~~AWT_seq_protein.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx~~
602		~~AWT_seq_protein.o: $(ARBHOME)/INCLUDE/aw_root.hxx~~
603		~~AWT_seq_protein.o: $(ARBHOME)/INCLUDE/inline.h~~
604		~~AWT_seq_protein.o: $(ARBHOME)/INCLUDE/smartptr.h~~
605
606		~~AWT_seq_simple_pro.o: awt_pro_a_nucs.hxx~~
607		~~AWT_seq_simple_pro.o: awt_seq_simple_pro.hxx~~
608		~~AWT_seq_simple_pro.o: awt_tree.hxx~~
609		~~AWT_seq_simple_pro.o: $(ARBHOME)/INCLUDE/ad_k_prot.h~~
610		~~AWT_seq_simple_pro.o: $(ARBHOME)/INCLUDE/ad_prot.h~~
611		~~AWT_seq_simple_pro.o: $(ARBHOME)/INCLUDE/ad_t_prot.h~~
612		~~AWT_seq_simple_pro.o: $(ARBHOME)/INCLUDE/arb_assert.h~~
613		~~AWT_seq_simple_pro.o: $(ARBHOME)/INCLUDE/arb_error.h~~
614		~~AWT_seq_simple_pro.o: $(ARBHOME)/INCLUDE/arbdb.h~~
615		~~AWT_seq_simple_pro.o: $(ARBHOME)/INCLUDE/arbdb_base.h~~
616		~~AWT_seq_simple_pro.o: $(ARBHOME)/INCLUDE/arbdbt.h~~
617		~~AWT_seq_simple_pro.o: $(ARBHOME)/INCLUDE/arbtools.h~~
618		~~AWT_seq_simple_pro.o: $(ARBHOME)/INCLUDE/attributes.h~~
619		~~AWT_seq_simple_pro.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx~~
620		~~AWT_seq_simple_pro.o: $(ARBHOME)/INCLUDE/aw_root.hxx~~
621		~~AWT_seq_simple_pro.o: $(ARBHOME)/INCLUDE/smartptr.h~~
622
623	426	AWT_tables.o: awt.hxx
624	427	AWT_tables.o: awt_sel_boxes.hxx
…	…
643	446	AWT_tables.o: $(ARBHOME)/INCLUDE/smartptr.h
644	447
645		~~AWT_translate.o: awt.hxx~~
646		~~AWT_translate.o: awt_codon_table.hxx~~
647		~~AWT_translate.o: awt_pro_a_nucs.hxx~~
648		~~AWT_translate.o: awt_translate.hxx~~
649		~~AWT_translate.o: $(ARBHOME)/INCLUDE/ad_k_prot.h~~
650		~~AWT_translate.o: $(ARBHOME)/INCLUDE/ad_prot.h~~
651		~~AWT_translate.o: $(ARBHOME)/INCLUDE/ad_t_prot.h~~
652		~~AWT_translate.o: $(ARBHOME)/INCLUDE/arb_assert.h~~
653		~~AWT_translate.o: $(ARBHOME)/INCLUDE/arb_error.h~~
654		~~AWT_translate.o: $(ARBHOME)/INCLUDE/arbdb.h~~
655		~~AWT_translate.o: $(ARBHOME)/INCLUDE/arbdb_base.h~~
656		~~AWT_translate.o: $(ARBHOME)/INCLUDE/arbdbt.h~~
657		~~AWT_translate.o: $(ARBHOME)/INCLUDE/arbtools.h~~
658		~~AWT_translate.o: $(ARBHOME)/INCLUDE/attributes.h~~
659		~~AWT_translate.o: $(ARBHOME)/INCLUDE/aw_device.hxx~~
660		~~AWT_translate.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx~~
661		~~AWT_translate.o: $(ARBHOME)/INCLUDE/aw_position.hxx~~
662		~~AWT_translate.o: $(ARBHOME)/INCLUDE/aw_root.hxx~~
663		~~AWT_translate.o: $(ARBHOME)/INCLUDE/aw_window.hxx~~
664		~~AWT_translate.o: $(ARBHOME)/INCLUDE/smartptr.h~~
665
666		~~AWT_tree.o: awt.hxx~~
667		~~AWT_tree.o: awt_attributes.hxx~~
668		~~AWT_tree.o: awt_canvas.hxx~~
669		~~AWT_tree.o: awt_pro_a_nucs.hxx~~
670		~~AWT_tree.o: awt_tree.hxx~~
671		~~AWT_tree.o: $(ARBHOME)/INCLUDE/ad_k_prot.h~~
672		~~AWT_tree.o: $(ARBHOME)/INCLUDE/ad_prot.h~~
673		~~AWT_tree.o: $(ARBHOME)/INCLUDE/ad_t_prot.h~~
674		~~AWT_tree.o: $(ARBHOME)/INCLUDE/arb_assert.h~~
675		~~AWT_tree.o: $(ARBHOME)/INCLUDE/arb_error.h~~
676		~~AWT_tree.o: $(ARBHOME)/INCLUDE/arbdb.h~~
677		~~AWT_tree.o: $(ARBHOME)/INCLUDE/arbdb_base.h~~
678		~~AWT_tree.o: $(ARBHOME)/INCLUDE/arbdbt.h~~
679		~~AWT_tree.o: $(ARBHOME)/INCLUDE/arbtools.h~~
680		~~AWT_tree.o: $(ARBHOME)/INCLUDE/attributes.h~~
681		~~AWT_tree.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx~~
682		~~AWT_tree.o: $(ARBHOME)/INCLUDE/aw_device.hxx~~
683		~~AWT_tree.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx~~
684		~~AWT_tree.o: $(ARBHOME)/INCLUDE/aw_position.hxx~~
685		~~AWT_tree.o: $(ARBHOME)/INCLUDE/aw_root.hxx~~
686		~~AWT_tree.o: $(ARBHOME)/INCLUDE/aw_window.hxx~~
687		~~AWT_tree.o: $(ARBHOME)/INCLUDE/smartptr.h~~
688
689		~~AWT_tree_cb.o: awt.hxx~~
690		~~AWT_tree_cb.o: awt_advice.hxx~~
691		~~AWT_tree_cb.o: awt_canvas.hxx~~
692		~~AWT_tree_cb.o: awt_dtree.hxx~~
693		~~AWT_tree_cb.o: awt_pro_a_nucs.hxx~~
694		~~AWT_tree_cb.o: awt_tree.hxx~~
695		~~AWT_tree_cb.o: awt_tree_cb.hxx~~
696		~~AWT_tree_cb.o: $(ARBHOME)/INCLUDE/ad_k_prot.h~~
697		~~AWT_tree_cb.o: $(ARBHOME)/INCLUDE/ad_prot.h~~
698		~~AWT_tree_cb.o: $(ARBHOME)/INCLUDE/ad_t_prot.h~~
699		~~AWT_tree_cb.o: $(ARBHOME)/INCLUDE/arb_assert.h~~
700		~~AWT_tree_cb.o: $(ARBHOME)/INCLUDE/arb_error.h~~
701		~~AWT_tree_cb.o: $(ARBHOME)/INCLUDE/arbdb.h~~
702		~~AWT_tree_cb.o: $(ARBHOME)/INCLUDE/arbdb_base.h~~
703		~~AWT_tree_cb.o: $(ARBHOME)/INCLUDE/arbdbt.h~~
704		~~AWT_tree_cb.o: $(ARBHOME)/INCLUDE/arbtools.h~~
705		~~AWT_tree_cb.o: $(ARBHOME)/INCLUDE/attributes.h~~
706		~~AWT_tree_cb.o: $(ARBHOME)/INCLUDE/aw_awars.hxx~~
707		~~AWT_tree_cb.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx~~
708		~~AWT_tree_cb.o: $(ARBHOME)/INCLUDE/aw_device.hxx~~
709		~~AWT_tree_cb.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx~~
710		~~AWT_tree_cb.o: $(ARBHOME)/INCLUDE/aw_position.hxx~~
711		~~AWT_tree_cb.o: $(ARBHOME)/INCLUDE/aw_root.hxx~~
712		~~AWT_tree_cb.o: $(ARBHOME)/INCLUDE/aw_window.hxx~~
713		~~AWT_tree_cb.o: $(ARBHOME)/INCLUDE/smartptr.h~~
714
715		~~AWT_tree_cmp.o: awt.hxx~~
716		~~AWT_tree_cmp.o: awt_pro_a_nucs.hxx~~
717		~~AWT_tree_cmp.o: awt_tree.hxx~~
718		~~AWT_tree_cmp.o: awt_tree_cmp.hxx~~
719		~~AWT_tree_cmp.o: $(ARBHOME)/INCLUDE/ad_k_prot.h~~
720		~~AWT_tree_cmp.o: $(ARBHOME)/INCLUDE/ad_prot.h~~
721		~~AWT_tree_cmp.o: $(ARBHOME)/INCLUDE/ad_t_prot.h~~
722		~~AWT_tree_cmp.o: $(ARBHOME)/INCLUDE/arb_assert.h~~
723		~~AWT_tree_cmp.o: $(ARBHOME)/INCLUDE/arb_error.h~~
724		~~AWT_tree_cmp.o: $(ARBHOME)/INCLUDE/arbdb.h~~
725		~~AWT_tree_cmp.o: $(ARBHOME)/INCLUDE/arbdb_base.h~~
726		~~AWT_tree_cmp.o: $(ARBHOME)/INCLUDE/arbdbt.h~~
727		~~AWT_tree_cmp.o: $(ARBHOME)/INCLUDE/arbtools.h~~
728		~~AWT_tree_cmp.o: $(ARBHOME)/INCLUDE/attributes.h~~
729		~~AWT_tree_cmp.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx~~
730		~~AWT_tree_cmp.o: $(ARBHOME)/INCLUDE/aw_device.hxx~~
731		~~AWT_tree_cmp.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx~~
732		~~AWT_tree_cmp.o: $(ARBHOME)/INCLUDE/aw_position.hxx~~
733		~~AWT_tree_cmp.o: $(ARBHOME)/INCLUDE/aw_root.hxx~~
734		~~AWT_tree_cmp.o: $(ARBHOME)/INCLUDE/aw_window.hxx~~
735		~~AWT_tree_cmp.o: $(ARBHOME)/INCLUDE/smartptr.h~~
736
737	448	AWT_www.o: awt.hxx
738	449	AWT_www.o: awt_config_manager.hxx

trunk/AWT/awt_canvas.hxx

r5901	r6280
24	24	AWT_MODE_ZOOM, // no command
25	25	AWT_MODE_LZOOM,
26		AWT_MODE_~~MOD~~, // species info
	26	AWT_MODE_EDIT, // species info
27	27	AWT_MODE_WWW,
28	28	AWT_MODE_LINE,

trunk/AWT/awt_item_sel_list.hxx

r6141	r6280
21	21	AWT_SF_HIDDEN = 2,
22	22	// continue with 4, 8
23		AWT_SF_ALL = ((AWT_SF_HIDDEN<<1)-1),
	23	AWT_SF_ALL = ((AWT_SF_HIDDEN<<1)-1),
24	24	};
	25
	26	#define AWT_NDS_FILTER (1<<GB_STRING)\|(1<<GB_BYTE)\|(1<<GB_INT)\|(1<<GB_FLOAT)\|(1<<GB_BITS)\|(1<<GB_LINK)
	27	#define AWT_PARS_FILTER (1<<GB_STRING)\|(1<<GB_BYTE)\|(1<<GB_INT)\|(1<<GB_FLOAT)\|(1<<GB_BITS)\|(1<<GB_LINK)
	28	#define AWT_STRING_FILTER (1<<GB_STRING)\|(1<<GB_BITS)\|(1<<GB_LINK)
	29
	30	struct ad_item_selector;
25	31
26	32	AW_CL awt_create_selection_list_on_scandb(GBDATA *gb_main,

trunk/AWT/awt_sel_boxes.hxx

r5901	r6280
14	14	#define AWT_SEL_BOXES_HXX
15	15
16		class AP_filter;
	16	#ifndef ARBDBT_H
	17	#include <arbdbt.h>
	18	#endif
	19	#ifndef AW_ROOT_HXX
	20	#include <aw_root.hxx>
	21	#endif
	22
	23	class AP_filter;
17	24	struct adfiltercbstruct;
18	25
…	…
69	76	AW_window* (create_popup)(AW_root , AW_default)); // .. or create_popup (both together not allowed)
70	77
71		~~/********************* FILTERS **********************/~~
72		~~adfiltercbstruct awt_create_select_filter(AW_root aw_root,GBDATA gb_main, const char def_name);~~
73		~~/* Create a data structure for filters (needed for awt_create_select_filter_win */~~
74		~~/* Create a filter selection box, this box needs 3 AWARS:~~
75		~~1. "$def_name"~~
76		~~2. "$def_name:/name=/filter"~~
77		~~3. "$def_name:/name=/alignment"~~
78		~~and some internal awars~~
79		*/
80		~~void awt_set_awar_to_valid_filter_good_for_tree_methods(GBDATA gb_main,AW_root awr, const char *awar_name);~~
81
82		~~AW_window awt_create_select_filter_win(AW_root aw_root, AW_CL cd_adfiltercbstruct);~~
83		~~/* not just the box, but the whole window */~~
84
85		~~AP_filter awt_get_filter(AW_root aw_root, adfiltercbstruct *acbs);~~
86
87		~~char AWT_get_combined_filter_name(AW_root aw_root, GB_CSTR prefix);~~
88
89		~~#define AWT_NDS_FILTER (1<<GB_STRING)\|(1<<GB_BYTE)\|(1<<GB_INT)\|(1<<GB_FLOAT)\|(1<<GB_BITS)\|(1<<GB_LINK)~~
90		~~#define AWT_PARS_FILTER (1<<GB_STRING)\|(1<<GB_BYTE)\|(1<<GB_INT)\|(1<<GB_FLOAT)\|(1<<GB_BITS)\|(1<<GB_LINK)~~
91		~~#define AWT_STRING_FILTER (1<<GB_STRING)\|(1<<GB_BITS)\|(1<<GB_LINK)~~
92
93	78	/********************* species fields **********************/
94	79

trunk/AWTI/AWTI_export.cxx

r6141	r6280
1		#include <stdio.h>
2		#include <stdlib.h>
3		#include <unistd.h>
4		#include <string.h>
5		// #include <malloc.h>
6		#include <arbdb.h>
7		#include <arbdbt.h>
8		#include <aw_root.hxx>
9		#include <aw_device.hxx>
10		#include <aw_window.hxx>
	1	#include "awti_export.hxx"
	2	#include "awti_exp_local.hxx"
	3
	4	#include <aw_awars.hxx>
11	5	#include <aw_global.hxx>
12	6	#include <awt.hxx>
13		#include <awt_tree.hxx>
	7	#include <awt_filter.hxx>
	8	#include <AP_filter.hxx>
	9	#include <xml.hxx>
14	10	#include <inline.h>
15
16		~~#include "awti_export.hxx"~~
17		~~#include "awti_exp_local.hxx"~~
18		~~#include "awt_sel_boxes.hxx"~~
19		~~#include "aw_awars.hxx"~~
20
21		~~#include "xml.hxx"~~
22	11
23	12	#define awte_assert(cond) arb_assert(cond)
…	…
173	162	int compress; // 0 = no;1 = vertical gaps; 2 = all gaps;
174	163
175		size_t max_ali_len; // length of alignment
176		~~int *export_column;~~ // list of exported seq data positions
177		~~int columns;~~ // how many columns get exported
178
179		GBDATA *single_species; // if != NULL -> first/next only return that species (used to export to multiple files)
	164	size_t max_ali_len; // length of alignment
	165	size_t *export_column; // list of exported seq data positions
	166	size_t columns; // how many columns get exported
	167
	168	GBDATA *single_species; // if != NULL -> first/next only return that species (used to export to multiple files)
180	169
181	170	public:
…	…
214	203	}
215	204
216		if (~~size_t(filter->filter_len~~) < max_ali_len) {
217		aw_message(GBS_global_string("Warning: Your filter is shorter than the alignment (%li<%zu)",
218		filter->~~filter_len~~, max_ali_len));
219		max_ali_len = filter->~~filter_len~~;
	205	if (filter->get_length() < max_ali_len) {
	206	aw_message(GBS_global_string("Warning: Your filter is shorter than the alignment (%zu<%zu)",
	207	filter->get_length(), max_ali_len));
	208	max_ali_len = filter->get_length();
220	209	}
221	210	}
…	…
276	265	awte_assert(!in_single_mode());
277	266
278		~~filter->calc_filter_2_seq();~~
279	267	if (compress == 1) { // compress vertical gaps!
280		int gap_columns = filter->real_len;
281		int *gap_column = new int[gap_columns+1];
282		memcpy(gap_column, filter->filterpos_2_seqpos, gap_columnssizeof(gap_column));
	268	size_t gap_columns = filter->get_filtered_length();
	269	size_t *gap_column = new size_t[gap_columns+1];
	270
	271	const size_t *filterpos_2_seqpos = filter->get_filterpos_2_seqpos();
	272	memcpy(gap_column, filterpos_2_seqpos, gap_columnssizeof(gap_column));
283	273	gap_column[gap_columns] = max_ali_len;
284	274
…	…
302	292
303	293	if (!err) {
304		int j = 0;
305		int i;
	294	size_t j = 0;
	295	size_t i;
306	296	for (i = 0; i<gap_columns; ++i) {
307	297	if (isGap(sdata[gap_column[i]])) {
…	…
311	301	}
312	302
313		int skipped_columns = i-j;
314		gap_columns -= skipped_columns;
315		awte_assert(gap_columns >= 0);
	303	awte_assert(i >= j);
	304	size_t skipped_columns = i-j;
	305	awte_assert(gap_columns >= skipped_columns);
	306	gap_columns -= skipped_columns;
316	307	}
317	308	++count;
…	…
325	316
326	317	if (!err) {
327		columns = filter->~~real_len~~ - gap_columns;
328		export_column = new int[columns];
329
330		int gpos = 0; // index into array of vertical gaps
331		int epos = 0; // index into array of exported columns
332		~~int flen = filter->real_len~~;
333		int a;
	318	columns = filter->get_filtered_length() - gap_columns;
	319	export_column = new size_t[columns];
	320
	321	size_t gpos = 0; // index into array of vertical gaps
	322	size_t epos = 0; // index into array of exported columns
	323	size_t flen = filter->get_filtered_length();
	324	size_t a;
334	325	for (a = 0; a<flen && gpos<gap_columns; ++a) {
335		~~int fpos = filter->~~filterpos_2_seqpos[a];
	326	size_t fpos = filterpos_2_seqpos[a];
336	327	if (fpos == gap_column[gpos]) { // only gaps here -> skip column
337	328	gpos++;
…	…
344	335	}
345	336	for (; a<flen; ++a) {
346		export_column[epos++] = filter~~->filter~~pos_2_seqpos[a];
	337	export_column[epos++] = filterpos_2_seqpos[a];
347	338	}
348	339
…	…
351	342
352	343	delete [] gap_column;
353		~~delete [] filter->filterpos_2_seqpos;~~
354		~~filter->filterpos_2_seqpos = 0;~~
355	344	}
356	345	else { // compress all or none (simply use filter)
357		export_column = filter->filterpos_2_seqpos;
358		filter->filterpos_2_seqpos = 0;
359		columns = filter->real_len;
	346	const size_t *filterpos_2_seqpos = filter->get_filterpos_2_seqpos();
	347
	348	columns = filter->get_filtered_length();
	349	export_column = new size_t[columns];
	350
	351	memcpy(export_column, filterpos_2_seqpos, columnssizeof(filterpos_2_seqpos));
360	352	}
361	353
…	…
377	369	}
378	370	else {
379		~~int~~ i;
380		const uchar *simplify = filter->~~simplify~~;
	371	size_t i;
	372	const uchar *simplify = filter->get_simplify_table();
381	373
382	374	if (cut_stop_codon) {
…	…
388	380
389	381	if (compress == 2) { // compress all gaps
390		int j = 0;
	382	size_t j = 0;
391	383	for (i = 0; i<columns; ++i) {
392	384	size_t seq_pos = export_column[i];

trunk/AWTI/Makefile

r6277	r6280
35	35	AWTI_export.o: $(ARBHOME)/INCLUDE/ad_prot.h
36	36	AWTI_export.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
	37	AWTI_export.o: $(ARBHOME)/INCLUDE/AP_filter.hxx
37	38	AWTI_export.o: $(ARBHOME)/INCLUDE/arb_assert.h
38	39	AWTI_export.o: $(ARBHOME)/INCLUDE/arb_error.h
…	…
43	44	AWTI_export.o: $(ARBHOME)/INCLUDE/attributes.h
44	45	AWTI_export.o: $(ARBHOME)/INCLUDE/aw_awars.hxx
45		~~AWTI_export.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx~~
46	46	AWTI_export.o: $(ARBHOME)/INCLUDE/aw_device.hxx
47	47	AWTI_export.o: $(ARBHOME)/INCLUDE/aw_global.hxx
…	…
51	51	AWTI_export.o: $(ARBHOME)/INCLUDE/aw_window.hxx
52	52	AWTI_export.o: $(ARBHOME)/INCLUDE/awt.hxx
53		AWTI_export.o: $(ARBHOME)/INCLUDE/awt_pro_a_nucs.hxx
54		AWTI_export.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx
55		AWTI_export.o: $(ARBHOME)/INCLUDE/awt_tree.hxx
	53	AWTI_export.o: $(ARBHOME)/INCLUDE/awt_filter.hxx
56	54	AWTI_export.o: $(ARBHOME)/INCLUDE/inline.h
57	55	AWTI_export.o: $(ARBHOME)/INCLUDE/smartptr.h

trunk/AWTI/awti_export.hxx

r6091	r6280
13	13	#define AWTI_EXPORT_HXX
14	14
15		#ifndef ARB~~_ASSER~~T_H
16		#include <arb~~_asser~~t.h>
	15	#ifndef ARBDBT_H
	16	#include <arbdbt.h>
17	17	#endif
	18
	19	class AW_window;
	20	class AW_root;
18	21
19	22	AW_window open_AWTC_export_window(AW_root awr,GBDATA *gb_main);

trunk/DIST/DI_clusters.cxx

r6252	r6280
48	48
49	49	void DI_create_cluster_awars(AW_root *aw_root, AW_default def, AW_default db) {
50		aw_root->awar_float(AWAR_CLUSTER_MAXDIST, ~~0.5~~, def)->set_minmax(0.0, 100.0);
	50	aw_root->awar_float(AWAR_CLUSTER_MAXDIST, 3.0, def)->set_minmax(0.0, 100.0);
51	51	aw_root->awar_int(AWAR_CLUSTER_MINSIZE, 7, def)->set_minmax(2, INT_MAX);
52	52	aw_root->awar_int(AWAR_CLUSTER_AUTOMARK, 1, def);

trunk/DIST/DI_compress_matrix.cxx

r6141	r6280
1		#include <stdio.h>
2		#include <string.h>
3		#include <stdlib.h>
4		#include <memory.h>
5
6		#include <arbdb.h>
7		#include <arbdbt.h>
8
9		#include <aw_root.hxx>
10		#include <aw_device.hxx>
11		#include <aw_window.hxx>
12		#include <aw_preset.hxx>
13
14		#include <awt_tree.hxx>
15		#include "dist.hxx"
16
17		#include <di_matr.hxx>
18		#include <di_view_matrix.hxx>
	1	#include "di_matr.hxx"
19	2
20	3	/* returns 1 only if groupname != null and there are species for that group */

trunk/DIST/DI_main.cxx

r6247	r6280
19	19
20	20	AW_window DI_create_matrix_window(AW_root aw_root);
21		void DI_create_matrix_variables(AW_root *aw_root, AW_default aw_def);
	21	void DI_create_matrix_variables(AW_root *aw_root, AW_default aw_def, AW_default db);
22	22	#ifdef FINDCORR
23	23	AW_window bc_create_main_window( AW_root awr);
…	…
81	81	}
82	82
83		DI_create_matrix_variables(aw_root,~~aw_default~~);
	83	DI_create_matrix_variables(aw_root, aw_default, GLOBAL_gb_main);
84	84	#ifdef FINDCORR
85	85	bc_create_bc_variables(aw_root,aw_default);

trunk/DIST/DI_matr.cxx

r6247	r6280
1		#include <stdio.h>
2		#include <stdlib.h>
3		#include <memory.h>
4		// #include <malloc.h>
5		#include <string.h>
6
7		#include <math.h>
8		#include <time.h>
9		#include <limits.h>
10
11		#include <arbdb.h>
12		#include <arbdbt.h>
13
14		#include <aw_root.hxx>
15		#include <aw_device.hxx>
16		#include <aw_window.hxx>
17		#include <aw_preset.hxx>
18		#include <aw_global.hxx>
19		#include <aw_awars.hxx>
20
21		#include <awt.hxx>
22		#include <awt_tree.hxx>
23		#include <awt_sel_boxes.hxx>
24		#include <awt_macro.hxx>
25		#include <awt_csp.hxx>
26
	1	// =============================================================== //
	2	// //
	3	// File : DI_matr.cxx //
	4	// Purpose : //
	5	// //
	6	// Institute of Microbiology (Technical University Munich) //
	7	// http://www.arb-home.de/ //
	8	// //
	9	// =============================================================== //
	10
	11	#include "di_protdist.hxx"
	12	#include "di_clusters.hxx"
27	13	#include "dist.hxx"
	14	#include "di_view_matrix.hxx"
	15	#include "di_matr.hxx"
	16	#include "di_awars.hxx"
	17
	18	#include <neighbourjoin.hxx>
	19	#include <AP_seq_dna.hxx>
	20	#include <AP_filter.hxx>
28	21	#include <BI_helix.hxx>
29	22	#include <CT_ctree.hxx>
30		#include "di_matr.hxx"
31		#include "di_protdist.hxx"
32		#include "di_view_matrix.hxx"
	23	#include <awt_macro.hxx>
	24	#include <awt.hxx>
	25	#include <awt_sel_boxes.hxx>
	26	#include <awt_filter.hxx>
	27	#include <awt_csp.hxx>
	28	#include <aw_preset.hxx>
	29	#include <aw_awars.hxx>
	30	#include <aw_global.hxx>
	31
	32	#include <gui_aliview.hxx>
	33
	34	#include <climits>
	35	#include <ctime>
33	36
34	37	#define di_assert(cond) arb_assert(cond)
…	…
36	39	// --------------------------------------------------------------------------------
37	40
38		~~#define AWAR_DIST_FILTER_PREFIX AWAR_DIST_PREFIX "filter/"~~
39		~~#define AWAR_DIST_COLUMN_STAT_PREFIX AWAR_DIST_PREFIX "col_stat/"~~
40		~~#define AWAR_DIST_TREE_PREFIX AWAR_DIST_PREFIX "tree/"~~
41
42		~~#define AWAR_DIST_MATRIX_DNA_BASE AWAR_DIST_PREFIX "dna/matrix"~~
43		~~#define AWAR_DIST_MATRIX_DNA_ENABLED "tmp/" AWAR_DIST_MATRIX_DNA_BASE "/enable"~~
44
45		~~#define AWAR_DIST_WHICH_SPECIES AWAR_DIST_PREFIX "which_species"~~
46		~~#define AWAR_DIST_ALIGNMENT AWAR_DIST_PREFIX "alignment"~~
47	41	#define AWAR_DIST_BOOTSTRAP_COUNT AWAR_DIST_PREFIX "bootstrap/count"
48	42	#define AWAR_DIST_CANCEL_CHARS AWAR_DIST_PREFIX "cancel/chars"
49	43
50		~~#define AWAR_DIST_FILTER_ALIGNMENT AWAR_DIST_FILTER_PREFIX "alignment"~~
51		~~#define AWAR_DIST_FILTER_NAME AWAR_DIST_FILTER_PREFIX "name"~~
52		~~#define AWAR_DIST_FILTER_FILTER AWAR_DIST_FILTER_PREFIX "filter"~~
53		~~#define AWAR_DIST_FILTER_SIMPLIFY AWAR_DIST_FILTER_PREFIX "simplify"~~
54
55	44	#define AWAR_DIST_COLUMN_STAT_ALIGNMENT AWAR_DIST_COLUMN_STAT_PREFIX "alignment"
56	45	#define AWAR_DIST_COLUMN_STAT_NAME AWAR_DIST_COLUMN_STAT_PREFIX "name"
57	46
58		~~#define AWAR_DIST_TREE_STD_NAME AWAR_DIST_TREE_PREFIX "tree_name"~~
59		~~#define AWAR_DIST_TREE_CURR_NAME "tmp/" AWAR_DIST_TREE_PREFIX "curr_tree_name"~~
60	47	#define AWAR_DIST_TREE_SORT_NAME "tmp/" AWAR_DIST_TREE_PREFIX "sort_tree_name"
61	48	#define AWAR_DIST_TREE_COMP_NAME "tmp/" AWAR_DIST_TREE_PREFIX "compr_tree_name"
	49	#define AWAR_DIST_TREE_STD_NAME AWAR_DIST_TREE_PREFIX "tree_name"
62	50
63	51	#define AWAR_DIST_SAVE_MATRIX_TYPE AWAR_DIST_SAVE_MATRIX_BASE "/type"
…	…
66	54	// --------------------------------------------------------------------------------
67	55
68		DI_MATRIX *DI_MATRIX::ROOT = 0;
69		DI_dmatrix *di_dmatrix = 0;
70		AWT_csp *global_csp = 0;
71
72		static adfiltercbstruct *dist_filter_cl = 0;
	56	DI_MATRIX *DI_MATRIX::ROOT = 0;
	57	DI_dmatrix *di_dmatrix = 0;
73	58
74	59	AP_matrix DI_dna_matrix(AP_MAX);
…	…
104	89	}
105	90
106		void DI_create_matrix_variables(AW_root *aw_root, AW_default def)
	91	void DI_create_matrix_variables(AW_root *aw_root, AW_default def, AW_default db)
107	92	{
108		GB_transaction dummy(~~GLOBAL_gb_main~~);
	93	GB_transaction dummy(db);
109	94	DI_dna_matrix.set_description("","");
110	95	DI_dna_matrix.x_description[AP_A] = strdup("A");
…	…
132	117	aw_root->awar_string(AWAR_DIST_WHICH_SPECIES, "marked", def)->add_callback(delete_matrix_cb);
133	118	{
134		char *default_ali = GBT_get_default_alignment(~~GLOBAL_gb_main~~);
	119	char *default_ali = GBT_get_default_alignment(db);
135	120	aw_root->awar_string( AWAR_DIST_ALIGNMENT,"",def) ->add_callback(delete_matrix_cb)->write_string(default_ali);
136	121	free(default_ali);
…	…
155	140	aw_root->awar_string(AWAR_DIST_TREE_STD_NAME, "tree_nj", def);
156	141	{
157		char *currentTree = aw_root->awar_string(AWAR_TREE, "", ~~GLOBAL_gb_main~~)->read_string();
	142	char *currentTree = aw_root->awar_string(AWAR_TREE, "", db)->read_string();
158	143	aw_root->awar_string(AWAR_DIST_TREE_CURR_NAME, currentTree, def);
159	144	aw_root->awar_string(AWAR_DIST_TREE_SORT_NAME, currentTree, def)->add_callback(delete_matrix_cb);
…	…
166	151	aw_root->awar_float(AWAR_DIST_MIN_DIST, 0.0);
167	152	aw_root->awar_float(AWAR_DIST_MAX_DIST, 0.0);
168
169		aw_root->awar_string(AWAR_SPECIES_NAME, "", GLOBAL_gb_main);
	153
	154	aw_root->awar_string(AWAR_SPECIES_NAME, "", db);
	155
	156	DI_create_cluster_awars(aw_root, def, db);
170	157
171	158	#if defined(DEBUG)
…	…
173	160	#endif // DEBUG
174	161
175		GB_push_transaction(GLOBAL_gb_main);
176
177		GBDATA *gb_species_data = GB_search(GLOBAL_gb_main,"species_data",GB_CREATE_CONTAINER);
178		GB_add_callback(gb_species_data,GB_CB_CHANGED,(GB_CB)delete_matrix_cb,0);
179
180		GB_pop_transaction(GLOBAL_gb_main);
181
182		}
183
184		DI_ENTRY::DI_ENTRY(GBDATA gbd,class DI_MATRIX phmatri) {
	162	{
	163	GB_push_transaction(db);
	164
	165	GBDATA *gb_species_data = GB_search(db,"species_data",GB_CREATE_CONTAINER);
	166	GB_add_callback(gb_species_data,GB_CB_CHANGED,(GB_CB)delete_matrix_cb,0);
	167
	168	GB_pop_transaction(db);
	169	}
	170	}
	171
	172	DI_ENTRY::DI_ENTRY(GBDATA gbd, DI_MATRIX phmatri) {
185	173	memset((char *)this,0,sizeof(DI_ENTRY));
186	174	phmatrix = phmatri;
187	175
188		GBDATA *gb_ali = GB_entry(gbd,~~phmatrix->use~~);
	176	GBDATA *gb_ali = GB_entry(gbd, phmatrix->get_aliname());
189	177	if (gb_ali) {
190	178	GBDATA *gb_data = GB_entry(gb_ali,"data");
191	179	if (gb_data) {
192		~~const char *seq = GB_read_char_pntr(gb_data);~~
193
194	180	if (phmatrix->is_AA) {
195		sequence = sequence_protein = new AP_sequence_simple_protein(phmatrix->~~tree_root~~);
	181	sequence = sequence_protein = new AP_sequence_simple_protein(phmatrix->get_aliview());
196	182	}
197	183	else {
198		sequence = sequence_parsimony = new AP_sequence_parsimony(phmatrix->tree_root);
199		}
200		sequence->set(seq);
	184	sequence = sequence_parsimony = new AP_sequence_parsimony(phmatrix->get_aliview());
	185	}
	186	sequence->bind_to_species(gbd);
	187	sequence->lazy_load_sequence(); // load sequence
201	188
202	189	name = GBT_read_string(gbd, "name");
…	…
206	193	}
207	194
208		DI_ENTRY::DI_ENTRY(char namei,~~class~~ DI_MATRIX phmatri)
	195	DI_ENTRY::DI_ENTRY(char namei, DI_MATRIX phmatri)
209	196	{
210	197	memset((char *)this,0,sizeof(DI_ENTRY));
…	…
222	209	}
223	210
224		DI_MATRIX::DI_MATRIX(GBDATA gb_maini,AW_root awr)
225		{
226		memset((char *)this,0,sizeof(DI_MATRIX));
	211	DI_MATRIX::DI_MATRIX(const AliView& aliview_, AW_root *awr) {
	212	memset((char )this, 0, sizeof(this));
227	213	aw_root = awr;
228		gb_main = gb_maini;
229		}
230
231		char *DI_MATRIX::unload(void)
232		{
233		freeset(use, 0);
234		long i;
235		for (i=0;i<nentries;i++){
	214	aliview = new AliView(aliview_);
	215	}
	216
	217	char *DI_MATRIX::unload() {
	218	for (long i=0; i<nentries; i++) {
236	219	delete entries[i];
237	220	}
238		~~delete tree_root;~~
239	221	freeset(entries, 0);
240	222	nentries = 0;
…	…
242	224	}
243	225
244		DI_MATRIX::~DI_MATRIX(~~void~~)
	226	DI_MATRIX::~DI_MATRIX()
245	227	{
246	228	unload();
247	229	delete matrix;
	230	delete aliview;
248	231	}
249	232
…	…
255	238	}
256	239
257		char DI_MATRIX::load(char usei, AP_filter filter, AP_weights weights, LoadWhat what, GB_CSTR sort_tree_name, bool show_warnings, GBDATA **species_list) {
258		delete tree_root;
259		tree_root = new AP_tree_root(gb_main,0,0);
260		tree_root->filter = filter;
261		tree_root->weights = weights;
262		this->use = strdup(usei);
263		this->gb_main = GLOBAL_gb_main;
	240	char DI_MATRIX::load(LoadWhat what, GB_CSTR sort_tree_name, bool show_warnings, GBDATA *species_list) {
	241	GBDATA *gb_main = get_gb_main();
	242	const char *use = get_aliname();
	243
264	244	GB_push_transaction(gb_main);
265	245
…	…
452	432	}
453	433
454		long DI_MATRIX::create_helix_filter(BI_helix helix,AP_filter *filter){
455		long result = (long )calloc(sizeof(long),(size_t)filter->real_len);
456		long temp = (long )calloc(sizeof(long),(size_t)filter->real_len);
457		int i,count;
458		count = 0;
459		for (i=0;i<filter->filter_len;i++) {
460		if (filter->filter_mask[i]) {
	434	long DI_MATRIX::create_helix_filter(BI_helix helix, const AP_filter *filter){
	435	long result = (long )calloc(sizeof(long), filter->get_filtered_length());
	436	long temp = (long )calloc(sizeof(long), filter->get_filtered_length());
	437	int count = 0;
	438	size_t i;
	439
	440	for (i=0; i<filter->get_length(); i++) {
	441	if (filter->use_position(i)) {
461	442	temp[i] = count;
462	443	if (helix->pairtype(i)== HELIX_PAIR) {
463	444	result[count] = helix->opposite_position(i);
464		}else{
	445	}
	446	else {
465	447	result[count] = -1;
466	448	}
…	…
482	464	return "There are no species selected";
483	465	}
484		long row,col,pos,s_len;
485		unsigned char seq1,seq2;
486		s_len = tree_root->filter->real_len;
	466	long row,col,pos,s_len;
	467
	468	const unsigned char seq1,seq2;
	469	s_len = aliview->get_length();
487	470	this->clear(hrates);
488	471	this->clear(nrates);
…	…
492	475	if (aw_status(gauge*gauge)) return "Aborted";
493	476	for (col=0; col<row; col++) {
494		seq1 = ~~(unsigned char *)entries[row]->sequence_parsimony->sequence~~;
495		seq2 = ~~(unsigned char *)entries[col]->sequence_parsimony->sequence~~;
	477	seq1 = entries[row]->sequence_parsimony->get_usequence();
	478	seq2 = entries[col]->sequence_parsimony->get_usequence();
496	479	for (pos = 0; pos < s_len; pos++){
497	480	if(filter[pos]>=0) {
…	…
505	488	}
506	489	for (row = 0; row<nentries;row++){
507		seq1 = ~~(unsigned char *)entries[row]->sequence_parsimony->sequence~~;
	490	seq1 = entries[row]->sequence_parsimony->get_usequence();
508	491	for (pos = 0; pos < s_len; pos++){
509	492	if(filter[pos]>=0) {
…	…
525	508	static BI_helix *helix = 0;
526	509	if (!helix) helix = new BI_helix();
527		const char *error = helix->init(g~~b_main~~);
	510	const char *error = helix->init(get_gb_main());
528	511	if (error) return error;
529	512
…	…
535	518
536	519	fprintf(out,"Pairs in helical regions:\n");
537		long *filter = create_helix_filter(helix,~~tree_root->filter~~);
	520	long *filter = create_helix_filter(helix, aliview->get_filter());
538	521	error = calculate_rates(temp,temp2,pairs,filter);
539	522	if (error){
…	…
549	532	rate_write(temp2,out);
550	533
551		long row,col,pos,s_len;
552		char seq1,seq2;
553		s_len = ~~tree_root->filter->real_len~~;
	534	long row,col,pos,s_len;
	535
	536	s_len = aliview->get_length();
554	537	fprintf(out,"\nDistance matrix (Helixdist Helixlen Nonhelixdist Nonhelixlen):");
555	538	fprintf(out,"\n%li",nentries);
	539
556	540	const int MAXDISTDEBUG = 1000;
557		double distdebug[MAXDISTDEBUG];
	541	double distdebug[MAXDISTDEBUG];
	542
558	543	for (pos = 0;pos<MAXDISTDEBUG;pos++) distdebug[pos] = 0.0;
	544
559	545	for (row = 0; row<nentries;row++){
560	546	if ( nentries > 100 \|\| ((row&0xf) == 0)){
…	…
568	554
569	555	for (col=0; col<row; col++) {
570		seq1 = entries[row]->sequence_parsimony->sequence;
571		seq2= entries[col]->sequence_parsimony->sequence;
	556	const unsigned char seq1,seq2;
	557
	558	seq1 = entries[row]->sequence_parsimony->get_usequence();
	559	seq2 = entries[col]->sequence_parsimony->get_usequence();
572	560	this->clear(temp);
573	561	this->clear(temp2);
	562
574	563	for (pos = 0; pos < s_len; pos++){
575		if(filter[pos]>=0) {
576		temp[(unsigned char)seq1][(unsigned char)seq2]++;
577		}else{
578		temp2[(unsigned char)seq1][(unsigned char)seq2]++;
579		}
	564	if (filter[pos]>=0) temp [seq1][seq2]++;
	565	else temp2[seq1][seq2]++;
580	566	seq1++; seq2++;
581	567	}
…	…
619	605	char DI_MATRIX::calculate_overall_freqs(double rel_frequencies[AP_MAX], char cancel)
620	606	{
621		long hits2[AP_MAX];
622		long sum = 0;
623		int i,row;
624		char *seq1;
625		int pos;
626		int b;
627		long s_len = tree_root->filter->real_len;
	607	long hits2[AP_MAX];
	608	long sum = 0;
	609	int i,row;
	610	int pos;
	611	int b;
	612	long s_len = aliview->get_length();
628	613
629	614	memset((char *) &hits2[0], 0, sizeof(hits2));
630	615	for (row = 0; row < nentries; row++) {
631		~~seq1 = entries[row]->sequence_parsimony->sequence~~;
	616	const char *seq1 = entries[row]->sequence_parsimony->get_sequence();
632	617	for (pos = 0; pos < s_len; pos++) {
633	618	b = *(seq1++);
…	…
678	663	matrix = new AP_smatrix(nentries);
679	664
680		long s_len = ~~tree_root->filter->real_len~~;
	665	long s_len = aliview->get_length();
681	666	long hits[AP_MAX][AP_MAX];
682	667	int row;
…	…
719	704	for (col=0; col<=row; col++) {
720	705	columns = 0;
721		c~~har *seq1 = entries[row]->sequence_parsimony->sequence~~;
722		c~~har *seq2 = entries[col]->sequence_parsimony->sequence~~;
	706	const unsigned char *seq1 = entries[row]->sequence_parsimony->get_usequence();
	707	const unsigned char *seq2 = entries[col]->sequence_parsimony->get_usequence();
723	708	b = 0.0;
724	709	switch(transformation){
…	…
732	717	int pos;
733	718	for (pos = s_len; pos >=0; pos--){
734		hits[~~(unsigned char)(seq1++)][(unsigned char)~~(seq2++)]++;
	719	hits[(seq1++)][(seq2++)]++;
735	720	}
736	721	int x,y;
…	…
782	767	memset((char )hits,0,sizeof(long) AP_MAX * AP_MAX);
783	768	for (pos = s_len; pos >=0; pos--){
784		hits[~~(unsigned char)(seq1++)][(unsigned char)~~(seq2++)]++;
	769	hits[(seq1++)][(seq2++)]++;
785	770	}
786	771	switch(transformation){
…	…
890	875	matrix = new AP_smatrix(nentries);
891	876
892		di_protdist prodist(whichcode, whichcat, nentries,~~entries, tree_root->filter->real_len,~~matrix);
	877	di_protdist prodist(whichcode, whichcat, nentries, entries, aliview->get_length(), matrix);
893	878	return prodist.makedists();
894	879	}
895	880
896		static GB_ERROR di_calculate_matrix_cb(AW_window *aww, AW_CL bootstrap_flag, AW_CL cl_show_warnings) // returns "Aborted" if stopped by user
897		{
898		bool show_warnings = (bool)cl_show_warnings;
	881	static GB_ERROR di_calculate_matrix(AW_window aww, const WeightedFilter weighted_filter, bool bootstrap_flag, bool show_warnings) {
	882	// returns "Aborted" if stopped by user
899	883	GB_push_transaction(GLOBAL_gb_main);
900	884	if (DI_MATRIX::ROOT){
…	…
918	902	char *cancel = aw_root->awar(AWAR_DIST_CANCEL_CHARS)->read_string();
919	903
920		AP_filter *ap_filter = awt_get_filter(aw_root, dist_filter_cl);
921		if (bootstrap_flag){
922		ap_filter->enable_bootstrap();
923		}
924
925		AP_weights *ap_weights = new AP_weights;
926		ap_weights->init(ap_filter);
	904	AliView *aliview = weighted_filter->create_aliview(use);
	905	if (bootstrap_flag) aliview->get_filter()->enable_bootstrap();
927	906
928	907	char *load_what = aw_root->awar(AWAR_DIST_WHICH_SPECIES)->read_string();
…	…
932	911	GB_ERROR error = 0;
933	912	{
934		DI_MATRIX *phm ~~= new DI_MATRIX(GLOBAL_gb_main,~~aw_root);
	913	DI_MATRIX phm = new DI_MATRIX(aliview, aw_root);
935	914	phm->matrix_type = DI_MATRIX_FULL;
936		phm->load(use, ap_filter, ap_weights, all_flag, sort_tree_name, show_warnings, NULL);
	915	phm->load(all_flag, sort_tree_name, show_warnings, NULL);
	916
937	917	free(sort_tree_name);
938	918	GB_pop_transaction(GLOBAL_gb_main);
939	919	if (aw_status()) {
940	920	phm->unload();
941		return "Aborted";
942		}
943
944		DI_TRANSFORMATION trans = (DI_TRANSFORMATION)aw_root->awar(AWAR_DIST_CORR_TRANS)->read_int();
945
946		if (phm->is_AA){
947		error = phm->calculate_pro(trans);
948		}else{
949		error = phm->calculate(aw_root,cancel,0.0,trans);
950		}
951		if (!bootstrap_flag){
952		aw_closestatus();
953		}
	921	error = "Aborted";
	922	}
	923	else {
	924	DI_TRANSFORMATION trans = (DI_TRANSFORMATION)aw_root->awar(AWAR_DIST_CORR_TRANS)->read_int();
	925
	926	if (phm->is_AA) error = phm->calculate_pro(trans);
	927	else error = phm->calculate(aw_root,cancel,0.0,trans);
	928	}
	929	if (!bootstrap_flag) aw_closestatus();
954	930	delete phm->ROOT;
955	931	if (error && strcmp(error,"Aborted")){
…	…
960	936	else {
961	937	phm->ROOT = phm;
962
963	938	}
964	939	}
…	…
966	941
967	942	free(cancel);
968		delete ap_filter;
969		delete ap_weights;
	943	delete aliview;
970	944
971	945	free(use);
…	…
973	947	}
974	948
975		static void di_mark_by_distance(AW_window *aww) {
	949	static void di_mark_by_distance(AW_window *aww, AW_CL cl_weightedFilter) {
976	950	AW_root *aw_root = aww->get_root();
977	951	double lowerBound = aw_root->awar(AWAR_DIST_MIN_DIST)->read_float();
…	…
1003	977	}
1004	978	else {
1005		char *use = aw_root->awar(AWAR_DIST_ALIGNMENT)->read_string();
1006		char *cancel = aw_root->awar(AWAR_DIST_CANCEL_CHARS)->read_string();
1007		AP_filter *ap_filter = awt_get_filter(aw_root,dist_filter_cl);
1008		AP_weights *ap_weights = new AP_weights;
1009		AP_smatrix *ap_ratematrix = 0;
1010		DI_TRANSFORMATION trans = (DI_TRANSFORMATION)aw_root->awar(AWAR_DIST_CORR_TRANS)->read_int();
1011
1012		ap_weights->init(ap_filter);
	979	char *use = aw_root->awar(AWAR_DIST_ALIGNMENT)->read_string();
	980	char *cancel = aw_root->awar(AWAR_DIST_CANCEL_CHARS)->read_string();
	981	AP_smatrix *ap_ratematrix = 0;
	982	DI_TRANSFORMATION trans = (DI_TRANSFORMATION)aw_root->awar(AWAR_DIST_CORR_TRANS)->read_int();
	983	WeightedFilter weighted_filter = (WeightedFilter)cl_weightedFilter;
	984	AliView *aliview = weighted_filter->create_aliview(use);
1013	985
1014	986	if (!error) {
…	…
1028	1000	gb_species = GBT_next_species(gb_species))
1029	1001	{
1030		DI_MATRIX *phm = new DI_MATRIX(~~GLOBAL_gb_main~~, aw_root);
	1002	DI_MATRIX phm = new DI_MATRIX(aliview, aw_root);
1031	1003	phm->matrix_type = DI_MATRIX_FULL;
1032	1004	GBDATA *species_pair[] = { gb_selected, gb_species, NULL };
1033	1005
1034		phm->load(~~use, ap_filter, ap_weights,~~ DI_LOAD_LIST, NULL, false, species_pair);
	1006	phm->load(DI_LOAD_LIST, NULL, false, species_pair);
1035	1007
1036	1008	if (phm->is_AA){
…	…
1064	1036
1065	1037	delete ap_ratematrix;
1066		delete ap_weights;
1067		delete ap_filter;
	1038	delete aliview;
1068	1039	free(cancel);
1069	1040	free(use);
…	…
1088	1059	}
1089	1060
1090		static void di_view_matrix_cb(AW_window *aww){
1091		GB_ERROR error = di_calculate_matrix_cb(aww,0,true);
	1061	static void di_view_matrix_cb(AW_window *aww, AW_CL cl_sparam) {
	1062	save_matrix_params sparam = (save_matrix_params)cl_sparam;
	1063	GB_ERROR error = di_calculate_matrix(aww, sparam->weighted_filter, 0, true);
1092	1064	if (error) return;
1093	1065
…	…
1097	1069	if (!viewer) {
1098	1070	AW_root *aw_root = aww->get_root();
1099		viewer = DI_create_view_matrix_window(aw_root, di_dmatrix);
	1071	viewer = DI_create_view_matrix_window(aw_root, di_dmatrix, sparam);
1100	1072
1101	1073	AW_awar *awar_sel = aw_root->awar(AWAR_SPECIES_NAME);
…	…
1109	1081	}
1110	1082
1111		static void di_save_matrix_cb(AW_window *aww)
1112		{
	1083	static void di_save_matrix_cb(AW_window *aww, AW_CL cl_weightedFilter) {
1113	1084	// save the matrix
1114		GB_ERROR error = di_calculate_matrix_cb(aww,0, true);
	1085	WeightedFilter weighted_filter = (WeightedFilter)cl_weightedFilter;
	1086	GB_ERROR error = di_calculate_matrix(aww, weighted_filter, 0, true);
1115	1087	if (!error) {
1116	1088	char *filename = aww->get_root()->awar(AWAR_DIST_SAVE_MATRIX_FILENAME)->read_string();
…	…
1124	1096	}
1125	1097
1126		AW_window DI_create_save_matrix_window(AW_root aw_root, char *base_name)
1127		{
	1098	AW_window DI_create_save_matrix_window(AW_root aw_root, save_matrix_params *save_params) {
1128	1099	static AW_window_simple *aws = 0;
1129		if (aws) return aws;
1130		aws = new AW_window_simple;
1131		aws->init( aw_root, "SAVE_MATRIX", "Save Matrix");
1132		aws->load_xfig("sel_box_user.fig");
1133
1134		aws->at("close");aws->callback((AW_CB0)AW_POPDOWN);
1135		aws->create_button("CLOSE", "CANCEL","C");
1136
1137
1138		aws->at("help");aws->callback(AW_POPUP_HELP,(AW_CL)"save_matrix.hlp");
1139		aws->create_button("HELP", "HELP","H");
1140
1141		aws->at("user");
1142		aws->create_option_menu(AWAR_DIST_SAVE_MATRIX_TYPE);
1143		aws->insert_default_option("Phylip Format (Lower Triangular Matrix)","P",DI_SAVE_PHYLIP_COMP);
1144		aws->insert_option("Readable (using NDS)","R",DI_SAVE_READABLE);
1145		aws->insert_option("Tabbed (using NDS)","R",DI_SAVE_TABBED);
1146		aws->update_option_menu();
1147
1148		awt_create_selection_box((AW_window *)aws,base_name);
1149
1150		aws->at("save2");aws->callback(di_save_matrix_cb);
1151		aws->create_button("SAVE", "SAVE","S");
1152
1153		aws->callback( (AW_CB0)AW_POPDOWN);
1154		aws->at("cancel2");
1155		aws->create_button("CLOSE", "CANCEL","C");
1156
	1100	if (!aws) {
	1101	aws = new AW_window_simple;
	1102	aws->init( aw_root, "SAVE_MATRIX", "Save Matrix");
	1103	aws->load_xfig("sel_box_user.fig");
	1104
	1105	aws->at("close");aws->callback((AW_CB0)AW_POPDOWN);
	1106	aws->create_button("CLOSE", "CANCEL","C");
	1107
	1108
	1109	aws->at("help");aws->callback(AW_POPUP_HELP,(AW_CL)"save_matrix.hlp");
	1110	aws->create_button("HELP", "HELP","H");
	1111
	1112	aws->at("user");
	1113	aws->create_option_menu(AWAR_DIST_SAVE_MATRIX_TYPE);
	1114	aws->insert_default_option("Phylip Format (Lower Triangular Matrix)","P",DI_SAVE_PHYLIP_COMP);
	1115	aws->insert_option("Readable (using NDS)","R",DI_SAVE_READABLE);
	1116	aws->insert_option("Tabbed (using NDS)","R",DI_SAVE_TABBED);
	1117	aws->update_option_menu();
	1118
	1119	awt_create_selection_box((AW_window *)aws, save_params->awar_base);
	1120
	1121	aws->at("save2");
	1122	aws->callback(di_save_matrix_cb, (AW_CL)save_params->weighted_filter);
	1123	aws->create_button("SAVE", "SAVE","S");
	1124
	1125	aws->callback( (AW_CB0)AW_POPDOWN);
	1126	aws->at("cancel2");
	1127	aws->create_button("CLOSE", "CANCEL","C");
	1128	}
1157	1129	return aws;
1158	1130	}
…	…
1206	1178	}
1207	1179
1208		static void di_calculate_tree_cb(AW_window *aww, AW_CL bootstrap_flag)
	1180	static void di_calculate_tree_cb(AW_window *aww, AW_CL cl_weightedFilter, AW_CL bootstrap_flag)
1209	1181	{
1210	1182	AW_root *aw_root = aww->get_root();
…	…
1226	1198	int last_status_upd = 0;
1227	1199
	1200	WeightedFilter weighted_filter = (WeightedFilter)cl_weightedFilter;
	1201
1228	1202	if (!error) {
1229	1203	{
…	…
1244	1218
1245	1219	gb_assert(DI_MATRIX::ROOT == 0);
1246		di_calculate_matrix~~_cb(aww,~~bootstrap_flag, true);
	1220	di_calculate_matrix(aww, weighted_filter, bootstrap_flag, true);
1247	1221
1248	1222	DI_MATRIX *matr = DI_MATRIX::ROOT;
…	…
1290	1264	DI_MATRIX::ROOT = 0;
1291	1265
1292		error = di_calculate_matrix~~_cb(aww~~, bootstrap_flag, bootstrap_flag ? false : true);
	1266	error = di_calculate_matrix(aww, weighted_filter, bootstrap_flag, bootstrap_flag ? false : true);
1293	1267	if (error && strcmp(error,"Aborted") == 0) {
1294	1268	error = 0; // clear error (otherwise no tree will be read below)
…	…
1384	1358	aw_status("Read the database");
1385	1359
1386		~~DI_MATRIX *phm = new DI_MATRIX(GLOBAL_gb_main,aw_root);~~
1387	1360	char *filter_str = aw_root->awar(AWAR_DIST_FILTER_FILTER)->read_string();
1388	1361	char *cancel = aw_root->awar(AWAR_DIST_CANCEL_CHARS)->read_string();
1389	1362
1390		AP_filter *ap_filter = new AP_filter;
1391		long flen = strlen(filter_str);
1392		if (flen == ali_len){
1393		ap_filter->init(filter_str,"0",ali_len);
1394		}else{
1395		if (flen){
1396		aw_message("WARNING: YOUR FILTER LEN IS NOT THE ALIGNMENT LEN\nFILTER IS TRUNCATED WITH ZEROS OR CUTTED");
1397		ap_filter->init(filter_str,"0",ali_len);
1398		}else{
1399		ap_filter->init(ali_len);
1400		}
1401		}
1402
1403		AP_weights *ap_weights = new AP_weights;
1404		ap_weights->init(ap_filter);
1405
	1363	AliView *aliview;
	1364	{
	1365	AP_filter *ap_filter = NULL;
	1366	long flen = strlen(filter_str);
	1367
	1368	if (flen == ali_len){
	1369	ap_filter = new AP_filter(filter_str, "0", ali_len);
	1370	}
	1371	else {
	1372	if (flen) {
	1373	aw_message("WARNING: YOUR FILTER LEN IS NOT THE ALIGNMENT LEN\nFILTER IS TRUNCATED WITH ZEROS OR CUTTED");
	1374	ap_filter = new AP_filter(filter_str, "0", ali_len);
	1375	}
	1376	else {
	1377	ap_filter = new AP_filter(ali_len); // unfiltered
	1378	}
	1379	}
	1380
	1381	AP_weights ap_weights(ap_filter);
	1382
	1383	aliview = new AliView(GLOBAL_gb_main, *ap_filter, ap_weights, use);
	1384	delete ap_filter;
	1385	}
	1386
	1387	DI_MATRIX phm = new DI_MATRIX(aliview,aw_root);
	1388
1406	1389	char *load_what = aw_root->awar(AWAR_DIST_WHICH_SPECIES)->read_string();
1407	1390	char *sort_tree_name = aw_root->awar(AWAR_DIST_TREE_SORT_NAME)->read_string();
1408
	1391
1409	1392	LoadWhat all_flag = (strcmp(load_what,"all") == 0) ? DI_LOAD_ALL : DI_LOAD_MARKED;
1410	1393
1411	1394	delete phm->ROOT;
1412	1395	phm->ROOT = 0;
1413		phm->load(use, ap_filter, ap_weights, all_flag, sort_tree_name, true, NULL);
	1396
	1397	phm->load(all_flag, sort_tree_name, true, NULL);
1414	1398	free(sort_tree_name);
1415	1399	GB_pop_transaction(GLOBAL_gb_main);
…	…
1420	1404	trans = (DI_TRANSFORMATION)aw_root->awar(AWAR_DIST_CORR_TRANS)->read_int();
1421	1405
1422
1423		char *error = phm->analyse(aw_root);
	1406	phm->analyse();
1424	1407	aw_closestatus();
1425	1408
1426	1409	delete phm;
1427		~~if (error) aw_message(error);~~
1428	1410
1429	1411	free(load_what);
1430	1412
1431	1413	free(cancel);
1432		delete ap_filter;
1433		delete ap_weights;
	1414	delete aliview;
1434	1415
1435	1416	free(use);
…	…
1445	1426	}
1446	1427
1447		static void di_calculate_full_matrix_cb(AW_window *aww){
	1428	static void di_calculate_full_matrix_cb(AW_window *aww, AW_CL cl_weightedFilter){
1448	1429	if (DI_MATRIX::ROOT && DI_MATRIX::ROOT->matrix_type == DI_MATRIX_FULL) return;
1449	1430	delete_matrix_cb(0);
1450		di_calculate_matrix_cb(aww,0, true);
	1431	WeightedFilter weighted_filter = (WeightedFilter)cl_weightedFilter;
	1432	di_calculate_matrix(aww, weighted_filter, 0, true);
1451	1433	if (di_dmatrix){
1452	1434	di_dmatrix->resized();
…	…
1455	1437	}
1456	1438
1457		static void di_compress_tree_cb(AW_window *aww){
	1439	static void di_compress_tree_cb(AW_window *aww, AW_CL cl_weightedFilter) {
1458	1440	GB_transaction dummy(GLOBAL_gb_main);
1459	1441	char *treename = aww->get_root()->awar(AWAR_DIST_TREE_COMP_NAME)->read_string();
…	…
1466	1448	}
1467	1449
1468		di_calculate_matrix_cb(aww,0, true);
	1450	WeightedFilter weighted_filter = (WeightedFilter)cl_weightedFilter;
	1451	di_calculate_matrix(aww, weighted_filter, 0, true);
1469	1452	if (!DI_MATRIX::ROOT) error = "Cannot calculate your matrix";
1470	1453
…	…
1538	1521	AW_window DI_create_matrix_window(AW_root aw_root) {
1539	1522	AW_window_simple_menu *aws = new AW_window_simple_menu;
1540		aws->init( aw_root, "NEIGHBOUR JOINING", "NEIGHBOUR JOINING");
	1523	aws->init( aw_root, "NEIGHBOUR JOINING", "NEIGHBOUR JOINING [ARB_DIST]");
1541	1524	aws->load_xfig("di_ge_ma.fig");
1542	1525	aws->button_length( 10 );
…	…
1569	1552
1570	1553	aws->insert_help_topic("help ...", "h", "dist.hlp", AWM_ALL, (AW_CB)AW_POPUP_HELP, (AW_CL)"dist.hlp", 0);
	1554
	1555	// ------------------
	1556	// left side
1571	1557
1572	1558	aws->at( "which_species" );
…	…
1579	1565	awt_create_selection_list_on_ad(GLOBAL_gb_main, (AW_window )aws,AWAR_DIST_ALIGNMENT,"=");
1580	1566
	1567	// filter & weights
	1568
	1569	WeightedFilter *weighted_filter = // do NOT free (bound to callbacks)
	1570	new WeightedFilter(GLOBAL_gb_main, aws->get_root(), AWAR_DIST_FILTER_NAME, AWAR_DIST_COLUMN_STAT_NAME);
	1571
1581	1572	aws->at("filter_select");
1582		dist_filter_cl = awt_create_select_filter(aws->get_root(), GLOBAL_gb_main, AWAR_DIST_FILTER_NAME);
1583		aws->callback(AW_POPUP, (AW_CL)awt_create_select_filter_win, (AW_CL)dist_filter_cl);
	1573	aws->callback(AW_POPUP, (AW_CL)awt_create_select_filter_win, (AW_CL)(weighted_filter->get_adfiltercbstruct()));
1584	1574	aws->create_button("SELECT_FILTER", AWAR_DIST_FILTER_NAME);
1585	1575
1586	1576	aws->at("weights_select");
1587	1577	aws->sens_mask(AWM_EXP);
1588		global_csp = new AWT_csp(GLOBAL_gb_main,aws->get_root(),AWAR_DIST_COLUMN_STAT_NAME);
1589		aws->callback(AW_POPUP,(AW_CL)create_csp_window, (AW_CL)global_csp);
	1578	aws->callback(AW_POPUP,(AW_CL)create_csp_window, (AW_CL)weighted_filter->get_csp());
1590	1579	aws->create_button("SELECT_COL_STAT",AWAR_DIST_COLUMN_STAT_NAME);
1591	1580	aws->sens_mask(AWM_ALL);
…	…
1625	1614	aws->update_option_menu();
1626	1615
	1616	aws->at("autodetect"); // auto
	1617	aws->callback(di_autodetect_callback);
	1618	aws->sens_mask(AWM_EXP);
	1619	aws->create_button("AUTODETECT_CORRECTION", "AUTODETECT","A");
	1620	aws->sens_mask(AWM_ALL);
	1621
1627	1622	// -------------------
1628	1623	// right side
1629		// -------------------
	1624
1630	1625
1631	1626	aws->at("mark_distance");
1632		aws->callback(di_mark_by_distance);
	1627	aws->callback(di_mark_by_distance, (AW_CL)weighted_filter);
1633	1628	aws->create_autosize_button("MARK_BY_DIST", "Mark all species");
1634	1629
…	…
1641	1636	// -----------------
1642	1637
1643		aws->button_length(18);
1644
1645		// aws->at("compress");
1646		// aws->callback(AW_POPUP, (AW_CL)create_select_compress_tree,0);
1647		// aws->help_text("compress_tree.hlp");
1648		// aws->create_button("CALC_COMPRESSED_MATRIX", "Calculate\nCompressed M. ...","C");
1649
1650		aws->at("compress");
1651		aws->callback(di_compress_tree_cb);
1652		aws->create_button("CALC_COMPRESSED_MATRIX", "Calculate\nCompressed Matrix","C");
1653
1654		aws->at("calculate");
1655		aws->callback(di_calculate_full_matrix_cb);
1656		aws->create_button("CALC_FULL_MATRIX", "Calculate\nFull Matrix","F");
1657
1658		aws->button_length(13);
1659
1660		aws->at("save_matrix");
1661		aws->callback(AW_POPUP, (AW_CL)DI_create_save_matrix_window,(AW_CL)AWAR_DIST_SAVE_MATRIX_BASE);
1662		aws->create_button("SAVE_MATRIX", "Save matrix","M");
1663
1664		aws->at("view_matrix");
1665		aws->callback(di_view_matrix_cb);
1666		aws->create_button("VIEW_MATRIX", "View matrix","V");
	1638	// tree selection
1667	1639
1668	1640	aws->at("tree_list");
1669	1641	awt_create_selection_list_on_trees(GLOBAL_gb_main,(AW_window *)aws,AWAR_DIST_TREE_CURR_NAME);
1670	1642
	1643	aws->at("detect_clusters");
	1644	aws->callback(AW_POPUP, (AW_CL)DI_create_cluster_detection_window, (AW_CL)weighted_filter);
	1645	aws->create_autosize_button("DETECT_CLUSTERS", "Detect homogenous clusters in tree","D");
	1646
	1647	// matrix calculation
	1648
1671	1649	aws->button_length(18);
1672
1673		aws->at("t_calculate");
1674		aws->callback(di_calculate_tree_cb,0);
1675		aws->create_button("CALC_TREE", "Calculate \ntree","C");
1676
1677		aws->at("bootstrap");
1678		aws->callback(di_calculate_tree_cb,1);
1679		aws->create_button("CALC_BOOTSTRAP_TREE", "Calculate \nbootstrap tree");
1680
1681		aws->at("bcount");
1682		aws->create_input_field(AWAR_DIST_BOOTSTRAP_COUNT, 7);
1683
1684		aws->at("autodetect"); // auto
1685		aws->callback(di_autodetect_callback);
1686		aws->sens_mask(AWM_EXP);
1687		aws->create_button("AUTODETECT_CORRECTION", "AUTODETECT","A");
1688		aws->sens_mask(AWM_ALL);
1689
1690		aws->at("sort_tree_name");
1691		aws->create_input_field(AWAR_DIST_TREE_SORT_NAME,12);
1692		aws->at("compr_tree_name");
1693		aws->create_input_field(AWAR_DIST_TREE_COMP_NAME,12);
1694		aws->at("calc_tree_name");
1695		aws->create_input_field(AWAR_DIST_TREE_STD_NAME,12);
	1650	aws->at("calculate");
	1651	aws->callback(di_calculate_full_matrix_cb, (AW_CL)weighted_filter);
	1652	aws->create_button("CALC_FULL_MATRIX", "Calculate\nFull Matrix","F");
	1653	aws->at("compress");
	1654	aws->callback(di_compress_tree_cb, (AW_CL)weighted_filter);
	1655	aws->create_button("CALC_COMPRESSED_MATRIX", "Calculate\nCompressed Matrix","C");
	1656
	1657	aws->button_length(13);
	1658
	1659	{
	1660	save_matrix_params *sparams = new save_matrix_params; // do not free (bound to callbacks)
	1661
	1662	sparams->awar_base = AWAR_DIST_SAVE_MATRIX_BASE;
	1663	sparams->weighted_filter = weighted_filter;
	1664
	1665	aws->at("save_matrix");
	1666	aws->callback(AW_POPUP, (AW_CL)DI_create_save_matrix_window,(AW_CL)sparams);
	1667	aws->create_button("SAVE_MATRIX", "Save matrix","M");
	1668
	1669	aws->at("view_matrix");
	1670	aws->callback(di_view_matrix_cb, (AW_CL)sparams);
	1671	aws->create_button("VIEW_MATRIX", "View matrix","V");
	1672	}
1696	1673
1697	1674	aws->button_length(22);
1698
1699	1675	aws->at("use_compr_tree");
1700	1676	aws->callback(di_define_compression_tree_name_cb);
1701	1677	aws->create_button("USE_COMPRESSION_TREE", "Use to compress", "");
1702
1703	1678	aws->at("use_sort_tree");
1704	1679	aws->callback(di_define_sort_tree_name_cb);
1705	1680	aws->create_button("USE_SORT_TREE", "Use to sort", "");
1706	1681
	1682	aws->at("compr_tree_name");
	1683	aws->create_input_field(AWAR_DIST_TREE_COMP_NAME,12);
	1684	aws->at("sort_tree_name");
	1685	aws->create_input_field(AWAR_DIST_TREE_SORT_NAME,12);
	1686
	1687	// tree calculation
	1688
	1689	aws->button_length(18);
	1690	aws->at("t_calculate");
	1691	aws->callback(di_calculate_tree_cb, (AW_CL)weighted_filter, 0);
	1692	aws->create_button("CALC_TREE", "Calculate \ntree","C");
	1693	aws->at("bootstrap");
	1694	aws->callback(di_calculate_tree_cb, (AW_CL)weighted_filter, 1);
	1695	aws->create_button("CALC_BOOTSTRAP_TREE", "Calculate \nbootstrap tree");
	1696
	1697	aws->button_length(22);
1707	1698	aws->at("use_existing");
1708	1699	aws->callback(di_define_save_tree_name_cb);
1709	1700	aws->create_button("USE_NAME", "Use as new tree name", "");
1710	1701
	1702	aws->at("calc_tree_name");
	1703	aws->create_input_field(AWAR_DIST_TREE_STD_NAME,12);
	1704
	1705	aws->at("bcount");
	1706	aws->create_input_field(AWAR_DIST_BOOTSTRAP_COUNT, 7);
	1707
1711	1708	GB_pop_transaction(GLOBAL_gb_main);
1712	1709	return (AW_window *)aws;

trunk/DIST/DI_mldist.cxx

r6141	r6280
1		#include <stdio.h>
2		#include <stdlib.h>
3		#include <memory.h>
4		// #include <malloc.h>
5		#include <string.h>
6
7		#include <math.h>
8
9		#include <arbdb.h>
10		#include <arbdbt.h>
11
12		#include <aw_root.hxx>
13		#include <aw_device.hxx>
14		#include <aw_window.hxx>
15		#include <aw_preset.hxx>
16		#include <awt.hxx>
17
18		#include <awt_tree.hxx>
19		#include "dist.hxx"
20		#include <awt_csp.hxx>
21
	1	// =============================================================== //
	2	// //
	3	// File : DI_mldist.cxx //
	4	// Purpose : //
	5	// //
	6	// Institute of Microbiology (Technical University Munich) //
	7	// http://www.arb-home.de/ //
	8	// //
	9	// =============================================================== //
	10
	11	#include "di_mldist.hxx"
22	12	#include "di_matr.hxx"
23		#include "di_mldist.hxx"
24
25		#define epsilon 0.000001/* a small number */
26
	13
	14	#include <AP_seq_simple_pro.hxx>
	15
	16	#include <cmath>
	17
	18
	19	#define epsilon 0.000001 // a small number
27	20
28	21	void di_mldist::givens(di_ml_matrix a,long i,long j,long n,double ctheta,double stheta,GB_BOOL left)
…	…
231	224	{
232	225	/* move all unknown characters to del */
233		ap_pro *seq~~1 = entries[i]->sequence_protein->sequence~~;
	226	ap_pro *seq = entries[i]->sequence_protein->get_sequence();
234	227	for (k = 0; k <chars ; k++) {
235		b1 = seq1[k];
	228	b1 = seq[k];
236	229	if (b1 <=val) continue;
237	230	if (b1 == asx \|\| b1 == glx) continue;
238		seq1[k] = del;
	231	seq[k] = del;
239	232	}
240	233	}
…	…
250	243	tt = pos_2_tt(pos);
251	244	build_akt_predikt(tt);
252		~~ap_pro *seq1 = entries[i]->sequence_protein->sequence~~;
253		~~ap_pro *seq2 = entries[j]->sequence_protein->sequence~~;
	245	const ap_pro *seq1 = entries[i]->sequence_protein->get_sequence();
	246	const ap_pro *seq2 = entries[j]->sequence_protein->get_sequence();
254	247	for (k = chars; k >0; k--) {
255	248	b1 = *(seq1++);

trunk/DIST/DI_protdist.cxx

r6141	r6280
1		#include <stdio.h>
2		#include <stdlib.h>
3		#include <memory.h>
4		// #include <malloc.h>
5		#include <string.h>
	1	// =============================================================== //
	2	// //
	3	// File : DI_protdist.cxx //
	4	// Purpose : //
	5	// //
	6	// Institute of Microbiology (Technical University Munich) //
	7	// http://www.arb-home.de/ //
	8	// //
	9	// =============================================================== //
	10
	11	#include "di_protdist.hxx"
	12	#include "di_matr.hxx"
6	13
7	14	#include <math.h>
8	15
9		#include <arbdb.h>
10		#include <arbdbt.h>
11
12		#include <aw_root.hxx>
13		#include <aw_device.hxx>
14		#include <aw_window.hxx>
15		#include <aw_preset.hxx>
16		#include <awt.hxx>
17
18		#include <awt_tree.hxx>
19		#include "dist.hxx"
20		#include <awt_csp.hxx>
21
22		#include "di_matr.hxx"
23		#include "di_protdist.hxx"
24
25		#define epsilon 0.000001/* a small number */
	16	#define di_assert(cond) arb_assert(cond)
	17
	18	#define epsilon 0.000001 /* a small number */
26	19
27	20	double di_protdist::pameigs[20] = {
…	…
676	669	{
677	670	/* move all unknown characters to del */
678		ap_pro *seq1 = entries[i]->sequence_protein->~~sequence~~;
	671	ap_pro *seq1 = entries[i]->sequence_protein->get_sequence();
679	672	for (k = 0; k <chars ; k++) {
680	673	b1 = seq1[k];
…	…
699	692	tt = pos_2_tt(pos);
700	693	build_akt_predikt(tt);
701		~~ap_pro *seq1 = entries[i]->sequence_protein->sequence~~;
702		~~ap_pro *seq2 = entries[j]->sequence_protein->sequence~~;
	694	const ap_pro *seq1 = entries[i]->sequence_protein->get_sequence();
	695	const ap_pro *seq2 = entries[j]->sequence_protein->get_sequence();
703	696	for (k = chars; k >0; k--) {
704	697	b1 = *(seq1++);
…	…
742	735	m = 0;
743	736	n = 0;
744		~~ap_pro *seq1 = entries[i]->sequence_protein->sequence~~;
745		~~ap_pro *seq2 = entries[j]->sequence_protein->sequence~~;
	737	const ap_pro *seq1 = entries[i]->sequence_protein->get_sequence();
	738	const ap_pro *seq2 = entries[j]->sequence_protein->get_sequence();
746	739	for (k = chars; k >0; k--) {
747	740	b1 = *(seq1++);

trunk/DIST/DI_save_matr.cxx

r5402	r6280
1		#include <stdio.h>
2		#include <stdlib.h>
3		// #include <malloc.h>
4		#include <memory.h>
5		#include <string.h>
6		#include <arbdb.h>
7		#include <arbdbt.h>
8
9		#include <aw_root.hxx>
10		#include <aw_device.hxx>
11		#include <aw_window.hxx>
12		#include <awt_tree.hxx>
13		#include "dist.hxx"
14		#include <awt_nds.hxx>
15		#include <awt_csp.hxx>
	1	// =============================================================== //
	2	// //
	3	// File : DI_save_matr.cxx //
	4	// Purpose : //
	5	// //
	6	// Institute of Microbiology (Technical University Munich) //
	7	// http://www.arb-home.de/ //
	8	// //
	9	// =============================================================== //
16	10
17	11	#include "di_matr.hxx"
18
	12	#include <awt_nds.hxx>
19	13
20	14	const char DI_MATRIX::save(char filename,enum DI_SAVE_TYPE type)
…	…
43	37	case DI_SAVE_TABBED:
44	38	{
	39	GBDATA *gb_main = get_gb_main();
45	40	GB_transaction dummy(gb_main);
46		size_t app_size = 200; // maximum width for NDS output (and max. height for vertical one)
	41	size_t app_size = 200; // maximum width for NDS output (and max. height for vertical one)
47	42	size_t maxnds = 0;
48	43	bool tabbed = (type == DI_SAVE_TABBED);
…	…
142	137	if (!tabbed) fputc(' ', out);
143	138
144		if (val2 > max) max = val2;
145		if (val2 < min) min = val2;
146		sum += val;
	139	if (val2 > max) max = val2;
	140	if (val2 < min) min = val2;
	141
	142	sum += val2; // ralf: before this added 'val' (which was included somehow)
147	143	}
148	144	fprintf(out,"\n");

trunk/DIST/DI_view_matrix.cxx

r6141	r6280
1		#include <stdio.h>
2		#include <stdlib.h>
3		#include <memory.h>
4		#include <string.h>
5
6		#include <arbdb.h>
7		#include <arbdbt.h>
8
9		#include <aw_root.hxx>
10		#include <aw_device.hxx>
	1	// =============================================================== //
	2	// //
	3	// File : DI_view_matrix.cxx //
	4	// Purpose : //
	5	// //
	6	// Institute of Microbiology (Technical University Munich) //
	7	// http://www.arb-home.de/ //
	8	// //
	9	// =============================================================== //
	10
	11	#include "di_view_matrix.hxx"
	12	#include "di_matr.hxx"
	13	#include "dist.hxx"
	14
11	15	#include <aw_window.hxx>
	16	#include <aw_awars.hxx>
12	17	#include <aw_preset.hxx>
13		#include <aw_awars.hxx>
14
15		#include <awt_tree.hxx>
	18
16	19	#include <awt_canvas.hxx>
17		~~#include "dist.hxx"~~
18
19		~~#include <di_matr.hxx>~~
20		~~#include <di_view_matrix.hxx>~~
21	20
22	21	void vertical_change_cb (AW_window aww,DI_dmatrix dis) { dis->monitor_vertical_scroll_cb(aww); }
…	…
550	549	}
551	550
552		AW_window DI_create_view_matrix_window(AW_root awr, DI_dmatrix *dmatrix){
	551	AW_window DI_create_view_matrix_window(AW_root awr, DI_dmatrix dmatrix, save_matrix_params sparam) {
553	552	di_bind_dist_awars(awr, dmatrix);
554	553	AW_window_menu *awm = new AW_window_menu();
…	…
580	579
581	580	awm->create_menu("File","F");
582		awm->insert_menu_topic("save_matrix", "Save Matrix to File", "S","save_matrix.hlp", AWM_ALL, AW_POPUP, (AW_CL)DI_create_save_matrix_window, (AW_CL)~~AWAR_DIST_SAVE_MATRIX_BASE~~);
	581	awm->insert_menu_topic("save_matrix", "Save Matrix to File", "S","save_matrix.hlp", AWM_ALL, AW_POPUP, (AW_CL)DI_create_save_matrix_window, (AW_CL)sparam);
583	582	awm->insert_menu_topic("close", "Close", "C",0, AWM_ALL, (AW_CB)AW_POPDOWN, (AW_CL)0, 0 );
584	583

trunk/DIST/Makefile

r6277	r6280
3	3	.SUFFIXES: .o .cxx .depend
4	4
5		CPP_OBJECTS = DI_mldist.o DI_protdist.o DI_compress_matrix.o DI_view_matrix.o DI_save_matr.o DI_main.o DI_matr.o distanalyse.o
	5	CPP_OBJECTS = \
	6	DI_foundclusters.o \
	7	DI_clusters.o \
	8	DI_clustertree.o \
	9	DI_compress_matrix.o \
	10	DI_main.o \
	11	DI_matr.o \
	12	DI_mldist.o \
	13	DI_protdist.o \
	14	DI_save_matr.o \
	15	DI_view_matrix.o \
	16	distanalyse.o \
6	17
7	18	$(MAIN): $(CPP_OBJECTS)
…	…
30	41	# For formatting issues see SOURCE_TOOLS/fix_depends.pl
31	42
	43	DI_clusters.o: di_awars.hxx
	44	DI_clusters.o: di_clusters.hxx
	45	DI_clusters.o: di_clustertree.hxx
	46	DI_clusters.o: di_foundclusters.hxx
	47	DI_clusters.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
	48	DI_clusters.o: $(ARBHOME)/INCLUDE/ad_prot.h
	49	DI_clusters.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
	50	DI_clusters.o: $(ARBHOME)/INCLUDE/AliView.hxx
	51	DI_clusters.o: $(ARBHOME)/INCLUDE/AP_filter.hxx
	52	DI_clusters.o: $(ARBHOME)/INCLUDE/AP_seq_dna.hxx
	53	DI_clusters.o: $(ARBHOME)/INCLUDE/AP_seq_simple_pro.hxx
	54	DI_clusters.o: $(ARBHOME)/INCLUDE/AP_sequence.hxx
	55	DI_clusters.o: $(ARBHOME)/INCLUDE/arb_assert.h
	56	DI_clusters.o: $(ARBHOME)/INCLUDE/arb_error.h
	57	DI_clusters.o: $(ARBHOME)/INCLUDE/ARB_Tree.hxx
	58	DI_clusters.o: $(ARBHOME)/INCLUDE/arbdb.h
	59	DI_clusters.o: $(ARBHOME)/INCLUDE/arbdb_base.h
	60	DI_clusters.o: $(ARBHOME)/INCLUDE/arbdbt.h
	61	DI_clusters.o: $(ARBHOME)/INCLUDE/arbtools.h
	62	DI_clusters.o: $(ARBHOME)/INCLUDE/attributes.h
	63	DI_clusters.o: $(ARBHOME)/INCLUDE/aw_awars.hxx
	64	DI_clusters.o: $(ARBHOME)/INCLUDE/aw_device.hxx
	65	DI_clusters.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
	66	DI_clusters.o: $(ARBHOME)/INCLUDE/aw_position.hxx
	67	DI_clusters.o: $(ARBHOME)/INCLUDE/aw_root.hxx
	68	DI_clusters.o: $(ARBHOME)/INCLUDE/aw_window.hxx
	69	DI_clusters.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx
	70	DI_clusters.o: $(ARBHOME)/INCLUDE/downcast.h
	71	DI_clusters.o: $(ARBHOME)/INCLUDE/gui_aliview.hxx
	72	DI_clusters.o: $(ARBHOME)/INCLUDE/smartptr.h
	73
	74	DI_clustertree.o: di_clustertree.hxx
	75	DI_clustertree.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
	76	DI_clustertree.o: $(ARBHOME)/INCLUDE/ad_prot.h
	77	DI_clustertree.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
	78	DI_clustertree.o: $(ARBHOME)/INCLUDE/AliView.hxx
	79	DI_clustertree.o: $(ARBHOME)/INCLUDE/AP_sequence.hxx
	80	DI_clustertree.o: $(ARBHOME)/INCLUDE/arb_assert.h
	81	DI_clustertree.o: $(ARBHOME)/INCLUDE/arb_error.h
	82	DI_clustertree.o: $(ARBHOME)/INCLUDE/ARB_Tree.hxx
	83	DI_clustertree.o: $(ARBHOME)/INCLUDE/arbdb.h
	84	DI_clustertree.o: $(ARBHOME)/INCLUDE/arbdb_base.h
	85	DI_clustertree.o: $(ARBHOME)/INCLUDE/arbdbt.h
	86	DI_clustertree.o: $(ARBHOME)/INCLUDE/arbtools.h
	87	DI_clustertree.o: $(ARBHOME)/INCLUDE/attributes.h
	88	DI_clustertree.o: $(ARBHOME)/INCLUDE/aw_root.hxx
	89	DI_clustertree.o: $(ARBHOME)/INCLUDE/downcast.h
	90	DI_clustertree.o: $(ARBHOME)/INCLUDE/smartptr.h
	91
32	92	DI_compress_matrix.o: di_matr.hxx
33		~~DI_compress_matrix.o: di_view_matrix.hxx~~
34		~~DI_compress_matrix.o: dist.hxx~~
35	93	DI_compress_matrix.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
36	94	DI_compress_matrix.o: $(ARBHOME)/INCLUDE/ad_prot.h
37	95	DI_compress_matrix.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
	96	DI_compress_matrix.o: $(ARBHOME)/INCLUDE/AliView.hxx
	97	DI_compress_matrix.o: $(ARBHOME)/INCLUDE/AP_matrix.hxx
	98	DI_compress_matrix.o: $(ARBHOME)/INCLUDE/AP_pro_a_nucs.hxx
	99	DI_compress_matrix.o: $(ARBHOME)/INCLUDE/AP_sequence.hxx
	100	DI_compress_matrix.o: $(ARBHOME)/INCLUDE/AP_Tree.hxx
38	101	DI_compress_matrix.o: $(ARBHOME)/INCLUDE/arb_assert.h
39	102	DI_compress_matrix.o: $(ARBHOME)/INCLUDE/arb_error.h
	103	DI_compress_matrix.o: $(ARBHOME)/INCLUDE/ARB_Tree.hxx
40	104	DI_compress_matrix.o: $(ARBHOME)/INCLUDE/arbdb.h
41	105	DI_compress_matrix.o: $(ARBHOME)/INCLUDE/arbdb_base.h
…	…
44	108	DI_compress_matrix.o: $(ARBHOME)/INCLUDE/attributes.h
45	109	DI_compress_matrix.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx
46		~~DI_compress_matrix.o: $(ARBHOME)/INCLUDE/aw_device.hxx~~
47		~~DI_compress_matrix.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx~~
48		~~DI_compress_matrix.o: $(ARBHOME)/INCLUDE/aw_position.hxx~~
49		~~DI_compress_matrix.o: $(ARBHOME)/INCLUDE/aw_preset.hxx~~
50	110	DI_compress_matrix.o: $(ARBHOME)/INCLUDE/aw_root.hxx
51		DI_compress_matrix.o: $(ARBHOME)/INCLUDE/aw_window.hxx
52		DI_compress_matrix.o: $(ARBHOME)/INCLUDE/awt_pro_a_nucs.hxx
53		DI_compress_matrix.o: $(ARBHOME)/INCLUDE/awt_seq_dna.hxx
54		DI_compress_matrix.o: $(ARBHOME)/INCLUDE/awt_seq_simple_pro.hxx
55		DI_compress_matrix.o: $(ARBHOME)/INCLUDE/awt_tree.hxx
	111	DI_compress_matrix.o: $(ARBHOME)/INCLUDE/downcast.h
56	112	DI_compress_matrix.o: $(ARBHOME)/INCLUDE/smartptr.h
	113
	114	DI_foundclusters.o: di_clustertree.hxx
	115	DI_foundclusters.o: di_foundclusters.hxx
	116	DI_foundclusters.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
	117	DI_foundclusters.o: $(ARBHOME)/INCLUDE/ad_prot.h
	118	DI_foundclusters.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
	119	DI_foundclusters.o: $(ARBHOME)/INCLUDE/AliView.hxx
	120	DI_foundclusters.o: $(ARBHOME)/INCLUDE/AP_sequence.hxx
	121	DI_foundclusters.o: $(ARBHOME)/INCLUDE/arb_assert.h
	122	DI_foundclusters.o: $(ARBHOME)/INCLUDE/arb_error.h
	123	DI_foundclusters.o: $(ARBHOME)/INCLUDE/ARB_Tree.hxx
	124	DI_foundclusters.o: $(ARBHOME)/INCLUDE/arbdb.h
	125	DI_foundclusters.o: $(ARBHOME)/INCLUDE/arbdb_base.h
	126	DI_foundclusters.o: $(ARBHOME)/INCLUDE/arbdbt.h
	127	DI_foundclusters.o: $(ARBHOME)/INCLUDE/arbtools.h
	128	DI_foundclusters.o: $(ARBHOME)/INCLUDE/attributes.h
	129	DI_foundclusters.o: $(ARBHOME)/INCLUDE/aw_device.hxx
	130	DI_foundclusters.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
	131	DI_foundclusters.o: $(ARBHOME)/INCLUDE/aw_position.hxx
	132	DI_foundclusters.o: $(ARBHOME)/INCLUDE/aw_root.hxx
	133	DI_foundclusters.o: $(ARBHOME)/INCLUDE/aw_window.hxx
	134	DI_foundclusters.o: $(ARBHOME)/INCLUDE/downcast.h
	135	DI_foundclusters.o: $(ARBHOME)/INCLUDE/gui_aliview.hxx
	136	DI_foundclusters.o: $(ARBHOME)/INCLUDE/smartptr.h
57	137
58	138	DI_main.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
…	…
75	155	DI_main.o: $(ARBHOME)/INCLUDE/smartptr.h
76	156
	157	DI_matr.o: di_awars.hxx
	158	DI_matr.o: di_clusters.hxx
77	159	DI_matr.o: di_matr.hxx
78	160	DI_matr.o: di_protdist.hxx
…	…
82	164	DI_matr.o: $(ARBHOME)/INCLUDE/ad_prot.h
83	165	DI_matr.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
	166	DI_matr.o: $(ARBHOME)/INCLUDE/AliView.hxx
	167	DI_matr.o: $(ARBHOME)/INCLUDE/AP_filter.hxx
	168	DI_matr.o: $(ARBHOME)/INCLUDE/AP_matrix.hxx
	169	DI_matr.o: $(ARBHOME)/INCLUDE/AP_pro_a_nucs.hxx
	170	DI_matr.o: $(ARBHOME)/INCLUDE/AP_seq_dna.hxx
	171	DI_matr.o: $(ARBHOME)/INCLUDE/AP_seq_simple_pro.hxx
	172	DI_matr.o: $(ARBHOME)/INCLUDE/AP_sequence.hxx
	173	DI_matr.o: $(ARBHOME)/INCLUDE/AP_Tree.hxx
84	174	DI_matr.o: $(ARBHOME)/INCLUDE/arb_assert.h
85	175	DI_matr.o: $(ARBHOME)/INCLUDE/arb_error.h
	176	DI_matr.o: $(ARBHOME)/INCLUDE/ARB_Tree.hxx
86	177	DI_matr.o: $(ARBHOME)/INCLUDE/arbdb.h
87	178	DI_matr.o: $(ARBHOME)/INCLUDE/arbdb_base.h
…	…
100	191	DI_matr.o: $(ARBHOME)/INCLUDE/awt.hxx
101	192	DI_matr.o: $(ARBHOME)/INCLUDE/awt_csp.hxx
	193	DI_matr.o: $(ARBHOME)/INCLUDE/awt_filter.hxx
102	194	DI_matr.o: $(ARBHOME)/INCLUDE/awt_macro.hxx
103		~~DI_matr.o: $(ARBHOME)/INCLUDE/awt_pro_a_nucs.hxx~~
104	195	DI_matr.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx
105		~~DI_matr.o: $(ARBHOME)/INCLUDE/awt_seq_dna.hxx~~
106		~~DI_matr.o: $(ARBHOME)/INCLUDE/awt_seq_simple_pro.hxx~~
107		~~DI_matr.o: $(ARBHOME)/INCLUDE/awt_tree.hxx~~
108	196	DI_matr.o: $(ARBHOME)/INCLUDE/BI_helix.hxx
109	197	DI_matr.o: $(ARBHOME)/INCLUDE/CT_ctree.hxx
	198	DI_matr.o: $(ARBHOME)/INCLUDE/downcast.h
	199	DI_matr.o: $(ARBHOME)/INCLUDE/gui_aliview.hxx
	200	DI_matr.o: $(ARBHOME)/INCLUDE/neighbourjoin.hxx
110	201	DI_matr.o: $(ARBHOME)/INCLUDE/smartptr.h
111	202
112	203	DI_mldist.o: di_matr.hxx
113	204	DI_mldist.o: di_mldist.hxx
114		~~DI_mldist.o: dist.hxx~~
115	205	DI_mldist.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
116	206	DI_mldist.o: $(ARBHOME)/INCLUDE/ad_prot.h
117	207	DI_mldist.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
	208	DI_mldist.o: $(ARBHOME)/INCLUDE/AliView.hxx
	209	DI_mldist.o: $(ARBHOME)/INCLUDE/AP_matrix.hxx
	210	DI_mldist.o: $(ARBHOME)/INCLUDE/AP_pro_a_nucs.hxx
	211	DI_mldist.o: $(ARBHOME)/INCLUDE/AP_seq_simple_pro.hxx
	212	DI_mldist.o: $(ARBHOME)/INCLUDE/AP_sequence.hxx
	213	DI_mldist.o: $(ARBHOME)/INCLUDE/AP_Tree.hxx
118	214	DI_mldist.o: $(ARBHOME)/INCLUDE/arb_assert.h
119	215	DI_mldist.o: $(ARBHOME)/INCLUDE/arb_error.h
	216	DI_mldist.o: $(ARBHOME)/INCLUDE/ARB_Tree.hxx
120	217	DI_mldist.o: $(ARBHOME)/INCLUDE/arbdb.h
121	218	DI_mldist.o: $(ARBHOME)/INCLUDE/arbdb_base.h
…	…
124	221	DI_mldist.o: $(ARBHOME)/INCLUDE/attributes.h
125	222	DI_mldist.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx
126		~~DI_mldist.o: $(ARBHOME)/INCLUDE/aw_device.hxx~~
127		~~DI_mldist.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx~~
128		~~DI_mldist.o: $(ARBHOME)/INCLUDE/aw_position.hxx~~
129		~~DI_mldist.o: $(ARBHOME)/INCLUDE/aw_preset.hxx~~
130	223	DI_mldist.o: $(ARBHOME)/INCLUDE/aw_root.hxx
131		DI_mldist.o: $(ARBHOME)/INCLUDE/aw_window.hxx
132		DI_mldist.o: $(ARBHOME)/INCLUDE/awt.hxx
133		DI_mldist.o: $(ARBHOME)/INCLUDE/awt_csp.hxx
134		DI_mldist.o: $(ARBHOME)/INCLUDE/awt_pro_a_nucs.hxx
135		DI_mldist.o: $(ARBHOME)/INCLUDE/awt_seq_dna.hxx
136		DI_mldist.o: $(ARBHOME)/INCLUDE/awt_seq_simple_pro.hxx
137		DI_mldist.o: $(ARBHOME)/INCLUDE/awt_tree.hxx
	224	DI_mldist.o: $(ARBHOME)/INCLUDE/downcast.h
138	225	DI_mldist.o: $(ARBHOME)/INCLUDE/smartptr.h
139	226
140	227	DI_protdist.o: di_matr.hxx
141	228	DI_protdist.o: di_protdist.hxx
142		~~DI_protdist.o: dist.hxx~~
143	229	DI_protdist.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
144	230	DI_protdist.o: $(ARBHOME)/INCLUDE/ad_prot.h
145	231	DI_protdist.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
	232	DI_protdist.o: $(ARBHOME)/INCLUDE/AliView.hxx
	233	DI_protdist.o: $(ARBHOME)/INCLUDE/AP_matrix.hxx
	234	DI_protdist.o: $(ARBHOME)/INCLUDE/AP_pro_a_nucs.hxx
	235	DI_protdist.o: $(ARBHOME)/INCLUDE/AP_seq_simple_pro.hxx
	236	DI_protdist.o: $(ARBHOME)/INCLUDE/AP_sequence.hxx
	237	DI_protdist.o: $(ARBHOME)/INCLUDE/AP_Tree.hxx
146	238	DI_protdist.o: $(ARBHOME)/INCLUDE/arb_assert.h
147	239	DI_protdist.o: $(ARBHOME)/INCLUDE/arb_error.h
	240	DI_protdist.o: $(ARBHOME)/INCLUDE/ARB_Tree.hxx
148	241	DI_protdist.o: $(ARBHOME)/INCLUDE/arbdb.h
149	242	DI_protdist.o: $(ARBHOME)/INCLUDE/arbdb_base.h
…	…
152	245	DI_protdist.o: $(ARBHOME)/INCLUDE/attributes.h
153	246	DI_protdist.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx
154		~~DI_protdist.o: $(ARBHOME)/INCLUDE/aw_device.hxx~~
155		~~DI_protdist.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx~~
156		~~DI_protdist.o: $(ARBHOME)/INCLUDE/aw_position.hxx~~
157		~~DI_protdist.o: $(ARBHOME)/INCLUDE/aw_preset.hxx~~
158	247	DI_protdist.o: $(ARBHOME)/INCLUDE/aw_root.hxx
159		DI_protdist.o: $(ARBHOME)/INCLUDE/aw_window.hxx
160		DI_protdist.o: $(ARBHOME)/INCLUDE/awt.hxx
161		DI_protdist.o: $(ARBHOME)/INCLUDE/awt_csp.hxx
162		DI_protdist.o: $(ARBHOME)/INCLUDE/awt_pro_a_nucs.hxx
163		DI_protdist.o: $(ARBHOME)/INCLUDE/awt_seq_dna.hxx
164		DI_protdist.o: $(ARBHOME)/INCLUDE/awt_seq_simple_pro.hxx
165		DI_protdist.o: $(ARBHOME)/INCLUDE/awt_tree.hxx
	248	DI_protdist.o: $(ARBHOME)/INCLUDE/downcast.h
166	249	DI_protdist.o: $(ARBHOME)/INCLUDE/smartptr.h
167	250
168	251	DI_save_matr.o: di_matr.hxx
169		~~DI_save_matr.o: dist.hxx~~
170	252	DI_save_matr.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
171	253	DI_save_matr.o: $(ARBHOME)/INCLUDE/ad_prot.h
172	254	DI_save_matr.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
	255	DI_save_matr.o: $(ARBHOME)/INCLUDE/AliView.hxx
	256	DI_save_matr.o: $(ARBHOME)/INCLUDE/AP_matrix.hxx
	257	DI_save_matr.o: $(ARBHOME)/INCLUDE/AP_pro_a_nucs.hxx
	258	DI_save_matr.o: $(ARBHOME)/INCLUDE/AP_sequence.hxx
	259	DI_save_matr.o: $(ARBHOME)/INCLUDE/AP_Tree.hxx
173	260	DI_save_matr.o: $(ARBHOME)/INCLUDE/arb_assert.h
174	261	DI_save_matr.o: $(ARBHOME)/INCLUDE/arb_error.h
	262	DI_save_matr.o: $(ARBHOME)/INCLUDE/ARB_Tree.hxx
175	263	DI_save_matr.o: $(ARBHOME)/INCLUDE/arbdb.h
176	264	DI_save_matr.o: $(ARBHOME)/INCLUDE/arbdb_base.h
…	…
179	267	DI_save_matr.o: $(ARBHOME)/INCLUDE/attributes.h
180	268	DI_save_matr.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx
181		~~DI_save_matr.o: $(ARBHOME)/INCLUDE/aw_device.hxx~~
182		~~DI_save_matr.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx~~
183		~~DI_save_matr.o: $(ARBHOME)/INCLUDE/aw_position.hxx~~
184	269	DI_save_matr.o: $(ARBHOME)/INCLUDE/aw_root.hxx
185		~~DI_save_matr.o: $(ARBHOME)/INCLUDE/aw_window.hxx~~
186		~~DI_save_matr.o: $(ARBHOME)/INCLUDE/awt_csp.hxx~~
187	270	DI_save_matr.o: $(ARBHOME)/INCLUDE/awt_nds.hxx
188		DI_save_matr.o: $(ARBHOME)/INCLUDE/awt_pro_a_nucs.hxx
189		DI_save_matr.o: $(ARBHOME)/INCLUDE/awt_seq_dna.hxx
190		DI_save_matr.o: $(ARBHOME)/INCLUDE/awt_seq_simple_pro.hxx
191		DI_save_matr.o: $(ARBHOME)/INCLUDE/awt_tree.hxx
	271	DI_save_matr.o: $(ARBHOME)/INCLUDE/downcast.h
192	272	DI_save_matr.o: $(ARBHOME)/INCLUDE/smartptr.h
193	273
…	…
198	278	DI_view_matrix.o: $(ARBHOME)/INCLUDE/ad_prot.h
199	279	DI_view_matrix.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
	280	DI_view_matrix.o: $(ARBHOME)/INCLUDE/AliView.hxx
	281	DI_view_matrix.o: $(ARBHOME)/INCLUDE/AP_matrix.hxx
	282	DI_view_matrix.o: $(ARBHOME)/INCLUDE/AP_pro_a_nucs.hxx
	283	DI_view_matrix.o: $(ARBHOME)/INCLUDE/AP_sequence.hxx
	284	DI_view_matrix.o: $(ARBHOME)/INCLUDE/AP_Tree.hxx
200	285	DI_view_matrix.o: $(ARBHOME)/INCLUDE/arb_assert.h
201	286	DI_view_matrix.o: $(ARBHOME)/INCLUDE/arb_error.h
	287	DI_view_matrix.o: $(ARBHOME)/INCLUDE/ARB_Tree.hxx
202	288	DI_view_matrix.o: $(ARBHOME)/INCLUDE/arbdb.h
203	289	DI_view_matrix.o: $(ARBHOME)/INCLUDE/arbdb_base.h
…	…
214	300	DI_view_matrix.o: $(ARBHOME)/INCLUDE/aw_window.hxx
215	301	DI_view_matrix.o: $(ARBHOME)/INCLUDE/awt_canvas.hxx
216		DI_view_matrix.o: $(ARBHOME)/INCLUDE/awt_pro_a_nucs.hxx
217		DI_view_matrix.o: $(ARBHOME)/INCLUDE/awt_seq_dna.hxx
218		DI_view_matrix.o: $(ARBHOME)/INCLUDE/awt_seq_simple_pro.hxx
219		DI_view_matrix.o: $(ARBHOME)/INCLUDE/awt_tree.hxx
	302	DI_view_matrix.o: $(ARBHOME)/INCLUDE/downcast.h
220	303	DI_view_matrix.o: $(ARBHOME)/INCLUDE/smartptr.h
221	304
222	305	distanalyse.o: di_matr.hxx
223		~~distanalyse.o: dist.hxx~~
224	306	distanalyse.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
225	307	distanalyse.o: $(ARBHOME)/INCLUDE/ad_prot.h
226	308	distanalyse.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
	309	distanalyse.o: $(ARBHOME)/INCLUDE/AliView.hxx
	310	distanalyse.o: $(ARBHOME)/INCLUDE/AP_filter.hxx
	311	distanalyse.o: $(ARBHOME)/INCLUDE/AP_matrix.hxx
	312	distanalyse.o: $(ARBHOME)/INCLUDE/AP_pro_a_nucs.hxx
	313	distanalyse.o: $(ARBHOME)/INCLUDE/AP_seq_dna.hxx
	314	distanalyse.o: $(ARBHOME)/INCLUDE/AP_sequence.hxx
	315	distanalyse.o: $(ARBHOME)/INCLUDE/AP_Tree.hxx
227	316	distanalyse.o: $(ARBHOME)/INCLUDE/arb_assert.h
228	317	distanalyse.o: $(ARBHOME)/INCLUDE/arb_error.h
	318	distanalyse.o: $(ARBHOME)/INCLUDE/ARB_Tree.hxx
229	319	distanalyse.o: $(ARBHOME)/INCLUDE/arbdb.h
230	320	distanalyse.o: $(ARBHOME)/INCLUDE/arbdb_base.h
…	…
233	323	distanalyse.o: $(ARBHOME)/INCLUDE/attributes.h
234	324	distanalyse.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx
235		~~distanalyse.o: $(ARBHOME)/INCLUDE/aw_device.hxx~~
236		~~distanalyse.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx~~
237		~~distanalyse.o: $(ARBHOME)/INCLUDE/aw_position.hxx~~
238	325	distanalyse.o: $(ARBHOME)/INCLUDE/aw_root.hxx
239		distanalyse.o: $(ARBHOME)/INCLUDE/aw_window.hxx
240		distanalyse.o: $(ARBHOME)/INCLUDE/awt.hxx
241		distanalyse.o: $(ARBHOME)/INCLUDE/awt_pro_a_nucs.hxx
242		distanalyse.o: $(ARBHOME)/INCLUDE/awt_seq_dna.hxx
243		distanalyse.o: $(ARBHOME)/INCLUDE/awt_seq_simple_pro.hxx
244		distanalyse.o: $(ARBHOME)/INCLUDE/awt_tree.hxx
	326	distanalyse.o: $(ARBHOME)/INCLUDE/downcast.h
245	327	distanalyse.o: $(ARBHOME)/INCLUDE/smartptr.h

trunk/DIST/di_matr.hxx

r5420	r6280
	1	// =============================================================== //
	2	// //
	3	// File : di_matr.hxx //
	4	// Purpose : //
	5	// //
	6	// Institute of Microbiology (Technical University Munich) //
	7	// http://www.arb-home.de/ //
	8	// //
	9	// =============================================================== //
	10
	11	#ifndef DI_MATR_HXX
	12	#define DI_MATR_HXX
	13
	14	#ifndef AP_PRO_A_NUCS_HXX
	15	#include <AP_pro_a_nucs.hxx>
	16	#endif
	17	#ifndef AP_TREE_HXX
	18	#include <AP_Tree.hxx>
	19	#endif
	20	#ifndef AP_MATRIX_HXX
	21	#include <AP_matrix.hxx>
	22	#endif
	23
1	24
2	25	#define AWAR_DIST_PREFIX "dist/"
…	…
30	53	enum DI_MATRIX_TYPE {
31	54	DI_MATRIX_FULL,
32		DI_MATRIX_COMPRESSED };
	55	DI_MATRIX_COMPRESSED
	56	};
33	57
34	58	class DI_MATRIX;
35	59	class AW_root;
	60	class AP_sequence_parsimony;
	61	class AP_sequence_simple_protein;
36	62
37	63	class DI_ENTRY {
…	…
64	90	enum LoadWhat { DI_LOAD_ALL, DI_LOAD_MARKED, DI_LOAD_LIST };
65	91
66		class DI_MATRIX {
67		private:
	92	class DI_MATRIX : Noncopyable {
68	93	friend class DI_ENTRY;
69	94
70		GBDATA *gb_main;
71		GBDATA *gb_species_data;
72		char *use;
73		long seq_len;
74		char cancel_columns[256];
75		AP_tree_root *tree_root;
76		AW_root *aw_root; // only link
77		long entries_mem_size;
	95	GBDATA *gb_species_data;
	96	long seq_len;
	97	char cancel_columns[256];
	98	AW_root *aw_root; // only link
	99	long entries_mem_size;
	100	AliView *aliview;
78	101
79	102	public:
…	…
85	108	DI_MATRIX_TYPE matrix_type;
86	109
87		DI_MATRIX(~~GBDATA gb_main,~~AW_root awr);
88		~DI_MATRIX(~~void~~);
	110	DI_MATRIX(const AliView& aliview, AW_root *awr);
	111	~DI_MATRIX();
89	112
90		char load(char use, AP_filter filter, AP_weights weights, LoadWhat what, GB_CSTR sort_tree_name, bool show_warnings, GBDATA **species_list);
	113	GBDATA *get_gb_main() const { return aliview->get_gb_main(); }
	114	const char *get_aliname() const { return aliview->get_aliname(); }
	115	const AliView *get_aliview() const { return aliview; }
	116
	117	char load(LoadWhat what, GB_CSTR sort_tree_name, bool show_warnings, GBDATA *species_list);
91	118	char *unload(void);
92	119	const char save(char filename,enum DI_SAVE_TYPE type);
…	…
95	122	void make_sym(DI_MUT_MATR &hits);
96	123	void rate_write(DI_MUT_MATR &hits,FILE *out);
97		long create_helix_filter(BI_helix helix,AP_filter *filter);
	124	long create_helix_filter(BI_helix helix, const AP_filter *filter);
98	125	// 0 non helix 1 helix; compressed filter
99	126	GB_ERROR calculate_rates(DI_MUT_MATR &hrates,DI_MUT_MATR &nrates,DI_MUT_MATR &pairs,long *filter);
…	…
103	130	char calculate_overall_freqs(double rel_frequencies[AP_MAX],char cancel_columns);
104	131	GB_ERROR calculate_pro(DI_TRANSFORMATION transformation);
105		~~char analyse(AW_root aw_root~~);
	132	void analyse();
106	133
107	134	int search_group(GBT_TREE node,GB_HASH hash, long groupcnt,char groupname, DI_ENTRY **groups); // @@ OLIVER
…	…
109	136	};
110	137
	138	class WeightedFilter;
	139	struct save_matrix_params {
	140	const char *awar_base;
	141	const WeightedFilter *weighted_filter;
	142	};
111	143
112		AW_window DI_create_save_matrix_window(AW_root aw_root, char *base_name);
	144	AW_window DI_create_save_matrix_window(AW_root aw_root, save_matrix_params *save_params);
	145
	146	#else
	147	#error di_matr.hxx included twice
	148	#endif // DI_MATR_HXX

trunk/DIST/di_mldist.hxx

r5392	r6280
	1	// =============================================================== //
	2	// //
	3	// File : di_mldist.hxx //
	4	// Purpose : //
	5	// //
	6	// Institute of Microbiology (Technical University Munich) //
	7	// http://www.arb-home.de/ //
	8	// //
	9	// =============================================================== //
	10
	11	#ifndef DI_MLDIST_HXX
	12	#define DI_MLDIST_HXX
	13
	14	#ifndef ARBDBT_H
	15	#include <arbdbt.h>
	16	#endif
	17
	18
1	19	const int DI_ML_RESOLUTION = 1000; // max res
2	20	const int DI_ML_MAX_DIST = 10; // max dist
…	…
7	25	typedef double di_pml_matrix[DI_ML_MAX_MAT_SIZE][DI_ML_MAX_MAT_SIZE];
8	26	typedef char di_bool_matrix[DI_ML_MAX_MAT_SIZE][DI_ML_MAX_MAT_SIZE];
	27
	28	class DI_ENTRY;
	29	class AP_smatrix;
9	30
10	31	class di_mldist {
…	…
64	85	const char *makedists(); // calculate the distance matrix
65	86	};
	87
	88	#else
	89	#error di_mldist.hxx included twice
	90	#endif // DI_MLDIST_HXX

trunk/DIST/di_protdist.hxx

r5392	r6280
	1	// =============================================================== //
	2	// //
	3	// File : di_protdist.hxx //
	4	// Purpose : //
	5	// //
	6	// Institute of Microbiology (Technical University Munich) //
	7	// http://www.arb-home.de/ //
	8	// //
	9	// =============================================================== //
1	10
2		const int di_max_aa = stop; // mussed be 20
	11	#ifndef DI_PROTDIST_HXX
	12	#define DI_PROTDIST_HXX
	13
	14	#ifndef AP_SEQ_SIMPLE_PRO_HXX
	15	#include <AP_seq_simple_pro.hxx>
	16	#endif
	17
	18	const int di_max_aa = stop; // must be 20
3	19	const int di_max_paa = unk; // includes virtual aa
4	20	const int di_resolution = 1000; // max res
…	…
18	34	typedef double di_paa_matrix[di_max_paa][di_max_paa];
19	35	typedef char di_bool_matrix[di_max_paa][di_max_paa];
	36
	37	class DI_ENTRY;
	38	class AP_smatrix;
20	39
21	40	class di_protdist {
…	…
86	105	const char *makedists(); // calculate the distance matrix
87	106	};
	107
	108	#else
	109	#error di_protdist.hxx included twice
	110	#endif // DI_PROTDIST_HXX

trunk/DIST/di_view_matrix.hxx

r5675	r6280
11	11	#define DI_VIEW_MATRIX_HXX
12	12
13		#ifndef AW_~~WINDOW~~_HXX
14		#include <aw_~~window~~.hxx>
	13	#ifndef AW_ROOT_HXX
	14	#include <aw_root.hxx>
15	15	#endif
16	16
…	…
26	26	DI_G_LAST // must be last
27	27	} DI_gc;
	28
	29	class AW_device;
	30	class AW_event;
	31	class DI_MATRIX;
28	32
29	33	class DI_dmatrix {
…	…
72	76	};
73	77
74		AW_window DI_create_view_matrix_window(AW_root awr, DI_dmatrix *dmatrix);
	78	struct save_matrix_params;
	79	AW_window DI_create_view_matrix_window(AW_root awr, DI_dmatrix dmatrix, save_matrix_params sparam);
75	80
76	81

trunk/DIST/dist.hxx

r5968	r6280
12	12	#define DIST_HXX
13	13
14		#ifndef AWT_SEQ_DNA_HXX
15		#include <awt_seq_dna.hxx>
16		#endif
17		#ifndef AWT_SEQ_SIMPLE_PRO_HXX
18		#include <awt_seq_simple_pro.hxx>
	14	#ifndef ARBDBT_H
	15	#include <arbdbt.h>
19	16	#endif
20	17
…	…
22	19
23	20	extern GBDATA *GLOBAL_gb_main;
24		~~GBT_TREE neighbourjoining(char names, AP_FLOAT *m, long size, size_t structure_size);~~
25	21
26	22	#else

trunk/DIST/distanalyse.cxx

r6141	r6280
1		#include <stdio.h>
2		#include <stdlib.h>
3		#include <memory.h>
4		#include <string.h>
	1	// =============================================================== //
	2	// //
	3	// File : distanalyse.cxx //
	4	// Purpose : //
	5	// //
	6	// Institute of Microbiology (Technical University Munich) //
	7	// http://www.arb-home.de/ //
	8	// //
	9	// =============================================================== //
5	10
6		~~#include <math.h>~~
7
8		~~#include <arbdb.h>~~
9		~~#include <arbdbt.h>~~
10
11		~~#include <aw_root.hxx>~~
12		~~#include <aw_device.hxx>~~
13		~~#include <aw_window.hxx>~~
14
15		~~#include <awt.hxx>~~
16
17		~~#include <awt_tree.hxx>~~
18		~~#include "dist.hxx"~~
19	11	#include "di_matr.hxx"
	12	#include <AP_seq_dna.hxx>
	13	#include <AP_filter.hxx>
20	14
21	15
22
23		char DI_MATRIX::analyse(AW_root awrdummy)
24		{
25		AWUSE(awrdummy);
26		long row, pos;
27		char *sequ, ch, dummy[280];
	16	void DI_MATRIX::analyse() {
	17	long row;
28	18
29	19	long act_gci, mean_gci=0;
…	…
35	25	aw_message("A lot of sequences!\n ==> fast Kimura selected! (instead of PAM)");
36	26	aw_root->awar(AWAR_DIST_CORR_TRANS)->write_int(DI_TRANSFORMATION_KIMURA);
37		}else{
38		aw_message( "Only limited number of sequences!\n"
39		" ==> slow PAM selected! (instead of Kimura)");
	27	}
	28	else{
	29	aw_message("Only limited number of sequences!\n"
	30	" ==> slow PAM selected! (instead of Kimura)");
40	31	aw_root->awar(AWAR_DIST_CORR_TRANS)->write_int(DI_TRANSFORMATION_PAM);
41	32	}
42		~~return 0;~~
43	33	}
	34	else {
	35	// calculate meanvalue of sequencelength:
	36	for(row=0; row<nentries; row++) {
	37	act_gci = 0;
	38	act_len = 0;
	39
	40	const char *sequ = entries[row]->sequence_parsimony->get_sequence();
44	41
	42	size_t flen = aliview->get_length();
	43	for (size_t pos=0; pos<flen; pos++) {
	44	char ch = sequ[pos];
	45	if(ch == AP_C \|\| ch == AP_G) act_gci++;
	46	if(ch == AP_A \|\| ch == AP_C \|\| ch == AP_G \|\| ch == AP_T) act_len++;
	47	}
	48	mean_gci += act_gci;
	49	act_gc = ((float) act_gci) / act_len;
	50	if(act_gc < min_gc) min_gc = act_gc;
	51	if(act_gc > max_gc) max_gc = act_gc;
	52	mean_len += act_len;
	53	if(act_len < min_len) min_len = act_len;
	54	if(act_len > max_len) max_len = act_len;
	55	}
45	56
46		//calculate meanvalue of sequencelength:
	57	if (min_len * 1.3 < max_len) {
	58	aw_message("Warning: The length of sequences differs significantly!\n"
	59	" Be careful: Neighbour Joining is sensitive to\n"
	60	" this kind of \"error\"");
	61	}
	62	mean_gc = ((float) mean_gci) / mean_len / nentries;
	63	mean_len /= nentries;
47	64
48		for(row=0; row<nentries; row++) {
49		act_gci = 0;
50		act_len = 0;
51		sequ = entries[row]->sequence_parsimony->sequence;
52		for(pos=0; pos<tree_root->filter->real_len; pos++) {
53		ch = sequ[pos];
54		if(ch == AP_C \|\| ch == AP_G) act_gci++;
55		if(ch == AP_A \|\| ch == AP_C \|\| ch == AP_G \|\| ch == AP_T) act_len++;
	65	if(mean_len < 100) {
	66	aw_message("Too short sequences!\n ==> No correction selected!");
	67	aw_root->awar(AWAR_DIST_CORR_TRANS)->write_int(DI_TRANSFORMATION_NONE);
56	68	}
57		mean_gci += act_gci;
58		act_gc = ((float) act_gci) / act_len;
59		if(act_gc < min_gc) min_gc = act_gc;
60		if(act_gc > max_gc) max_gc = act_gc;
61		mean_len += act_len;
62		if(act_len < min_len) min_len = act_len;
63		if(act_len > max_len) max_len = act_len;
	69	else if(mean_len < 300) {
	70	aw_message("Meanlength shorter than 300\n ==> Jukes Cantor selected!");
	71	aw_root->awar(AWAR_DIST_CORR_TRANS)->write_int(DI_TRANSFORMATION_JUKES_CANTOR);
	72	}
	73	else if ((mean_len < 1000) \|\| ((max_gc / min_gc) < 1.2)) {
	74	const char *reason;
	75	if(mean_len < 1000) reason = "Sequences are too short for Olsen!";
	76	else reason = GBS_global_string("Maximal GC (%f) : Minimal GC (%f) < 1.2", max_gc, min_gc);
	77
	78	reason = GBS_global_string("%s ==> Felsenstein selected!", reason);
	79	aw_message(reason);
	80	aw_root->awar(AWAR_DIST_CORR_TRANS)->write_int(DI_TRANSFORMATION_FELSENSTEIN);
	81	}
	82	else {
	83	aw_message("Olsen selected!");
	84	aw_root->awar(AWAR_DIST_CORR_TRANS)->write_int(DI_TRANSFORMATION_OLSEN);
	85	}
64	86	}
65
66		~~if (min_len * 1.3 < max_len) {~~
67		~~aw_message("Warning: The length of sequences differs significantly\n"~~
68		~~" be careful, neighbour joining is sensitive to\n"~~
69		~~" this kind of error");~~
70		}
71		~~mean_gc = ((float) mean_gci) / mean_len / nentries;~~
72		~~mean_len /= nentries;~~
73
74
75		~~if(mean_len < 100) {~~
76		~~aw_root->awar(AWAR_DIST_CORR_TRANS)->write_int(DI_TRANSFORMATION_NONE);~~
77		~~aw_message("Too short sequences!\n ==> No correction selected!");~~
78		~~return NULL;~~
79		}
80
81		~~if(mean_len < 300) {~~
82		~~aw_root->awar(AWAR_DIST_CORR_TRANS)->write_int(DI_TRANSFORMATION_JUKES_CANTOR);~~
83		~~aw_message("Meanlength shorter than 300\n ==> Jukes Cantor selected!");~~
84		~~return NULL;~~
85		}
86
87		~~if((mean_len < 1000) \|\| ((max_gc / min_gc) < 1.2)) {~~
88		~~if(mean_len < 1000)~~
89		~~sprintf(dummy, "Too short sequences for Olsen! \n");~~
90		~~else~~
91		~~sprintf(dummy, "Maximal GC (%f) : Minimal GC (%f) < 1.2\n", max_gc, min_gc);~~
92		~~sprintf(dummy, "%s ==> Felsenstein selected!", dummy);~~
93		~~aw_root->awar(AWAR_DIST_CORR_TRANS)->write_int(DI_TRANSFORMATION_FELSENSTEIN);~~
94		~~aw_message(dummy);~~
95		~~return NULL;~~
96		}
97
98		~~aw_root->awar(AWAR_DIST_CORR_TRANS)->write_int(DI_TRANSFORMATION_OLSEN);~~
99		~~aw_message("Olsen selected!");~~
100		~~return NULL;~~
101
102	87	}

trunk/EDIT4/ED4_ProteinViewer.cxx

r6141	r6280
14	14	#include "ed4_class.hxx"
15	15
16		#include <~~awt~~_pro_a_nucs.hxx>
17		#include <~~awt~~_codon_table.hxx>
18		#include <~~awt_t~~ranslate.hxx>
	16	#include <AP_pro_a_nucs.hxx>
	17	#include <AP_codon_table.hxx>
	18	#include <Translate.hxx>
19	19	#include <awt_seq_colors.hxx>
20	20	#include <aw_question.hxx>
21	21	#include <aw_preset.hxx>
22	22	#include <aw_awars.hxx>
23		~~#include <arbdbt.h>~~
24	23
25	24	#include <iostream>
…	…
633	632	const char *AAname = 0;
634	633	if(base>='A' && base<='Z') {
635		AAname = AWT_get_protein_name(base);
	634	AAname = AP_get_protein_name(base);
636	635	}
637	636	else if (base=='*') {

trunk/EDIT4/ED4_main.cxx

r6208	r6280
20	20	#include <st_window.hxx>
21	21	#include <gde.hxx>
22		#include~~<awt~~_pro_a_nucs.hxx>
	22	#include <AP_pro_a_nucs.hxx>
23	23
24	24	#include <ed4_extern.hxx>

trunk/EDIT4/ED4_manager.cxx

r6279	r6280
1813	1813	e4_assert(gbd);
1814	1814
1815		#if defined(ASSERTION_USED)
1816		GB_ERROR error =
1817		#endif // ASSERTION_USED
1818		GB_write_flag(gbd, mark ? 1 : 0);
1819		e4_assert(!error);
1820
	1815	GB_write_flag(gbd, mark ? 1 : 0);
1821	1816	sel++;
1822	1817	}

trunk/EDIT4/ED4_search.cxx

r6257	r6280
1446	1446	ED4_SearchPositionType pattern = ED4_SearchPositionType(cl_pattern);
1447	1447	ED4_terminal *terminal = ED4_ROOT->root_group_man->get_first_terminal();
1448		~~GB_ERROR error = 0;~~
1449	1448	GB_transaction ta(GLOBAL_gb_main);
1450	1449
1451		while (terminal ~~&& !error~~) {
	1450	while (terminal) {
1452	1451	if (terminal->is_sequence_terminal()) {
1453	1452	ED4_sequence_terminal *seq_terminal = terminal->to_sequence_terminal();
…	…
1462	1461	GBDATA *gbd = species_man->get_species_pointer();
1463	1462	e4_assert(gbd);
1464		~~error =~~ GB_write_flag(gbd, 1);
	1463	GB_write_flag(gbd, 1);
1465	1464	}
1466	1465	}
…	…
1468	1467
1469	1468	terminal = terminal->get_next_terminal();
1470		}
1471
1472		~~if (error) {~~
1473		~~error = ta.close(error);~~
1474		~~aw_message(error);~~
1475	1469	}
1476	1470	}

trunk/EDIT4/Makefile

r6277	r6280
252	252	ED4_main.o: $(ARBHOME)/INCLUDE/ad_prot.h
253	253	ED4_main.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
	254	ED4_main.o: $(ARBHOME)/INCLUDE/AP_pro_a_nucs.hxx
254	255	ED4_main.o: $(ARBHOME)/INCLUDE/arb_assert.h
255	256	ED4_main.o: $(ARBHOME)/INCLUDE/arb_error.h
…	…
271	272	ED4_main.o: $(ARBHOME)/INCLUDE/awt.hxx
272	273	ED4_main.o: $(ARBHOME)/INCLUDE/awt_map_key.hxx
273		~~ED4_main.o: $(ARBHOME)/INCLUDE/awt_pro_a_nucs.hxx~~
274	274	ED4_main.o: $(ARBHOME)/INCLUDE/awt_seq_colors.hxx
275	275	ED4_main.o: $(ARBHOME)/INCLUDE/BI_helix.hxx
…	…
443	443	ED4_ProteinViewer.o: $(ARBHOME)/INCLUDE/ad_prot.h
444	444	ED4_ProteinViewer.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
	445	ED4_ProteinViewer.o: $(ARBHOME)/INCLUDE/AP_codon_table.hxx
	446	ED4_ProteinViewer.o: $(ARBHOME)/INCLUDE/AP_pro_a_nucs.hxx
445	447	ED4_ProteinViewer.o: $(ARBHOME)/INCLUDE/arb_assert.h
446	448	ED4_ProteinViewer.o: $(ARBHOME)/INCLUDE/arb_error.h
…	…
461	463	ED4_ProteinViewer.o: $(ARBHOME)/INCLUDE/aw_window.hxx
462	464	ED4_ProteinViewer.o: $(ARBHOME)/INCLUDE/awt.hxx
463		~~ED4_ProteinViewer.o: $(ARBHOME)/INCLUDE/awt_codon_table.hxx~~
464		~~ED4_ProteinViewer.o: $(ARBHOME)/INCLUDE/awt_pro_a_nucs.hxx~~
465	465	ED4_ProteinViewer.o: $(ARBHOME)/INCLUDE/awt_seq_colors.hxx
466		~~ED4_ProteinViewer.o: $(ARBHOME)/INCLUDE/awt_translate.hxx~~
467	466	ED4_ProteinViewer.o: $(ARBHOME)/INCLUDE/smartptr.h
	467	ED4_ProteinViewer.o: $(ARBHOME)/INCLUDE/Translate.hxx
468	468
469	469	ED4_RNA3D.o: ../RNA3D/RNA3D_Main.hxx

trunk/GENOM/EXP_interface.cxx

r6188	r6280
13	13	// ==================================================================== //
14	14
15		#include <awt.hxx>
16		#include <awt_canvas.hxx>
17		#include <awt_item_sel_list.hxx>
18		#include <awt_sel_boxes.hxx>
19		#include <arbdbt.h>
20		#include <aw_awars.hxx>
21		#include <db_scanner.hxx>
22
23		#include "EXP.hxx"
	15	#include "EXP_local.hxx"
24	16	#include "EXP_interface.hxx"
25		#include "EXP_local.hxx"
26
27		#include "GEN.hxx"
	17
28	18	#include "GEN_local.hxx"
29	19	#include "GEN_interface.hxx"
30	20
	21	#include <db_scanner.hxx>
	22
	23	#include <awt_sel_boxes.hxx>
	24	#include <awt_item_sel_list.hxx>
	25	#include <awt.hxx>
	26
	27	#include <aw_awars.hxx>
	28
31	29	#include "../NTREE/ad_spec.hxx"
32	30	#include <../NTREE/nt_internal.h>
33
34		~~#include <cstdlib>~~
35		~~#include <cstring>~~
36	31
37	32	using namespace std;

trunk/GENOM/EXP_local.hxx

r5675	r6280
16	16	#define EXP_LOCAL_HXX
17	17
	18	#ifndef EXP_HXX
	19	#include <EXP.hxx>
	20	#endif
	21	#ifndef AW_ROOT_HXX
	22	#include <aw_root.hxx>
	23	#endif
18	24	#ifndef ARB_ASSERT_H
19	25	#include <arb_assert.h>

trunk/GENOM/GEN_graphic.cxx

r5942	r6280
117	117	}
118	118	case AWT_MODE_SELECT:
119		case AWT_MODE_~~MOD~~: {
	119	case AWT_MODE_EDIT: {
120	120	if(button==AWT_M_LEFT) {
121	121	GEN_gene *gene = 0;
…	…
127	127	aw_root->awar(AWAR_LOCAL_GENE_NAME(window_nr))->write_string(gene->Name().c_str());
128	128
129		if (cmd == AWT_MODE_~~MOD~~) {
	129	if (cmd == AWT_MODE_EDIT) {
130	130	GEN_create_gene_window(aw_root)->activate();
131	131	}

trunk/GENOM/GEN_interface.cxx

r6188	r6280
1		#include <cstdlib>
2		#include <cstring>
3		#include <awt.hxx>
4		#include <awt_canvas.hxx>
	1	#include "GEN_local.hxx"
	2
5	3	#include <awt_item_sel_list.hxx>
6	4	#include <awt_sel_boxes.hxx>
…	…
8	6	#include <db_scanner.hxx>
9	7
10		~~#include <arbdbt.h>~~
11		~~#include <probe_design.hxx>~~
12
13	8	#include <ntree.hxx>
14	9	#include <../NTREE/ad_spec.hxx>
15	10	#include <../NTREE/nt_internal.h>
16	11
17		~~#ifndef GEN_LOCAL_HXX~~
18		~~#include "GEN_local.hxx"~~
19		~~#endif~~
20		~~#ifndef GEN_NDS_HXX~~
21		~~#include "GEN_nds.hxx"~~
22		~~#endif~~
23	12
24	13	using namespace std;

trunk/GENOM/GEN_interface.hxx

r312	r6280
8	8	#define GEN_INTERFACE_HXX
9	9
	10	#ifndef ARBDBT_H
	11	#include <arbdbt.h>
	12	#endif
	13
	14
10	15	extern struct ad_item_selector GEN_item_selector;
11	16

trunk/GENOM/GEN_map.cxx

r6188	r6280
522	522	break;
523	523	}
524		case AWT_MODE_~~MOD~~: {
	524	case AWT_MODE_EDIT: {
525	525	text="INFO MODE LEFT: click for info";
526	526	break;
…	…
922	922
923	923	static void do_mark_command_for_one_species(int imode, GBDATA *gb_species, AW_CL cl_user) {
924		GEN_MARK_MODE mode = (GEN_MARK_MODE)imode;
925		GB_ERROR error = 0;
	924	GEN_MARK_MODE mode = (GEN_MARK_MODE)imode;
926	925
927	926	for (GBDATA *gb_gene = GEN_first_gene(gb_species);
928		~~!error &&~~ gb_gene;
	927	gb_gene;
929	928	gb_gene = GEN_next_gene(gb_gene))
930	929	{
…	…
975	974	}
976	975
977		if (mark_flag != org_mark_flag) {
978		error = GB_write_flag(gb_gene, mark_flag?1:0);
979		}
980		}
981
982		if (error) aw_message(error);
	976	if (mark_flag != org_mark_flag) GB_write_flag(gb_gene, mark_flag?1:0);
	977	}
983	978	}
984	979
…	…
1666	1661	create_mode("select.bitmap", "gen_mode.hlp", AWM_ALL, GEN_mode_event, (AW_CL)this, (AW_CL)AWT_MODE_SELECT);
1667	1662	create_mode("pzoom.bitmap", "gen_mode.hlp", AWM_ALL, GEN_mode_event, (AW_CL)this, (AW_CL)AWT_MODE_ZOOM);
1668		create_mode("info.bitmap", "gen_mode.hlp", AWM_ALL, GEN_mode_event, (AW_CL)this, (AW_CL)AWT_MODE_~~MOD~~);
	1663	create_mode("info.bitmap", "gen_mode.hlp", AWM_ALL, GEN_mode_event, (AW_CL)this, (AW_CL)AWT_MODE_EDIT);
1669	1664
1670	1665	// ------------------

trunk/GENOM/GEN_translations.cxx

r6141	r6280
11	11	// =============================================================== //
12	12
	13	#include "GEN_local.hxx"
	14
	15	#include <Translate.hxx>
	16	#include <AP_codon_table.hxx>
	17	#include <aw_question.hxx>
13	18	#include <arbdbt.h>
14		~~#include <awt_translate.hxx>~~
15		~~#include <awt_codon_table.hxx>~~
16		~~#include <aw_question.hxx>~~
17
18		~~#include "GEN.hxx"~~
19		~~#include "GEN_local.hxx"~~
20	19
21	20	using namespace std;

trunk/GENOM/Makefile

r6277	r6280
40	40	$(MAKEDEPEND) -f- $(MAKEDEPENDFLAGS) $< 2>/dev/null >$@
41	41
42		# DO NOT DELETE
	42	# DO NOT DELETE THIS LINE -- make depend depends on it.
43	43
44	44	# Do not add dependencies manually - use 'make depend' in $ARBHOME
…	…
71	71	EXP_interface.o: $(ARBHOME)/INCLUDE/aw_window.hxx
72	72	EXP_interface.o: $(ARBHOME)/INCLUDE/awt.hxx
73		~~EXP_interface.o: $(ARBHOME)/INCLUDE/awt_canvas.hxx~~
74	73	EXP_interface.o: $(ARBHOME)/INCLUDE/awt_item_sel_list.hxx
75	74	EXP_interface.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx
…	…
158	157	GEN_interface.o: GEN.hxx
159	158	GEN_interface.o: GEN_local.hxx
160		~~GEN_interface.o: GEN_nds.hxx~~
161	159	GEN_interface.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
162	160	GEN_interface.o: $(ARBHOME)/INCLUDE/ad_prot.h
…	…
177	175	GEN_interface.o: $(ARBHOME)/INCLUDE/aw_window.hxx
178	176	GEN_interface.o: $(ARBHOME)/INCLUDE/awt.hxx
179		~~GEN_interface.o: $(ARBHOME)/INCLUDE/awt_canvas.hxx~~
180	177	GEN_interface.o: $(ARBHOME)/INCLUDE/awt_item_sel_list.hxx
181	178	GEN_interface.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx
182	179	GEN_interface.o: $(ARBHOME)/INCLUDE/db_scanner.hxx
183	180	GEN_interface.o: $(ARBHOME)/INCLUDE/ntree.hxx
184		~~GEN_interface.o: $(ARBHOME)/INCLUDE/probe_design.hxx~~
185	181	GEN_interface.o: $(ARBHOME)/INCLUDE/smartptr.h
186	182
…	…
249	245	GEN_translations.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
250	246	GEN_translations.o: $(ARBHOME)/INCLUDE/adGene.h
	247	GEN_translations.o: $(ARBHOME)/INCLUDE/AP_codon_table.hxx
251	248	GEN_translations.o: $(ARBHOME)/INCLUDE/arb_assert.h
252	249	GEN_translations.o: $(ARBHOME)/INCLUDE/arb_error.h
…	…
263	260	GEN_translations.o: $(ARBHOME)/INCLUDE/aw_window.hxx
264	261	GEN_translations.o: $(ARBHOME)/INCLUDE/awt.hxx
265		~~GEN_translations.o: $(ARBHOME)/INCLUDE/awt_codon_table.hxx~~
266		~~GEN_translations.o: $(ARBHOME)/INCLUDE/awt_translate.hxx~~
267	262	GEN_translations.o: $(ARBHOME)/INCLUDE/smartptr.h
	263	GEN_translations.o: $(ARBHOME)/INCLUDE/Translate.hxx

trunk/GENOM_IMPORT/DBwriter.cxx

r6141	r6280
16	16	#include <arbdbt.h>
17	17	#include <adGene.h>
18		#include <~~awt_t~~ranslate.hxx>
	18	#include <Translate.hxx>
19	19	#include <aw_question.hxx>
20	20	#include <GEN.hxx>
…	…
48	48	if (!gb_container) throw DBerror(GBS_global_string("Failed to create container '%s'", name));
49	49
50		if (mark) {
51		GB_ERROR err = GB_write_flag(gb_container, 1);
52		if (err) throw DBerror(GBS_global_string("Failed to mark %s", name), err);
53		}
	50	if (mark) GB_write_flag(gb_container, 1);
54	51
55	52	return gb_container;

trunk/GENOM_IMPORT/Makefile

r6277	r6280
84	84	DBwriter.o: $(ARBHOME)/INCLUDE/aw_root.hxx
85	85	DBwriter.o: $(ARBHOME)/INCLUDE/aw_window.hxx
86		~~DBwriter.o: $(ARBHOME)/INCLUDE/awt_translate.hxx~~
87	86	DBwriter.o: $(ARBHOME)/INCLUDE/FileBuffer.h
88	87	DBwriter.o: $(ARBHOME)/INCLUDE/GEN.hxx
89	88	DBwriter.o: $(ARBHOME)/INCLUDE/smartptr.h
	89	DBwriter.o: $(ARBHOME)/INCLUDE/Translate.hxx
90	90
91	91	Feature.o: defs.h

trunk/MERGE/MG_checkfield.cxx

r6141	r6280
247	247	GBS_diff_strings(s1,s2,exclude,ToUpper,correct,&positions1,&positions2,&corrected);
248	248	if (corrected) {
249		error = GB_write_as_string(gb_field2,s2);
250		if (!error) ~~error =~~ GB_write_flag(gb_species2,1);
	249	error = GB_write_as_string(gb_field2,s2);
	250	if (!error) GB_write_flag(gb_species2,1);
251	251	}
252	252	}

trunk/MERGE/MG_species.cxx

r6141	r6280
686	686	else {
687	687	if (!GBS_find_string(s2,s1,0)) {
688		error = GB_write_string(gb_field2, GBS_global_string("%s %s", s2, s1));
689		if (!error) ~~error =~~ GB_write_flag(gb_species2,1);
	688	error = GB_write_string(gb_field2, GBS_global_string("%s %s", s2, s1));
	689	if (!error) GB_write_flag(gb_species2,1);
690	690	}
691	691	}
…	…
695	695	}
696	696	else { // not GB_STRING
697		error = GB_copy(gb_field2,gb_field1);
698		if (!error) ~~error =~~ GB_write_flag(gb_species2, 1);
	697	error = GB_copy(gb_field2,gb_field1);
	698	if (!error) GB_write_flag(gb_species2, 1);
699	699	if (transfer_of_alignment && !error){
700	700	error = MG_transfer_sequence(&rm,gb_species1,gb_species2);
…	…
827	827	}
828	828	}
829		if (!error) ~~error =~~ GB_write_flag(gb_species2,1);
	829	if (!error) GB_write_flag(gb_species2,1);
830	830	}
831	831	}
…	…
1160	1160	else {
1161	1161	error = GB_copy_with_protection(D_species, M_species, GB_TRUE);
1162		if (!error) ~~error =~~ GB_write_flag(D_species,1); // mark species
	1162	if (!error) GB_write_flag(D_species,1); // mark species
1163	1163	if (!error) error = GB_write_usr_private(D_species,255); // put in hitlist
1164	1164	if (!error) error = GBT_write_string(D_species, "name", m_name);

trunk/MULTI_PROBE/MP_noclass.cxx

r6160	r6280
11	11	#include <awt.hxx>
12	12	#include <awt_canvas.hxx>
13		#include <awt_tree.hxx>
14		#include <awt_dtree.hxx>
15		#include <awt_tree_cb.hxx>
	13	#include <AP_Tree.hxx>
	14	#include <TreeCallbacks.hxx>
16	15
17	16	#include "MultiProbe.hxx"
…	…
63	62	GB_transaction dummy(ntw->gb_main);
64	63
65		AP_tree *ap_tree = AWT_TREE(ntw)->~~tree_root~~;
	64	AP_tree *ap_tree = AWT_TREE(ntw)->get_root_node();
66	65	if (ap_tree) ap_tree->calc_color();
67	66
…	…
540	539
541	540	GB_transaction dummy(ntw->gb_main);
542		AWT_TREE(ntw)->~~tree_root~~->calc_color_probes(mp_main->get_stc()->sondentopf->get_color_hash());
	541	AWT_TREE(ntw)->get_root_node()->calc_color_probes(mp_main->get_stc()->sondentopf->get_color_hash());
543	542
544	543	if (ntw->gb_main)
…	…
826	825	GB_transaction dummy(ntw->gb_main);
827	826
828		AWT_TREE(ntw)->~~tree_root~~->calc_color();
	827	AWT_TREE(ntw)->get_root_node()->calc_color();
829	828
830	829	if (ntw->gb_main)

trunk/MULTI_PROBE/MP_sonde.cxx

r6137	r6280
4	4	#include <arbdbt.h>
5	5	#include <aw_root.hxx>
6		~~#include <awt_tree.hxx>~~
7	6	#include <math.h>
8	7

trunk/MULTI_PROBE/MP_sondentopf.cxx

r5356	r6280
3	3	#include <string.h>
4	4	#include <arbdbt.h>
5		#include <awt_tree.hxx>
	5	#include <aw_root.hxx>
	6	#include <AP_Tree.hxx> // needed for GCs
6	7	#include <math.h>
7	8

trunk/MULTI_PROBE/Makefile

r6277	r6280
126	126	MP_noclass.o: $(ARBHOME)/INCLUDE/ad_prot.h
127	127	MP_noclass.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
	128	MP_noclass.o: $(ARBHOME)/INCLUDE/AliView.hxx
	129	MP_noclass.o: $(ARBHOME)/INCLUDE/AP_sequence.hxx
	130	MP_noclass.o: $(ARBHOME)/INCLUDE/AP_Tree.hxx
128	131	MP_noclass.o: $(ARBHOME)/INCLUDE/arb_assert.h
129	132	MP_noclass.o: $(ARBHOME)/INCLUDE/arb_error.h
	133	MP_noclass.o: $(ARBHOME)/INCLUDE/ARB_Tree.hxx
130	134	MP_noclass.o: $(ARBHOME)/INCLUDE/arbdb.h
131	135	MP_noclass.o: $(ARBHOME)/INCLUDE/arbdb_base.h
…	…
142	146	MP_noclass.o: $(ARBHOME)/INCLUDE/awt.hxx
143	147	MP_noclass.o: $(ARBHOME)/INCLUDE/awt_canvas.hxx
144		~~MP_noclass.o: $(ARBHOME)/INCLUDE/awt_dtree.hxx~~
145		~~MP_noclass.o: $(ARBHOME)/INCLUDE/awt_pro_a_nucs.hxx~~
146		~~MP_noclass.o: $(ARBHOME)/INCLUDE/awt_tree.hxx~~
147		~~MP_noclass.o: $(ARBHOME)/INCLUDE/awt_tree_cb.hxx~~
148	148	MP_noclass.o: $(ARBHOME)/INCLUDE/client.h
	149	MP_noclass.o: $(ARBHOME)/INCLUDE/downcast.h
149	150	MP_noclass.o: $(ARBHOME)/INCLUDE/PT_com.h
150	151	MP_noclass.o: $(ARBHOME)/INCLUDE/servercntrl.h
151	152	MP_noclass.o: $(ARBHOME)/INCLUDE/smartptr.h
	153	MP_noclass.o: $(ARBHOME)/INCLUDE/TreeCallbacks.hxx
	154	MP_noclass.o: $(ARBHOME)/INCLUDE/TreeDisplay.hxx
152	155
153	156	MP_permute.o: MP_externs.hxx
…	…
239	242	MP_sonde.o: $(ARBHOME)/INCLUDE/attributes.h
240	243	MP_sonde.o: $(ARBHOME)/INCLUDE/aw_awars.hxx
241		~~MP_sonde.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx~~
242	244	MP_sonde.o: $(ARBHOME)/INCLUDE/aw_root.hxx
243		~~MP_sonde.o: $(ARBHOME)/INCLUDE/awt_pro_a_nucs.hxx~~
244		~~MP_sonde.o: $(ARBHOME)/INCLUDE/awt_tree.hxx~~
245	245	MP_sonde.o: $(ARBHOME)/INCLUDE/client.h
246	246	MP_sonde.o: $(ARBHOME)/INCLUDE/PT_com.h
…	…
256	256	MP_sondentopf.o: $(ARBHOME)/INCLUDE/ad_prot.h
257	257	MP_sondentopf.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
	258	MP_sondentopf.o: $(ARBHOME)/INCLUDE/AliView.hxx
	259	MP_sondentopf.o: $(ARBHOME)/INCLUDE/AP_sequence.hxx
	260	MP_sondentopf.o: $(ARBHOME)/INCLUDE/AP_Tree.hxx
258	261	MP_sondentopf.o: $(ARBHOME)/INCLUDE/arb_assert.h
259	262	MP_sondentopf.o: $(ARBHOME)/INCLUDE/arb_error.h
	263	MP_sondentopf.o: $(ARBHOME)/INCLUDE/ARB_Tree.hxx
260	264	MP_sondentopf.o: $(ARBHOME)/INCLUDE/arbdb.h
261	265	MP_sondentopf.o: $(ARBHOME)/INCLUDE/arbdb_base.h
…	…
266	270	MP_sondentopf.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx
267	271	MP_sondentopf.o: $(ARBHOME)/INCLUDE/aw_root.hxx
268		~~MP_sondentopf.o: $(ARBHOME)/INCLUDE/awt_pro_a_nucs.hxx~~
269		~~MP_sondentopf.o: $(ARBHOME)/INCLUDE/awt_tree.hxx~~
270	272	MP_sondentopf.o: $(ARBHOME)/INCLUDE/client.h
	273	MP_sondentopf.o: $(ARBHOME)/INCLUDE/downcast.h
271	274	MP_sondentopf.o: $(ARBHOME)/INCLUDE/PT_com.h
272	275	MP_sondentopf.o: $(ARBHOME)/INCLUDE/servercntrl.h
…	…
281	284	MP_Window.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
282	285	MP_Window.o: $(ARBHOME)/INCLUDE/ad_prot.h
	286	MP_Window.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
283	287	MP_Window.o: $(ARBHOME)/INCLUDE/arb_assert.h
284	288	MP_Window.o: $(ARBHOME)/INCLUDE/arb_error.h
285	289	MP_Window.o: $(ARBHOME)/INCLUDE/arbdb.h
286	290	MP_Window.o: $(ARBHOME)/INCLUDE/arbdb_base.h
	291	MP_Window.o: $(ARBHOME)/INCLUDE/arbdbt.h
287	292	MP_Window.o: $(ARBHOME)/INCLUDE/arbtools.h
288	293	MP_Window.o: $(ARBHOME)/INCLUDE/attributes.h

trunk/Makefile

r6277	r6280
631	631	XML/XML.a \
632	632
	633	# -----------------------
	634	# library packets
	635
633	636	ARCHS_CLIENT_PROBE = PROBE_COM/client.a
634	637	ARCHS_CLIENT_NAMES = NAMES_COM/client.a
…	…
640	643	# communication libs need aisc and aisc_mkpts:
641	644	$(ARCHS_COMMUNICATION:.a=.dummy) : $(ARCHS_MAKEBIN:.a=.dummy)
	645
	646	ARCHS_SEQUENCE = \
	647	SL/SEQUENCE/SEQUENCE.a \
	648	SL/ALIVIEW/ALIVIEW.a \
	649	SL/PRONUC/PRONUC.a \
	650
	651	ARCHS_TREE = \
	652	$(ARCHS_SEQUENCE) \
	653	SL/FILTER/FILTER.a \
	654	SL/ARB_TREE/ARB_TREE.a \
	655
	656	# parsimony tree (used by NTREE, PARSIMONY, STAT(->EDIT[4]), DIST(obsolete!))
	657	ARCHS_AP_TREE = \
	658	$(ARCHS_TREE) \
	659	SL/AP_TREE/AP_TREE.a \
642	660
643	661	#***************************************************************************************
…	…
649	667	ARCHS_NTREE = \
650	668	$(ARCHS_CLIENT_PROBE) \
	669	$(ARCHS_AP_TREE) \
651	670	ARB_GDE/ARB_GDE.a \
652	671	AWTC/AWTC.a \
…	…
664	683	SL/DB_SCANNER/DB_SCANNER.a \
665	684	SL/FILE_BUFFER/FILE_BUFFER.a \
	685	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
666	686	SL/HELIX/HELIX.a \
667	687	SL/REGEXPR/REGEXPR.a \
	688	SL/TRANSLATE/TRANSLATE.a \
	689	SL/TREEDISP/TREEDISP.a \
668	690	SL/TREE_READ/TREE_READ.a \
669	691	SL/TREE_WRITE/TREE_WRITE.a \
…	…
690	712	EDIT = bin/arb_edit
691	713	ARCHS_EDIT = \
	714	$(ARCHS_AP_TREE) \
	715	ARB_GDE/ARB_GDE.a \
	716	EDIT/EDIT.a \
692	717	NAMES_COM/client.a \
693	718	SERVERCNTRL/SERVERCNTRL.a \
694		EDIT/EDIT.a \
695		ARB_GDE/ARB_GDE.a \
	719	SL/AW_HELIX/AW_HELIX.a \
	720	SL/AW_NAME/AW_NAME.a \
	721	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
	722	SL/HELIX/HELIX.a \
696	723	STAT/STAT.a \
697	724	XML/XML.a \
698		~~SL/HELIX/HELIX.a \~~
699		~~SL/AW_HELIX/AW_HELIX.a \~~
700		~~SL/AW_NAME/AW_NAME.a \~~
701	725
702	726	$(EDIT): $(ARCHS_EDIT:.a=.dummy) shared_libs
…	…
711	735
712	736	ARCHS_EDIT4 := \
713		NAMES_COM/client.a \
	737	$(ARCHS_AP_TREE) \
	738	ARB_GDE/ARB_GDE.a \
714	739	AWTC/AWTC.a \
715	740	EDIT4/EDIT4.a \
	741	ISLAND_HOPPING/ISLAND_HOPPING.a \
	742	NAMES_COM/client.a \
716	743	SECEDIT/SECEDIT.a \
717	744	SERVERCNTRL/SERVERCNTRL.a \
718		~~STAT/STAT.a \~~
719		~~ARB_GDE/ARB_GDE.a \~~
720		~~ISLAND_HOPPING/ISLAND_HOPPING.a \~~
721		~~SL/FAST_ALIGNER/FAST_ALIGNER.a \~~
722		~~SL/HELIX/HELIX.a \~~
723	745	SL/AW_HELIX/AW_HELIX.a \
724	746	SL/AW_NAME/AW_NAME.a \
	747	SL/FAST_ALIGNER/FAST_ALIGNER.a \
725	748	SL/FILE_BUFFER/FILE_BUFFER.a \
	749	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
	750	SL/HELIX/HELIX.a \
	751	SL/TRANSLATE/TRANSLATE.a \
	752	STAT/STAT.a \
726	753	XML/XML.a \
727	754
…	…
759	786	WETC/WETC.a \
760	787	SL/HELIX/HELIX.a \
	788	SL/FILTER/FILTER.a \
761	789	XML/XML.a \
762	790
…	…
772	800	ARCHS_DIST = \
773	801	$(ARCHS_CLIENT_PROBE) \
	802	$(ARCHS_AP_TREE) \
	803	CONSENSUS_TREE/CONSENSUS_TREE.a \
774	804	DIST/DIST.a \
	805	EISPACK/EISPACK.a \
775	806	SERVERCNTRL/SERVERCNTRL.a \
776		CONSENSUS_TREE/CONSENSUS_TREE.a \
777		EISPACK/EISPACK.a \
	807	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
778	808	SL/HELIX/HELIX.a \
	809	SL/MATRIX/MATRIX.a \
	810	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.a \
779	811	XML/XML.a \
780	812
…	…
789	821	PARSIMONY = bin/arb_pars
790	822	ARCHS_PARSIMONY = \
	823	$(ARCHS_AP_TREE) \
791	824	NAMES_COM/client.a \
	825	PARSIMONY/PARSIMONY.a \
792	826	SERVERCNTRL/SERVERCNTRL.a \
793		PARSIMONY/PARSIMONY.a \
	827	SL/AW_NAME/AW_NAME.a \
	828	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
794	829	SL/HELIX/HELIX.a \
795		SL/AW_NAME/AW_NAME.a \
	830	SL/TRANSLATE/TRANSLATE.a \
	831	SL/TREEDISP/TREEDISP.a \
796	832	XML/XML.a \
797	833
…	…
846	882	PHYLO/PHYLO.a \
847	883	SL/HELIX/HELIX.a \
	884	SL/FILTER/FILTER.a \
	885	SL/MATRIX/MATRIX.a \
848	886	XML/XML.a \
849	887
…	…
1126	1164	xmlin: XML_IMPORT/XML_IMPORT.dummy# broken
1127	1165	templ: TEMPLATES/TEMPLATES.dummy
	1166	stat: STAT/STAT.a $(NTREE) $(EDIT) $(EDIT4)
1128	1167
1129	1168	#********************************************************************************
…	…
1171	1210	AISC_COM/AISC_COM.proto \
1172	1211	GDE/GDE.proto \
	1212	SL/SL.proto \
1173	1213
1174	1214	#********************************************************************************

trunk/NTREE/AP_conservProfile2Gnuplot.cxx

r6141	r6280
1		#include <stdio.h>
2		#include <stdlib.h>
3		#include <string.h>
4		#include <math.h>
5		#include <unistd.h>
6		#include <sys/types.h>
	1	// =============================================================== //
	2	// //
	3	// File : AP_conservProfile2Gnuplot.cxx //
	4	// Purpose : //
	5	// //
	6	// Institute of Microbiology (Technical University Munich) //
	7	// http://www.arb-home.de/ //
	8	// //
	9	// =============================================================== //
7	10
8		#include <arbdb.h>
9		#include <arbdbt.h>
10		#include <aw_root.hxx>
11		#include <aw_device.hxx>
12		#include <aw_window.hxx>
13		#include <aw_awars.hxx>
	11	#include "nt_internal.h"
	12
	13	#include <awt.hxx>
	14	#include "ap_conservProfile2Gnuplot.hxx"
	15
14	16	#include <aw_global.hxx>
15		~~#include <awt.hxx>~~
16		~~#include <awt_tree.hxx>~~
17		~~#include <awt_canvas.hxx>~~
18		~~#include <awt_csp.hxx>~~
19		~~#include "ap_conservProfile2Gnuplot.hxx"~~
20		~~//#include "nt_cb.hxx"~~
21	17
22	18	extern GBDATA *GLOBAL_gb_main;

trunk/NTREE/AP_csp_2_gnuplot.cxx

r6141	r6280
1		#include <stdio.h>
2		#include <stdlib.h>
3		#include <string.h>
4		#include <math.h>
	1	// =============================================================== //
	2	// //
	3	// File : AP_csp_2_gnuplot.cxx //
	4	// Purpose : //
	5	// //
	6	// Institute of Microbiology (Technical University Munich) //
	7	// http://www.arb-home.de/ //
	8	// //
	9	// =============================================================== //
	10
	11	#include "nt_internal.h"
	12	#include "ap_csp_2_gnuplot.hxx"
	13
	14	#include <awt_filter.hxx>
	15	#include <awt.hxx>
	16	#include <awt_csp.hxx>
	17	#include <AP_filter.hxx>
	18	#include <aw_global.hxx>
	19	#include <aw_awars.hxx>
	20
5	21	#include <unistd.h>
6		#include <sys/types.h>
7
8		#include <arbdb.h>
9		#include <arbdbt.h>
10		#include <aw_root.hxx>
11		#include <aw_device.hxx>
12		#include <aw_window.hxx>
13		#include <aw_awars.hxx>
14		#include <aw_global.hxx>
15		#include <awt.hxx>
16		#include <awt_tree.hxx>
17		#include <awt_csp.hxx>
18		#include <awt_sel_boxes.hxx>
19		#include "ap_csp_2_gnuplot.hxx"
20
21		#ifndef ARB_ASSERT_H
22		#include <arb_assert.h>
23		#endif
	22
24	23	#define nt_assert(bed) arb_assert(bed)
25	24
26	25	extern GBDATA *GLOBAL_gb_main;
27	26
28
29		~~// ------------------------------------------------------------------------------------------------------------------------------~~
30		~~// static GB_ERROR split_stat_filename(const char fname, char dirPtr, char name_prefixPtr, char *name_postfixPtr)~~
31		~~// ------------------------------------------------------------------------------------------------------------------------------~~
32	27	static GB_ERROR split_stat_filename(const char fname, char dirPtr, char name_prefixPtr, char *name_postfixPtr) {
33	28	// 'fname' is sth like 'directory/prefix.sth_gnu'
…	…
66	61	return 0;
67	62	}
68		// -------------------------------------------------------------------------------------------
69		// static char * get_overlay_files(AW_root awr, const char fname, GB_ERROR& error)
70		// -------------------------------------------------------------------------------------------
	63
71	64	static char * get_overlay_files(AW_root awr, const char fname, GB_ERROR& error) {
72	65	nt_assert(!error);
…	…
219	212	}
220	213
221		// ------------------------------------------------------------------------------
222		// void AP_csp_2_gnuplot_cb(AW_window *aww, AW_CL cspcd, AW_CL cl_mode)
223		// ------------------------------------------------------------------------------
	214	// -------------------
	215	// SortedFreq
	216
	217	class SortedFreq {
	218	float *freq[4];
	219
	220	public:
	221	SortedFreq(const AWT_csp *csp);
	222	~SortedFreq();
	223
	224	float get(PlotType plot_type, size_t pos) const {
	225	float f;
	226	switch (plot_type) {
	227	case PT_MOST_FREQUENT_BASE: f = freq[0][pos]; break;
	228	case PT_SECOND_FREQUENT_BASE: f = freq[1][pos]; break;
	229	case PT_THIRD_FREQUENT_BASE: f = freq[2][pos]; break;
	230	case PT_LEAST_FREQUENT_BASE: f = freq[3][pos]; break;
	231	default: nt_assert(0); break;
	232	}
	233	return f;
	234	}
	235	};
	236
	237	SortedFreq::SortedFreq(const AWT_csp *csp) {
	238	size_t len = csp->get_length();
	239	for (int i = 0; i<4; ++i) { // 4 best frequencies
	240	freq[i] = new float[len];
	241	for (size_t p = 0; p<len; ++p) freq[i][p] = 0.0; // clear
	242	}
	243
	244	for (unsigned int c = 0; c<256; ++c) { // all character stats
	245	const float *cfreq = csp->get_frequencies((unsigned char)c);
	246	if (cfreq) {
	247	for (size_t p = 0; p<len; ++p) { // all positions
	248	if (freq[3][p] < cfreq[p]) {
	249	freq[3][p] = cfreq[p]; // found higher freq
	250
	251	for (int i = 3; i > 0; --i) { // bubble upwards to sort
	252	if (freq[i-1][p] >= freq[i][p]) break; // sorted!
	253
	254	float f = freq[i][p];
	255	freq[i][p] = freq[i-1][p];
	256	freq[i-1][p] = f;
	257	}
	258	}
	259	}
	260	}
	261	}
	262
	263	#if defined(DEBUG)
	264	for (size_t p = 0; p<len; ++p) { // all positions
	265	nt_assert(freq[0][p] >= freq[1][p]);
	266	nt_assert(freq[1][p] >= freq[2][p]);
	267	nt_assert(freq[2][p] >= freq[3][p]);
	268	}
	269	#endif // DEBUG
	270	}
	271	SortedFreq::~SortedFreq() {
	272	for (int i = 0; i<4; ++i) delete [] freq[i];
	273	}
	274
	275	// ----------------------------
	276	// AP_csp_2_gnuplot_cb
	277
224	278	void AP_csp_2_gnuplot_cb(AW_window *aww, AW_CL cspcd, AW_CL cl_mode) {
225	279	// cl_mode = 0 -> write file
…	…
230	284	AWT_csp csp = (AWT_csp )cspcd;
231	285	GB_ERROR error = 0;
232		~~AP_filter filter;~~
233	286	int mode = int(cl_mode);
234	287
…	…
237	290	char *alignment_name = aww->get_root()->awar(AP_AWAR_FILTER_ALIGNMENT)->read_string();
238	291	long alignment_length = GBT_get_alignment_len(GLOBAL_gb_main,alignment_name);
239		error = filter.init(filterstring,"0",alignment_length);
	292
	293	AP_filter filter(filterstring, "0", alignment_length);
	294
240	295	free(alignment_name);
241	296	free(filterstring);
242	297
243		~~if (!error)~~ error = csp->go(&filter);
244
245		if (!error && !csp->~~seq_len~~) error = "Please select column statistic";
	298	error = csp->go(&filter);
	299
	300	if (!error && !csp->get_length()) error = "Please select column statistic";
246	301	}
247	302
…	…
276	331
277	332	if (!error) {
278		char *type = aww->get_root()->awar(AP_AWAR_CSP_SUFFIX)->read_string();
279		long smooth = aww->get_root()->awar(AP_AWAR_CSP_SMOOTH)->read_int()+1;
280		double val;
281		double smoothed = 0;
282		unsigned int j;
283		float *f[4];
284
285		if (type[0] == 'f') { // sort frequencies
286		int wf;
287		int c = 0;
288
289		for (wf = 0; wf <256 && c <4; wf++) {
290		if (csp->frequency[wf]) f[c++] = csp->frequency[wf];
291		}
292		int k,l;
293		for (k=3;k>0;k--) {
294		for (l=0;l<k;l++) {
295		for (j=0;j<csp->seq_len; j++) {
296		if (f[l][j] > f[l+1][j]) {
297		float h;
298		h = f[l][j];
299		f[l][j] = f[l+1][j];
300		f[l+1][j] = h;
	333	char *type = aww->get_root()->awar(AP_AWAR_CSP_SUFFIX)->read_string();
	334	long smooth = aww->get_root()->awar(AP_AWAR_CSP_SMOOTH)->read_int()+1;
	335	size_t csplen = csp->get_length();
	336
	337	enum {
	338	STAT_AMOUNT,
	339	STAT_SIMPLE_FLOAT,
	340	STAT_SIMPLE_BOOL,
	341	STAT_SORT,
	342	STAT_UNKNOWN
	343	} stat_type = STAT_UNKNOWN;
	344	union {
	345	struct {
	346	const float *A;
	347	const float *C;
	348	const float *G;
	349	const float *TU;
	350	} amount; // STAT_AMOUNT
	351	const float *floatVals; // STAT_SIMPLE_FLOAT
	352	const bool *boolVals; // STAT_SIMPLE_BOOL
	353	SortedFreq *sorted; // STAT_SORT
	354	} data;
	355
	356	PlotType plot_type = string2PlotType(type);
	357	switch (plot_type) {
	358	case PT_GC_RATIO:
	359	case PT_GA_RATIO:
	360	case PT_BASE_A:
	361	case PT_BASE_C:
	362	case PT_BASE_G:
	363	case PT_BASE_TU: {
	364	stat_type = STAT_AMOUNT;
	365
	366	data.amount.A = csp->get_frequencies('A');
	367	data.amount.C = csp->get_frequencies('C');
	368	data.amount.G = csp->get_frequencies('G');
	369	data.amount.TU = csp->get_frequencies('U');
	370	break;
	371	}
	372	case PT_RATE:
	373	stat_type = STAT_SIMPLE_FLOAT;
	374	data.floatVals = csp->get_rates();
	375	break;
	376
	377	case PT_TT_RATIO:
	378	stat_type = STAT_SIMPLE_FLOAT;
	379	data.floatVals = csp->get_ttratio();
	380	break;
	381
	382	case PT_HELIX: {
	383	stat_type = STAT_SIMPLE_BOOL;
	384	data.boolVals = csp->get_is_helix();
	385	break;
	386	}
	387	case PT_MOST_FREQUENT_BASE:
	388	case PT_SECOND_FREQUENT_BASE:
	389	case PT_THIRD_FREQUENT_BASE:
	390	case PT_LEAST_FREQUENT_BASE: {
	391	stat_type = STAT_SORT;
	392	data.sorted = new SortedFreq(csp);
	393	break;
	394	}
	395	case PT_PLOT_TYPES:
	396	case PT_UNKNOWN:
	397	error = "Please select what to plot";
	398	break;
	399	}
	400
	401	const GB_UINT4 *weights = csp->get_weights();
	402
	403	if (!error) {
	404	for (size_t j=0; j<csplen; ++j) {
	405	if (!weights[j]) continue;
	406	fprintf(out,"%i ",j); // print X coordinate
	407
	408	double val;
	409	switch (stat_type) {
	410	case STAT_AMOUNT: {
	411	float A = data.amount.A[j];
	412	float C = data.amount.C[j];
	413	float G = data.amount.G[j];
	414	float TU = data.amount.TU[j];
	415
	416	float amount = A+C+G+TU;
	417
	418	switch (plot_type) {
	419	case PT_GC_RATIO: val = (G+C)/amount; break;
	420	case PT_GA_RATIO: val = (G+A)/amount; break;
	421	case PT_BASE_A: val = A/amount; break;
	422	case PT_BASE_C: val = C/amount; break;
	423	case PT_BASE_G: val = G/amount; break;
	424	case PT_BASE_TU: val = TU/amount; break;
	425
	426	default: nt_assert(0); break;
301	427	}
	428	break;
302	429	}
	430	case STAT_SIMPLE_FLOAT: val = data.floatVals[j]; break;
	431	case STAT_SIMPLE_BOOL: val = data.boolVals[j]; break;
	432	case STAT_SORT: val = data.sorted->get(plot_type, j); break;
	433
	434	case STAT_UNKNOWN: nt_assert(0); break;
303	435	}
304		}
305		}
306
307		PlotType plot_type = string2PlotType(type);
308		nt_assert(plot_type != PT_UNKNOWN); // 'type' is not a PlotType
309
310		for (j=0;j<csp->seq_len; j++) {
311		if (!csp->weights[j]) continue;
312		fprintf(out,"%i ",j);
313
314		double amount =
315		csp->frequency[(unsigned char)'A'][j] + csp->frequency[(unsigned char)'C'][j] +
316		csp->frequency[(unsigned char)'G'][j] + csp->frequency[(unsigned char)'U'][j] ;
317
318		switch (plot_type) {
319		case PT_GC_RATIO:
320		val = ( csp->frequency[(unsigned char)'G'][j] + csp->frequency[(unsigned char)'C'][j] ) / amount;
321		break;
322		case PT_GA_RATIO:
323		val = ( csp->frequency[(unsigned char)'G'][j] + csp->frequency[(unsigned char)'A'][j] ) / amount;
324		break;
325
326		case PT_BASE_A: val = csp->frequency[(unsigned char)'A'][j] / amount; break;
327		case PT_BASE_C: val = csp->frequency[(unsigned char)'C'][j] / amount; break;
328		case PT_BASE_G: val = csp->frequency[(unsigned char)'G'][j] / amount; break;
329		case PT_BASE_TU: val = csp->frequency[(unsigned char)'U'][j] / amount; break;
330
331		case PT_RATE: val = csp->rates[j]; break;
332		case PT_TT_RATIO: val = csp->ttratio[j]; break;
333		case PT_HELIX: val = csp->is_helix[j]; break;
334
335		case PT_MOST_FREQUENT_BASE: val = f[3][j]; break;
336		case PT_SECOND_FREQUENT_BASE: val = f[2][j]; break;
337		case PT_THIRD_FREQUENT_BASE: val = f[1][j]; break;
338		case PT_LEAST_FREQUENT_BASE: val = f[0][j]; break;
339		default: {
340		nt_assert(0); // unknown calculation requested..
341		val = 0;
342		}
343		}
344		smoothed = val/smooth + smoothed *(smooth-1)/(smooth);
345		fprintf(out,"%f\n",smoothed);
346		}
347
	436
	437	double smoothed = val/smooth + smoothed *(smooth-1)/(smooth);
	438	fprintf(out,"%f\n",smoothed); // print Y coordinate
	439	}
	440	}
	441
	442	if (stat_type == STAT_SORT) delete data.sorted;
348	443	free(type);
349	444	fclose(out);
350	445	out = 0;
351	446	}
352
	447
353	448	if (!error) {
354	449	aww->get_root()->awar(AP_AWAR_CSP_DIRECTORY)->touch(); // reload file selection box
…	…
380	475
381	476	fprintf(out, "%s \"%s\" %s title \"%s\"\n", plot_command[int(plotted)], fname, smooth, makeTitle(fname));
382		fprintf(out, "pause ~~-1 \"Press RETURN to clos~~e gnuplot\"\n");
	477	fprintf(out, "pause mouse any \"Any key or button will terminate gnuplot\"\n");
383	478	fclose(out);
384	479	out = 0;
…	…
499	594	return (AW_window *)aws;
500	595	}
	596
	597

trunk/NTREE/AP_pos_var_pars.cxx

r5825	r6280
1		#include <stdlib.h>
2		#include <stdio.h>
3		#include <ctype.h>
4		#include <string.h>
5		// #include <malloc.h>
6		#include <memory.h>
7		#include <math.h>
8		#include <arbdb.h>
9		#include <arbdbt.h>
10		#include <aw_root.hxx>
11		#include <aw_device.hxx>
	1	// =============================================================== //
	2	// //
	3	// File : AP_pos_var_pars.cxx //
	4	// Purpose : //
	5	// //
	6	// Institute of Microbiology (Technical University Munich) //
	7	// http://www.arb-home.de/ //
	8	// //
	9	// =============================================================== //
	10
	11	#include "ap_pos_var_pars.hxx"
	12
	13	#include <AP_pro_a_nucs.hxx>
	14	#include <awt_sel_boxes.hxx>
12	15	#include <aw_window.hxx>
13		#include <awt.hxx>
14		#include <awt_tree.hxx>
15		#include <awt_sel_boxes.hxx>
16
17		#include "ap_pos_var_pars.hxx"
	16
	17	#include <cctype>
18	18
19	19	#define ap_assert(cond) arb_assert(cond)

trunk/NTREE/Makefile

r6277	r6280
3	3	.SUFFIXES: .o .cxx .depend
4	4
5
	5	# Note: NT_cb.o should be first object (needed by 'proto')
6	6	CPP_OBJECTS = \
	7	NT_cb.o \
7	8	AP_consensus.o \
8	9	AP_conservProfile2Gnuplot.o \
…	…
10	11	AP_csp_2_gnuplot.o \
11	12	AP_pos_var_pars.o \
12		~~NT_cb.o \~~
13	13	NT_concatenate.o \
14	14	NT_dbrepair.o \
…	…
24	24	NT_validNameParser.o \
25	25	NT_validNames.o \
	26	NT_tree_cmp.o \
26	27	ad_ali.o \
27	28	ad_ext.o \
…	…
40	41
41	42	proto:
42		../MAKEBIN/aisc_mkpt -A -E -g -F NT_,AP_ -w nt_internal.h $(CPP_SOURCES) >nt_internal.h.tmp
	43	../MAKEBIN/aisc_mkpt -P -A -E -g -F NT_,AP_ -w nt_internal.h $(CPP_SOURCES) >nt_internal.h.tmp
43	44	../SOURCE_TOOLS/mv_if_diff nt_internal.h.tmp nt_internal.h
44		../MAKEBIN/aisc_mkpt -A -E -g -w nt_cb.hxx NT_cb.cxx NT_extern.cxx >nt_cb.hxx.tmp
	45	../MAKEBIN/aisc_mkpt -P -A -E -g -w nt_cb.hxx NT_cb.cxx NT_extern.cxx >nt_cb.hxx.tmp
45	46	../SOURCE_TOOLS/mv_if_diff nt_cb.hxx.tmp nt_cb.hxx
46	47
…	…
63	64	# DO NOT DELETE THIS LINE -- make depend depends on it.
64	65
65		# Do not add dependencies manually - use 'make depend' in $ARBHOME
66		# For formatting issues see SOURCE_TOOLS/fix_depends.pl
67
68		ad_ali.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
69		ad_ali.o: $(ARBHOME)/INCLUDE/ad_prot.h
70		ad_ali.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
71		ad_ali.o: $(ARBHOME)/INCLUDE/arb_assert.h
72		ad_ali.o: $(ARBHOME)/INCLUDE/arb_error.h
73		ad_ali.o: $(ARBHOME)/INCLUDE/arbdb.h
74		ad_ali.o: $(ARBHOME)/INCLUDE/arbdb_base.h
75		ad_ali.o: $(ARBHOME)/INCLUDE/arbdbt.h
76		ad_ali.o: $(ARBHOME)/INCLUDE/arbtools.h
77		ad_ali.o: $(ARBHOME)/INCLUDE/attributes.h
78		ad_ali.o: $(ARBHOME)/INCLUDE/aw_device.hxx
79		ad_ali.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
80		ad_ali.o: $(ARBHOME)/INCLUDE/aw_position.hxx
81		ad_ali.o: $(ARBHOME)/INCLUDE/aw_root.hxx
82		ad_ali.o: $(ARBHOME)/INCLUDE/aw_window.hxx
83		ad_ali.o: $(ARBHOME)/INCLUDE/awt.hxx
84		ad_ali.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx
85		ad_ali.o: $(ARBHOME)/INCLUDE/smartptr.h
86
87		ad_ext.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
88		ad_ext.o: $(ARBHOME)/INCLUDE/ad_prot.h
89		ad_ext.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
90		ad_ext.o: $(ARBHOME)/INCLUDE/arb_assert.h
91		ad_ext.o: $(ARBHOME)/INCLUDE/arb_error.h
92		ad_ext.o: $(ARBHOME)/INCLUDE/arbdb.h
93		ad_ext.o: $(ARBHOME)/INCLUDE/arbdb_base.h
94		ad_ext.o: $(ARBHOME)/INCLUDE/arbdbt.h
95		ad_ext.o: $(ARBHOME)/INCLUDE/arbtools.h
96		ad_ext.o: $(ARBHOME)/INCLUDE/attributes.h
97		ad_ext.o: $(ARBHOME)/INCLUDE/aw_awars.hxx
98		ad_ext.o: $(ARBHOME)/INCLUDE/aw_device.hxx
99		ad_ext.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
100		ad_ext.o: $(ARBHOME)/INCLUDE/aw_position.hxx
101		ad_ext.o: $(ARBHOME)/INCLUDE/aw_root.hxx
102		ad_ext.o: $(ARBHOME)/INCLUDE/aw_window.hxx
103		ad_ext.o: $(ARBHOME)/INCLUDE/awt.hxx
104		ad_ext.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx
105		ad_ext.o: $(ARBHOME)/INCLUDE/db_scanner.hxx
106		ad_ext.o: $(ARBHOME)/INCLUDE/smartptr.h
107
108		ad_spec.o: ad_spec.hxx
	66	NT_cb.o: nt_internal.h
	67	NT_cb.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdbt.h
	68	NT_cb.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdb.h
	69	NT_cb.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdb_base.h
	70	NT_cb.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/attributes.h
	71	NT_cb.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_k_prot.h
	72	NT_cb.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arb_assert.h
	73	NT_cb.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_prot.h
	74	NT_cb.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_t_prot.h
	75	NT_cb.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_root.hxx
	76	NT_cb.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbtools.h
	77	NT_cb.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arb_error.h
	78	NT_cb.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/smartptr.h nt_cb.hxx
	79	NT_cb.o: ntree.hxx
	80	NT_cb.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_window.hxx
	81	NT_cb.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_device.hxx
	82	NT_cb.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_position.hxx
	83	NT_cb.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_keysym.hxx
	84	NT_cb.o: ad_trees.hxx
	85	NT_cb.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awt_canvas.hxx
	86	NT_cb.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awt_sel_boxes.hxx
	87	NT_cb.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_awars.hxx
	88
	89	AP_consensus.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdb.h
	90	AP_consensus.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdb_base.h
	91	AP_consensus.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/attributes.h
	92	AP_consensus.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_k_prot.h
	93	AP_consensus.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arb_assert.h
	94	AP_consensus.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_prot.h
	95	AP_consensus.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdbt.h
	96	AP_consensus.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_t_prot.h
	97	AP_consensus.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_root.hxx
	98	AP_consensus.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbtools.h
	99	AP_consensus.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arb_error.h
	100	AP_consensus.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/smartptr.h
	101	AP_consensus.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_device.hxx
	102	AP_consensus.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_position.hxx
	103	AP_consensus.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_window.hxx
	104	AP_consensus.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_keysym.hxx
	105	AP_consensus.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awt.hxx
	106	AP_consensus.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awt_sel_boxes.hxx
	107
	108	AP_conservProfile2Gnuplot.o: nt_internal.h
	109	AP_conservProfile2Gnuplot.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdbt.h
	110	AP_conservProfile2Gnuplot.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdb.h
	111	AP_conservProfile2Gnuplot.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdb_base.h
	112	AP_conservProfile2Gnuplot.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/attributes.h
	113	AP_conservProfile2Gnuplot.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_k_prot.h
	114	AP_conservProfile2Gnuplot.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arb_assert.h
	115	AP_conservProfile2Gnuplot.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_prot.h
	116	AP_conservProfile2Gnuplot.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_t_prot.h
	117	AP_conservProfile2Gnuplot.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_root.hxx
	118	AP_conservProfile2Gnuplot.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbtools.h
	119	AP_conservProfile2Gnuplot.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arb_error.h
	120	AP_conservProfile2Gnuplot.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/smartptr.h
	121	AP_conservProfile2Gnuplot.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awt.hxx
	122	AP_conservProfile2Gnuplot.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_window.hxx
	123	AP_conservProfile2Gnuplot.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_device.hxx
	124	AP_conservProfile2Gnuplot.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_position.hxx
	125	AP_conservProfile2Gnuplot.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_keysym.hxx
	126	AP_conservProfile2Gnuplot.o: ap_conservProfile2Gnuplot.hxx
	127	AP_conservProfile2Gnuplot.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_global.hxx
	128
	129	AP_cprofile.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdb.h
	130	AP_cprofile.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdb_base.h
	131	AP_cprofile.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/attributes.h
	132	AP_cprofile.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_k_prot.h
	133	AP_cprofile.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arb_assert.h
	134	AP_cprofile.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_prot.h
	135	AP_cprofile.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdbt.h
	136	AP_cprofile.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_t_prot.h
	137	AP_cprofile.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_root.hxx
	138	AP_cprofile.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbtools.h
	139	AP_cprofile.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arb_error.h
	140	AP_cprofile.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/smartptr.h
	141	AP_cprofile.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_device.hxx
	142	AP_cprofile.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_position.hxx
	143	AP_cprofile.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_window.hxx
	144	AP_cprofile.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_keysym.hxx
	145	AP_cprofile.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_awars.hxx
	146	AP_cprofile.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_global.hxx
	147	AP_cprofile.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awt.hxx
	148	AP_cprofile.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awt_sel_boxes.hxx
	149
	150	AP_csp_2_gnuplot.o: nt_internal.h
	151	AP_csp_2_gnuplot.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdbt.h
	152	AP_csp_2_gnuplot.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdb.h
	153	AP_csp_2_gnuplot.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdb_base.h
	154	AP_csp_2_gnuplot.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/attributes.h
	155	AP_csp_2_gnuplot.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_k_prot.h
	156	AP_csp_2_gnuplot.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arb_assert.h
	157	AP_csp_2_gnuplot.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_prot.h
	158	AP_csp_2_gnuplot.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_t_prot.h
	159	AP_csp_2_gnuplot.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_root.hxx
	160	AP_csp_2_gnuplot.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbtools.h
	161	AP_csp_2_gnuplot.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arb_error.h
	162	AP_csp_2_gnuplot.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/smartptr.h
	163	AP_csp_2_gnuplot.o: ap_csp_2_gnuplot.hxx
	164	AP_csp_2_gnuplot.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awt_filter.hxx
	165	AP_csp_2_gnuplot.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awt.hxx
	166	AP_csp_2_gnuplot.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_window.hxx
	167	AP_csp_2_gnuplot.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_device.hxx
	168	AP_csp_2_gnuplot.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_position.hxx
	169	AP_csp_2_gnuplot.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_keysym.hxx
	170	AP_csp_2_gnuplot.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awt_csp.hxx
	171	AP_csp_2_gnuplot.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/AP_filter.hxx
	172	AP_csp_2_gnuplot.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_global.hxx
	173	AP_csp_2_gnuplot.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_awars.hxx
	174
	175	AP_pos_var_pars.o: ap_pos_var_pars.hxx
	176	AP_pos_var_pars.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdbt.h
	177	AP_pos_var_pars.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdb.h
	178	AP_pos_var_pars.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdb_base.h
	179	AP_pos_var_pars.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/attributes.h
	180	AP_pos_var_pars.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_k_prot.h
	181	AP_pos_var_pars.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arb_assert.h
	182	AP_pos_var_pars.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_prot.h
	183	AP_pos_var_pars.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_t_prot.h
	184	AP_pos_var_pars.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/AP_pro_a_nucs.hxx
	185	AP_pos_var_pars.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awt_sel_boxes.hxx
	186	AP_pos_var_pars.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_root.hxx
	187	AP_pos_var_pars.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbtools.h
	188	AP_pos_var_pars.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arb_error.h
	189	AP_pos_var_pars.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/smartptr.h
	190	AP_pos_var_pars.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_window.hxx
	191	AP_pos_var_pars.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_device.hxx
	192	AP_pos_var_pars.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_position.hxx
	193	AP_pos_var_pars.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_keysym.hxx
	194
	195	NT_concatenate.o: nt_internal.h
	196	NT_concatenate.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdbt.h
	197	NT_concatenate.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdb.h
	198	NT_concatenate.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdb_base.h
	199	NT_concatenate.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/attributes.h
	200	NT_concatenate.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_k_prot.h
	201	NT_concatenate.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arb_assert.h
	202	NT_concatenate.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_prot.h
	203	NT_concatenate.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_t_prot.h
	204	NT_concatenate.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_root.hxx
	205	NT_concatenate.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbtools.h
	206	NT_concatenate.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arb_error.h
	207	NT_concatenate.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/smartptr.h
	208	NT_concatenate.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awt.hxx
	209	NT_concatenate.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_window.hxx
	210	NT_concatenate.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_device.hxx
	211	NT_concatenate.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_position.hxx
	212	NT_concatenate.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_keysym.hxx
	213	NT_concatenate.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awt_item_sel_list.hxx
	214	NT_concatenate.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awt_sel_boxes.hxx
	215	NT_concatenate.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/AW_rename.hxx
	216	NT_concatenate.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_question.hxx
	217
	218	NT_dbrepair.o: NT_dbrepair.hxx
	219	NT_dbrepair.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdb.h
	220	NT_dbrepair.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdb_base.h
	221	NT_dbrepair.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/attributes.h
	222	NT_dbrepair.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_k_prot.h
	223	NT_dbrepair.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arb_assert.h
	224	NT_dbrepair.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_prot.h
	225	NT_dbrepair.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_window.hxx
	226	NT_dbrepair.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_root.hxx
	227	NT_dbrepair.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbtools.h
	228	NT_dbrepair.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arb_error.h
	229	NT_dbrepair.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/smartptr.h
	230	NT_dbrepair.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_device.hxx
	231	NT_dbrepair.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_position.hxx
	232	NT_dbrepair.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_keysym.hxx
	233	NT_dbrepair.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdbt.h
	234	NT_dbrepair.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_t_prot.h
	235	NT_dbrepair.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/adGene.h
	236	NT_dbrepair.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awt.hxx
	237	NT_dbrepair.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/GEN.hxx
	238	NT_dbrepair.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/EXP.hxx
	239	NT_dbrepair.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_color_groups.hxx
	240	NT_dbrepair.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/inline.h
	241
	242	NT_edconf.o: nt_cb.hxx
	243	NT_edconf.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdbt.h
	244	NT_edconf.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdb.h
	245	NT_edconf.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdb_base.h
	246	NT_edconf.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/attributes.h
	247	NT_edconf.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_k_prot.h
	248	NT_edconf.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arb_assert.h
	249	NT_edconf.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_prot.h
	250	NT_edconf.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_t_prot.h
	251	NT_edconf.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_root.hxx
	252	NT_edconf.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbtools.h
	253	NT_edconf.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arb_error.h
	254	NT_edconf.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/smartptr.h
	255	NT_edconf.o: nt_internal.h
	256	NT_edconf.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awt_sel_boxes.hxx
	257	NT_edconf.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_window.hxx
	258	NT_edconf.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_device.hxx
	259	NT_edconf.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_position.hxx
	260	NT_edconf.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_keysym.hxx
	261	NT_edconf.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_awars.hxx
	262	NT_edconf.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_config.h
	263
	264	NT_extern.o: nt_internal.h
	265	NT_extern.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdbt.h
	266	NT_extern.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdb.h
	267	NT_extern.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdb_base.h
	268	NT_extern.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/attributes.h
	269	NT_extern.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_k_prot.h
	270	NT_extern.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arb_assert.h
	271	NT_extern.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_prot.h
	272	NT_extern.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_t_prot.h
	273	NT_extern.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_root.hxx
	274	NT_extern.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbtools.h
	275	NT_extern.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arb_error.h
	276	NT_extern.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/smartptr.h
	277	NT_extern.o: ntree.hxx
	278	NT_extern.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_window.hxx
	279	NT_extern.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_device.hxx
	280	NT_extern.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_position.hxx
	281	NT_extern.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_keysym.hxx
	282	NT_extern.o: ad_spec.hxx
	283	NT_extern.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awt.hxx
	284	NT_extern.o: ad_trees.hxx ap_consensus.hxx
	285	NT_extern.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/seq_quality.h
	286	NT_extern.o: nt_join.hxx
	287	NT_extern.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/st_window.hxx
	288	NT_extern.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/GEN.hxx
	289	NT_extern.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/adGene.h
	290	NT_extern.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/EXP.hxx
	291	NT_extern.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/TreeCallbacks.hxx
	292	NT_extern.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/TreeDisplay.hxx
	293	NT_extern.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/AP_Tree.hxx
	294	NT_extern.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ARB_Tree.hxx
	295	NT_extern.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/AliView.hxx
	296	NT_extern.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/AP_sequence.hxx
	297	NT_extern.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_color_groups.hxx
	298	NT_extern.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/downcast.h
	299	NT_extern.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awt_canvas.hxx
	300	NT_extern.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/AW_rename.hxx
	301	NT_extern.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/probe_design.hxx
	302	NT_extern.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/primer_design.hxx
	303	NT_extern.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/gde.hxx
	304	NT_extern.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awtc_submission.hxx
	305	NT_extern.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awti_export.hxx
	306	NT_extern.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awt_preset.hxx
	307	NT_extern.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awt_macro.hxx
	308	NT_extern.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awt_advice.hxx
	309	NT_extern.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awt_config_manager.hxx
	310	NT_extern.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awt_input_mask.hxx
	311	NT_extern.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awt_sel_boxes.hxx
	312	NT_extern.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awt_www.hxx
	313	NT_extern.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awt_nds.hxx
	314	NT_extern.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_preset.hxx
	315	NT_extern.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_global.hxx
	316	NT_extern.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_awars.hxx
	317	NT_extern.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arb_version.h
	318	NT_extern.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arb_build.h
	319	NT_extern.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/svn_revision.h
	320
	321	NT_import.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdb.h
	322	NT_import.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdb_base.h
	323	NT_import.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/attributes.h
	324	NT_import.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_k_prot.h
	325	NT_import.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arb_assert.h
	326	NT_import.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_prot.h
	327	NT_import.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdbt.h
	328	NT_import.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_t_prot.h
	329	NT_import.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_root.hxx
	330	NT_import.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbtools.h
	331	NT_import.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arb_error.h
	332	NT_import.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/smartptr.h
	333	NT_import.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_window.hxx
	334	NT_import.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_device.hxx
	335	NT_import.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_position.hxx
	336	NT_import.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_keysym.hxx
	337	NT_import.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awti_import.hxx
	338	NT_import.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awt_canvas.hxx
	339	NT_import.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/mg_merge.hxx
	340	NT_import.o: nt_internal.h ad_spec.hxx
	341	NT_import.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awt.hxx
	342	NT_import.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/GEN.hxx
	343	NT_import.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/adGene.h
	344
	345	NT_ins_col.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdb.h
	346	NT_ins_col.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdb_base.h
	347	NT_ins_col.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/attributes.h
	348	NT_ins_col.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_k_prot.h
	349	NT_ins_col.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arb_assert.h
	350	NT_ins_col.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_prot.h
	351	NT_ins_col.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdbt.h
	352	NT_ins_col.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_t_prot.h
	353	NT_ins_col.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_root.hxx
	354	NT_ins_col.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbtools.h
	355	NT_ins_col.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arb_error.h
	356	NT_ins_col.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/smartptr.h
	357	NT_ins_col.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_device.hxx
	358	NT_ins_col.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_position.hxx
	359	NT_ins_col.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_window.hxx
	360	NT_ins_col.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_keysym.hxx
	361	NT_ins_col.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_awars.hxx
	362
	363	NT_join.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdb.h
	364	NT_join.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdb_base.h
	365	NT_join.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/attributes.h
	366	NT_join.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_k_prot.h
	367	NT_join.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arb_assert.h
	368	NT_join.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_prot.h
	369	NT_join.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdbt.h
	370	NT_join.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_t_prot.h
	371	NT_join.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_root.hxx
	372	NT_join.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbtools.h
	373	NT_join.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arb_error.h
	374	NT_join.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/smartptr.h
	375	NT_join.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_device.hxx
	376	NT_join.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_position.hxx
	377	NT_join.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_window.hxx
	378	NT_join.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_keysym.hxx
	379	NT_join.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_awars.hxx
	380	NT_join.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awt.hxx
	381	NT_join.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awt_item_sel_list.hxx
	382	NT_join.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awt_sel_boxes.hxx
	383
	384	NT_main.o: nt_internal.h
	385	NT_main.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdbt.h
	386	NT_main.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdb.h
	387	NT_main.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdb_base.h
	388	NT_main.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/attributes.h
	389	NT_main.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_k_prot.h
	390	NT_main.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arb_assert.h
	391	NT_main.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_prot.h
	392	NT_main.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_t_prot.h
	393	NT_main.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_root.hxx
	394	NT_main.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbtools.h
	395	NT_main.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arb_error.h
	396	NT_main.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/smartptr.h
	397	NT_main.o: ntree.hxx
	398	NT_main.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_window.hxx
	399	NT_main.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_device.hxx
	400	NT_main.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_position.hxx
	401	NT_main.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_keysym.hxx
	402	NT_main.o: nt_cb.hxx
	403	NT_main.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/mg_merge.hxx
	404	NT_main.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awti_import.hxx
	405	NT_main.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awt_advice.hxx
	406	NT_main.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awt.hxx
	407	NT_main.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_global.hxx
	408	NT_main.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_question.hxx
	409	NT_main.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_awars.hxx
	410	NT_main.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/adGene.h
	411	NT_main.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arb_version.h
	412	NT_main.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arb_build.h
	413	NT_main.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/svn_revision.h
	414
	415	NT_trackAliChanges.o: NT_trackAliChanges.h
	416	NT_trackAliChanges.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_root.hxx
	417	NT_trackAliChanges.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arb_assert.h
	418	NT_trackAliChanges.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdb_base.h
	419	NT_trackAliChanges.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/attributes.h
	420	NT_trackAliChanges.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_k_prot.h
	421	NT_trackAliChanges.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbtools.h
	422	NT_trackAliChanges.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arb_error.h
	423	NT_trackAliChanges.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/smartptr.h
	424	NT_trackAliChanges.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awt_sel_boxes.hxx
	425	NT_trackAliChanges.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdbt.h
	426	NT_trackAliChanges.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdb.h
	427	NT_trackAliChanges.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_prot.h
	428	NT_trackAliChanges.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_t_prot.h
	429	NT_trackAliChanges.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_window.hxx
	430	NT_trackAliChanges.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_device.hxx
	431	NT_trackAliChanges.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_position.hxx
	432	NT_trackAliChanges.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_keysym.hxx
	433
	434	NT_validManual.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdb.h
	435	NT_validManual.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdb_base.h
	436	NT_validManual.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/attributes.h
	437	NT_validManual.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_k_prot.h
	438	NT_validManual.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arb_assert.h
	439	NT_validManual.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_prot.h
	440	NT_validManual.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdbt.h
	441	NT_validManual.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_t_prot.h
	442	NT_validManual.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_root.hxx
	443	NT_validManual.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbtools.h
	444	NT_validManual.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arb_error.h
	445	NT_validManual.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/smartptr.h
	446	NT_validManual.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_device.hxx
	447	NT_validManual.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_position.hxx
	448	NT_validManual.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_window.hxx
	449	NT_validManual.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_keysym.hxx
	450	NT_validManual.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_awars.hxx
	451	NT_validManual.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awt.hxx
	452
	453	NT_validNameParser.o: nt_validNameParser.hxx
	454
	455	NT_validNames.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdb.h
	456	NT_validNames.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdb_base.h
	457	NT_validNames.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/attributes.h
	458	NT_validNames.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_k_prot.h
	459	NT_validNames.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arb_assert.h
	460	NT_validNames.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_prot.h
	461	NT_validNames.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdbt.h
	462	NT_validNames.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_t_prot.h
	463	NT_validNames.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_root.hxx
	464	NT_validNames.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbtools.h
	465	NT_validNames.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arb_error.h
	466	NT_validNames.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/smartptr.h
	467	NT_validNames.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_device.hxx
	468	NT_validNames.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_position.hxx
	469	NT_validNames.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_window.hxx
	470	NT_validNames.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_keysym.hxx
	471	NT_validNames.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_awars.hxx
	472	NT_validNames.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awt.hxx
	473	NT_validNames.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awt_www.hxx
	474	NT_validNames.o: nt_validNameParser.hxx
	475
	476	NT_tree_cmp.o: nt_tree_cmp.hxx
	477	NT_tree_cmp.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdbt.h
	478	NT_tree_cmp.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdb.h
	479	NT_tree_cmp.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdb_base.h
	480	NT_tree_cmp.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/attributes.h
	481	NT_tree_cmp.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_k_prot.h
	482	NT_tree_cmp.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arb_assert.h
	483	NT_tree_cmp.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_prot.h
	484	NT_tree_cmp.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_t_prot.h
	485	NT_tree_cmp.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/AP_Tree.hxx
	486	NT_tree_cmp.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ARB_Tree.hxx
	487	NT_tree_cmp.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/AliView.hxx
	488	NT_tree_cmp.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/AP_sequence.hxx
	489	NT_tree_cmp.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_color_groups.hxx
	490	NT_tree_cmp.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_root.hxx
	491	NT_tree_cmp.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbtools.h
	492	NT_tree_cmp.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arb_error.h
	493	NT_tree_cmp.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/smartptr.h
	494	NT_tree_cmp.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/downcast.h
	495
	496	ad_ali.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_root.hxx
	497	ad_ali.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arb_assert.h
	498	ad_ali.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdb_base.h
	499	ad_ali.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/attributes.h
	500	ad_ali.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_k_prot.h
	501	ad_ali.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbtools.h
	502	ad_ali.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arb_error.h
	503	ad_ali.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/smartptr.h
	504	ad_ali.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_device.hxx
	505	ad_ali.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_position.hxx
	506	ad_ali.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_window.hxx
	507	ad_ali.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_keysym.hxx
	508	ad_ali.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdbt.h
	509	ad_ali.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdb.h
	510	ad_ali.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_prot.h
	511	ad_ali.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_t_prot.h
	512	ad_ali.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awt.hxx
	513	ad_ali.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awt_sel_boxes.hxx
	514
	515	ad_ext.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdb.h
	516	ad_ext.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdb_base.h
	517	ad_ext.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/attributes.h
	518	ad_ext.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_k_prot.h
	519	ad_ext.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arb_assert.h
	520	ad_ext.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_prot.h
	521	ad_ext.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdbt.h
	522	ad_ext.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_t_prot.h
	523	ad_ext.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_root.hxx
	524	ad_ext.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbtools.h
	525	ad_ext.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arb_error.h
	526	ad_ext.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/smartptr.h
	527	ad_ext.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_device.hxx
	528	ad_ext.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_position.hxx
	529	ad_ext.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_window.hxx
	530	ad_ext.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_keysym.hxx
	531	ad_ext.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awt.hxx
	532	ad_ext.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awt_sel_boxes.hxx
	533	ad_ext.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_awars.hxx
	534	ad_ext.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/db_scanner.hxx
	535
	536	ad_spec.o: ad_spec.hxx /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awt.hxx
	537	ad_spec.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arb_assert.h
	538	ad_spec.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdb_base.h
	539	ad_spec.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/attributes.h
	540	ad_spec.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_k_prot.h
	541	ad_spec.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_window.hxx
	542	ad_spec.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_root.hxx
	543	ad_spec.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbtools.h
	544	ad_spec.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arb_error.h
	545	ad_spec.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/smartptr.h
	546	ad_spec.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_device.hxx
	547	ad_spec.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_position.hxx
	548	ad_spec.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_keysym.hxx
	549	ad_spec.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdb.h
	550	ad_spec.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_prot.h
109	551	ad_spec.o: nt_internal.h
	552	ad_spec.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdbt.h
	553	ad_spec.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_t_prot.h
110	554	ad_spec.o: ntree.hxx
111		ad_spec.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
112		ad_spec.o: $(ARBHOME)/INCLUDE/ad_prot.h
113		ad_spec.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
114		ad_spec.o: $(ARBHOME)/INCLUDE/arb_assert.h
115		ad_spec.o: $(ARBHOME)/INCLUDE/arb_error.h
116		ad_spec.o: $(ARBHOME)/INCLUDE/arbdb.h
117		ad_spec.o: $(ARBHOME)/INCLUDE/arbdb_base.h
118		ad_spec.o: $(ARBHOME)/INCLUDE/arbdbt.h
119		ad_spec.o: $(ARBHOME)/INCLUDE/arbtools.h
120		ad_spec.o: $(ARBHOME)/INCLUDE/attributes.h
121		ad_spec.o: $(ARBHOME)/INCLUDE/aw_awars.hxx
122		ad_spec.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx
123		ad_spec.o: $(ARBHOME)/INCLUDE/aw_device.hxx
124		ad_spec.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
125		ad_spec.o: $(ARBHOME)/INCLUDE/aw_position.hxx
126		ad_spec.o: $(ARBHOME)/INCLUDE/AW_rename.hxx
127		ad_spec.o: $(ARBHOME)/INCLUDE/aw_root.hxx
128		ad_spec.o: $(ARBHOME)/INCLUDE/aw_window.hxx
129		ad_spec.o: $(ARBHOME)/INCLUDE/awt.hxx
130		ad_spec.o: $(ARBHOME)/INCLUDE/awt_canvas.hxx
131		ad_spec.o: $(ARBHOME)/INCLUDE/awt_dtree.hxx
132		ad_spec.o: $(ARBHOME)/INCLUDE/awt_item_sel_list.hxx
133		ad_spec.o: $(ARBHOME)/INCLUDE/awt_pro_a_nucs.hxx
134		ad_spec.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx
135		ad_spec.o: $(ARBHOME)/INCLUDE/awt_tree.hxx
136		ad_spec.o: $(ARBHOME)/INCLUDE/awt_www.hxx
137		ad_spec.o: $(ARBHOME)/INCLUDE/awtc_next_neighbours.hxx
138		ad_spec.o: $(ARBHOME)/INCLUDE/awtlocal.hxx
139		ad_spec.o: $(ARBHOME)/INCLUDE/db_scanner.hxx
140		ad_spec.o: $(ARBHOME)/INCLUDE/probe_design.hxx
141		ad_spec.o: $(ARBHOME)/INCLUDE/smartptr.h
142
143		ad_transpro.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
144		ad_transpro.o: $(ARBHOME)/INCLUDE/ad_prot.h
145		ad_transpro.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
146		ad_transpro.o: $(ARBHOME)/INCLUDE/arb_assert.h
147		ad_transpro.o: $(ARBHOME)/INCLUDE/arb_error.h
148		ad_transpro.o: $(ARBHOME)/INCLUDE/arbdb.h
149		ad_transpro.o: $(ARBHOME)/INCLUDE/arbdb_base.h
150		ad_transpro.o: $(ARBHOME)/INCLUDE/arbdbt.h
151		ad_transpro.o: $(ARBHOME)/INCLUDE/arbtools.h
152		ad_transpro.o: $(ARBHOME)/INCLUDE/attributes.h
153		ad_transpro.o: $(ARBHOME)/INCLUDE/aw_awars.hxx
154		ad_transpro.o: $(ARBHOME)/INCLUDE/aw_device.hxx
155		ad_transpro.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
156		ad_transpro.o: $(ARBHOME)/INCLUDE/aw_position.hxx
157		ad_transpro.o: $(ARBHOME)/INCLUDE/aw_root.hxx
158		ad_transpro.o: $(ARBHOME)/INCLUDE/aw_window.hxx
159		ad_transpro.o: $(ARBHOME)/INCLUDE/awt.hxx
160		ad_transpro.o: $(ARBHOME)/INCLUDE/awt_codon_table.hxx
161		ad_transpro.o: $(ARBHOME)/INCLUDE/awt_pro_a_nucs.hxx
162		ad_transpro.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx
163		ad_transpro.o: $(ARBHOME)/INCLUDE/awt_translate.hxx
164		ad_transpro.o: $(ARBHOME)/INCLUDE/smartptr.h
	555	ad_spec.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awtc_next_neighbours.hxx
	556	ad_spec.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/AW_rename.hxx
	557	ad_spec.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/db_scanner.hxx
	558	ad_spec.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awt_item_sel_list.hxx
	559	ad_spec.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awtlocal.hxx
	560	ad_spec.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awt_www.hxx
	561	ad_spec.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awt_canvas.hxx
	562	ad_spec.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awt_sel_boxes.hxx
	563	ad_spec.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_awars.hxx
	564	ad_spec.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/probe_design.hxx
	565
	566	ad_transpro.o: nt_internal.h
	567	ad_transpro.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdbt.h
	568	ad_transpro.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdb.h
	569	ad_transpro.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdb_base.h
	570	ad_transpro.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/attributes.h
	571	ad_transpro.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_k_prot.h
	572	ad_transpro.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arb_assert.h
	573	ad_transpro.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_prot.h
	574	ad_transpro.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_t_prot.h
	575	ad_transpro.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_root.hxx
	576	ad_transpro.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbtools.h
	577	ad_transpro.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arb_error.h
	578	ad_transpro.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/smartptr.h
	579	ad_transpro.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awt_sel_boxes.hxx
	580	ad_transpro.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/Translate.hxx
	581	ad_transpro.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/AP_codon_table.hxx
	582	ad_transpro.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awt.hxx
	583	ad_transpro.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_window.hxx
	584	ad_transpro.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_device.hxx
	585	ad_transpro.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_position.hxx
	586	ad_transpro.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_keysym.hxx
	587	ad_transpro.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/AP_pro_a_nucs.hxx
	588	ad_transpro.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_awars.hxx
165	589
166	590	ad_trees.o: ad_trees.hxx
167		ad_trees.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
168		ad_trees.o: $(ARBHOME)/INCLUDE/ad_prot.h
169		ad_trees.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
170		ad_trees.o: $(ARBHOME)/INCLUDE/arb_assert.h
171		ad_trees.o: $(ARBHOME)/INCLUDE/arb_error.h
172		ad_trees.o: $(ARBHOME)/INCLUDE/arbdb.h
173		ad_trees.o: $(ARBHOME)/INCLUDE/arbdb_base.h
174		ad_trees.o: $(ARBHOME)/INCLUDE/arbdbt.h
175		ad_trees.o: $(ARBHOME)/INCLUDE/arbtools.h
176		ad_trees.o: $(ARBHOME)/INCLUDE/attributes.h
177		ad_trees.o: $(ARBHOME)/INCLUDE/aw_awars.hxx
178		ad_trees.o: $(ARBHOME)/INCLUDE/aw_device.hxx
179		ad_trees.o: $(ARBHOME)/INCLUDE/aw_global.hxx
180		ad_trees.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
181		ad_trees.o: $(ARBHOME)/INCLUDE/aw_position.hxx
182		ad_trees.o: $(ARBHOME)/INCLUDE/aw_root.hxx
183		ad_trees.o: $(ARBHOME)/INCLUDE/aw_window.hxx
184		ad_trees.o: $(ARBHOME)/INCLUDE/awt.hxx
185		ad_trees.o: $(ARBHOME)/INCLUDE/awt_nds.hxx
186		ad_trees.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx
187		ad_trees.o: $(ARBHOME)/INCLUDE/awt_tree_cmp.hxx
188		ad_trees.o: $(ARBHOME)/INCLUDE/smartptr.h
189		ad_trees.o: $(ARBHOME)/INCLUDE/TreeRead.h
190		ad_trees.o: $(ARBHOME)/INCLUDE/TreeWrite.h
191
192		AP_consensus.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
193		AP_consensus.o: $(ARBHOME)/INCLUDE/ad_prot.h
194		AP_consensus.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
195		AP_consensus.o: $(ARBHOME)/INCLUDE/arb_assert.h
196		AP_consensus.o: $(ARBHOME)/INCLUDE/arb_error.h
197		AP_consensus.o: $(ARBHOME)/INCLUDE/arbdb.h
198		AP_consensus.o: $(ARBHOME)/INCLUDE/arbdb_base.h
199		AP_consensus.o: $(ARBHOME)/INCLUDE/arbdbt.h
200		AP_consensus.o: $(ARBHOME)/INCLUDE/arbtools.h
201		AP_consensus.o: $(ARBHOME)/INCLUDE/attributes.h
202		AP_consensus.o: $(ARBHOME)/INCLUDE/aw_device.hxx
203		AP_consensus.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
204		AP_consensus.o: $(ARBHOME)/INCLUDE/aw_position.hxx
205		AP_consensus.o: $(ARBHOME)/INCLUDE/aw_root.hxx
206		AP_consensus.o: $(ARBHOME)/INCLUDE/aw_window.hxx
207		AP_consensus.o: $(ARBHOME)/INCLUDE/awt.hxx
208		AP_consensus.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx
209		AP_consensus.o: $(ARBHOME)/INCLUDE/smartptr.h
210
211		AP_conservProfile2Gnuplot.o: ap_conservProfile2Gnuplot.hxx
212		AP_conservProfile2Gnuplot.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
213		AP_conservProfile2Gnuplot.o: $(ARBHOME)/INCLUDE/ad_prot.h
214		AP_conservProfile2Gnuplot.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
215		AP_conservProfile2Gnuplot.o: $(ARBHOME)/INCLUDE/arb_assert.h
216		AP_conservProfile2Gnuplot.o: $(ARBHOME)/INCLUDE/arb_error.h
217		AP_conservProfile2Gnuplot.o: $(ARBHOME)/INCLUDE/arbdb.h
218		AP_conservProfile2Gnuplot.o: $(ARBHOME)/INCLUDE/arbdb_base.h
219		AP_conservProfile2Gnuplot.o: $(ARBHOME)/INCLUDE/arbdbt.h
220		AP_conservProfile2Gnuplot.o: $(ARBHOME)/INCLUDE/arbtools.h
221		AP_conservProfile2Gnuplot.o: $(ARBHOME)/INCLUDE/attributes.h
222		AP_conservProfile2Gnuplot.o: $(ARBHOME)/INCLUDE/aw_awars.hxx
223		AP_conservProfile2Gnuplot.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx
224		AP_conservProfile2Gnuplot.o: $(ARBHOME)/INCLUDE/aw_device.hxx
225		AP_conservProfile2Gnuplot.o: $(ARBHOME)/INCLUDE/aw_global.hxx
226		AP_conservProfile2Gnuplot.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
227		AP_conservProfile2Gnuplot.o: $(ARBHOME)/INCLUDE/aw_position.hxx
228		AP_conservProfile2Gnuplot.o: $(ARBHOME)/INCLUDE/aw_root.hxx
229		AP_conservProfile2Gnuplot.o: $(ARBHOME)/INCLUDE/aw_window.hxx
230		AP_conservProfile2Gnuplot.o: $(ARBHOME)/INCLUDE/awt.hxx
231		AP_conservProfile2Gnuplot.o: $(ARBHOME)/INCLUDE/awt_canvas.hxx
232		AP_conservProfile2Gnuplot.o: $(ARBHOME)/INCLUDE/awt_csp.hxx
233		AP_conservProfile2Gnuplot.o: $(ARBHOME)/INCLUDE/awt_pro_a_nucs.hxx
234		AP_conservProfile2Gnuplot.o: $(ARBHOME)/INCLUDE/awt_tree.hxx
235		AP_conservProfile2Gnuplot.o: $(ARBHOME)/INCLUDE/smartptr.h
236
237		AP_cprofile.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
238		AP_cprofile.o: $(ARBHOME)/INCLUDE/ad_prot.h
239		AP_cprofile.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
240		AP_cprofile.o: $(ARBHOME)/INCLUDE/arb_assert.h
241		AP_cprofile.o: $(ARBHOME)/INCLUDE/arb_error.h
242		AP_cprofile.o: $(ARBHOME)/INCLUDE/arbdb.h
243		AP_cprofile.o: $(ARBHOME)/INCLUDE/arbdb_base.h
244		AP_cprofile.o: $(ARBHOME)/INCLUDE/arbdbt.h
245		AP_cprofile.o: $(ARBHOME)/INCLUDE/arbtools.h
246		AP_cprofile.o: $(ARBHOME)/INCLUDE/attributes.h
247		AP_cprofile.o: $(ARBHOME)/INCLUDE/aw_awars.hxx
248		AP_cprofile.o: $(ARBHOME)/INCLUDE/aw_device.hxx
249		AP_cprofile.o: $(ARBHOME)/INCLUDE/aw_global.hxx
250		AP_cprofile.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
251		AP_cprofile.o: $(ARBHOME)/INCLUDE/aw_position.hxx
252		AP_cprofile.o: $(ARBHOME)/INCLUDE/aw_root.hxx
253		AP_cprofile.o: $(ARBHOME)/INCLUDE/aw_window.hxx
254		AP_cprofile.o: $(ARBHOME)/INCLUDE/awt.hxx
255		AP_cprofile.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx
256		AP_cprofile.o: $(ARBHOME)/INCLUDE/smartptr.h
257
258		AP_csp_2_gnuplot.o: ap_csp_2_gnuplot.hxx
259		AP_csp_2_gnuplot.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
260		AP_csp_2_gnuplot.o: $(ARBHOME)/INCLUDE/ad_prot.h
261		AP_csp_2_gnuplot.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
262		AP_csp_2_gnuplot.o: $(ARBHOME)/INCLUDE/arb_assert.h
263		AP_csp_2_gnuplot.o: $(ARBHOME)/INCLUDE/arb_error.h
264		AP_csp_2_gnuplot.o: $(ARBHOME)/INCLUDE/arbdb.h
265		AP_csp_2_gnuplot.o: $(ARBHOME)/INCLUDE/arbdb_base.h
266		AP_csp_2_gnuplot.o: $(ARBHOME)/INCLUDE/arbdbt.h
267		AP_csp_2_gnuplot.o: $(ARBHOME)/INCLUDE/arbtools.h
268		AP_csp_2_gnuplot.o: $(ARBHOME)/INCLUDE/attributes.h
269		AP_csp_2_gnuplot.o: $(ARBHOME)/INCLUDE/aw_awars.hxx
270		AP_csp_2_gnuplot.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx
271		AP_csp_2_gnuplot.o: $(ARBHOME)/INCLUDE/aw_device.hxx
272		AP_csp_2_gnuplot.o: $(ARBHOME)/INCLUDE/aw_global.hxx
273		AP_csp_2_gnuplot.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
274		AP_csp_2_gnuplot.o: $(ARBHOME)/INCLUDE/aw_position.hxx
275		AP_csp_2_gnuplot.o: $(ARBHOME)/INCLUDE/aw_root.hxx
276		AP_csp_2_gnuplot.o: $(ARBHOME)/INCLUDE/aw_window.hxx
277		AP_csp_2_gnuplot.o: $(ARBHOME)/INCLUDE/awt.hxx
278		AP_csp_2_gnuplot.o: $(ARBHOME)/INCLUDE/awt_csp.hxx
279		AP_csp_2_gnuplot.o: $(ARBHOME)/INCLUDE/awt_pro_a_nucs.hxx
280		AP_csp_2_gnuplot.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx
281		AP_csp_2_gnuplot.o: $(ARBHOME)/INCLUDE/awt_tree.hxx
282		AP_csp_2_gnuplot.o: $(ARBHOME)/INCLUDE/smartptr.h
283
284		AP_pos_var_pars.o: ap_pos_var_pars.hxx
285		AP_pos_var_pars.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
286		AP_pos_var_pars.o: $(ARBHOME)/INCLUDE/ad_prot.h
287		AP_pos_var_pars.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
288		AP_pos_var_pars.o: $(ARBHOME)/INCLUDE/arb_assert.h
289		AP_pos_var_pars.o: $(ARBHOME)/INCLUDE/arb_error.h
290		AP_pos_var_pars.o: $(ARBHOME)/INCLUDE/arbdb.h
291		AP_pos_var_pars.o: $(ARBHOME)/INCLUDE/arbdb_base.h
292		AP_pos_var_pars.o: $(ARBHOME)/INCLUDE/arbdbt.h
293		AP_pos_var_pars.o: $(ARBHOME)/INCLUDE/arbtools.h
294		AP_pos_var_pars.o: $(ARBHOME)/INCLUDE/attributes.h
295		AP_pos_var_pars.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx
296		AP_pos_var_pars.o: $(ARBHOME)/INCLUDE/aw_device.hxx
297		AP_pos_var_pars.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
298		AP_pos_var_pars.o: $(ARBHOME)/INCLUDE/aw_position.hxx
299		AP_pos_var_pars.o: $(ARBHOME)/INCLUDE/aw_root.hxx
300		AP_pos_var_pars.o: $(ARBHOME)/INCLUDE/aw_window.hxx
301		AP_pos_var_pars.o: $(ARBHOME)/INCLUDE/awt.hxx
302		AP_pos_var_pars.o: $(ARBHOME)/INCLUDE/awt_pro_a_nucs.hxx
303		AP_pos_var_pars.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx
304		AP_pos_var_pars.o: $(ARBHOME)/INCLUDE/awt_tree.hxx
305		AP_pos_var_pars.o: $(ARBHOME)/INCLUDE/smartptr.h
306
307		NT_cb.o: ad_trees.hxx
308		NT_cb.o: nt_cb.hxx
309		NT_cb.o: nt_internal.h
310		NT_cb.o: ntree.hxx
311		NT_cb.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
312		NT_cb.o: $(ARBHOME)/INCLUDE/ad_prot.h
313		NT_cb.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
314		NT_cb.o: $(ARBHOME)/INCLUDE/arb_assert.h
315		NT_cb.o: $(ARBHOME)/INCLUDE/arb_error.h
316		NT_cb.o: $(ARBHOME)/INCLUDE/arbdb.h
317		NT_cb.o: $(ARBHOME)/INCLUDE/arbdb_base.h
318		NT_cb.o: $(ARBHOME)/INCLUDE/arbdbt.h
319		NT_cb.o: $(ARBHOME)/INCLUDE/arbtools.h
320		NT_cb.o: $(ARBHOME)/INCLUDE/attributes.h
321		NT_cb.o: $(ARBHOME)/INCLUDE/aw_awars.hxx
322		NT_cb.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx
323		NT_cb.o: $(ARBHOME)/INCLUDE/aw_device.hxx
324		NT_cb.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
325		NT_cb.o: $(ARBHOME)/INCLUDE/aw_position.hxx
326		NT_cb.o: $(ARBHOME)/INCLUDE/aw_root.hxx
327		NT_cb.o: $(ARBHOME)/INCLUDE/aw_window.hxx
328		NT_cb.o: $(ARBHOME)/INCLUDE/awt.hxx
329		NT_cb.o: $(ARBHOME)/INCLUDE/awt_canvas.hxx
330		NT_cb.o: $(ARBHOME)/INCLUDE/awt_dtree.hxx
331		NT_cb.o: $(ARBHOME)/INCLUDE/awt_pro_a_nucs.hxx
332		NT_cb.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx
333		NT_cb.o: $(ARBHOME)/INCLUDE/awt_tree.hxx
334		NT_cb.o: $(ARBHOME)/INCLUDE/smartptr.h
335
336		NT_concatenate.o: nt_internal.h
337		NT_concatenate.o: nt_sort.hxx
338		NT_concatenate.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
339		NT_concatenate.o: $(ARBHOME)/INCLUDE/ad_prot.h
340		NT_concatenate.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
341		NT_concatenate.o: $(ARBHOME)/INCLUDE/arb_assert.h
342		NT_concatenate.o: $(ARBHOME)/INCLUDE/arb_error.h
343		NT_concatenate.o: $(ARBHOME)/INCLUDE/arbdb.h
344		NT_concatenate.o: $(ARBHOME)/INCLUDE/arbdb_base.h
345		NT_concatenate.o: $(ARBHOME)/INCLUDE/arbdbt.h
346		NT_concatenate.o: $(ARBHOME)/INCLUDE/arbtools.h
347		NT_concatenate.o: $(ARBHOME)/INCLUDE/attributes.h
348		NT_concatenate.o: $(ARBHOME)/INCLUDE/aw_awars.hxx
349		NT_concatenate.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx
350		NT_concatenate.o: $(ARBHOME)/INCLUDE/aw_device.hxx
351		NT_concatenate.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
352		NT_concatenate.o: $(ARBHOME)/INCLUDE/aw_position.hxx
353		NT_concatenate.o: $(ARBHOME)/INCLUDE/aw_question.hxx
354		NT_concatenate.o: $(ARBHOME)/INCLUDE/AW_rename.hxx
355		NT_concatenate.o: $(ARBHOME)/INCLUDE/aw_root.hxx
356		NT_concatenate.o: $(ARBHOME)/INCLUDE/aw_window.hxx
357		NT_concatenate.o: $(ARBHOME)/INCLUDE/awt.hxx
358		NT_concatenate.o: $(ARBHOME)/INCLUDE/awt_canvas.hxx
359		NT_concatenate.o: $(ARBHOME)/INCLUDE/awt_item_sel_list.hxx
360		NT_concatenate.o: $(ARBHOME)/INCLUDE/awt_pro_a_nucs.hxx
361		NT_concatenate.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx
362		NT_concatenate.o: $(ARBHOME)/INCLUDE/awt_tree.hxx
363		NT_concatenate.o: $(ARBHOME)/INCLUDE/awtlocal.hxx
364		NT_concatenate.o: $(ARBHOME)/INCLUDE/smartptr.h
365
366		NT_dbrepair.o: NT_dbrepair.hxx
367		NT_dbrepair.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
368		NT_dbrepair.o: $(ARBHOME)/INCLUDE/ad_prot.h
369		NT_dbrepair.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
370		NT_dbrepair.o: $(ARBHOME)/INCLUDE/adGene.h
371		NT_dbrepair.o: $(ARBHOME)/INCLUDE/arb_assert.h
372		NT_dbrepair.o: $(ARBHOME)/INCLUDE/arb_error.h
373		NT_dbrepair.o: $(ARBHOME)/INCLUDE/arbdb.h
374		NT_dbrepair.o: $(ARBHOME)/INCLUDE/arbdb_base.h
375		NT_dbrepair.o: $(ARBHOME)/INCLUDE/arbdbt.h
376		NT_dbrepair.o: $(ARBHOME)/INCLUDE/arbtools.h
377		NT_dbrepair.o: $(ARBHOME)/INCLUDE/attributes.h
378		NT_dbrepair.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx
379		NT_dbrepair.o: $(ARBHOME)/INCLUDE/aw_device.hxx
380		NT_dbrepair.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
381		NT_dbrepair.o: $(ARBHOME)/INCLUDE/aw_position.hxx
382		NT_dbrepair.o: $(ARBHOME)/INCLUDE/aw_root.hxx
383		NT_dbrepair.o: $(ARBHOME)/INCLUDE/aw_window.hxx
384		NT_dbrepair.o: $(ARBHOME)/INCLUDE/awt.hxx
385		NT_dbrepair.o: $(ARBHOME)/INCLUDE/EXP.hxx
386		NT_dbrepair.o: $(ARBHOME)/INCLUDE/GEN.hxx
387		NT_dbrepair.o: $(ARBHOME)/INCLUDE/inline.h
388		NT_dbrepair.o: $(ARBHOME)/INCLUDE/smartptr.h
389
390		NT_edconf.o: nt_edconf.hxx
391		NT_edconf.o: $(ARBHOME)/INCLUDE/ad_config.h
392		NT_edconf.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
393		NT_edconf.o: $(ARBHOME)/INCLUDE/ad_prot.h
394		NT_edconf.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
395		NT_edconf.o: $(ARBHOME)/INCLUDE/arb_assert.h
396		NT_edconf.o: $(ARBHOME)/INCLUDE/arb_error.h
397		NT_edconf.o: $(ARBHOME)/INCLUDE/arbdb.h
398		NT_edconf.o: $(ARBHOME)/INCLUDE/arbdb_base.h
399		NT_edconf.o: $(ARBHOME)/INCLUDE/arbdbt.h
400		NT_edconf.o: $(ARBHOME)/INCLUDE/arbtools.h
401		NT_edconf.o: $(ARBHOME)/INCLUDE/attributes.h
402		NT_edconf.o: $(ARBHOME)/INCLUDE/aw_awars.hxx
403		NT_edconf.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx
404		NT_edconf.o: $(ARBHOME)/INCLUDE/aw_device.hxx
405		NT_edconf.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
406		NT_edconf.o: $(ARBHOME)/INCLUDE/aw_position.hxx
407		NT_edconf.o: $(ARBHOME)/INCLUDE/aw_root.hxx
408		NT_edconf.o: $(ARBHOME)/INCLUDE/aw_window.hxx
409		NT_edconf.o: $(ARBHOME)/INCLUDE/awt.hxx
410		NT_edconf.o: $(ARBHOME)/INCLUDE/awt_canvas.hxx
411		NT_edconf.o: $(ARBHOME)/INCLUDE/awt_dtree.hxx
412		NT_edconf.o: $(ARBHOME)/INCLUDE/awt_pro_a_nucs.hxx
413		NT_edconf.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx
414		NT_edconf.o: $(ARBHOME)/INCLUDE/awt_tree.hxx
415		NT_edconf.o: $(ARBHOME)/INCLUDE/smartptr.h
416
417		NT_extern.o: ad_spec.hxx
418		NT_extern.o: ad_trees.hxx
419		NT_extern.o: ap_consensus.hxx
420		NT_extern.o: ap_conservProfile2Gnuplot.hxx
421		NT_extern.o: ap_csp_2_gnuplot.hxx
422		NT_extern.o: ap_pos_var_pars.hxx
423		NT_extern.o: nt_cb.hxx
424		NT_extern.o: NT_dbrepair.hxx
425		NT_extern.o: nt_edconf.hxx
426		NT_extern.o: nt_internal.h
427		NT_extern.o: nt_join.hxx
428		NT_extern.o: nt_sort.hxx
429		NT_extern.o: NT_trackAliChanges.h
430		NT_extern.o: ntree.hxx
431		NT_extern.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
432		NT_extern.o: $(ARBHOME)/INCLUDE/ad_prot.h
433		NT_extern.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
434		NT_extern.o: $(ARBHOME)/INCLUDE/adGene.h
435		NT_extern.o: $(ARBHOME)/INCLUDE/arb_assert.h
436		NT_extern.o: $(ARBHOME)/INCLUDE/arb_build.h
437		NT_extern.o: $(ARBHOME)/INCLUDE/arb_error.h
438		NT_extern.o: $(ARBHOME)/INCLUDE/arb_version.h
439		NT_extern.o: $(ARBHOME)/INCLUDE/arbdb.h
440		NT_extern.o: $(ARBHOME)/INCLUDE/arbdb_base.h
441		NT_extern.o: $(ARBHOME)/INCLUDE/arbdbt.h
442		NT_extern.o: $(ARBHOME)/INCLUDE/arbtools.h
443		NT_extern.o: $(ARBHOME)/INCLUDE/attributes.h
444		NT_extern.o: $(ARBHOME)/INCLUDE/aw_awars.hxx
445		NT_extern.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx
446		NT_extern.o: $(ARBHOME)/INCLUDE/aw_device.hxx
447		NT_extern.o: $(ARBHOME)/INCLUDE/aw_global.hxx
448		NT_extern.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
449		NT_extern.o: $(ARBHOME)/INCLUDE/aw_position.hxx
450		NT_extern.o: $(ARBHOME)/INCLUDE/aw_preset.hxx
451		NT_extern.o: $(ARBHOME)/INCLUDE/AW_rename.hxx
452		NT_extern.o: $(ARBHOME)/INCLUDE/aw_root.hxx
453		NT_extern.o: $(ARBHOME)/INCLUDE/aw_window.hxx
454		NT_extern.o: $(ARBHOME)/INCLUDE/awt.hxx
455		NT_extern.o: $(ARBHOME)/INCLUDE/awt_advice.hxx
456		NT_extern.o: $(ARBHOME)/INCLUDE/awt_canvas.hxx
457		NT_extern.o: $(ARBHOME)/INCLUDE/awt_config_manager.hxx
458		NT_extern.o: $(ARBHOME)/INCLUDE/awt_dtree.hxx
459		NT_extern.o: $(ARBHOME)/INCLUDE/awt_input_mask.hxx
460		NT_extern.o: $(ARBHOME)/INCLUDE/awt_macro.hxx
461		NT_extern.o: $(ARBHOME)/INCLUDE/awt_nds.hxx
462		NT_extern.o: $(ARBHOME)/INCLUDE/awt_preset.hxx
463		NT_extern.o: $(ARBHOME)/INCLUDE/awt_pro_a_nucs.hxx
464		NT_extern.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx
465		NT_extern.o: $(ARBHOME)/INCLUDE/awt_tree.hxx
466		NT_extern.o: $(ARBHOME)/INCLUDE/awt_tree_cb.hxx
467		NT_extern.o: $(ARBHOME)/INCLUDE/awt_www.hxx
468		NT_extern.o: $(ARBHOME)/INCLUDE/awtc_submission.hxx
469		NT_extern.o: $(ARBHOME)/INCLUDE/awti_export.hxx
470		NT_extern.o: $(ARBHOME)/INCLUDE/EXP.hxx
471		NT_extern.o: $(ARBHOME)/INCLUDE/gde.hxx
472		NT_extern.o: $(ARBHOME)/INCLUDE/GEN.hxx
473		NT_extern.o: $(ARBHOME)/INCLUDE/primer_design.hxx
474		NT_extern.o: $(ARBHOME)/INCLUDE/probe_design.hxx
475		NT_extern.o: $(ARBHOME)/INCLUDE/seq_quality.h
476		NT_extern.o: $(ARBHOME)/INCLUDE/smartptr.h
477		NT_extern.o: $(ARBHOME)/INCLUDE/st_window.hxx
478		NT_extern.o: $(ARBHOME)/INCLUDE/svn_revision.h
479
480		NT_import.o: ad_spec.hxx
481		NT_import.o: nt_internal.h
482		NT_import.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
483		NT_import.o: $(ARBHOME)/INCLUDE/ad_prot.h
484		NT_import.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
485		NT_import.o: $(ARBHOME)/INCLUDE/adGene.h
486		NT_import.o: $(ARBHOME)/INCLUDE/arb_assert.h
487		NT_import.o: $(ARBHOME)/INCLUDE/arb_error.h
488		NT_import.o: $(ARBHOME)/INCLUDE/arbdb.h
489		NT_import.o: $(ARBHOME)/INCLUDE/arbdb_base.h
490		NT_import.o: $(ARBHOME)/INCLUDE/arbdbt.h
491		NT_import.o: $(ARBHOME)/INCLUDE/arbtools.h
492		NT_import.o: $(ARBHOME)/INCLUDE/attributes.h
493		NT_import.o: $(ARBHOME)/INCLUDE/aw_device.hxx
494		NT_import.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
495		NT_import.o: $(ARBHOME)/INCLUDE/aw_position.hxx
496		NT_import.o: $(ARBHOME)/INCLUDE/aw_root.hxx
497		NT_import.o: $(ARBHOME)/INCLUDE/aw_window.hxx
498		NT_import.o: $(ARBHOME)/INCLUDE/awt.hxx
499		NT_import.o: $(ARBHOME)/INCLUDE/awt_canvas.hxx
500		NT_import.o: $(ARBHOME)/INCLUDE/awti_import.hxx
501		NT_import.o: $(ARBHOME)/INCLUDE/GEN.hxx
502		NT_import.o: $(ARBHOME)/INCLUDE/mg_merge.hxx
503		NT_import.o: $(ARBHOME)/INCLUDE/smartptr.h
504
505		NT_ins_col.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
506		NT_ins_col.o: $(ARBHOME)/INCLUDE/ad_prot.h
507		NT_ins_col.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
508		NT_ins_col.o: $(ARBHOME)/INCLUDE/arb_assert.h
509		NT_ins_col.o: $(ARBHOME)/INCLUDE/arb_error.h
510		NT_ins_col.o: $(ARBHOME)/INCLUDE/arbdb.h
511		NT_ins_col.o: $(ARBHOME)/INCLUDE/arbdb_base.h
512		NT_ins_col.o: $(ARBHOME)/INCLUDE/arbdbt.h
513		NT_ins_col.o: $(ARBHOME)/INCLUDE/arbtools.h
514		NT_ins_col.o: $(ARBHOME)/INCLUDE/attributes.h
515		NT_ins_col.o: $(ARBHOME)/INCLUDE/aw_awars.hxx
516		NT_ins_col.o: $(ARBHOME)/INCLUDE/aw_device.hxx
517		NT_ins_col.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
518		NT_ins_col.o: $(ARBHOME)/INCLUDE/aw_position.hxx
519		NT_ins_col.o: $(ARBHOME)/INCLUDE/aw_root.hxx
520		NT_ins_col.o: $(ARBHOME)/INCLUDE/aw_window.hxx
521		NT_ins_col.o: $(ARBHOME)/INCLUDE/smartptr.h
522
523		NT_join.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
524		NT_join.o: $(ARBHOME)/INCLUDE/ad_prot.h
525		NT_join.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
526		NT_join.o: $(ARBHOME)/INCLUDE/arb_assert.h
527		NT_join.o: $(ARBHOME)/INCLUDE/arb_error.h
528		NT_join.o: $(ARBHOME)/INCLUDE/arbdb.h
529		NT_join.o: $(ARBHOME)/INCLUDE/arbdb_base.h
530		NT_join.o: $(ARBHOME)/INCLUDE/arbdbt.h
531		NT_join.o: $(ARBHOME)/INCLUDE/arbtools.h
532		NT_join.o: $(ARBHOME)/INCLUDE/attributes.h
533		NT_join.o: $(ARBHOME)/INCLUDE/aw_awars.hxx
534		NT_join.o: $(ARBHOME)/INCLUDE/aw_device.hxx
535		NT_join.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
536		NT_join.o: $(ARBHOME)/INCLUDE/aw_position.hxx
537		NT_join.o: $(ARBHOME)/INCLUDE/aw_root.hxx
538		NT_join.o: $(ARBHOME)/INCLUDE/aw_window.hxx
539		NT_join.o: $(ARBHOME)/INCLUDE/awt.hxx
540		NT_join.o: $(ARBHOME)/INCLUDE/awt_item_sel_list.hxx
541		NT_join.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx
542		NT_join.o: $(ARBHOME)/INCLUDE/smartptr.h
543
544		NT_main.o: nt_cb.hxx
545		NT_main.o: NT_dbrepair.hxx
546		NT_main.o: nt_internal.h
547		NT_main.o: ntree.hxx
548		NT_main.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
549		NT_main.o: $(ARBHOME)/INCLUDE/ad_prot.h
550		NT_main.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
551		NT_main.o: $(ARBHOME)/INCLUDE/adGene.h
552		NT_main.o: $(ARBHOME)/INCLUDE/arb_assert.h
553		NT_main.o: $(ARBHOME)/INCLUDE/arb_build.h
554		NT_main.o: $(ARBHOME)/INCLUDE/arb_error.h
555		NT_main.o: $(ARBHOME)/INCLUDE/arb_version.h
556		NT_main.o: $(ARBHOME)/INCLUDE/arbdb.h
557		NT_main.o: $(ARBHOME)/INCLUDE/arbdb_base.h
558		NT_main.o: $(ARBHOME)/INCLUDE/arbdbt.h
559		NT_main.o: $(ARBHOME)/INCLUDE/arbtools.h
560		NT_main.o: $(ARBHOME)/INCLUDE/attributes.h
561		NT_main.o: $(ARBHOME)/INCLUDE/aw_awars.hxx
562		NT_main.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx
563		NT_main.o: $(ARBHOME)/INCLUDE/aw_device.hxx
564		NT_main.o: $(ARBHOME)/INCLUDE/aw_global.hxx
565		NT_main.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
566		NT_main.o: $(ARBHOME)/INCLUDE/aw_position.hxx
567		NT_main.o: $(ARBHOME)/INCLUDE/aw_question.hxx
568		NT_main.o: $(ARBHOME)/INCLUDE/aw_root.hxx
569		NT_main.o: $(ARBHOME)/INCLUDE/aw_window.hxx
570		NT_main.o: $(ARBHOME)/INCLUDE/awt.hxx
571		NT_main.o: $(ARBHOME)/INCLUDE/awt_advice.hxx
572		NT_main.o: $(ARBHOME)/INCLUDE/awt_canvas.hxx
573		NT_main.o: $(ARBHOME)/INCLUDE/awt_dtree.hxx
574		NT_main.o: $(ARBHOME)/INCLUDE/awt_pro_a_nucs.hxx
575		NT_main.o: $(ARBHOME)/INCLUDE/awt_tree.hxx
576		NT_main.o: $(ARBHOME)/INCLUDE/awti_import.hxx
577		NT_main.o: $(ARBHOME)/INCLUDE/mg_merge.hxx
578		NT_main.o: $(ARBHOME)/INCLUDE/servercntrl.h
579		NT_main.o: $(ARBHOME)/INCLUDE/smartptr.h
580		NT_main.o: $(ARBHOME)/INCLUDE/svn_revision.h
581
582		NT_sort.o: nt_sort.hxx
583		NT_sort.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
584		NT_sort.o: $(ARBHOME)/INCLUDE/ad_prot.h
585		NT_sort.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
586		NT_sort.o: $(ARBHOME)/INCLUDE/arb_assert.h
587		NT_sort.o: $(ARBHOME)/INCLUDE/arb_error.h
588		NT_sort.o: $(ARBHOME)/INCLUDE/arbdb.h
589		NT_sort.o: $(ARBHOME)/INCLUDE/arbdb_base.h
590		NT_sort.o: $(ARBHOME)/INCLUDE/arbdbt.h
591		NT_sort.o: $(ARBHOME)/INCLUDE/arbtools.h
592		NT_sort.o: $(ARBHOME)/INCLUDE/attributes.h
593		NT_sort.o: $(ARBHOME)/INCLUDE/aw_awars.hxx
594		NT_sort.o: $(ARBHOME)/INCLUDE/aw_device.hxx
595		NT_sort.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
596		NT_sort.o: $(ARBHOME)/INCLUDE/aw_position.hxx
597		NT_sort.o: $(ARBHOME)/INCLUDE/aw_root.hxx
598		NT_sort.o: $(ARBHOME)/INCLUDE/aw_window.hxx
599		NT_sort.o: $(ARBHOME)/INCLUDE/awt.hxx
600		NT_sort.o: $(ARBHOME)/INCLUDE/awt_item_sel_list.hxx
601		NT_sort.o: $(ARBHOME)/INCLUDE/smartptr.h
602
603		NT_trackAliChanges.o: NT_trackAliChanges.h
604		NT_trackAliChanges.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
605		NT_trackAliChanges.o: $(ARBHOME)/INCLUDE/ad_prot.h
606		NT_trackAliChanges.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
607		NT_trackAliChanges.o: $(ARBHOME)/INCLUDE/arb_assert.h
608		NT_trackAliChanges.o: $(ARBHOME)/INCLUDE/arb_error.h
609		NT_trackAliChanges.o: $(ARBHOME)/INCLUDE/arbdb.h
610		NT_trackAliChanges.o: $(ARBHOME)/INCLUDE/arbdb_base.h
611		NT_trackAliChanges.o: $(ARBHOME)/INCLUDE/arbdbt.h
612		NT_trackAliChanges.o: $(ARBHOME)/INCLUDE/arbtools.h
613		NT_trackAliChanges.o: $(ARBHOME)/INCLUDE/attributes.h
614		NT_trackAliChanges.o: $(ARBHOME)/INCLUDE/aw_device.hxx
615		NT_trackAliChanges.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
616		NT_trackAliChanges.o: $(ARBHOME)/INCLUDE/aw_position.hxx
617		NT_trackAliChanges.o: $(ARBHOME)/INCLUDE/aw_root.hxx
618		NT_trackAliChanges.o: $(ARBHOME)/INCLUDE/aw_window.hxx
619		NT_trackAliChanges.o: $(ARBHOME)/INCLUDE/awt.hxx
620		NT_trackAliChanges.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx
621		NT_trackAliChanges.o: $(ARBHOME)/INCLUDE/smartptr.h
622
623		NT_validManual.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
624		NT_validManual.o: $(ARBHOME)/INCLUDE/ad_prot.h
625		NT_validManual.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
626		NT_validManual.o: $(ARBHOME)/INCLUDE/arb_assert.h
627		NT_validManual.o: $(ARBHOME)/INCLUDE/arb_error.h
628		NT_validManual.o: $(ARBHOME)/INCLUDE/arbdb.h
629		NT_validManual.o: $(ARBHOME)/INCLUDE/arbdb_base.h
630		NT_validManual.o: $(ARBHOME)/INCLUDE/arbdbt.h
631		NT_validManual.o: $(ARBHOME)/INCLUDE/arbtools.h
632		NT_validManual.o: $(ARBHOME)/INCLUDE/attributes.h
633		NT_validManual.o: $(ARBHOME)/INCLUDE/aw_awars.hxx
634		NT_validManual.o: $(ARBHOME)/INCLUDE/aw_device.hxx
635		NT_validManual.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
636		NT_validManual.o: $(ARBHOME)/INCLUDE/aw_position.hxx
637		NT_validManual.o: $(ARBHOME)/INCLUDE/aw_root.hxx
638		NT_validManual.o: $(ARBHOME)/INCLUDE/aw_window.hxx
639		NT_validManual.o: $(ARBHOME)/INCLUDE/awt.hxx
640		NT_validManual.o: $(ARBHOME)/INCLUDE/smartptr.h
641
642		NT_validNameParser.o: nt_validNameParser.hxx
643
644		NT_validNames.o: nt_validNameParser.hxx
645		NT_validNames.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
646		NT_validNames.o: $(ARBHOME)/INCLUDE/ad_prot.h
647		NT_validNames.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
648		NT_validNames.o: $(ARBHOME)/INCLUDE/arb_assert.h
649		NT_validNames.o: $(ARBHOME)/INCLUDE/arb_error.h
650		NT_validNames.o: $(ARBHOME)/INCLUDE/arbdb.h
651		NT_validNames.o: $(ARBHOME)/INCLUDE/arbdb_base.h
652		NT_validNames.o: $(ARBHOME)/INCLUDE/arbdbt.h
653		NT_validNames.o: $(ARBHOME)/INCLUDE/arbtools.h
654		NT_validNames.o: $(ARBHOME)/INCLUDE/attributes.h
655		NT_validNames.o: $(ARBHOME)/INCLUDE/aw_awars.hxx
656		NT_validNames.o: $(ARBHOME)/INCLUDE/aw_device.hxx
657		NT_validNames.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
658		NT_validNames.o: $(ARBHOME)/INCLUDE/aw_position.hxx
659		NT_validNames.o: $(ARBHOME)/INCLUDE/aw_root.hxx
660		NT_validNames.o: $(ARBHOME)/INCLUDE/aw_window.hxx
661		NT_validNames.o: $(ARBHOME)/INCLUDE/awt.hxx
662		NT_validNames.o: $(ARBHOME)/INCLUDE/awt_www.hxx
663		NT_validNames.o: $(ARBHOME)/INCLUDE/smartptr.h
	591	ad_trees.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_root.hxx
	592	ad_trees.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arb_assert.h
	593	ad_trees.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdb_base.h
	594	ad_trees.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/attributes.h
	595	ad_trees.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_k_prot.h
	596	ad_trees.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbtools.h
	597	ad_trees.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arb_error.h
	598	ad_trees.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/smartptr.h
	599	ad_trees.o: nt_tree_cmp.hxx
	600	ad_trees.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdbt.h
	601	ad_trees.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/arbdb.h
	602	ad_trees.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_prot.h
	603	ad_trees.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/ad_t_prot.h
	604	ad_trees.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/TreeRead.h
	605	ad_trees.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/TreeWrite.h
	606	ad_trees.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awt_sel_boxes.hxx
	607	ad_trees.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awt_nds.hxx
	608	ad_trees.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/awt.hxx
	609	ad_trees.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_window.hxx
	610	ad_trees.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_device.hxx
	611	ad_trees.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_position.hxx
	612	ad_trees.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_keysym.hxx
	613	ad_trees.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_awars.hxx
	614	ad_trees.o: /home/ralf/ARB-saphira/ARB.quickChange/INCLUDE/aw_global.hxx

trunk/NTREE/NT_cb.cxx

r5794	r6280
1		#include <stdio.h>
2		#include <stdlib.h>
	1	// =============================================================== //
	2	// //
	3	// File : NT_cb.cxx //
	4	// Purpose : //
	5	// //
	6	// Institute of Microbiology (Technical University Munich) //
	7	// http://www.arb-home.de/ //
	8	// //
	9	// =============================================================== //
3	10
4		~~#include <arbdb.h>~~
5		~~#include <arbdbt.h>~~
6
7		~~#include <aw_root.hxx>~~
8		~~#include <aw_device.hxx>~~
9		~~#include <aw_window.hxx>~~
10		~~#include <aw_awars.hxx>~~
11		~~#include <awt_canvas.hxx>~~
12		~~#include <awt.hxx>~~
13
14		~~#include <awt_tree.hxx>~~
15		~~#include <awt_dtree.hxx>~~
16		~~#include <awt_sel_boxes.hxx>~~
17		~~#include "ad_trees.hxx"~~
18		~~#include "ntree.hxx"~~
19	11	#include "nt_internal.h"
20	12	#include "nt_cb.hxx"
	13	#include "ntree.hxx"
	14	#include "ad_trees.hxx"
21	15
	16	#include <awt_canvas.hxx>
	17	#include <awt_sel_boxes.hxx>
	18	#include <aw_awars.hxx>
22	19
23		#define AWT_TREE(ntw) ((AWT_graphic_tree *)ntw->tree_disp)
	20	/AISC_MKPT_PROMOTE:#ifndef ARBDBT_H/
	21	/AISC_MKPT_PROMOTE:#include <arbdbt.h>/
	22	/AISC_MKPT_PROMOTE:#endif/
	23	/AISC_MKPT_PROMOTE:#ifndef AW_ROOT_HXX/
	24	/AISC_MKPT_PROMOTE:#include <aw_root.hxx>/
	25	/AISC_MKPT_PROMOTE:#endif/
	26	/AISC_MKPT_PROMOTE:/
	27	/AISC_MKPT_PROMOTE:class AW_window;/
	28	/AISC_MKPT_PROMOTE:class AWT_canvas;/
	29
	30	// #define AWT_TREE(ntw) ((AWT_graphic_tree *)ntw->tree_disp)
	31	#define AWT_TREE(ntw) DOWNCAST(AWT_graphic_tree *, (ntw)->tree_disp)
24	32
25	33	void NT_delete_mark_all_cb(void , AWT_canvas ntw) {

trunk/NTREE/NT_concatenate.cxx

r6141	r6280
11	11	/=======================================================================================/
12	12
13		#include <stdio.h>
14		#include <stdlib.h>
15		#include <unistd.h>
16		#include <time.h>
17		#include <string.h>
18		#include <memory.h>
19		#include <iostream>
20
21		#include <arbdb.h>
22		#include <arbdbt.h>
23		#include <aw_root.hxx>
24		#include <aw_device.hxx>
25		#include <aw_window.hxx>
26		#include <aw_awars.hxx>
	13	#include "nt_internal.h"
	14
27	15	#include <awt.hxx>
28		~~#include <AW_rename.hxx>~~
29		~~#include <awt_tree.hxx>~~
30		~~#include <awt_canvas.hxx>~~
31	16	#include <awt_item_sel_list.hxx>
32	17	#include <awt_sel_boxes.hxx>
33		#include ~~"awtlocal.hxx"~~
	18	#include <AW_rename.hxx>
34	19	#include <aw_question.hxx>
35		#include "nt_internal.h"
36		#include <nt_sort.hxx> // for sorting database entries
37
38		#ifndef ARB_ASSERT_H
39		#include <arb_assert.h>
40		#endif
	20
41	21	#define nt_assert(bed) arb_assert(bed)
42	22

trunk/NTREE/NT_edconf.cxx

r6158	r6280
1		#include <stdio.h>
2		#include <stdlib.h>
3		#include <string.h>
4
5		#include <arbdb.h>
6		#include <arbdbt.h>
	1	// =============================================================== //
	2	// //
	3	// File : NT_edconf.cxx //
	4	// Purpose : //
	5	// //
	6	// Institute of Microbiology (Technical University Munich) //
	7	// http://www.arb-home.de/ //
	8	// //
	9	// =============================================================== //
	10
	11	#include "nt_cb.hxx"
	12	#include "nt_internal.h"
	13
	14	#include <awt_sel_boxes.hxx>
	15	#include <aw_window.hxx>
	16	#include <aw_awars.hxx>
7	17	#include <ad_config.h>
8		#include <aw_awars.hxx>
9		#include <aw_root.hxx>
10		#include <aw_device.hxx>
11		#include <aw_window.hxx>
12
13		#include "nt_edconf.hxx"
14
15		#include <awt.hxx>
16		#include <awt_canvas.hxx>
17		#include <awt_tree.hxx>
18		#include <awt_dtree.hxx>
19		#include <awt_sel_boxes.hxx>
20
21		#ifndef ARB_ASSERT_H
22		#include <arb_assert.h>
23		#endif
	18
24	19	#define nt_assert(bed) arb_assert(bed)
25	20
…	…
379	374	}
380	375
381		void NT_start_editor_on_tree(AW_window , GBT_TREE *ptree, int use_species_aside){
382		GB_ERROR error = NT_create_configuration(0,ptree,CONFNAME, use_species_aside);
383		if (!error) {
384		GBCMC_system(GLOBAL_gb_main, "arb_edit4 -c "CONFNAME" &");
385		}
	376	void NT_start_editor_on_tree(AW_window *, AW_CL cl_use_species_aside, AW_CL) {
	377	GB_ERROR error = NT_create_configuration(0, nt_get_current_tree_root(), CONFNAME, (int)cl_use_species_aside);
	378	if (!error) GBCMC_system(GLOBAL_gb_main, "arb_edit4 -c "CONFNAME" &");
386	379	}
387	380
…	…
477	470
478	471
479		GB_ERROR NT_create_configuration(AW_window , GBT_TREE ptree,const char conf_name, int use_species_aside){
480		GBT_TREE tree = ptree;
481		char *to_free = 0;
	472	GB_ERROR NT_create_configuration(AW_window , GBT_TREE tree, const char *conf_name, int use_species_aside) {
	473	char *to_free = 0;
482	474
483	475	if (!conf_name) {
…	…
492	484	{
493	485	const char *val = GBS_global_string("%i", last_used_species_aside);
494		char *use_species = aw_input("~~Enter number of~~ extra species to view aside marked:", val);
	486	char *use_species = aw_input("How many extra species to view aside marked:", val);
495	487	if (use_species) use_species_aside = atoi(use_species);
496	488	free(use_species);
…	…
551	543	}
552	544
553		void nt_store_configuration(AW_window /aww*/, AW_CL cl_GBT_TREE_ptr) {
554		GBT_TREE ptree = (GBT_TREE)cl_GBT_TREE_ptr;
555		GB_ERROR err = NT_create_configuration(0, ptree, 0, 0);
	545	static void nt_store_configuration(AW_window *) {
	546	GB_ERROR err = NT_create_configuration(0, nt_get_current_tree_root(), 0, 0);
556	547	if (err) aw_message(err);
557	548	}
…	…
586	577	free(old_name);
587	578	}
588		// --------------------------------------------------------------------------------------
589		// AW_window create_configuration_admin_window(AW_root root, GBT_TREE **ptree)
590		// --------------------------------------------------------------------------------------
591		AW_window create_configuration_admin_window(AW_root root, GBT_TREE **ptree) {
	579
	580	static AW_window create_configuration_admin_window(AW_root root) {
592	581	static AW_window_simple *aws = 0;
593		if (aws) return aws;
594
595		init_config_awars(root);
596
597		aws = new AW_window_simple;
598		aws->init(root, "SPECIES_SELECTIONS", "Species Selections");
599		aws->load_xfig("nt_selection.fig");
600
601		aws->at("close");
602		aws->callback( (AW_CB0)AW_POPDOWN);
603		aws->create_button("CLOSE","CLOSE","C");
604
605		aws->at("help");
606		aws->callback(AW_POPUP_HELP,(AW_CL)"configuration.hlp");
607		aws->create_button("HELP","HELP","H");
608
609		aws->at("list");
610		awt_create_selection_list_on_configurations(GLOBAL_gb_main, aws, AWAR_CONFIGURATION);
611
612		aws->at("store");
613		aws->callback(nt_store_configuration, (AW_CL)ptree);
614		aws->create_button("STORE","STORE","S");
615
616		aws->at("extract");
617		aws->callback(nt_extract_configuration, CONF_EXTRACT);
618		aws->create_button("EXTRACT","EXTRACT","E");
619
620		aws->at("mark");
621		aws->callback(nt_extract_configuration, CONF_MARK);
622		aws->create_button("MARK","MARK","M");
623
624		aws->at("unmark");
625		aws->callback(nt_extract_configuration, CONF_UNMARK);
626		aws->create_button("UNMARK","UNMARK","U");
627
628		aws->at("invert");
629		aws->callback(nt_extract_configuration, CONF_INVERT);
630		aws->create_button("INVERT","INVERT","I");
631
632		aws->at("combine");
633		aws->callback(nt_extract_configuration, CONF_COMBINE);
634		aws->create_button("COMBINE","COMBINE","C");
635
636		aws->at("delete");
637		aws->callback(nt_delete_configuration);
638		aws->create_button("DELETE","DELETE","D");
639
640		aws->at("rename");
641		aws->callback(nt_rename_configuration);
642		aws->create_button("RENAME","RENAME","R");
643
	582	if (!aws) {
	583	init_config_awars(root);
	584
	585	aws = new AW_window_simple;
	586	aws->init(root, "SPECIES_SELECTIONS", "Species Selections");
	587	aws->load_xfig("nt_selection.fig");
	588
	589	aws->at("close");
	590	aws->callback( (AW_CB0)AW_POPDOWN);
	591	aws->create_button("CLOSE","CLOSE","C");
	592
	593	aws->at("help");
	594	aws->callback(AW_POPUP_HELP,(AW_CL)"configuration.hlp");
	595	aws->create_button("HELP","HELP","H");
	596
	597	aws->at("list");
	598	awt_create_selection_list_on_configurations(GLOBAL_gb_main, aws, AWAR_CONFIGURATION);
	599
	600	aws->at("store");
	601	aws->callback(nt_store_configuration);
	602	aws->create_button("STORE","STORE","S");
	603
	604	aws->at("extract");
	605	aws->callback(nt_extract_configuration, CONF_EXTRACT);
	606	aws->create_button("EXTRACT","EXTRACT","E");
	607
	608	aws->at("mark");
	609	aws->callback(nt_extract_configuration, CONF_MARK);
	610	aws->create_button("MARK","MARK","M");
	611
	612	aws->at("unmark");
	613	aws->callback(nt_extract_configuration, CONF_UNMARK);
	614	aws->create_button("UNMARK","UNMARK","U");
	615
	616	aws->at("invert");
	617	aws->callback(nt_extract_configuration, CONF_INVERT);
	618	aws->create_button("INVERT","INVERT","I");
	619
	620	aws->at("combine");
	621	aws->callback(nt_extract_configuration, CONF_COMBINE);
	622	aws->create_button("COMBINE","COMBINE","C");
	623
	624	aws->at("delete");
	625	aws->callback(nt_delete_configuration);
	626	aws->create_button("DELETE","DELETE","D");
	627
	628	aws->at("rename");
	629	aws->callback(nt_rename_configuration);
	630	aws->create_button("RENAME","RENAME","R");
	631	}
644	632	return aws;
645	633	}
646	634
647		void NT_popup_configuration_admin(AW_window *aw_main, AW_CL cl_GBT_TREE_ptr, AW_CL) {
648		GBT_TREE ptree = (GBT_TREE)cl_GBT_TREE_ptr;
649		AW_root *aw_root = aw_main->get_root();
650		AW_window *aww = create_configuration_admin_window(aw_root, ptree);
651
	635	void NT_popup_configuration_admin(AW_window *aw_main, AW_CL, AW_CL) {
	636	AW_window *aww = create_configuration_admin_window(aw_main->get_root());
652	637	aww->activate();
653	638	}

trunk/NTREE/NT_extern.cxx

r6200	r6280
1		#include <stdio.h>
2		#include <stdlib.h>
3		#include <string.h>
4
5		#include <arbdb.h>
6		#include <arbdbt.h>
7		#include <aw_root.hxx>
8		#include <aw_device.hxx>
9		#include <aw_window.hxx>
10		#include <aw_awars.hxx>
11
	1	// =============================================================== //
	2	// //
	3	// File : NT_extern.cxx //
	4	// Purpose : //
	5	// //
	6	// Institute of Microbiology (Technical University Munich) //
	7	// http://www.arb-home.de/ //
	8	// //
	9	// =============================================================== //
	10
	11	#include "nt_internal.h"
	12	#include "ntree.hxx"
	13	#include "ad_spec.hxx"
12	14	#include "ad_trees.hxx"
13		#include "ad_spec.hxx"
	15	#include "ap_consensus.hxx"
	16	#include "seq_quality.h"
	17	#include "nt_join.hxx"
	18
	19	#include <st_window.hxx>
	20	#include <GEN.hxx>
	21	#include <EXP.hxx>
	22
	23	#include <TreeCallbacks.hxx>
	24	#include <AW_rename.hxx>
	25	#include <probe_design.hxx>
	26	#include <primer_design.hxx>
	27	#include <gde.hxx>
	28	#include <awtc_submission.hxx>
	29
	30	#include <awti_export.hxx>
	31
	32	#include <awt_preset.hxx>
	33	#include <awt_macro.hxx>
	34	#include <awt_advice.hxx>
	35	#include <awt_config_manager.hxx>
	36	#include <awt_input_mask.hxx>
	37	#include <awt_sel_boxes.hxx>
	38	#include <awt_www.hxx>
14	39	#include <awt_nds.hxx>
15		#include <awt_canvas.hxx>
	40
16	41	#include <aw_preset.hxx>
17	42	#include <aw_global.hxx>
18		#include <awt_preset.hxx>
19		#include <awt_advice.hxx>
20		#include <awt_config_manager.hxx>
21		#include <awt_sel_boxes.hxx>
22		#include <awt_macro.hxx>
23
24		#include <AW_rename.hxx>
25		#include <awtc_submission.hxx>
26		#include <gde.hxx>
27
28		#include <awt_www.hxx>
29		#include <awt_tree.hxx>
30		#include <awt_dtree.hxx>
31		#include <awt_tree_cb.hxx>
32		#include "ntree.hxx"
33		#include "nt_cb.hxx"
34		#include "nt_sort.hxx"
35		#include "ap_consensus.hxx"
36		#include "ap_csp_2_gnuplot.hxx"
37		#include "ap_conservProfile2Gnuplot.hxx"
38		#include <awti_export.hxx>
39		#include "nt_join.hxx"
40		#include "nt_edconf.hxx"
41		#include "ap_pos_var_pars.hxx"
	43	#include <aw_awars.hxx>
	44
42	45	#include <arb_version.h>
43		#include "nt_internal.h"
44		#include <st_window.hxx>
45		#include <probe_design.hxx>
46		#include <primer_design.hxx>
47		#include <GEN.hxx>
48		#include <EXP.hxx>
49		#include <awt_input_mask.hxx>
50
51		#include "seq_quality.h"
52		#include "NT_trackAliChanges.h"
53		#include "NT_dbrepair.hxx"
54
55		#ifndef ARB_ASSERT_H
56		#include <arb_assert.h>
57		#endif
	46
58	47	#define nt_assert(bed) arb_assert(bed)
59	48
…	…
813	802	AWT_canvas ntw = (AWT_canvas )ntwcl;
814	803	GB_transaction dummy(ntw->gb_main);
815
	804
816	805	NT_mark_all_cb(aww,(AW_CL)ntw, (AW_CL)0);
817		AWT_TREE(ntw)->tree_root->mark_degenerated_branches(ntw->gb_main,atof(val));
818		AWT_TREE(ntw)->tree_root->compute_tree(ntw->gb_main);
	806	AP_tree *tree_root = AWT_TREE(ntw)->get_root_node();
	807	tree_root->mark_degenerated_branches(ntw->gb_main,atof(val));
	808	tree_root->compute_tree(ntw->gb_main);
819	809	free(val);
820	810	ntw->refresh();
…	…
829	819
830	820	NT_mark_all_cb(aww,(AW_CL)ntw, (AW_CL)0);
831		AWT_TREE(ntw)->tree_root->mark_deep_branches(ntw->gb_main,atoi(val));
832		AWT_TREE(ntw)->tree_root->compute_tree(ntw->gb_main);
	821	AP_tree *tree_root = AWT_TREE(ntw)->get_root_node();
	822	tree_root->mark_deep_branches(ntw->gb_main,atoi(val));
	823	tree_root->compute_tree(ntw->gb_main);
833	824	free(val);
834	825	ntw->refresh();
…	…
851	842
852	843	NT_mark_all_cb(aww,(AW_CL)ntw, (AW_CL)0);
853		AWT_TREE(ntw)->tree_root->mark_long_branches(ntw->gb_main, min_rel_diff, min_abs_diff);
854		AWT_TREE(ntw)->tree_root->compute_tree(ntw->gb_main);
	844	AP_tree *tree_root = AWT_TREE(ntw)->get_root_node();
	845	tree_root->mark_long_branches(ntw->gb_main, min_rel_diff, min_abs_diff);
	846	tree_root->compute_tree(ntw->gb_main);
855	847	ntw->refresh();
856	848	}
…	…
864	856	GB_transaction dummy(ntw->gb_main);
865	857	NT_mark_all_cb(aww,(AW_CL)ntw, (AW_CL)0);
866		AWT_TREE(ntw)->tree_root->mark_duplicates(ntw->gb_main);
867		AWT_TREE(ntw)->tree_root->compute_tree(ntw->gb_main);
	858	AP_tree *tree_root = AWT_TREE(ntw)->get_root_node();
	859	tree_root->mark_duplicates(ntw->gb_main);
	860	tree_root->compute_tree(ntw->gb_main);
868	861	ntw->refresh();
869	862	}
870	863
871	864	void NT_justify_branch_lenghs(AW_window *, AW_CL cl_ntw, AW_CL){
872		AWT_canvas ntw = (AWT_canvas )cl_ntw;
873		GB_transaction dummy(ntw->gb_main);
874		if (AWT_TREE(ntw)->tree_root){
875		AWT_TREE(ntw)->tree_root->justify_branch_lenghs(ntw->gb_main);
876		AWT_TREE(ntw)->tree_root->compute_tree(ntw->gb_main);
	865	AWT_canvas ntw = (AWT_canvas )cl_ntw;
	866	GB_transaction dummy(ntw->gb_main);
	867	AP_tree *tree_root = AWT_TREE(ntw)->get_root_node();
	868
	869	if (tree_root){
	870	tree_root->justify_branch_lenghs(ntw->gb_main);
	871	tree_root->compute_tree(ntw->gb_main);
877	872	GB_ERROR error = AWT_TREE(ntw)->save(ntw->gb_main,0,0,0);
878	873	if (error) aw_message(error);
…	…
905	900
906	901	void NT_pseudo_species_to_organism(AW_window *, AW_CL ntwcl){
907		AWT_canvas ntw = (AWT_canvas )ntwcl;
	902	AWT_canvas ntw = (AWT_canvas )ntwcl;
908	903	GB_transaction dummy(ntw->gb_main);
909		if (AWT_TREE(ntw)->tree_root){
	904	AP_tree *tree_root = AWT_TREE(ntw)->get_root_node();
	905
	906	if (tree_root){
910	907	GB_HASH *organism_hash = GBT_create_organism_hash(ntw->gb_main);
911		~~AWT_TREE(ntw)->~~tree_root->relink_tree(ntw->gb_main, relink_pseudo_species_to_organisms, organism_hash);
912		~~AWT_TREE(ntw)->~~tree_root->compute_tree(ntw->gb_main);
	908	tree_root->relink_tree(ntw->gb_main, relink_pseudo_species_to_organisms, organism_hash);
	909	tree_root->compute_tree(ntw->gb_main);
913	910	GB_ERROR error = AWT_TREE(ntw)->save(ntw->gb_main,0,0,0);
914	911	if (error) aw_message(error);
…	…
1056	1053	}
1057	1054
	1055	GBT_TREE *nt_get_current_tree_root() {
	1056	if (GLOBAL_NT.tree) {
	1057	AP_tree *root = GLOBAL_NT.tree->get_root_node();
	1058	if (root) {
	1059	return (GBT_TREE*)root;
	1060	}
	1061	}
	1062	return NULL;
	1063	}
	1064
1058	1065	//--------------------------------------------------------------------------------------------------
1059	1066
…	…
1090	1097	if (!clone) AW_init_color_group_defaults("arb_ntree");
1091	1098
1092		GLOBAL_NT.tree = NT_generate_tree(awr,GLOBAL_gb_main);
	1099	GLOBAL_NT.tree = NT_generate_tree(awr, GLOBAL_gb_main);
1093	1100
1094	1101	AWT_canvas *ntw;
…	…
1108	1115	if (existing_tree_name) {
1109	1116	awr->awar(awar_tree)->write_string(existing_tree_name);
1110		NT_reload_tree_event(awr,ntw,GB_FALSE); // load first tree !!!!!!!
1111		}else{
	1117	NT_reload_tree_event(awr, ntw); // load first tree
	1118	}
	1119	else {
1112	1120	AWT_advice("Your database contains no tree.", AWT_ADVICE_TOGGLE\|AWT_ADVICE_HELP, 0, "no_tree.hlp");
1113		}
1114
1115		awr->awar( awar_tree)->add_callback( (AW_RCB)NT_reload_tree_event, (AW_CL)ntw,(AW_CL)GB_FALSE);
	1121	GLOBAL_NT.tree->set_tree_type(AP_LIST_NDS); // no tree -> show NDS list
	1122	}
	1123
	1124	awr->awar( awar_tree)->add_callback( (AW_RCB)NT_reload_tree_event, (AW_CL)ntw, 0);
1116	1125
1117	1126	free(existing_tree_name);
…	…
1217	1226
1218	1227	NT_insert_mark_submenus(awm, ntw, 1);
1219		AWMIMT("species_colors", "Set Colors", "l", "mark_colors.hlp", AWM_ALL, AW_POPUP, (AW_CL)NT_create_species_colorize_window, 0);
1220		AWMIMT("selection_admin", "Configurations", "o", "configuration.hlp", AWM_ALL, NT_popup_configuration_admin, ~~(AW_CL)&(GLOBAL_NT.tree->tree_root), (AW_CL)~~0);
	1228	AWMIMT("species_colors", "Set Colors", "l", "mark_colors.hlp", AWM_ALL, AW_POPUP, (AW_CL)NT_create_species_colorize_window, 0);
	1229	AWMIMT("selection_admin", "Configurations", "o", "configuration.hlp", AWM_ALL, NT_popup_configuration_admin, 0, 0);
1221	1230
1222	1231	SEP________________________SEP();
…	…
1233	1242	awm->insert_sub_menu("Sort Species", "r");
1234	1243	{
1235		AWMIMT("sort_by_field", "According to Database Entries", "D", "sp_sort_fld.hlp", AWM_ALL, AW_POPUP, ~~(AW_CL)NT_build_resort_window,~~ 0);
1236		AWMIMT("sort_by_tree", "According to Phylogeny", "P", "sp_sort_phyl.hlp", AWM_ALL, ~~(AW_CB)NT_resort_data_by_phylogeny, (AW_CL)&(GLOBAL_NT.tree->tree_root),~~ 0);
	1244	AWMIMT("sort_by_field", "According to Database Entries", "D", "sp_sort_fld.hlp", AWM_ALL, AW_POPUP, (AW_CL)NT_build_resort_window, 0);
	1245	AWMIMT("sort_by_tree", "According to Phylogeny", "P", "sp_sort_phyl.hlp", AWM_ALL, NT_resort_data_by_phylogeny, 0, 0);
1237	1246	}
1238	1247	awm->close_sub_menu();
…	…
1279	1288	awm->insert_sub_menu("Edit Sequences","E");
1280	1289	{
1281		AWMIMT("new_arb_edit4", "Using marked species and tree", "m", "arb_edit4.hlp", AWM_ALL, ~~(AW_CB)NT_start_editor_on_tree, (AW_CL)&(GLOBAL_NT.tree->tree_root),~~ 0);
1282		AWMIMT("new2_arb_edit4", "... plus relatives", "r", "arb_edit4.hlp", AWM_ALL, ~~(AW_CB)NT_start_editor_on_tree, (AW_CL)&(GLOBAL_NT.tree->tree_root), -1~~);
	1290	AWMIMT("new_arb_edit4", "Using marked species and tree", "m", "arb_edit4.hlp", AWM_ALL, NT_start_editor_on_tree, 0, 0);
	1291	AWMIMT("new2_arb_edit4", "... plus relatives", "r", "arb_edit4.hlp", AWM_ALL, NT_start_editor_on_tree, -1, 0);
1283	1292	AWMIMT("old_arb_edit4", "Using earlier configuration", "c", "arb_edit4.hlp", AWM_ALL, AW_POPUP, (AW_CL)NT_start_editor_on_old_configuration, 0);
1284	1293	}
…	…
1552	1561	awm->create_mode("pzoom.bitmap", "mode_pzoom.hlp", AWM_ALL, (AW_CB)nt_mode_event, (AW_CL)ntw, (AW_CL)AWT_MODE_ZOOM);
1553	1562	awm->create_mode("lzoom.bitmap", "mode_lzoom.hlp", AWM_ALL, (AW_CB)nt_mode_event, (AW_CL)ntw, (AW_CL)AWT_MODE_LZOOM);
1554		awm->create_mode("modify.bitmap", "mode_info.hlp", AWM_ALL, (AW_CB)NT_modify_cb, (AW_CL)ntw, (AW_CL)AWT_MODE_~~MOD~~);
	1563	awm->create_mode("modify.bitmap", "mode_info.hlp", AWM_ALL, (AW_CB)NT_modify_cb, (AW_CL)ntw, (AW_CL)AWT_MODE_EDIT);
1555	1564	awm->create_mode("www_mode.bitmap", "mode_www.hlp", AWM_ALL, (AW_CB)nt_mode_event, (AW_CL)ntw, (AW_CL)AWT_MODE_WWW);
1556	1565
…	…
1708	1717
1709	1718	awm->at_set_to(false, false, ((2-is_genome_db)*EDIT_XSIZE), EDIT_YSIZE);
1710		awm->callback(~~(AW_CB)NT_start_editor_on_tree, (AW_CL)&(GLOBAL_NT.tree->tree_root)~~, 0);
	1719	awm->callback(NT_start_editor_on_tree, 0, 0);
1711	1720	awm->help_text("arb_edit4.hlp");
1712	1721	awm->create_button("EDIT_SEQUENCES", "#edit.xpm");
…	…
1765	1774	awm->button_length(13);
1766	1775	awm->help_text("marked_species.hlp");
1767		awm->callback(NT_popup_configuration_admin, ~~(AW_CL)&(GLOBAL_NT.tree->tree_root)~~, 0);
	1776	awm->callback(NT_popup_configuration_admin, 0, 0);
1768	1777	awm->create_button(0, AWAR_MARKED_SPECIES_COUNTER);
1769	1778	{

trunk/NTREE/NT_main.cxx

r6206	r6280
1		#include <string.h>
2		#include <stdio.h>
3		#include <stdlib.h>
4		#include <arbdb.h>
5		#include <arbdbt.h>
6		#include <adGene.h>
7
8		#include <servercntrl.h>
9		#include <aw_root.hxx>
10		#include <aw_device.hxx>
11		#include <aw_window.hxx>
12		#include <aw_awars.hxx>
13		#include <aw_question.hxx>
14		#include <aw_global.hxx>
15		#include <awt_canvas.hxx>
16		#include <awt_advice.hxx>
17
18		#include <awt_tree.hxx>
19		#include <awt_dtree.hxx>
20		#include <awt.hxx>
21		#include <awti_import.hxx>
22
23		#include <mg_merge.hxx>
	1	// =============================================================== //
	2	// //
	3	// File : NT_main.cxx //
	4	// Purpose : //
	5	// //
	6	// Institute of Microbiology (Technical University Munich) //
	7	// http://www.arb-home.de/ //
	8	// //
	9	// =============================================================== //
24	10
25	11	#include "nt_internal.h"
26	12	#include "ntree.hxx"
27	13	#include "nt_cb.hxx"
28		#include "NT_dbrepair.hxx"
29
	14
	15	#include <mg_merge.hxx>
	16	#include <awti_import.hxx>
	17	#include <awt_advice.hxx>
	18	#include <awt.hxx>
	19	#include <aw_global.hxx>
	20	#include <aw_question.hxx>
	21	#include <aw_awars.hxx>
	22	#include <adGene.h>
30	23	#include <arb_version.h>
31	24

trunk/NTREE/NT_trackAliChanges.cxx

r5851	r6280
10	10	// =============================================================== //
11	11
12		#include <cstdlib>
13		#include <cstring>
	12	#include "NT_trackAliChanges.h"
	13
	14	#include <awt_sel_boxes.hxx>
	15	#include <aw_window.hxx>
14	16	#include <ctime>
15
16
17		~~#include <awt.hxx>~~
18		~~#include <awt_sel_boxes.hxx>~~
19		~~#include <arbdbt.h>~~
20
21		~~#include "NT_trackAliChanges.h"~~
22	17
23	18	extern GBDATA *GLOBAL_gb_main;

trunk/NTREE/NT_trackAliChanges.h

r5675	r6280
13	13	#define NT_TRACKALICHANGES_H
14	14
	15	#ifndef AW_ROOT_HXX
	16	#include <aw_root.hxx>
	17	#endif
	18
	19	class AW_window;
	20
15	21	void NT_create_trackAliChanges_Awars(AW_root *root, AW_default aw_def);
16	22	AW_window NT_create_trackAliChanges_window(AW_root root);

trunk/NTREE/ad_spec.cxx

r6188	r6280
	1	// =============================================================== //
	2	// //
	3	// File : ad_spec.cxx //
	4	// Purpose : //
	5	// //
	6	// Institute of Microbiology (Technical University Munich) //
	7	// http://www.arb-home.de/ //
	8	// //
	9	// =============================================================== //
	10
	11
1	12	#include "ad_spec.hxx"
2
3		#include <stdio.h>
4		#include <stdlib.h>
5		#include <string.h>
6		#include <arbdbt.h>
7		#include <aw_awars.hxx>
8		#include <awt_www.hxx>
9		#include <awt_tree.hxx>
10		#include <awt_canvas.hxx>
11		#include <awt_dtree.hxx>
12		#include <awtlocal.hxx>
13		#include <awt_item_sel_list.hxx>
14		#include <awt_sel_boxes.hxx>
15		#include <db_scanner.hxx>
	13	#include "nt_internal.h"
	14	#include "ntree.hxx"
	15
16	16	#include <awtc_next_neighbours.hxx>
17	17	#include <AW_rename.hxx>
18		#include <ntree.hxx>
19		#include <nt_internal.h>
20
21		#ifndef ARB_ASSERT_H
22		#include <arb_assert.h>
23		#endif
	18	#include <db_scanner.hxx>
	19	#include <awt_item_sel_list.hxx>
	20	#include <awtlocal.hxx>
	21	#include <awt_www.hxx>
	22	#include <awt_canvas.hxx>
	23	#include <awt_sel_boxes.hxx>
	24	#include <aw_awars.hxx>
	25
24	26	#define nt_assert(bed) arb_assert(bed)
25	27

trunk/NTREE/ad_transpro.cxx

r6141	r6280
1		#include <stdio.h>
2		#include <stdlib.h>
3		#include <string.h>
4		#include <ctype.h>
5
6		#include <arbdb.h>
7		#include <arbdbt.h>
8		#include <aw_root.hxx>
9		#include <aw_device.hxx>
	1	// =============================================================== //
	2	// //
	3	// File : ad_transpro.cxx //
	4	// Purpose : //
	5	// //
	6	// Institute of Microbiology (Technical University Munich) //
	7	// http://www.arb-home.de/ //
	8	// //
	9	// =============================================================== //
	10
	11	#include "nt_internal.h"
	12
	13	#include <awt_sel_boxes.hxx>
	14	#include <Translate.hxx>
	15	#include <AP_codon_table.hxx>
	16	#include <AP_pro_a_nucs.hxx>
10	17	#include <aw_awars.hxx>
11		#include <aw_window.hxx>
12		#include <awt.hxx>
13		#include <awt_codon_table.hxx>
14		#include <awt_sel_boxes.hxx>
15		#include <awt_pro_a_nucs.hxx>
16		#include <awt_translate.hxx>
17
18		#ifndef ARB_ASSERT_H
19		#include <arb_assert.h>
20		#endif
	18	#include <cctype>
	19
21	20	#define nt_assert(bed) arb_assert(bed)
22	21
…	…
343	342	GB_ERROR arb_transdna(GBDATA gb_main, char ali_source, char ali_dest, long neededLength)
344	343	{
345		AWT_initialize_codon_tables();
	344	AP_initialize_codon_tables();
346	345
347	346	GBDATA *gb_source = GBT_get_alignment(gb_main,ali_source); if (!gb_source) return "Please select a valid source alignment";

trunk/NTREE/ad_trees.cxx

r6200	r6280
1		#include <stdio.h>
2		#include <stdlib.h>
3		#include <memory.h>
4		// #include <malloc.h>
5		#include <string.h>
6		#include <unistd.h>
7
8		#include <arbdb.h>
9		#include <arbdbt.h>
10		#include <aw_root.hxx>
11		#include <aw_device.hxx>
12		#include <aw_window.hxx>
	1	// =============================================================== //
	2	// //
	3	// File : ad_trees.cxx //
	4	// Purpose : //
	5	// //
	6	// Institute of Microbiology (Technical University Munich) //
	7	// http://www.arb-home.de/ //
	8	// //
	9	// =============================================================== //
	10
	11	#include "ad_trees.hxx"
	12	#include "nt_tree_cmp.hxx"
	13
	14	#include <TreeRead.h>
	15	#include <TreeWrite.h>
	16	#include <awt_sel_boxes.hxx>
	17	#include <awt_nds.hxx>
	18	#include <awt.hxx>
13	19	#include <aw_awars.hxx>
14	20	#include <aw_global.hxx>
15		#include <awt.hxx>
16		#include <TreeRead.h>
17		#include <TreeWrite.h>
18		#include <awt_tree_cmp.hxx>
19		#include <awt_sel_boxes.hxx>
20		#include <awt_nds.hxx>
21
22		#include "ad_trees.hxx"
23
24		#ifndef ARB_ASSERT_H
25		#include <arb_assert.h>
26		#endif
	21
27	22	#define nt_assert(bed) arb_assert(bed)
28	23
…	…
184	179
185	180	void tree_rename_cb(AW_window *aww) {
186		char *source = aww->get_root()->awar(AWAR_TREE_NAME)->read_string();
187		char *dest = aww->get_root()->awar(AWAR_TREE_DEST)->read_string();
188		GB_ERROR error = GBT_check_tree_name(dest);
	181	AW_root *aw_root = aww->get_root();
	182	AW_awar *awar_tree = aw_root->awar(AWAR_TREE_NAME);
	183	char *source = awar_tree->read_string();
	184	char *dest = aw_root->awar(AWAR_TREE_DEST)->read_string();
	185	GB_ERROR error = GBT_check_tree_name(dest);
189	186
190	187	if (!error) {
…	…
211	208	}
212	209	}
	210
	211	if (!error) awar_tree->write_string(dest);
213	212	error = GB_end_transaction(GLOBAL_gb_main, error);
214	213	}
215	214
216	215	aww->hide_or_notify(error);
217
	216
218	217	free(dest);
219	218	free(source);
…	…
679	678	}
680	679	void ad_tr_delete_cb(AW_window *aww){
681		GB_ERROR error = 0;
682		char *source = aww->get_root()->awar(AWAR_TREE_NAME)->read_string();
683
684		GB_begin_transaction(GLOBAL_gb_main);
685
686		GBDATA *gb_tree = GBT_get_tree(GLOBAL_gb_main,source);
687		if (gb_tree) {
688		char *newname = GBT_get_next_tree_name(GLOBAL_gb_main,source);
689		error = GB_delete(gb_tree);
690		if (!error && newname) {
691		aww->get_root()->awar(AWAR_TREE_NAME)->write_string(strcmp(newname, source) == 0 ? "" : newname);
692		}
	680	AW_awar *awar_tree = aww->get_root()->awar(AWAR_TREE_NAME);
	681	char *source = awar_tree->read_string();
	682
	683	// 1. switch to next tree
	684	{
	685	GB_transaction ta(GLOBAL_gb_main);
	686	char *newname = GBT_get_next_tree_name(GLOBAL_gb_main, source);
	687
	688	awar_tree->write_string(!newname \|\| (strcmp(newname, source) == 0) ? "" : newname);
693	689	free(newname);
694	690	}
695		else {
696		error = "Please select a tree first";
697		}
698
699		if (!error) GB_commit_transaction(GLOBAL_gb_main);
700		else GB_abort_transaction(GLOBAL_gb_main);
701
702		if (error) aw_message(error);
	691
	692	// 2. delete old tree
	693	{
	694	GB_ERROR error = GB_begin_transaction(GLOBAL_gb_main);
	695	GBDATA *gb_tree = GBT_get_tree(GLOBAL_gb_main,source);
	696	if (gb_tree) {
	697	char *newname = GBT_get_next_tree_name(GLOBAL_gb_main,source);
	698	error = GB_delete(gb_tree);
	699	if (!error && newname) {
	700	awar_tree->write_string(strcmp(newname, source) == 0 ? "" : newname);
	701	}
	702	free(newname);
	703	}
	704	else {
	705	error = "Please select a tree first";
	706	}
	707
	708	error = GB_end_transaction(GLOBAL_gb_main, error);
	709	if (error) {
	710	aw_message(error);
	711	awar_tree->write_string(source); // switch back to failed tree
	712	}
	713	}
	714
703	715	free(source);
704	716	}

trunk/NTREE/ad_trees.hxx

r6033	r6280
12	12	#define AD_TREES_HXX
13	13
	14	#ifndef AW_ROOT_HXX
	15	#include <aw_root.hxx>
	16	#endif
	17
14	18	#define AWAR_TREE_NAME "tmp/ad_tree/tree_name"
15	19

trunk/NTREE/ap_csp_2_gnuplot.hxx

r5390	r6280
	1	// ================================================================ //
	2	// //
	3	// File : ap_csp_2_gnuplot.hxx //
	4	// Purpose : //
	5	// //
	6	// Institute of Microbiology (Technical University Munich) //
	7	// http://www.arb-home.de/ //
	8	// //
	9	// ================================================================ //
	10
	11	#ifndef AP_CSP_2_GNUPLOT_HXX
	12	#define AP_CSP_2_GNUPLOT_HXX
	13
1	14	#define AP_AWAR_CSP "tmp/ntree/csp_2_gnuplot"
2	15	#define AP_AWAR_CSP_NAME AP_AWAR_CSP "/name"
…	…
15	28
16	29	AW_window AP_open_csp_2_gnuplot_window( AW_root root );
	30
	31	#else
	32	#error ap_csp_2_gnuplot.hxx included twice
	33	#endif // AP_CSP_2_GNUPLOT_HXX

trunk/NTREE/ap_pos_var_pars.hxx

r6141	r6280
1		#define AWAR_PVP_SAI "tmp/pos_var_pars/sai"
	1	// =============================================================== //
	2	// //
	3	// File : ap_pos_var_pars.hxx //
	4	// Purpose : //
	5	// //
	6	// Institute of Microbiology (Technical University Munich) //
	7	// http://www.arb-home.de/ //
	8	// //
	9	// =============================================================== //
	10
	11	#ifndef AP_POS_VAR_PARS_HXX
	12	#define AP_POS_VAR_PARS_HXX
	13
	14	#ifndef ARBDBT_H
	15	#include <arbdbt.h>
	16	#endif
	17
	18	class AW_window;
	19	class AW_root;
	20
	21	#define AWAR_PVP_SAI "tmp/pos_var_pars/sai"
2	22	#define AWAR_PVP_TREE "tmp/pos_var_pars/tree"
3	23
…	…
32	52	GB_ERROR save_sai(const char *sai_name);
33	53	};
	54
	55	#else
	56	#error ap_pos_var_pars.hxx included twice
	57	#endif // AP_POS_VAR_PARS_HXX

trunk/NTREE/nt_cb.hxx

r5968	r6280
17	17
18	18	/* NT_cb.cxx */
	19
	20	#ifndef ARBDBT_H
	21	#include <arbdbt.h>
	22	#endif
	23	#ifndef AW_ROOT_HXX
	24	#include <aw_root.hxx>
	25	#endif
	26
	27	class AW_window;
	28	class AWT_canvas;
	29
19	30	void NT_delete_mark_all_cb(void , AWT_canvas ntw);
20	31	AW_window NT_open_select_tree_window(AW_root awr, char *awar_tree);
…	…
59	70	void NT_popup_species_window(AW_window *aww, AW_CL dummy_1x, AW_CL dummy_2x);
60	71	void NT_alltree_remove_leafs(AW_window *, AW_CL cl_mode, AW_CL cl_gb_main);
	72	GBT_TREE *nt_get_current_tree_root(void);
61	73	AW_window create_nt_main_window(AW_root awr, AW_CL clone);
62	74

trunk/NTREE/nt_internal.h

r6019	r6280
15	15	#endif
16	16
	17
	18	/* NT_cb.cxx */
	19
	20	#ifndef ARBDBT_H
	21	#include <arbdbt.h>
	22	#endif
	23	#ifndef AW_ROOT_HXX
	24	#include <aw_root.hxx>
	25	#endif
	26
	27	class AW_window;
	28	class AWT_canvas;
	29
	30	void NT_delete_mark_all_cb(void , AWT_canvas ntw);
	31	AW_window NT_open_select_tree_window(AW_root awr, char *awar_tree);
	32	void NT_select_last_tree(AW_window aww, char awar_tree);
	33	AW_window NT_open_select_alignment_window(AW_root awr);
	34	void NT_system_cb(AW_window *aww, AW_CL command, AW_CL auto_help_file);
	35	void NT_system_cb2(AW_window *aww, AW_CL command, AW_CL auto_help_file);
17	36
18	37	/* AP_consensus.cxx */
…	…
36	55	AW_window AP_open_pos_var_pars_window(AW_root root);
37	56
38		~~/* NT_cb.cxx */~~
39		~~void NT_delete_mark_all_cb(void , AWT_canvas ntw);~~
40		~~AW_window NT_open_select_tree_window(AW_root awr, char *awar_tree);~~
41		~~void NT_select_last_tree(AW_window aww, char awar_tree);~~
42		~~AW_window NT_open_select_alignment_window(AW_root awr);~~
43		~~void NT_system_cb(AW_window *aww, AW_CL command, AW_CL auto_help_file);~~
44		~~void NT_system_cb2(AW_window *aww, AW_CL command, AW_CL auto_help_file);~~
45
46	57	/* NT_concatenate.cxx */
47	58	void NT_createConcatenationAwars(AW_root *aw_root, AW_default aw_def);
…	…
56	67	/* NT_edconf.cxx */
57	68	AW_window NT_start_editor_on_old_configuration(AW_root awr);
58		void NT_start_editor_on_tree(AW_window , ~~GBT_TREE *ptree, int use_species_aside~~);
59		GB_ERROR NT_create_configuration(AW_window , GBT_TREE ptree, const char conf_name, int use_species_aside);
60		void NT_popup_configuration_admin(AW_window *aw_main, AW_CL ~~cl_GBT_TREE_ptr, AW_CL dummy_1~~x);
	69	void NT_start_editor_on_tree(AW_window *, AW_CL cl_use_species_aside, AW_CL dummy_1x);
	70	GB_ERROR NT_create_configuration(AW_window , GBT_TREE tree, const char *conf_name, int use_species_aside);
	71	void NT_popup_configuration_admin(AW_window *aw_main, AW_CL dummy_1x, AW_CL dummy_2x);
61	72
62	73	/* NT_extern.cxx */
…	…
97	108	/* NT_sort.cxx */
98	109	GB_ERROR NT_resort_data_base(GBT_TREE tree, const char key1, const char key2, const char key3);
99		void NT_resort_data_by_phylogeny(AW_window ~~dummy, GBT_TREE *ptree~~);
	110	void NT_resort_data_by_phylogeny(AW_window *, AW_CL dummy_1x, AW_CL dummy_2x);
100	111	void NT_resort_data_by_user_criteria(AW_window *aw);
101	112	void NT_build_resort_awars(AW_root *awr, AW_default aw_def);

trunk/NTREE/nt_sort.hxx

r5646	r6280
	1	#error "bad header"
	2
1	3	extern GBDATA *GLOBAL_gb_main;
2		~~#define NT_RESORT_FILTER (1<<GB_STRING)\|(1<<GB_INT)\|(1<<GB_FLOAT)~~
3	4
4	5	AW_window NT_build_resort_window(AW_root awr);

trunk/NTREE/ntree.hxx

r5968	r6280
11	11	#ifndef NTREE_HXX
12	12	#define NTREE_HXX
	13
	14	#ifndef AW_WINDOW_HXX
	15	#include <aw_window.hxx>
	16	#endif
13	17
14	18	#define NT_AW_TRUE 1

trunk/PARSIMONY/AP_buffer.cxx

r6141	r6280
1		#include <cstdio>
2		#include <memory.h>
3		#include <iostream>
4
5		#include <arbdb.h>
6		#include <arbdbt.h>
7		#include <awt_tree.hxx>
	1	// =============================================================== //
	2	// //
	3	// File : AP_buffer.cxx //
	4	// Purpose : //
	5	// //
	6	// Institute of Microbiology (Technical University Munich) //
	7	// http://www.arb-home.de/ //
	8	// //
	9	// =============================================================== //
8	10
9	11	#include "AP_buffer.hxx"
10	12	#include "AP_error.hxx"
	13
	14	#include <iostream>
11	15
12	16	using namespace std;

trunk/PARSIMONY/AP_buffer.hxx

r5390	r6280
1		#ifndef _AP_BUFFER_INC
2		#define _AP_BUFFER_INC
	1	// =============================================================== //
	2	// //
	3	// File : AP_buffer.hxx //
	4	// Purpose : //
	5	// //
	6	// Institute of Microbiology (Technical University Munich) //
	7	// http://www.arb-home.de/ //
	8	// //
	9	// =============================================================== //
	10
	11	#ifndef AP_BUFFER_HXX
	12	#define AP_BUFFER_HXX
	13
	14	#ifndef AP_SEQUENCE_HXX
	15	#include <AP_sequence.hxx>
	16	#endif
	17	#ifndef AP_TREE_HXX
	18	#include <AP_Tree.hxx>
	19	#endif
	20
3	21
4	22	/*******************
…	…
96	114
97	115	struct AP_tree_buffer {
98		unsigned long controll; // used for internal buffer check
99		unsigned int count; // counts how often the entry is buffered
	116	unsigned long controll; // used for internal buffer check
	117	unsigned int count; // counts how often the entry is buffered
100	118	AP_STACK_MODE mode;
101	119	AP_sequence *sequence;
…	…
105	123	AP_tree *leftson;
106	124	AP_tree *rightson;
	125	AP_tree_root *root;
107	126	GBDATA *gb_node;
108	127
…	…
128	147	};
129	148
130
	149	class AP_tree_nlen;
131	150
132	151	class AP_main_stack : public AP_STACK {
…	…
135	154	public:
136	155	friend class AP_main;
137		void push(AP_tree value) { AP_STACK::push((void )value); }
138		AP_tree * pop() { return (AP_tree *) AP_STACK::pop(); }
139		AP_tree * get() { return (AP_tree *) AP_STACK::get(); }
140		AP_tree * get_first() { return (AP_tree *) AP_STACK::get_first(); }
	156	void push(AP_tree_nlen value) { AP_STACK::push((void )value); }
	157	AP_tree_nlen pop() { return (AP_tree_nlen)AP_STACK::pop(); }
	158	AP_tree_nlen get() { return (AP_tree_nlen)AP_STACK::get(); }
	159	AP_tree_nlen get_first() { return (AP_tree_nlen)AP_STACK::get_first(); }
141	160	void print();
142	161	};
…	…
151	170	};
152	171
153		#endif
	172	#else
	173	#error AP_buffer.hxx included twice
	174	#endif // AP_BUFFER_HXX

trunk/PARSIMONY/AP_main.cxx

r6141	r6280
1		#include <cstdio>
2		#include <cmath>
3		#include <cstring>
4		#include <memory.h>
	1	// =============================================================== //
	2	// //
	3	// File : AP_main.cxx //
	4	// Purpose : //
	5	// //
	6	// Institute of Microbiology (Technical University Munich) //
	7	// http://www.arb-home.de/ //
	8	// //
	9	// =============================================================== //
	10
	11	#include "AP_error.hxx"
	12	#include "ap_main.hxx"
	13	#include "ap_tree_nlen.hxx"
	14
	15	#include <TreeDisplay.hxx>
	16
5	17	#include <iostream>
6
7		~~#include <arbdb.h>~~
8		~~#include <arbdbt.h>~~
9		~~#include <awt_tree.hxx>~~
10
11		~~#include "AP_buffer.hxx"~~
12		~~#include "parsimony.hxx"~~
13		~~#include "AP_error.hxx"~~
14	18
15	19	using namespace std;
…	…
79	83	***************/
80	84
81		AP_main::AP_main(~~void~~) {
	85	AP_main::AP_main() {
82	86	memset((char *)this,0,sizeof(AP_main));
83	87	}
84	88
85		AP_main::~AP_main(void) {
86		if (use) delete use;
	89	AP_main::~AP_main() {
87	90	if (stack) delete stack;
88	91	}
…	…
95	98	}
96	99
97		void AP_main::user_push(~~void~~) {
	100	void AP_main::user_push() {
98	101	this->user_push_counter = stack_level + 1;
99	102	this->push();
100	103	}
101	104
102		void AP_main::user_pop(~~void~~) {
	105	void AP_main::user_pop() {
103	106	// checks if user_pop possible
104	107	if (user_push_counter == stack_level) {
…	…
110	113	}
111	114
112		void AP_main::push(~~void~~) {
	115	void AP_main::push() {
113	116	// if count > 1 the nodes are buffered more than once
114	117	// WARNING:: node only has to be buffered once in the stack
…	…
121	124	}
122	125
123		void AP_main::pop(~~void~~) {
124		AP_tree *knoten;
	126	void AP_main::pop() {
	127	AP_tree_nlen *knoten;
125	128	if (!stack) {
126	129	new AP_ERR("AP_main::pop()","Stack underflow !");
…	…
147	150	}
148	151
149		void AP_main::clear(~~void~~) {
	152	void AP_main::clear() {
150	153	// removes count elements from the list
151	154	// because the current tree is used
…	…
155	158	// previous stack
156	159
157		AP_tree * knoten;
158		AP_main_stack * new_stack;
	160	AP_tree_nlen *knoten;
	161	AP_main_stack *new_stack;
	162
159	163	if (!stack) {
160	164	new AP_ERR("AP_main::clear","Stack underflow !");
…	…
166	170	while (stack->size() > 0) {
167	171	knoten = stack->pop();
168		~~//if (buffer_cout == AP_TRUE) knoten->printl();~~
169	172	knoten->clear(stack_level,user_push_counter);
170	173	}
…	…
195	198	}
196	199
197		void AP_main::push_node(AP_tree * node,AP_STACK_MODE mode) {
	200	void AP_main::push_node(AP_tree_nlen *node, AP_STACK_MODE mode) {
198	201	//
199	202	// stores node
…	…
212	215	}
213	216
214
215		void AP_main::set_tree_root(AP_tree *new_root) {
216		// removes old root and sets it
217		// to the father of the new_root
218		*ap_main->tree_root = new_root;
219		}
	217	AP_tree_nlen *AP_main::get_root_node() {
	218	return DOWNCAST(AP_tree_nlen*, agt->get_root_node());
	219	}
	220
	221	void AP_main::set_tree_root(AWT_graphic_tree *agt_) {
	222	ap_assert(agt == 0 && agt_ != 0); // do only once
	223	agt = agt_;
	224	}
	225
	226	const char *AP_main::get_aliname() const {
	227	return agt->tree_static->get_aliview()->get_aliname();
	228	}
	229

trunk/PARSIMONY/AP_tree_edge.cxx

r6141	r6280
1		#include <stdio.h>
2		#include <stdlib.h>
3		#include <math.h>
4		#include <iostream>
	1	// =============================================================== //
	2	// //
	3	// File : AP_tree_edge.cxx //
	4	// Purpose : //
	5	// //
	6	// Coded by Ralf Westram (coder@reallysoft.de) in Summer 1995 //
	7	// Institute of Microbiology (Technical University Munich) //
	8	// http://www.arb-home.de/ //
	9	// //
	10	// =============================================================== //
	11
	12	#include "ap_tree_nlen.hxx"
	13
	14	#include <AP_filter.hxx>
	15
	16	#include <cmath>
5	17	#include <iomanip>
6		~~#include <memory.h>~~
7		~~#include <arbdb.h>~~
8		~~#include <arbdbt.h>~~
9		~~#include <string.h>~~
10		~~#include <awt_tree.hxx>~~
11
12		~~#include "AP_buffer.hxx"~~
13		~~#include "parsimony.hxx"~~
14		~~#include "ap_tree_nlen.hxx"~~
15
16		~~// #include <aw_root.hxx>~~
17	18
18	19	using namespace std;
…	…
444	445	}
445	446
446		int AP_tree_edge::dumpChain(~~void~~) const
	447	int AP_tree_edge::dumpChain() const
447	448	{
448	449	// cout << this << '\n';
…	…
479	480	}
480	481
481		long AP_tree_edge::sizeofChain(~~void~~){
	482	long AP_tree_edge::sizeofChain(){
482	483	AP_tree_edge *f;
483	484	long c= 0;
…	…
553	554	tree optimization
554	555	**************************/
555		void ap_init_bootstrap_remark(AP_tree_nlen *son_node){
556		int seq_len = son_node->sequence->root->filter->real_len;
557		AP_sequence::static_mutation_per_site[0] = (char *)GB_calloc(sizeof(char),seq_len);
558		AP_sequence::static_mutation_per_site[1] = (char *)GB_calloc(sizeof(char),seq_len);
559		AP_sequence::static_mutation_per_site[2] = (char *)GB_calloc(sizeof(char),seq_len);
560		}
561
562		double fak(int n,int m){
563		double res = 1.0;
564		while (n>m){
565		res *= n;
566		n--;
567		}
568		return res;
569		}
570
571
572		double ap_calc_bootstrap_remark_sub(int seq_len, char old, char ne){
	556
	557	class MutationsPerSite {
	558	char *Data;
	559	size_t length;
	560
	561	public:
	562	MutationsPerSite(size_t len)
	563	: Data((char)GB_calloc(sizeof(char), len3))
	564	, length(len)
	565	{ }
	566	~MutationsPerSite() {
	567	free(Data);
	568	}
	569
	570	char *data(int block) {
	571	ap_assert(block >= 0 && block<3);
	572	return Data+block*length;
	573	}
	574	const char *data(int block) const {
	575	return const_cast<MutationsPerSite*>(this)->data(block);
	576	}
	577	};
	578
	579	double ap_calc_bootstrap_remark_sub(int seq_len, const char old, const char ne){
573	580	int i;
574	581	int sum[3];
…	…
653	660	}
654	661
655		~~void ap_calc_bootstrap_remark(AP_tree_nlen *son_node,AP_BL_MODE mode)~~{
	662	static void ap_calc_bootstrap_remark(AP_tree_nlen *son_node, AP_BL_MODE mode, const MutationsPerSite& mps) {
656	663	if (!son_node->is_leaf){
657		int seq_len = son_node->sequence->root->filter->real_len;
658		float one = ap_calc_bootstrap_remark_sub(seq_len,
659		&AP_sequence::static_mutation_per_site[0][0],
660		&AP_sequence::static_mutation_per_site[1][0]);
661		float two = ap_calc_bootstrap_remark_sub(seq_len,
662		&AP_sequence::static_mutation_per_site[0][0],
663		&AP_sequence::static_mutation_per_site[2][0]);
	664	size_t seq_len = son_node->get_seq()->get_sequence_length();
	665	float one = ap_calc_bootstrap_remark_sub(seq_len, mps.data(0), mps.data(1));
	666	float two = ap_calc_bootstrap_remark_sub(seq_len, mps.data(0), mps.data(2));
	667
664	668	if ((mode & AP_BL_BOOTSTRAP_ESTIMATE) == AP_BL_BOOTSTRAP_ESTIMATE){
665	669	one = one * two; // assume independent bootstrap values for both nnis
666		}else{
	670	}
	671	else {
667	672	if (two<one) one = two; // dependent bootstrap values, take minimum (safe)
668	673	}
…	…
677	682	freedup(son_node->Brother()->remark_branch, text);
678	683	}
679
680		~~freeset(AP_sequence::static_mutation_per_site[0], NULL);~~
681		~~freeset(AP_sequence::static_mutation_per_site[1], NULL);~~
682		~~freeset(AP_sequence::static_mutation_per_site[2], NULL);~~
683	684	}
684	685
685	686
686	687	void ap_calc_leaf_branch_length(AP_tree_nlen *leaf){
687		AP_FLOAT Seq_len = leaf->~~sequence->real_len~~();
	688	AP_FLOAT Seq_len = leaf->get_seq()->weighted_base_count();
688	689	if (Seq_len <=1.0) Seq_len = 1.0;
689	690
…	…
719	720	static double s_old = 0.0;
720	721
721		AP_FLOAT seq_len = son->~~sequence->real_len~~();
	722	AP_FLOAT seq_len = son->get_seq()->weighted_base_count();
722	723	if (seq_len <=1.0) seq_len = 1.0;
723	724	blen = 0.5 / seq_len 2.0; // doubled counted sum * corr
…	…
819	820	}
820	821	}
821		if (mode & AP_BL_BOOTSTRAP_LIMIT){
	822	if (mode & AP_BL_BOOTSTRAP_LIMIT) {
822	823	if (fath->father){
823	824	son->set_root();
824	825	new_parsimony = rootNode()->costs();
825	826	}
826		ap_init_bootstrap_remark(son);
827		}
828		new_parsimony = follow->nni(new_parsimony, mode);
829		if (mode & AP_BL_BOOTSTRAP_LIMIT){
830		ap_calc_bootstrap_remark(son,mode);
831		}
	827
	828	MutationsPerSite mps(son->get_seq()->get_sequence_length());
	829	new_parsimony = follow->nni_mutPerSite(new_parsimony, mode, &mps);
	830	ap_calc_bootstrap_remark(son, mode, mps);
	831	}
	832	else {
	833	new_parsimony = follow->nni(new_parsimony, mode);
	834	}
	835
832	836	if (useStatus ? aw_status(++count/(double)cs) : aw_status()) { Abort = 1; break; }
833	837	}
…	…
857	861	int AP_tree_edge::nodesInTree;
858	862
859		AP_FLOAT AP_tree_edge::nni~~(AP_FLOAT pars_one, AP_BL_MODE mode~~)
860		{
861		AP_tree_nlen root = ~~(AP_tree_nlen ) (*ap_main->tree_root~~);
	863	AP_FLOAT AP_tree_edge::nni_mutPerSite(AP_FLOAT pars_one, AP_BL_MODE mode, MutationsPerSite *mps)
	864	{
	865	AP_tree_nlen *root = rootNode();
862	866
863	867	if (node[0]->is_leaf \|\| node[1]->is_leaf) { // a son at root
…	…
890	894	int betterValueFound = 0;
891	895	{ // ******** original tree
892		if ( ~~(mode & AP_BL_BOOTSTRAP_LIMIT))~~{
	896	if ((mode & AP_BL_BOOTSTRAP_LIMIT)) {
893	897	root->costs();
894		~~char *ms = AP_sequence::static_mutation_per_site[0];~~
895		~~AP_sequence::mutation_per_site = ms;~~
896	898	son->unhash_sequence();
897		son->~~father~~->unhash_sequence();
	899	son->Father()->unhash_sequence();
898	900	ap_assert(!son->father->father);
899	901	AP_tree_nlen *brother = son->Brother();
900	902	brother->unhash_sequence();
901		pars_one = 0.0;
902		}
903		if (pars_one==0.0) pars_one = root->costs();
	903
	904	ap_assert(mps);
	905	pars_one = root->costs(mps->data(0));
	906	}
	907	else if (pars_one==0.0) {
	908	pars_one = root->costs();
	909	}
904	910	}
905	911	{ // ********* first nni
906	912	ap_main->push();
907	913	son->swap_assymetric(AP_LEFT);
908		char *ms = AP_sequence::static_mutation_per_site[1];
909		AP_sequence::mutation_per_site = ms;
910		pars_two = root->costs();
	914	pars_two = root->costs(mps ? mps->data(1) : NULL);
911	915
912	916	if (pars_two <= parsbest){
913		if ((mode & AP_BL_NNI_ONLY)==0) ap_main->pop();
914		else ap_main->clear();
915		parsbest = pars_two;
	917	if ((mode & AP_BL_NNI_ONLY) == 0) ap_main->pop();
	918	else ap_main->clear();
	919
	920	parsbest = pars_two;
916	921	betterValueFound = (int)(pars_one-pars_two);
917		}else{
	922	}
	923	else {
918	924	ap_main->pop();
919	925	}
…	…
922	928	ap_main->push();
923	929	son->swap_assymetric(AP_RIGHT);
924		char *ms = AP_sequence::static_mutation_per_site[2];
925		AP_sequence::mutation_per_site = ms;
926		pars_three = root->costs();
	930	pars_three = root->costs(mps ? mps->data(2) : NULL);
927	931
928	932	if (pars_three <= parsbest){
929		if ((mode & AP_BL_NNI_ONLY)==0) ap_main->pop();
930		else ap_main->clear();
931		parsbest = pars_three;
	933	if ((mode & AP_BL_NNI_ONLY) == 0) ap_main->pop();
	934	else ap_main->clear();
	935
	936	parsbest = pars_three;
932	937	betterValueFound = (int)(pars_one-pars_three);
933		}else{
	938	}
	939	else {
934	940	ap_main->pop();
935	941	}
936		~~AP_sequence::mutation_per_site = 0;~~
937	942	}
938	943
…	…
1029	1034	}
1030	1035	}
	1036

trunk/PARSIMONY/AP_tree_nlen.cxx

r6234	r6280
1		#include <stdio.h>
2		#include <stdlib.h>
3		// #include <malloc.h>
4		#include <string.h>
5		#include <iostream>
6		#include <math.h>
7		#include <arbdb.h>
8		#include <arbdbt.h>
9		//
10		#include <awt_tree.hxx>
11		#include <awt_seq_dna.hxx>
12		#include "AP_buffer.hxx"
13		#include "parsimony.hxx"
	1	// =============================================================== //
	2	// //
	3	// File : AP_tree_nlen.cxx //
	4	// Purpose : //
	5	// //
	6	// Coded by Ralf Westram (coder@reallysoft.de) in Summer 1995 //
	7	// Institute of Microbiology (Technical University Munich) //
	8	// http://www.arb-home.de/ //
	9	// //
	10	// =============================================================== //
	11
	12	#include "ap_tree_nlen.hxx"
14	13	#include "pars_debug.hxx"
15		#include "ap_tree_nlen.hxx"
16		~~// #include <aw_root~~.hxx>
	14
	15	#include <AP_seq_dna.hxx>
17	16
18	17	using namespace std;
19	18
20		#define ap_assert(x) arb_assert(x)
	19	// #define ap_assert(x) arb_assert(x)
21	20
22	21	// ---------------------------------
…	…
32	31	AP_tree_nlen::AP_tree_nlen(AP_tree_root *Tree_root)
33	32	: AP_tree(Tree_root)
	33	, kernighan(AP_NONE)
	34	, distance(INT_MAX)
	35	, mutation_rate(0)
34	36	{
35		// this->init();
36		kernighan = AP_NONE;
37		sequence = NULL;
38
39		edge[0] = edge[1] = edge[2] = NULL;
	37	edge[0] = edge[1] = edge[2] = NULL;
40	38	index[0] = index[1] = index[2] = 0;
41		distance = INT_MAX;
42
43		// cout << "AP_tree_nlen-constructor\n";
44		}
45
46		AP_tree *AP_tree_nlen::dup(void)
47		{
48		return (AP_tree *) new AP_tree_nlen(this->tree_root);
49		}
50
51		AP_UPDATE_FLAGS AP_tree_nlen::check_update(void)
52		{
53		AP_UPDATE_FLAGS res = this->AP_tree::check_update();
54
55		if (res == AP_UPDATE_RELOADED) {
56		return AP_UPDATE_OK;
57		}
58
59		return res;
	39	}
	40
	41	AP_tree_nlen *AP_tree_nlen::dup() const {
	42	return new AP_tree_nlen(get_tree_root());
	43	}
	44
	45	AP_UPDATE_FLAGS AP_tree_nlen::check_update() {
	46	AP_UPDATE_FLAGS res = AP_tree::check_update();
	47
	48	return res == AP_UPDATE_RELOADED ? AP_UPDATE_OK : res;
60	49	}
61	50
…	…
78	67
79	68	if (is_leaf == GB_TRUE) {
80		if (tree->sequence) {
81		this->sequence = tree->sequence;
82		}
83		else {
84		cout << "empty sequence at leaf";
85		this->sequence = 0;
86		}
	69	ap_assert(tree->get_seq()); /* oops - AP_tree_nlen expects to have sequences at leafs!
	70	* did you forget to remove_leafs() ? */
	71
	72	set_seq(tree->get_seq());
	73	// dangerous - no copy, just moves pointer
	74	// will result in undefined behavior
	75
	76	ap_assert(0); // this will not work, but is only used in GA_genetic.
	77	// Use some kind of SmartPtr there!
	78
	79	// if (tree->sequence) {
	80	// this->sequence = tree->sequence;
	81	// }
	82	// else {
	83	// cout << "empty sequence at leaf";
	84	// this->sequence = 0;
	85	// }
87	86	}
88	87	}
…	…
149	148	for (e=0; e<3; e++) if (edge[e]==NULL) return e;
150	149
151		cout << "No unused edge found at" << *this << '\n';
	150	// cout << "No unused edge found at" << *this << '\n';
152	151	return -1;
153	152	}
…	…
162	161	}
163	162	}
164		cout << "AP_tree_nlen::edgeTo: " << this << "\nhas no edge to " << neighbour << '\n';
	163	// cout << "AP_tree_nlen::edgeTo: " << this << "\nhas no edge to " << neighbour << '\n';
165	164	ap_assert(0);
166	165	return NULL;
…	…
211	210	********************************************/
212	211
	212	#if defined(CHECK_TREE_STRUCTURE)
	213
	214	void AP_tree_nlen::assert_edges_valid() const {
	215	if (!is_root()) { // root has no edges
	216	if (Father()->is_root()) { // sons of root have one edge between them
	217	ap_assert(edgeTo(Brother()) == Brother()->edgeTo(this));
	218	}
	219	else {
	220	ap_assert(edgeTo(Father()) == Father()->edgeTo(this));
	221	if (!is_leaf) {
	222	ap_assert(edgeTo(Leftson()) == Leftson()->edgeTo(this));
	223	ap_assert(edgeTo(Rightson()) == Rightson()->edgeTo(this));
	224	}
	225	}
	226	}
	227
	228	if (!is_leaf) {
	229	Leftson()->assert_edges_valid();
	230	Rightson()->assert_edges_valid();
	231	}
	232	}
	233
	234	void AP_tree_nlen::assert_valid() const {
	235	assert_edges_valid();
	236	AP_tree::assert_valid();
	237	}
	238
	239	#endif
	240
213	241	void AP_tree_nlen::insert(AP_tree *new_brother) {
214	242	// inserts a node at the father-edge of new_brother
215	243
216		AP_tree *pntr;
	244	AP_tree_nlen *pntr;
217	245	AP_tree_nlen newBrother = dynamic_cast<AP_tree_nlen>(new_brother);
218	246	ap_assert(new_brother);
…	…
220	248	AP_tree_edge *oldEdge;
221	249
222		ap_main->push_node(new_brother, STRUCTURE);
	250	ap_main->push_node(newBrother, STRUCTURE);
223	251
224	252	if (new_brother->father) {
225		ap_main->push_node(new_brother->father, BOTH);
226		for (pntr = new_brother->father->father; pntr; pntr = pntr->father) {
	253	ap_main->push_node(newBrother->Father(), BOTH);
	254	AP_tree_nlen *newGrandpa = newBrother->Father()->Father();
	255	for (pntr = newGrandpa; pntr; pntr = pntr->Father()) {
227	256	ap_main->push_node(pntr, SEQUENCE);
228	257	}
229	258
230		if (new~~_brother->father->father~~) {
	259	if (newGrandpa) {
231	260	oldEdge = newBrother->edgeTo(newBrother->Father())->unlink();
232	261	AP_tree::insert(new_brother);
…	…
242	271	new AP_tree_edge(Father(),newBrother);
243	272	}
244		else { // insert at root
245		AP_tree_nlen *lson = newBrother->Leftson();
246		AP_tree_nlen *rson = newBrother->Rightson();
247
248		ap_main->push_node(lson, STRUCTURE);
249		ap_main->push_node(rson, STRUCTURE);
250
251		oldEdge = lson->edgeTo(rson)->unlink();
	273	else { // insert at root
	274	if (newBrother->is_leaf) { // tree contains exactly one species (only legal during insert)
	275	AP_tree::insert(new_brother);
	276	new AP_tree_edge(newBrother, this); // build the root edge
	277	}
	278	else {
	279	AP_tree_nlen *lson = newBrother->Leftson();
	280	AP_tree_nlen *rson = newBrother->Rightson();
	281
	282	ap_main->push_node(lson, STRUCTURE);
	283	ap_main->push_node(rson, STRUCTURE);
	284
	285	oldEdge = lson->edgeTo(rson)->unlink();
252	286	#if defined(DEBUG)
253		cout << "old Edge = " << oldEdge << '\n';
	287	cout << "old Edge = " << oldEdge << '\n';
254	288	#endif // DEBUG
255	289
256		AP_tree::insert(new_brother);
257
258		oldEdge->relink(this,newBrother);
259		new AP_tree_edge(newBrother,rson);
260		new AP_tree_edge(newBrother,lson);
261		}
262		}
263
264		void AP_tree_nlen::remove(void) {
	290	AP_tree::insert(new_brother);
	291
	292	oldEdge->relink(this,newBrother);
	293	new AP_tree_edge(newBrother,rson);
	294	new AP_tree_edge(newBrother,lson);
	295	}
	296	}
	297	}
	298
	299	void AP_tree_nlen::remove() {
265	300	// Removes the node and its father from the tree:
266	301	//
…	…
280	315	// memory location was stored in the tree-stack.
281	316
282		AP_tree *pntr;
	317	AP_tree_nlen *oldBrother = Brother();
	318
	319	ASSERT_VALID_TREE(this);
	320
	321	ap_assert(father); // can't remove complete tree,
	322
	323	ap_main->push_node(this, STRUCTURE);
	324	ap_main->push_node(oldBrother, STRUCTURE);
	325
	326	AP_tree_nlen *grandPa = Father()->Father();
	327	for (AP_tree_nlen *pntr = grandPa; pntr; pntr = pntr->Father()) {
	328	ap_main->push_node(pntr, SEQUENCE);
	329	}
	330
283	331	AP_tree_edge *oldEdge;
284		AP_tree_nlen *oldBrother = Brother();
285
286		ap_assert(father);
287
288		ap_main->push_node(this, STRUCTURE);
289		ap_main->push_node(brother(), STRUCTURE);
290
291		for (pntr = father->father; pntr; pntr = pntr->father) {
292		ap_main->push_node(pntr, SEQUENCE);
293		}
294
295		if (father->father) {
296		AP_tree_nlen *grandPa = Father()->Father();
297
298		ap_main->push_node(father, BOTH);
	332	if (grandPa) {
	333	ASSERT_VALID_TREE(grandPa);
	334
	335	ap_main->push_node(Father(), BOTH);
299	336	ap_main->push_node(grandPa, STRUCTURE);
300	337
301		edgeTo(Father())->unlink();
302		Father()->edgeTo(oldBrother)->unlink();
	338	edgeTo(Father())->unlink(); // LOST_EDGE
	339	Father()->edgeTo(oldBrother)->unlink(); // LOST_EDGE
303	340
304	341	if (grandPa->father) {
…	…
315	352	oldEdge->relink(oldBrother,uncle);
316	353	}
317		}
318		else { // remove son of root
319		AP_tree_nlen *lson = Brother()->Leftson();
320		AP_tree_nlen *rson = Brother()->Rightson();
321
322		ap_assert(lson && rson);
323
324		ap_main->push_node(lson,STRUCTURE);
325		ap_main->push_node(rson,STRUCTURE);
326		ap_main->push_node(father, ROOT);
327
328		ap_main->set_tree_root(oldBrother);
329
330		// delete edgeTo(oldBrother);
331		oldBrother->edgeTo(lson)->unlink();
332		// delete oldBrother->edgeTo(lson);
333		oldEdge = oldBrother->edgeTo(rson)->unlink();
334		AP_tree::remove();
335		oldEdge->relink(lson,rson);
336		}
	354	ASSERT_VALID_TREE(grandPa);
	355	}
	356	else { // remove son of root
	357	AP_tree_nlen *oldRoot = Father();
	358	ASSERT_VALID_TREE(oldRoot);
	359
	360	if (oldBrother->is_leaf) {
	361	// root
	362	// oo
	363	// o o
	364	// o o
	365	// oldBrother --- this -----> NULL
	366	//
	367	ap_main->push_node(oldRoot, ROOT);
	368
	369	edgeTo(oldBrother)->unlink(); // LOST_EDGE
	370
	371	#if defined(DEBUG)
	372	AP_tree_root *troot = get_tree_root();
	373	#endif // DEBUG
	374	AP_tree::remove();
	375	ap_assert(!troot->get_root_node()); // tree should have been removed
	376	}
	377	else {
	378	//
	379	// root
	380	// oo .
	381	// o o root (=oldBrother)
	382	// o o oo .
	383	// oldBrother --- this -----> o o .
	384	// /\ o o .
	385	// / \ lson ----- rson
	386	// / \ .
	387	// lson rson
	388	//
	389	AP_tree_nlen *lson = oldBrother->Leftson();
	390	AP_tree_nlen *rson = oldBrother->Rightson();
	391
	392	ap_assert(lson && rson);
	393
	394	ap_main->push_node(lson,STRUCTURE);
	395	ap_main->push_node(rson,STRUCTURE);
	396	ap_main->push_node(oldRoot, ROOT);
	397
	398	// get_tree_root()->change_root(get_father(), oldBrother);
	399	// don't do this here (already done in AP_tree::remove())
	400
	401	edgeTo(oldBrother)->unlink(); // LOST_EDGE
	402	oldBrother->edgeTo(lson)->unlink(); // LOST_EDGE
	403
	404	oldEdge = oldBrother->edgeTo(rson)->unlink();
	405	AP_tree::remove();
	406	oldEdge->relink(lson,rson);
	407
	408	ap_assert(lson->get_tree_root()->get_root_node() == oldBrother);
	409	ASSERT_VALID_TREE(oldBrother);
	410	}
	411	}
	412
337	413	}
338	414
…	…
357	433	ap_main->push_node(this, BOTH);
358	434	ap_main->push_node(movedSon,STRUCTURE);
359		ap_main->push_node(~~father~~, SEQUENCE);
	435	ap_main->push_node(Father(), SEQUENCE);
360	436	ap_main->push_node(nephew, STRUCTURE);
361	437	ap_main->push_node(oldBrother, BOTH);
…	…
372	448	else {
373	449	ap_main->push_node(this, BOTH);
374		ap_main->push_node(~~father~~, BOTH);
	450	ap_main->push_node(Father(), BOTH);
375	451	ap_main->push_node(oldBrother, STRUCTURE);
376	452	ap_main->push_node(movedSon,STRUCTURE);
…	…
378	454	// from father to root buffer all sequences
379	455
380		for (AP_tree *pntr = father->father; pntr ; pntr = pntr->father) {
	456	for (AP_tree_nlen *pntr = Father()->Father(); pntr ; pntr = pntr->Father()) {
381	457	ap_main->push_node(pntr, SEQUENCE);
382	458	}
…	…
401	477	// from this to root buffer the nodes
402	478	ap_main->push_node(this , STRUCTURE);
403
404		AP_tree *old_brother = 0;
405		AP_tree *old_root;
	479
	480	AP_tree_nlen *old_brother = 0;
	481	AP_tree_nlen *old_root = 0;
406	482	{
407		AP_tree *pntr;
408		for (pntr = ~~father; pntr->father; pntr = pntr->father~~) {
	483	AP_tree_nlen *pntr;
	484	for (pntr = Father(); pntr->father; pntr = pntr->Father()) {
409	485	ap_main->push_node(pntr, BOTH);
410	486	old_brother = pntr;
…	…
414	490
415	491	if (old_brother) {
416		old_brother = old_brother->brother();
	492	old_brother = old_brother->Brother();
417	493	ap_main->push_node(old_brother , STRUCTURE);
418	494	}
…	…
443	519	ap_assert(new_brother->father);
444	520
445		AP_tree *pntr;
	521	AP_tree_nlen *pntr;
446	522
447	523	ap_main->push_node(this , STRUCTURE);
448		ap_main->push_node(brother(), STRUCTURE);
	524	ap_main->push_node(Brother(), STRUCTURE);
449	525
450	526	if (father->father) {
451		AP_tree *grandpa = father->father;
452
453		ap_main->push_node(~~father~~ , BOTH);
	527	AP_tree_nlen *grandpa = Father()->Father();
	528
	529	ap_main->push_node(Father(), BOTH);
454	530
455	531	if (grandpa->father) {
456	532	ap_main->push_node(grandpa, BOTH);
457		for (pntr = grandpa->~~father; pntr; pntr = pntr->father~~) {
	533	for (pntr = grandpa->Father(); pntr; pntr = pntr->Father()) {
458	534	ap_main->push_node( pntr, SEQUENCE);
459	535	}
…	…
461	537	else { // grandson of root
462	538	ap_main->push_node(grandpa, ROOT);
463		ap_main->push_node(~~father->b~~rother(), STRUCTURE);
	539	ap_main->push_node(Father()->Brother(), STRUCTURE);
464	540	}
465	541	}
466	542	else { // son of root
467		ap_main->push_node(father , ROOT);
468
469		if (!brother()->is_leaf) {
470		ap_main->push_node(brother()->leftson, STRUCTURE);
471		ap_main->push_node(brother()->rightson, STRUCTURE);
472		}
473		}
474
475		ap_main->push_node(new_brother , STRUCTURE);
	543	ap_main->push_node(Father(), ROOT);
	544
	545	if (!get_brother()->is_leaf) {
	546	ap_main->push_node(Brother()->Leftson(), STRUCTURE);
	547	ap_main->push_node(Brother()->Rightson(), STRUCTURE);
	548	}
	549	}
	550
	551	AP_tree_nlen *newBrother = AP_TREE_NLEN_CAST(new_brother);
	552
	553	ap_main->push_node(newBrother , STRUCTURE);
476	554	if (new_brother->father) {
477	555	if (new_brother->father->father) {
478		ap_main->push_node(new~~_brother->father~~ , BOTH);
	556	ap_main->push_node(newBrother->Father(), BOTH);
479	557	}
480	558	else { // move to son of root
481		ap_main->push_node(new~~_brother->father~~ , BOTH);
482		ap_main->push_node(new~~_brother->b~~rother(), STRUCTURE);
483		}
484
485		for ~~(pntr = new_brother->father->father; pntr; pntr = pntr->father~~) {
486		ap_main->push_node( pntr, SEQUENCE);
	559	ap_main->push_node(newBrother->Father(), BOTH);
	560	ap_main->push_node(newBrother->Brother(), STRUCTURE);
	561	}
	562
	563	for (pntr = newBrother->Father()->Father(); pntr; pntr = pntr->Father()) {
	564	ap_main->push_node(pntr, SEQUENCE);
487	565	}
488	566	}
489	567
490	568	AP_tree_nlen *thisFather = Father();
491		~~AP_tree_nlen newBrother = (AP_tree_nlen)new_brother;~~
492	569	AP_tree_nlen *grandFather = thisFather->Father();
493	570	AP_tree_nlen *oldBrother = Brother();
…	…
616	693	}
617	694
618		~~/*-----------------------~~
619		~~costs~~
620		~~-----------------------*/~~
621
622		~~AP_FLOAT AP_tree_nlen::costs(void) { /* cost of a tree (number of changes ..) */~~
623		~~if (! this->tree_root->sequence_template) return 0.0;~~
624		~~this->parsimony_rek();~~
625		~~return (AP_FLOAT)this->mutation_rate;~~
626		}
627
628	695	/*******************************************
629	696
…	…
638	705
639	706	void AP_tree_nlen::unhash_sequence() {
640		//removes the current sequence
641		//(not leaf)
642
643		if (sequence != 0) {
644		if (!is_leaf) {
645		sequence->is_set_flag = AP_FALSE;
646		}
647		}
648
649		return;
	707	// removes the sequence from inner node (not for leafs!)
	708	AP_sequence *sequence = get_seq();
	709	if (sequence && !is_leaf) sequence->forget_sequence();
650	710	}
651	711
…	…
655	715	// according if user_buffer is greater than datum
656	716
657		~~// cout << "clear\n";~~
658
659	717	AP_tree_buffer * buff;
660	718	AP_BOOL result;
…	…
698	756	if (this->stack_level == datum) {
699	757	AP_tree_buffer *last_buffer = stack.get_first();
700		if (sequence &&(mode & SEQUENCE)) sequence->is_set_flag = AP_FALSE;
	758	AP_sequence *sequence = get_seq();
	759
	760	if (sequence && (mode & SEQUENCE)) sequence->forget_sequence();
701	761	if (0 == (mode & ~last_buffer->mode)) { // already buffered
702	762	return AP_FALSE;
…	…
717	777
718	778	if ( (mode & STRUCTURE) && !(new_buff->mode & STRUCTURE) ) {
719		// cout << "push structure " << *this << '\n';
720		new_buff->father = father;
721		new_buff->leftson = leftson;
722		new_buff->rightson = rightson;
	779	new_buff->father = get_father();
	780	new_buff->leftson = get_leftson();
	781	new_buff->rightson = get_rightson();
723	782	new_buff->leftlen = leftlen;
724	783	new_buff->rightlen = rightlen;
	784	new_buff->root = get_tree_root();
725	785	new_buff->gb_node = gb_node;
726	786	new_buff->distance = distance;
…	…
736	796
737	797	if ( (mode & SEQUENCE) && !(new_buff->mode & SEQUENCE) ) {
738		if (sequence) {
739		new_buff->sequence = sequence;
740		new_buff->mutation_rate = mutation_rate;
741		mutation_rate = 0.0;
742		sequence = 0;
743		}
744		else {
745		new_buff->sequence = 0;
746		AW_ERROR("Sequence not found %s",this->name);
747		}
	798	AP_sequence *sequence = take_seq();
	799	new_buff->sequence = sequence;
	800	new_buff->mutation_rate = mutation_rate;
	801	mutation_rate = 0.0;
748	802	}
749	803
…	…
765	819
766	820	if (mode&STRUCTURE) {
767		~~// cout << "pop structure " << this << '\n';~~
768
769	821	father = buff->father;
770	822	leftson = buff->leftson;
…	…
772	824	leftlen = buff->leftlen;
773	825	rightlen = buff->rightlen;
	826	set_tree_root(buff->root);
774	827	gb_node = buff->gb_node;
775	828	distance = buff->distance;
…	…
789	842
790	843	if (mode&SEQUENCE) {
791		if (sequence) delete sequence;
792
793		sequence = buff->sequence;
	844	replace_seq(buff->sequence);
794	845	mutation_rate = buff->mutation_rate;
795	846	}
796	847
797	848	if (ROOT==mode) {
798		// cout << "root popped:" << this << "\n";
799		ap_main->set_tree_root(this);
	849	buff->root->change_root(buff->root->get_root_node(), this);
800	850	}
801	851
…	…
808	858	********************************************************/
809	859
810		void AP_tree_nlen::parsimony_rek(void)
811		{
812		if (sequence && sequence->is_set_flag) return;
	860	void AP_tree_nlen::parsimony_rek(char *mutPerSite) {
	861	AP_sequence *sequence = get_seq();
813	862
814	863	if (is_leaf) {
815		sequence->is_set_flag = AP_TRUE;
816		return;
817		}
818
819		if (!Leftson()->sequence \|\| !Leftson()->sequence->is_set_flag ) Leftson()->parsimony_rek();
820		if (!Rightson()->sequence\|\| !Rightson()->sequence->is_set_flag ) Rightson()->parsimony_rek();
821
822		if (!Leftson()->sequence->is_set_flag \|\| !Rightson()->sequence->is_set_flag) {
823		AW_ERROR("AP_tree_nlen::parsimony_rek: Cannot set sequence");
824		return;
825		}
826
827		if (sequence == 0) sequence = tree_root->sequence_template->dup();
828
829		AP_FLOAT mutations_for_combine = sequence->combine(Leftson()->sequence, Rightson()->sequence);
830		mutation_rate = Leftson()->mutation_rate + Rightson()->mutation_rate + mutations_for_combine;
831
832		#if defined(DEBUG) && 0
833		printf("mutation-rates: left=%f right=%f combine=%f overall=%f %s\n",
834		Leftson()->mutation_rate, Rightson()->mutation_rate, mutations_for_combine, mutation_rate,
835		fullname());
836		#endif // DEBUG
837
838		sequence->is_set_flag = AP_TRUE;
	864	ap_assert(sequence); // tree w/o aliview?
	865	sequence->ensure_sequence_loaded();
	866	}
	867	else {
	868	if (!sequence) {
	869	sequence = set_seq(get_tree_root()->get_seqTemplate()->dup());
	870	ap_assert(sequence);
	871	}
	872
	873	if (!sequence->got_sequence()) {
	874	AP_tree_nlen *lson = Leftson();
	875	AP_tree_nlen *rson = Rightson();
	876
	877	ap_assert(lson);
	878	ap_assert(rson);
	879
	880	lson->parsimony_rek(mutPerSite);
	881	rson->parsimony_rek(mutPerSite);
	882
	883	AP_sequence *lseq = lson->get_seq();
	884	AP_sequence *rseq = rson->get_seq();
	885
	886	ap_assert(lseq);
	887	ap_assert(rseq);
	888
	889	AP_FLOAT mutations_for_combine = sequence->combine(lseq, rseq, mutPerSite);
	890	mutation_rate = lson->mutation_rate + rson->mutation_rate + mutations_for_combine;
	891	}
	892	}
	893	}
	894
	895	AP_FLOAT AP_tree_nlen::costs(char *mutPerSite) {
	896	// returns costs of a tree ( = number of mutations)
	897
	898	ap_assert(get_tree_root()->get_seqTemplate()); // forgot to set_seqTemplate() ? (previously returned 0.0 in this case)
	899	parsimony_rek(mutPerSite);
	900	return mutation_rate;
839	901	}
840	902
…	…
910	972	// zwei swapmoeglichkeiten initialisieren
911	973	//
912		AP_tree *this_brother = this->brother();
	974	AP_tree *this_brother = this->get_brother();
913	975	if (rek_deep == 0) {
914	976	for (i = 0; i < 8; i+=2) {
…	…
930	992	} else {
931	993	//an der Wurzel nehme linken und rechten Sohns des Bruders
932		if (this->brother()->is_leaf == GB_FALSE) {
	994	if (this->get_brother()->is_leaf == GB_FALSE) {
933	995	pars_refpntr[4] = pars_refpntr[5] = static_cast<AP_tree_nlen *>(this_brother->leftson);
934	996	pars_refpntr[6] = pars_refpntr[7] = static_cast<AP_tree_nlen *>(this_brother->rightson);
…	…
951	1013	ap_main->push();
952	1014	this->set_root();
953		~~(*ap_main->tree_root~~)->costs();
	1015	rootNode()->costs();
954	1016
955	1017	int visited_subtrees = 0;
…	…
963	1025	if (!pars_refpntr[i]->kernighan == AP_NONE) continue;
964	1026	if (pars_refpntr[i]->gr.hidden) continue;
965		if (pars_refpntr[i]->~~father~~->gr.hidden) continue;
	1027	if (pars_refpntr[i]->get_father()->gr.hidden) continue;
966	1028
967	1029	//nur wenn kein Blatt ist
968	1030	ap_main->push();
969	1031	pars_refpntr[i]->swap_assymetric(pars_side_ref[i]);
970		pars[i] = ~~(*ap_main->tree_root~~)->costs();
	1032	pars[i] = rootNode()->costs();
971	1033	if (pars[i] < pars_best) {
972	1034	better_subtrees++;
…	…
1049	1111	pars_refpntr[pars_ref[i]]->swap_assymetric(pars_side_ref[pars_ref[i]]);
1050	1112	//vertausche seite
1051		~~(*ap_main->tree_root~~)->parsimony_rek();
	1113	rootNode()->parsimony_rek();
1052	1114	switch (rek_width_type) {
1053	1115	case AP_BETTER:{
…	…
1243	1305	}
1244	1306
1245		~~int AP_tree_nlen::test(void) const~~
1246		{
1247		~~int edges = 0;~~
1248
1249		~~for (int e=0; e<3; e++) if (edge[e]!=NULL) edges++;~~
1250
1251		~~if (!sequence) cout << "Node" << *this << "has no sequence\n";~~
1252
1253		~~if (father) {~~
1254		~~if (father->father == (AP_tree *)this) {~~
1255		~~cout << "Ooops! I am my own grandfather! How is this possible?\n" <<~~
1256		*this << '\n' <<
1257		*Father() << '\n';
1258		}
1259
1260		~~if (is_leaf) {~~
1261		~~if (edges!=1) cout << "Leaf-Node" << *this << "has" << edges << " edges\n";~~
1262		}
1263		~~else {~~
1264		~~if (edges!=3) cout << "Inner-Node" << *this << "has" << edges << " edges\n";~~
1265		}
1266
1267		~~int e;~~
1268
1269		~~for (e=0; e<3; e++) {~~
1270		~~if (edge[e]) {~~
1271		~~if (edge[e]->isConnectedTo(this)) {~~
1272		~~AP_tree_nlen *neighbour = edge[e]->otherNode(this);~~
1273
1274		~~if ( ! (neighbour==father \|\| neighbour==leftson \|\| neighbour==rightson)) {~~
1275		~~if (father->father==NULL) {~~
1276		~~if (!(father->leftson==neighbour \|\| father->rightson==neighbour)) {~~
1277		~~cout << "Neighbour is not brother (at root)\n";~~
1278		}
1279		}
1280		~~else {~~
1281		~~cout << "Edge " << edge[e] << " connects the nodes"~~
1282		~~<< this << "and" << (edge[e]->otherNode(this))~~
1283		~~<< "(they are not neighbours)\n";~~
1284		}
1285		}
1286		}
1287		~~else {~~
1288		~~cout << "Node" << *this~~
1289		~~<< "is connected to wrong edge"~~
1290		~~<< edge[e] << '\n';~~
1291		}
1292		}
1293		}
1294		}
1295		~~else {~~
1296		~~if (edges) {~~
1297		~~cout << "Root" << *this << "has edges!\n";~~
1298		}
1299		}
1300
1301		~~test_tree(); // AP_tree::~~
1302
1303		~~return 0;~~
1304		}
1305
1306	1307	const char *AP_tree_nlen::fullname() const
1307	1308	{
…	…
1332	1333
1333	1334
1334		char* AP_tree_nlen::getSequence()
1335		{
1336		char *s;
1337
	1335	char* AP_tree_nlen::getSequenceCopy() {
1338	1336	costs();
1339		AP_sequence_parsimony pseq = (AP_sequence_parsimony)sequence;
1340		ap_assert(pseq->is_set_flag);
1341		s = new char[pseq->sequence_len];
1342		memcpy(s,pseq->sequence,(unsigned int)pseq->sequence_len);
	1337
	1338	AP_sequence_parsimony pseq = DOWNCAST(AP_sequence_parsimony, get_seq());
	1339	ap_assert(pseq->got_sequence());
	1340
	1341	size_t len = pseq->get_sequence_length();
	1342	char *s = new char[len];
	1343	memcpy(s, pseq->get_sequence(), len);
1343	1344
1344	1345	return s;

trunk/PARSIMONY/GA_genetic.cxx

r6141	r6280
8	8	#include <iostream.h>
9	9	#include "AP_buffer.hxx"
10		#include "~~parsimony~~.hxx"
	10	#include "ap_main.hxx"
11	11	#include "ap_tree_nlen.hxx"
12	12	#include "GA_genetic.hxx"
…	…
16	16
17	17
18		GA_genetic::GA_genetic(~~void~~) {
	18	GA_genetic::GA_genetic() {
19	19	gb_tree_start = 0;
20	20	gb_tree_opt = 0;
…	…
27	27	}
28	28
29		GA_genetic::~GA_genetic(~~void~~) {
	29	GA_genetic::~GA_genetic() {
30	30	if (fout) {
31	31	if (fclose(fout) != 0) {

trunk/PARSIMONY/GA_main.cxx

r6141	r6280
8	8	#include <iostream.h>
9	9	#include "AP_buffer.hxx"
10		#include "~~parsimony~~.hxx"
	10	#include "ap_main.hxx"
11	11	#include "ap_tree_nlen.hxx"
12	12	#include "GA_genetic.hxx"

trunk/PARSIMONY/GA_window.cxx

r5390	r6280
15	15	// #include <malloc.h>
16	16	#include "AP_buffer.hxx"
17		#include "~~parsimony~~.hxx"
	17	#include "ap_main.hxx"
18	18	#include "ap_tree_nlen.hxx"
19	19	#include "GA_genetic.hxx"
…	…
27	27	extern GA_genetic *GAgenetic;
28	28
29		void start_genetic_cb(AW_window *aww,AW_CL cld1) {
30		AWUSE(cld1);
31		AW_root *aw_root = aww->get_root();
32		//aw_root->awar("kh/costs")->write_string((long)ap_main->combineCount);
	29	void start_genetic_cb(AW_window *,AW_CL ) {
33	30	start_genetic(ap_main->gb_main);
34	31	}

trunk/PARSIMONY/Makefile

r6277	r6280
34	34	AP_buffer.o: $(ARBHOME)/INCLUDE/ad_prot.h
35	35	AP_buffer.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
	36	AP_buffer.o: $(ARBHOME)/INCLUDE/AliView.hxx
	37	AP_buffer.o: $(ARBHOME)/INCLUDE/AP_sequence.hxx
	38	AP_buffer.o: $(ARBHOME)/INCLUDE/AP_Tree.hxx
36	39	AP_buffer.o: $(ARBHOME)/INCLUDE/arb_assert.h
37	40	AP_buffer.o: $(ARBHOME)/INCLUDE/arb_error.h
	41	AP_buffer.o: $(ARBHOME)/INCLUDE/ARB_Tree.hxx
38	42	AP_buffer.o: $(ARBHOME)/INCLUDE/arbdb.h
39	43	AP_buffer.o: $(ARBHOME)/INCLUDE/arbdb_base.h
…	…
43	47	AP_buffer.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx
44	48	AP_buffer.o: $(ARBHOME)/INCLUDE/aw_root.hxx
45		AP_buffer.o: $(ARBHOME)/INCLUDE/awt_pro_a_nucs.hxx
46		AP_buffer.o: $(ARBHOME)/INCLUDE/awt_tree.hxx
	49	AP_buffer.o: $(ARBHOME)/INCLUDE/downcast.h
47	50	AP_buffer.o: $(ARBHOME)/INCLUDE/smartptr.h
48	51
49	52	AP_main.o: AP_buffer.hxx
50	53	AP_main.o: AP_error.hxx
51		AP_main.o: parsimony.hxx
	54	AP_main.o: ap_main.hxx
	55	AP_main.o: ap_tree_nlen.hxx
52	56	AP_main.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
53	57	AP_main.o: $(ARBHOME)/INCLUDE/ad_prot.h
54	58	AP_main.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
	59	AP_main.o: $(ARBHOME)/INCLUDE/AliView.hxx
	60	AP_main.o: $(ARBHOME)/INCLUDE/AP_sequence.hxx
	61	AP_main.o: $(ARBHOME)/INCLUDE/AP_Tree.hxx
55	62	AP_main.o: $(ARBHOME)/INCLUDE/arb_assert.h
56	63	AP_main.o: $(ARBHOME)/INCLUDE/arb_error.h
	64	AP_main.o: $(ARBHOME)/INCLUDE/ARB_Tree.hxx
57	65	AP_main.o: $(ARBHOME)/INCLUDE/arbdb.h
58	66	AP_main.o: $(ARBHOME)/INCLUDE/arbdb_base.h
…	…
61	69	AP_main.o: $(ARBHOME)/INCLUDE/attributes.h
62	70	AP_main.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx
	71	AP_main.o: $(ARBHOME)/INCLUDE/aw_device.hxx
	72	AP_main.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
	73	AP_main.o: $(ARBHOME)/INCLUDE/aw_position.hxx
63	74	AP_main.o: $(ARBHOME)/INCLUDE/aw_root.hxx
64		AP_main.o: $(ARBHOME)/INCLUDE/awt_pro_a_nucs.hxx
65		AP_main.o: $(ARBHOME)/INCLUDE/awt_tree.hxx
	75	AP_main.o: $(ARBHOME)/INCLUDE/aw_window.hxx
	76	AP_main.o: $(ARBHOME)/INCLUDE/awt_canvas.hxx
	77	AP_main.o: $(ARBHOME)/INCLUDE/downcast.h
66	78	AP_main.o: $(ARBHOME)/INCLUDE/smartptr.h
	79	AP_main.o: $(ARBHOME)/INCLUDE/TreeDisplay.hxx
67	80
68	81	AP_tree_edge.o: AP_buffer.hxx
	82	AP_tree_edge.o: ap_main.hxx
69	83	AP_tree_edge.o: ap_tree_nlen.hxx
70		~~AP_tree_edge.o: parsimony.hxx~~
71	84	AP_tree_edge.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
72	85	AP_tree_edge.o: $(ARBHOME)/INCLUDE/ad_prot.h
73	86	AP_tree_edge.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
	87	AP_tree_edge.o: $(ARBHOME)/INCLUDE/AliView.hxx
	88	AP_tree_edge.o: $(ARBHOME)/INCLUDE/AP_filter.hxx
	89	AP_tree_edge.o: $(ARBHOME)/INCLUDE/AP_sequence.hxx
	90	AP_tree_edge.o: $(ARBHOME)/INCLUDE/AP_Tree.hxx
74	91	AP_tree_edge.o: $(ARBHOME)/INCLUDE/arb_assert.h
75	92	AP_tree_edge.o: $(ARBHOME)/INCLUDE/arb_error.h
	93	AP_tree_edge.o: $(ARBHOME)/INCLUDE/ARB_Tree.hxx
76	94	AP_tree_edge.o: $(ARBHOME)/INCLUDE/arbdb.h
77	95	AP_tree_edge.o: $(ARBHOME)/INCLUDE/arbdb_base.h
…	…
81	99	AP_tree_edge.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx
82	100	AP_tree_edge.o: $(ARBHOME)/INCLUDE/aw_root.hxx
83		AP_tree_edge.o: $(ARBHOME)/INCLUDE/awt_pro_a_nucs.hxx
84		AP_tree_edge.o: $(ARBHOME)/INCLUDE/awt_tree.hxx
	101	AP_tree_edge.o: $(ARBHOME)/INCLUDE/downcast.h
85	102	AP_tree_edge.o: $(ARBHOME)/INCLUDE/smartptr.h
86	103
87	104	AP_tree_nlen.o: AP_buffer.hxx
	105	AP_tree_nlen.o: ap_main.hxx
88	106	AP_tree_nlen.o: ap_tree_nlen.hxx
89	107	AP_tree_nlen.o: pars_debug.hxx
90		~~AP_tree_nlen.o: parsimony.hxx~~
91	108	AP_tree_nlen.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
92	109	AP_tree_nlen.o: $(ARBHOME)/INCLUDE/ad_prot.h
93	110	AP_tree_nlen.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
	111	AP_tree_nlen.o: $(ARBHOME)/INCLUDE/AliView.hxx
	112	AP_tree_nlen.o: $(ARBHOME)/INCLUDE/AP_seq_dna.hxx
	113	AP_tree_nlen.o: $(ARBHOME)/INCLUDE/AP_sequence.hxx
	114	AP_tree_nlen.o: $(ARBHOME)/INCLUDE/AP_Tree.hxx
94	115	AP_tree_nlen.o: $(ARBHOME)/INCLUDE/arb_assert.h
95	116	AP_tree_nlen.o: $(ARBHOME)/INCLUDE/arb_error.h
	117	AP_tree_nlen.o: $(ARBHOME)/INCLUDE/ARB_Tree.hxx
96	118	AP_tree_nlen.o: $(ARBHOME)/INCLUDE/arbdb.h
97	119	AP_tree_nlen.o: $(ARBHOME)/INCLUDE/arbdb_base.h
…	…
101	123	AP_tree_nlen.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx
102	124	AP_tree_nlen.o: $(ARBHOME)/INCLUDE/aw_root.hxx
103		AP_tree_nlen.o: $(ARBHOME)/INCLUDE/awt_pro_a_nucs.hxx
104		AP_tree_nlen.o: $(ARBHOME)/INCLUDE/awt_seq_dna.hxx
105		AP_tree_nlen.o: $(ARBHOME)/INCLUDE/awt_tree.hxx
	125	AP_tree_nlen.o: $(ARBHOME)/INCLUDE/downcast.h
106	126	AP_tree_nlen.o: $(ARBHOME)/INCLUDE/smartptr.h
107	127
…	…
123	143
124	144	PARS_dtree.o: AP_buffer.hxx
	145	PARS_dtree.o: ap_main.hxx
125	146	PARS_dtree.o: ap_tree_nlen.hxx
126	147	PARS_dtree.o: pars_debug.hxx
127	148	PARS_dtree.o: pars_dtree.hxx
128	149	PARS_dtree.o: pars_main.hxx
129		~~PARS_dtree.o: parsimony.hxx~~
130	150	PARS_dtree.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
131	151	PARS_dtree.o: $(ARBHOME)/INCLUDE/ad_prot.h
132	152	PARS_dtree.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
	153	PARS_dtree.o: $(ARBHOME)/INCLUDE/AliView.hxx
	154	PARS_dtree.o: $(ARBHOME)/INCLUDE/AP_filter.hxx
	155	PARS_dtree.o: $(ARBHOME)/INCLUDE/AP_seq_dna.hxx
	156	PARS_dtree.o: $(ARBHOME)/INCLUDE/AP_seq_protein.hxx
	157	PARS_dtree.o: $(ARBHOME)/INCLUDE/AP_sequence.hxx
	158	PARS_dtree.o: $(ARBHOME)/INCLUDE/AP_Tree.hxx
133	159	PARS_dtree.o: $(ARBHOME)/INCLUDE/arb_assert.h
134	160	PARS_dtree.o: $(ARBHOME)/INCLUDE/arb_error.h
	161	PARS_dtree.o: $(ARBHOME)/INCLUDE/ARB_Tree.hxx
135	162	PARS_dtree.o: $(ARBHOME)/INCLUDE/arbdb.h
136	163	PARS_dtree.o: $(ARBHOME)/INCLUDE/arbdb_base.h
…	…
145	172	PARS_dtree.o: $(ARBHOME)/INCLUDE/aw_root.hxx
146	173	PARS_dtree.o: $(ARBHOME)/INCLUDE/aw_window.hxx
147		~~PARS_dtree.o: $(ARBHOME)/INCLUDE/awt.hxx~~
148	174	PARS_dtree.o: $(ARBHOME)/INCLUDE/awt_canvas.hxx
149	175	PARS_dtree.o: $(ARBHOME)/INCLUDE/awt_csp.hxx
150		PARS_dtree.o: $(ARBHOME)/INCLUDE/awt_dtree.hxx
151		PARS_dtree.o: $(ARBHOME)/INCLUDE/awt_pro_a_nucs.hxx
	176	PARS_dtree.o: $(ARBHOME)/INCLUDE/awt_filter.hxx
152	177	PARS_dtree.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx
153		PARS_dtree.o: $(ARBHOME)/INCLUDE/awt_seq_dna.hxx
154		PARS_dtree.o: $(ARBHOME)/INCLUDE/awt_seq_protein.hxx
155		PARS_dtree.o: $(ARBHOME)/INCLUDE/awt_tree.hxx
	178	PARS_dtree.o: $(ARBHOME)/INCLUDE/downcast.h
	179	PARS_dtree.o: $(ARBHOME)/INCLUDE/gui_aliview.hxx
156	180	PARS_dtree.o: $(ARBHOME)/INCLUDE/smartptr.h
157
158		PARS_klprops.o: AP_buffer.hxx
159		PARS_klprops.o: ap_tree_nlen.hxx
160		PARS_klprops.o: pars_dtree.hxx
161		PARS_klprops.o: pars_main.hxx
162		PARS_klprops.o: parsimony.hxx
	181	PARS_dtree.o: $(ARBHOME)/INCLUDE/TreeDisplay.hxx
	182
	183	PARS_klprops.o: pars_klprops.hxx
163	184	PARS_klprops.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
164		~~PARS_klprops.o: $(ARBHOME)/INCLUDE/ad_prot.h~~
165		~~PARS_klprops.o: $(ARBHOME)/INCLUDE/ad_t_prot.h~~
166	185	PARS_klprops.o: $(ARBHOME)/INCLUDE/arb_assert.h
167	186	PARS_klprops.o: $(ARBHOME)/INCLUDE/arb_error.h
168		~~PARS_klprops.o: $(ARBHOME)/INCLUDE/arbdb.h~~
169	187	PARS_klprops.o: $(ARBHOME)/INCLUDE/arbdb_base.h
170		~~PARS_klprops.o: $(ARBHOME)/INCLUDE/arbdbt.h~~
171	188	PARS_klprops.o: $(ARBHOME)/INCLUDE/arbtools.h
172	189	PARS_klprops.o: $(ARBHOME)/INCLUDE/attributes.h
173		~~PARS_klprops.o: $(ARBHOME)/INCLUDE/aw_awars.hxx~~
174		~~PARS_klprops.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx~~
175	190	PARS_klprops.o: $(ARBHOME)/INCLUDE/aw_device.hxx
176	191	PARS_klprops.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
177	192	PARS_klprops.o: $(ARBHOME)/INCLUDE/aw_position.hxx
178		~~PARS_klprops.o: $(ARBHOME)/INCLUDE/aw_preset.hxx~~
179	193	PARS_klprops.o: $(ARBHOME)/INCLUDE/aw_root.hxx
180	194	PARS_klprops.o: $(ARBHOME)/INCLUDE/aw_window.hxx
181		~~PARS_klprops.o: $(ARBHOME)/INCLUDE/awt.hxx~~
182		~~PARS_klprops.o: $(ARBHOME)/INCLUDE/awt_canvas.hxx~~
183		~~PARS_klprops.o: $(ARBHOME)/INCLUDE/awt_dtree.hxx~~
184		~~PARS_klprops.o: $(ARBHOME)/INCLUDE/awt_nds.hxx~~
185		~~PARS_klprops.o: $(ARBHOME)/INCLUDE/awt_pro_a_nucs.hxx~~
186		~~PARS_klprops.o: $(ARBHOME)/INCLUDE/awt_tree.hxx~~
187		~~PARS_klprops.o: $(ARBHOME)/INCLUDE/awt_tree_cb.hxx~~
188	195	PARS_klprops.o: $(ARBHOME)/INCLUDE/smartptr.h
189	196
190	197	PARS_main.o: AP_buffer.hxx
	198	PARS_main.o: ap_main.hxx
191	199	PARS_main.o: ap_tree_nlen.hxx
192	200	PARS_main.o: pars_dtree.hxx
	201	PARS_main.o: pars_klprops.hxx
193	202	PARS_main.o: pars_main.hxx
194		~~PARS_main.o: parsimony.hxx~~
195	203	PARS_main.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
196	204	PARS_main.o: $(ARBHOME)/INCLUDE/ad_prot.h
197	205	PARS_main.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
	206	PARS_main.o: $(ARBHOME)/INCLUDE/AliView.hxx
	207	PARS_main.o: $(ARBHOME)/INCLUDE/AP_sequence.hxx
	208	PARS_main.o: $(ARBHOME)/INCLUDE/AP_Tree.hxx
198	209	PARS_main.o: $(ARBHOME)/INCLUDE/arb_assert.h
199	210	PARS_main.o: $(ARBHOME)/INCLUDE/arb_error.h
	211	PARS_main.o: $(ARBHOME)/INCLUDE/ARB_Tree.hxx
200	212	PARS_main.o: $(ARBHOME)/INCLUDE/arbdb.h
201	213	PARS_main.o: $(ARBHOME)/INCLUDE/arbdb_base.h
…	…
214	226	PARS_main.o: $(ARBHOME)/INCLUDE/awt_canvas.hxx
215	227	PARS_main.o: $(ARBHOME)/INCLUDE/awt_csp.hxx
216		PARS_main.o: $(ARBHOME)/INCLUDE/awt_~~dtree~~.hxx
	228	PARS_main.o: $(ARBHOME)/INCLUDE/awt_filter.hxx
217	229	PARS_main.o: $(ARBHOME)/INCLUDE/awt_nds.hxx
218		~~PARS_main.o: $(ARBHOME)/INCLUDE/awt_pro_a_nucs.hxx~~
219	230	PARS_main.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx
220		PARS_main.o: $(ARBHOME)/INCLUDE/~~awt_tree.hxx~~
221		PARS_main.o: $(ARBHOME)/INCLUDE/~~awt_tree_cb~~.hxx
	231	PARS_main.o: $(ARBHOME)/INCLUDE/downcast.h
	232	PARS_main.o: $(ARBHOME)/INCLUDE/gui_aliview.hxx
222	233	PARS_main.o: $(ARBHOME)/INCLUDE/smartptr.h
	234	PARS_main.o: $(ARBHOME)/INCLUDE/TreeCallbacks.hxx
	235	PARS_main.o: $(ARBHOME)/INCLUDE/TreeDisplay.hxx

trunk/PARSIMONY/PARS_dtree.cxx

r6141	r6280
1		#include <stdio.h>
2		#include <stdlib.h>
3		#include <string.h>
4
5		#include <arbdb.h>
6		#include <arbdbt.h>
7		#include <aw_root.hxx>
8		#include <aw_device.hxx>
9		#include <aw_window.hxx>
10		#include <aw_preset.hxx>
11		#include <awt_canvas.hxx>
12		#include <awt_tree.hxx>
13		#include <awt_seq_dna.hxx>
14		#include <awt_seq_protein.hxx>
15
16		#include <awt_csp.hxx>
17		#include <awt.hxx>
18		#include <awt_dtree.hxx>
19		#include <awt_sel_boxes.hxx>
	1	// =============================================================== //
	2	// //
	3	// File : PARS_dtree.cxx //
	4	// Purpose : //
	5	// //
	6	// Institute of Microbiology (Technical University Munich) //
	7	// http://www.arb-home.de/ //
	8	// //
	9	// =============================================================== //
	10
	11	#include "ap_main.hxx"
20	12	#include "pars_dtree.hxx"
21
22		~~#include "AP_buffer.hxx"~~
23		~~#include "parsimony.hxx"~~
24		~~#include "ap_tree_nlen.hxx"~~
25	13	#include "pars_main.hxx"
26	14	#include "pars_debug.hxx"
27
28		extern AWT_csp *awt_csp;
29
30		char AWT_graphic_parsimony_root_changed(void cd, AP_tree old, AP_tree newroot)
31		{
	15	#include "ap_tree_nlen.hxx"
	16
	17	#include <AP_seq_dna.hxx>
	18	#include <AP_seq_protein.hxx>
	19	#include <AP_filter.hxx>
	20
	21	#include <awt_csp.hxx>
	22	#include <awt_sel_boxes.hxx>
	23	#include <awt_filter.hxx>
	24
	25	#include <gui_aliview.hxx>
	26
	27	#include <aw_preset.hxx>
	28
	29	static void AWT_graphic_parsimony_root_changed(void cd, AP_tree old, AP_tree *newroot) {
32	30	AWT_graphic_tree agt = (AWT_graphic_tree)cd;
	31
33	32	if (old == agt->tree_root_display) agt->tree_root_display = newroot;
34		if (old == agt->tree_root) agt->tree_root = newroot;
35		if (old == GLOBAL_NT->tree->tree_root) GLOBAL_NT->tree->tree_root = newroot;
36		return 0;
37		}
38
	33	}
	34
	35	static AliView pars_generate_aliview(WeightedFilter pars_weighted_filter) {
	36	GBDATA *gb_main = pars_weighted_filter->get_gb_main();
	37	char *ali_name;
	38	{
	39	GB_transaction ta(gb_main);
	40	ali_name = GBT_read_string(gb_main,AWAR_ALIGNMENT);
	41	}
	42	AliView *aliview = pars_weighted_filter->create_aliview(ali_name);
	43	if (!aliview) aw_popup_exit(GB_await_error());
	44	free(ali_name);
	45	return aliview;
	46	}
39	47
40	48	/**************************
…	…
47	55
48	56	**************************/
49		void NT_tree_init(AWT_graphic_tree agt, adfiltercbstruct pars_global_filter) {
50
51		AP_tree *tree = agt->tree_root;
	57
	58	void PARS_tree_init(AWT_graphic_tree *agt) {
	59	ap_assert(agt->get_root_node());
	60	ap_assert(agt == ap_main->get_tree_root());
	61
52	62	GB_transaction dummy(GLOBAL_gb_main);
53
54		if (!tree) {
55		return;
56		}
57		char *use = GBT_read_string(GLOBAL_gb_main,AWAR_ALIGNMENT);
58
59		long ali_len = GBT_get_alignment_len(GLOBAL_gb_main,use);
	63
	64	const char *use = ap_main->get_aliname();
	65	long ali_len = GBT_get_alignment_len(GLOBAL_gb_main, use);
60	66	if (ali_len <=1) {
61	67	aw_popup_exit("No valid alignment selected! Try again");
62	68	}
63	69
64
65		GB_BOOL is_aa = GBT_is_alignment_protein(GLOBAL_gb_main,use);
66		//
67		// filter & weights setup
68		//
69		if (!tree->tree_root->sequence_template) {
70		AP_tree_root *tr = tree->tree_root;
71		AP_sequence *sproto;
72		if (is_aa) {
73		sproto = (AP_sequence *)new AP_sequence_protein(tr);
74		}else{
75		sproto = (AP_sequence *)new AP_sequence_parsimony(tr);
76		}
77
78		tr->sequence_template = sproto;
79		tr->filter = awt_get_filter(agt->aw_root, pars_global_filter);
80		tr->weights = new AP_weights();
81
82		awt_csp->go(0);
83		int i;
84		if (awt_csp->rates){
85		for (i=0;i<ali_len;i++){
86		if (awt_csp->rates[i]>0.0000001){
87		awt_csp->weights[i] *= (int)(2.0/ awt_csp->rates[i]);
88		}
89		}
90		tr->weights->init(awt_csp->weights , tr->filter);
91		}else{
92		tr->weights->init(tr->filter);
93		}
94		tree->load_sequences_rek(use,GB_FALSE,GB_TRUE); // load with sequences
95		}
96		tree->tree_root->root_changed_cd = (void*)agt;
97		tree->tree_root->root_changed = AWT_graphic_parsimony_root_changed;
98
99		ap_main->use = use;
	70	agt->tree_static->set_root_changed_callback(AWT_graphic_parsimony_root_changed, agt);
100	71	}
101	72
…	…
115	86
116	87	void PARS_kernighan_cb(AP_tree *tree) {
117
118	88	GB_push_transaction(GLOBAL_gb_main);
119	89
120		~~AP_sequence::global_combineCount = 0~~;
	90	long prevCombineCount = AP_sequence::combine_count();
121	91
122	92	AP_FLOAT pars_start, pars_prev;
123		pars_prev = pars_start = ~~GLOBAL_NT->tree->tree_root~~->costs();
	93	pars_prev = pars_start = AP_TREE_NLEN_CAST(GLOBAL_PARS->tree->get_root_node())->costs();
124	94
125	95	int rek_deep_max = *GBT_read_int(GLOBAL_gb_main,"genetic/kh/maxdepth");
…	…
195	165
196	166	if (tree_elem->gr.hidden \|\|
197		(tree_elem->father && tree_elem->~~father~~->gr.hidden)){
	167	(tree_elem->father && tree_elem->get_father()->gr.hidden)){
198	168	continue; // within a folded group
199	169	}
…	…
211	181	if (better_tree_found) {
212	182	ap_main->clear();
213		pars_start = ~~GLOBAL_NT->tree->tree_root~~->costs();
	183	pars_start = AP_TREE_NLEN_CAST(GLOBAL_PARS->tree->get_root_node())->costs();
214	184	char buffer[100];
215	185	sprintf(buffer,"New Parsimony: %f",pars_start);
…	…
223	193	delete list;
224	194	ap_global_abort_flag \|= abort_flag;
225		printf("Combines: %li\n", AP_sequence::global_combineCount);
226		return;
	195	printf("Combines: %li\n", AP_sequence::combine_count()-prevCombineCount);
227	196	}
228	197
229	198	void PARS_optimizer_cb(AP_tree *tree) {
230		AP_tree *oldrootleft = GLOBAL_NT->tree->tree_root->leftson;
231		AP_tree *oldrootright = GLOBAL_NT->tree->tree_root->rightson;
	199	AWT_graphic_tree *agt = GLOBAL_PARS->tree;
	200	AP_tree *oldrootleft = agt->get_root_node()->get_leftson();
	201	AP_tree *oldrootright = agt->get_root_node()->get_rightson();
232	202
233	203	for (ap_global_abort_flag = 0;!ap_global_abort_flag;){
234		AP_FLOAT old_pars = ~~GLOBAL_NT->tree->tree_root~~->costs();
235
236		((AP_tree_nlen *)tree)->nn_interchange_rek(AP_TRUE,~~ap_global_abort_flag,-1,AP_BL_NNI_ONLY, GB_TRUE); // only not hidden~~
	204	AP_FLOAT old_pars = AP_TREE_NLEN_CAST(agt->get_root_node())->costs();
	205
	206	((AP_tree_nlen *)tree)->nn_interchange_rek(AP_TRUE, ap_global_abort_flag, -1);
237	207	if (ap_global_abort_flag) break;
	208
	209	if (old_pars != AP_TREE_NLEN_CAST(agt->get_root_node())->costs()) { // NNI found better tree
	210	continue;
	211	}
	212
238	213	PARS_kernighan_cb(tree);
239		if (old_pars == ~~GLOBAL_NT->tree->tree_root~~->costs()) {
	214	if (old_pars == AP_TREE_NLEN_CAST(agt->get_root_node())->costs()) {
240	215	ap_global_abort_flag = 1;
241	216	}
…	…
243	218	if (oldrootleft->father == oldrootright) oldrootleft->set_root();
244	219	else oldrootright->set_root();
245		~~GLOBAL_NT->tree->tree_root~~->costs();
	220	AP_TREE_NLEN_CAST(agt->get_root_node())->costs();
246	221	aw_closestatus();
247	222	}
248	223
249		AWT_graphic_parsimony::AWT_graphic_parsimony(AW_root root, GBDATA gb_maini):AWT_graphic_tree(root,gb_maini)
250		{;}
251
252		AWT_graphic_tree PARS_generate_tree(AW_root root) {
253		AWT_graphic_parsimony *apdt = new AWT_graphic_parsimony(root,GLOBAL_gb_main);
254		AP_tree_nlen *aptnl = new AP_tree_nlen(0);
255
256		apdt->init((AP_tree *)aptnl);
257		ap_main->tree_root = &apdt->tree_root;
258
259		delete aptnl;
	224	AWT_graphic_parsimony::AWT_graphic_parsimony(AW_root root, GBDATA gb_maini)
	225	: AWT_graphic_tree(root,gb_maini)
	226	{}
	227
	228	AWT_graphic_tree PARS_generate_tree(AW_root root, WeightedFilter *pars_weighted_filter) {
	229	AliView *aliview = pars_generate_aliview(pars_weighted_filter);
	230	AP_sequence *seq_templ = 0;
	231
	232	GBDATA *gb_main = aliview->get_gb_main();
	233	{
	234	GB_transaction ta(gb_main);
	235	GB_BOOL is_aa = GBT_is_alignment_protein(gb_main, aliview->get_aliname());
	236
	237	if (is_aa) seq_templ = new AP_sequence_protein(aliview);
	238	else seq_templ = new AP_sequence_parsimony(aliview);
	239	}
	240
	241	AWT_graphic_parsimony *apdt = new AWT_graphic_parsimony(root, aliview->get_gb_main());
	242
	243	apdt->init(AP_tree_nlen(0), aliview, seq_templ, true, false);
	244
	245	ap_main->set_tree_root(apdt);
260	246	return apdt;
261	247	}
…	…
297	283	void AWT_graphic_parsimony::show(AW_device *device)
298	284	{
299		long parsval = 0;
300		if (GLOBAL_NT->tree->tree_root) parsval = (long)GLOBAL_NT->tree->tree_root->costs();
301		GLOBAL_NT->awr->awar(AWAR_PARSIMONY)->write_int( parsval);
302		long best = GLOBAL_NT->awr->awar(AWAR_BEST_PARSIMONY)->read_int();
	285	long parsval = 0;
	286	AP_tree_nlen *root_node = AP_TREE_NLEN_CAST(GLOBAL_PARS->tree->get_root_node());
	287	if (root_node) parsval = root_node->costs();
	288
	289	GLOBAL_PARS->awr->awar(AWAR_PARSIMONY)->write_int(parsval);
	290	long best = GLOBAL_PARS->awr->awar(AWAR_BEST_PARSIMONY)->read_int();
303	291	if (parsval < best \|\| 0==best) {
304		GLOBAL_NT->awr->awar(AWAR_BEST_PARSIMONY)->write_int( parsval);
	292	GLOBAL_PARS->awr->awar(AWAR_BEST_PARSIMONY)->write_int( parsval);
305	293	}
306	294	this->AWT_graphic_tree::show(device);
…	…
368	356	break;
369	357	}
370		// if ( dest->is_~~son~~(source)) {
	358	// if ( dest->is_inside(source)) {
371	359	// aw_message("This operation is only allowed with two independent subtrees");
372	360	// break;
…	…
388	376	error = source->move_group_info(dest);
389	377	break;
390		~~default:~~
391		~~error = "????? 45338";~~
392	378	}
393	379
…	…
398	384	if (error) aw_message(error);
399	385	this->exports.refresh = 1;
400		this->exports.save = 1;
401		this->exports.resize = 1;
402		~~this->tree_root->test_tree(~~);
	386	this->exports.save = 1;
	387	this->exports.resize = 1;
	388	ASSERT_VALID_TREE(get_root_node());
403	389	//this->tree_root->compute_tree(gb_main);
404	390	compute_tree = true;
…	…
415	401	GB_pop_transaction(gb_main);
416	402	switch(button){
417		case AWT_M_LEFT:
418		if (!cl->exists) break;
419		at = (AP_tree *)cl->client_data1;
420		ap_global_abort_flag = AP_FALSE;
421		((AP_tree_nlen *)at)->nn_interchange_rek(AP_TRUE,ap_global_abort_flag,-1);
422		this->exports.refresh = 1;
423		this->exports.save = 1;
424		this->tree_root->test_tree();
	403	case AWT_M_LEFT: {
	404	if (cl->exists) {
	405	at = (AP_tree *)cl->client_data1;
	406	ap_global_abort_flag = AP_FALSE;
	407	AP_tree_nlen atn = DOWNCAST(AP_tree_nlen, at);
	408	atn->nn_interchange_rek(AP_TRUE,ap_global_abort_flag,-1);
	409	exports.refresh = 1;
	410	exports.save = 1;
	411	ASSERT_VALID_TREE(get_root_node());
	412	recalc_branch_lengths = true;
	413	}
	414	break;
	415	}
	416	case AWT_M_RIGHT: {
	417	long prevCombineCount = AP_sequence::combine_count();
	418	ap_global_abort_flag = AP_FALSE;
	419	AP_tree_nlen atn = DOWNCAST(AP_tree_nlen, get_root_node());
	420
	421	atn->nn_interchange_rek(AP_TRUE,ap_global_abort_flag,-1);
	422	printf("Combines: %li\n", AP_sequence::combine_count()-prevCombineCount);
	423
	424	exports.refresh = 1;
	425	exports.save = 1;
	426	ASSERT_VALID_TREE(get_root_node());
425	427	recalc_branch_lengths = true;
426	428	break;
427		case AWT_M_RIGHT:
428		AP_sequence::global_combineCount = 0;
429		ap_global_abort_flag = AP_FALSE;
430		((AP_tree_nlen *)this->tree_root)->nn_interchange_rek(AP_TRUE,ap_global_abort_flag,-1);
431		printf("Combines: %li\n", AP_sequence::global_combineCount);
432		this->exports.refresh = 1;
433		this->exports.save = 1;
434		this->tree_root->test_tree();
435		recalc_branch_lengths = true;
436		break;
	429	}
437	430	}
438	431	GB_begin_transaction(gb_main);
…	…
449	442	this->exports.refresh = 1;
450	443	this->exports.save = 1;
451		~~this->tree_root->test_tree(~~);
	444	ASSERT_VALID_TREE(get_root_node());
452	445	recalc_branch_lengths = true;
453	446	break;
454	447	case AWT_M_RIGHT:
455		PARS_kernighan_cb(~~this->tree_root~~);
	448	PARS_kernighan_cb(get_root_node());
456	449	this->exports.refresh = 1;
457	450	this->exports.save = 1;
458		~~this->tree_root->test_tree(~~);
	451	ASSERT_VALID_TREE(get_root_node());
459	452	recalc_branch_lengths = true;
460	453	break;
…	…
473	466	this->exports.refresh = 1;
474	467	this->exports.save = 1;
475		~~this->tree_root->test_tree(~~);
	468	ASSERT_VALID_TREE(get_root_node());
476	469	recalc_branch_lengths = true;
477	470	break;
478	471	case AWT_M_RIGHT:
479		PARS_optimizer_cb(~~this->tree_root~~);
	472	PARS_optimizer_cb(get_root_node());
480	473	this->exports.refresh = 1;
481	474	this->exports.save = 1;
482		~~this->tree_root->test_tree(~~);
	475	ASSERT_VALID_TREE(get_root_node());
483	476	recalc_branch_lengths = true;
484	477	break;
…	…
509	502
510	503	if (compute_tree) {
511		~~this->tree_root~~->compute_tree(gb_main);
512		~~this->~~exports.refresh = 1;
513		}
514		}
	504	get_root_node()->compute_tree(gb_main);
	505	exports.refresh = 1;
	506	}
	507	}

trunk/PARSIMONY/PARS_klprops.cxx

r6089	r6280
1		#include <stdio.h>
2		#include <stdlib.h>
3		// #include <malloc.h>
4		#include <arbdb.h>
5		#include <arbdbt.h>
	1	// =============================================================== //
	2	// //
	3	// File : PARS_klprops.cxx //
	4	// Purpose : //
	5	// //
	6	// Institute of Microbiology (Technical University Munich) //
	7	// http://www.arb-home.de/ //
	8	// //
	9	// =============================================================== //
6	10
7		#include ~~<aw_root.hxx>~~
8		#include <aw_device.hxx>
	11	#include "pars_klprops.hxx"
	12
9	13	#include <aw_window.hxx>
10		~~#include <aw_preset.hxx>~~
11		~~#include <aw_awars.hxx>~~
12		~~#include <awt_canvas.hxx>~~
13		~~#include <awt.hxx>~~
14		~~#include <awt_nds.hxx>~~
15	14
16		~~#include <awt_tree.hxx>~~
17		~~#include <awt_dtree.hxx>~~
18		~~#include <awt_tree_cb.hxx>~~
19
20		~~#include "AP_buffer.hxx"~~
21		~~#include "parsimony.hxx"~~
22		~~#include "ap_tree_nlen.hxx"~~
23		~~#include "pars_main.hxx"~~
24		~~#include "pars_dtree.hxx"~~
25
26		~~extern AW_window preset_window( AW_root root );~~
27		~~extern AW_window genetic_window(AW_root root);~~
28	15
29	16	AW_window create_kernighan_window(AW_root aw_root) {

trunk/PARSIMONY/PARS_main.cxx

r6236	r6280
1		#include <stdio.h>
2		#include <stdlib.h>
3		#include <string.h>
4		// #include <malloc.h>
5		#include <iostream>
6		#include <limits.h>
7		#include <arbdb.h>
8		#include <arbdbt.h>
9
10		#include <aw_root.hxx>
11		#include <aw_device.hxx>
12		#include <aw_window.hxx>
13		#include <aw_preset.hxx>
14		#include <aw_awars.hxx>
15		#include <awt_canvas.hxx>
16		#include <awt.hxx>
17		#include <awt_nds.hxx>
18
19		#include <awt_tree.hxx>
20		#include <awt_dtree.hxx>
21		#include <awt_tree_cb.hxx>
22		#include <awt_sel_boxes.hxx>
23
24		#include <awt_csp.hxx>
25
26		#include "AP_buffer.hxx"
27		#include "parsimony.hxx"
28		#include "ap_tree_nlen.hxx"
	1	// =============================================================== //
	2	// //
	3	// File : PARS_main.cxx //
	4	// Purpose : //
	5	// //
	6	// Institute of Microbiology (Technical University Munich) //
	7	// http://www.arb-home.de/ //
	8	// //
	9	// =============================================================== //
	10
	11	#include "ap_main.hxx"
29	12	#include "pars_main.hxx"
30	13	#include "pars_dtree.hxx"
	14	#include "pars_klprops.hxx"
	15	#include "ap_tree_nlen.hxx"
	16
	17	#include <aw_awars.hxx>
	18	#include <aw_preset.hxx>
	19
	20	#include <awt.hxx>
	21	#include <awt_csp.hxx>
	22	#include <awt_nds.hxx>
	23	#include <awt_sel_boxes.hxx>
	24	#include <awt_filter.hxx>
	25	#include <gui_aliview.hxx>
	26
	27	#include <TreeCallbacks.hxx>
31	28
32	29	#include <list>
…	…
36	33	#endif // DEBUG
37	34
38
39	35	using namespace std;
40	36
41	37	AW_HEADER_MAIN
42	38
43		GBDATA *GLOBAL_gb_main; // global gb_main for arb_pars
44		NT_global *GLOBAL_NT;
	39	#define AWAR_CSP_NAME "tmp/pars/csp/name"
	40
	41	GBDATA *GLOBAL_gb_main; // global gb_main for arb_pars
	42
	43
	44
	45	#if defined(DEVEL_RALF)
	46	#warning make GLOBAL_PARS static!
	47	#endif // DEVEL_RALF
	48	PARS_global *GLOBAL_PARS;
45	49
46	50	// waaah more globals :(
47	51	AP_main *ap_main;
48		AWT_csp *awt_csp = 0;
49
50		AW_window create_kernighan_window(AW_root aw_root);
51
52		static void pars_export_tree(void){
53		// GB_ERROR error = GLOBAL_NT->tree->tree_root->AP_tree::saveTree();
54		GB_ERROR error = GLOBAL_NT->tree->save(0, 0, 0, 0);
	52
	53	static void pars_saveNrefresh_changed_tree(AWT_canvas *ntw) {
	54	ap_assert((AWT_TREE(ntw) == GLOBAL_PARS->tree));
	55
	56	GB_ERROR error = GLOBAL_PARS->tree->save(ntw->gb_main,0,0,0);
	57	if (error) aw_message(error);
	58
	59	ntw->zoom_reset();
	60	ntw->refresh();
	61	}
	62
	63	static void pars_export_tree(){
	64	GB_ERROR error = GLOBAL_PARS->tree->save(0, 0, 0, 0);
55	65	if (error) aw_message(error);
56	66	}
…	…
78	88	{
79	89	ap_main->user_push();
80		aww->get_root()->awar(AWAR_STACKPOINTER)->write_int(ap_main->~~user_push_counter~~);
	90	aww->get_root()->awar(AWAR_STACKPOINTER)->write_int(ap_main->get_user_push_counter());
81	91	}
82	92
83	93	void AP_user_pop_cb(AW_window aww,AWT_canvas ntw)
84	94	{
85		if (ap_main->~~user_push_counter~~<=0) {
	95	if (ap_main->get_user_push_counter()<=0) {
86	96	aw_message("No tree on stack.");
87	97	return;
88	98	}
89	99	ap_main->user_pop();
90		(*ap_main->tree_root)->compute_tree(GLOBAL_gb_main);
91		ntw->zoom_reset();
92		ntw->refresh();
93		(*ap_main->tree_root)->test_tree();
94		aww->get_root()->awar(AWAR_STACKPOINTER)->write_int(ap_main->user_push_counter);
95		pars_export_tree();
96
97		if (ap_main->user_push_counter <= 0) { // last tree was popped => push again
	100	rootNode()->compute_tree(GLOBAL_gb_main);
	101	ASSERT_VALID_TREE(rootNode());
	102	aww->get_root()->awar(AWAR_STACKPOINTER)->write_int(ap_main->get_user_push_counter());
	103
	104	pars_saveNrefresh_changed_tree(ntw);
	105
	106	if (ap_main->get_user_push_counter() <= 0) { // last tree was popped => push again
98	107	AP_user_push_cb(aww, ntw);
99	108	}
…	…
123	132	if (isits->abort_flag) return val;
124	133
125		AP_tree tree = (ap_main->tree_root);
126		GBDATA gb_node = (GBDATA )val;
127
128		GB_begin_transaction(GLOBAL_gb_main);
129
130		GBDATA *gb_data = GBT_read_sequence(gb_node,ap_main->use);
131		if (!gb_data)
132		{
133		sprintf(AW_ERROR_BUFFER,"Warning Species '%s' has no sequence '%s'",
134		key,ap_main->use);
135		aw_message();
136		GB_commit_transaction(GLOBAL_gb_main);
137		return val;
138		}
139
	134	GBDATA gb_node = (GBDATA )val;
	135
	136	#if defined(DEVEL_RALF)
	137	#warning following code could be a method ..
	138	// ARB_tree ARB_tree_root::create_linked_leaf(GBDATA gb_species, const char *name)
	139	#endif // DEVEL_RALF
	140
	141	AP_tree *tree = rootNode();
140	142	AP_tree *leaf = tree->dup();
141	143	leaf->gb_node = gb_node;
142		leaf->name = strdup(key);
	144	leaf->name = strdup(key);
143	145	leaf->is_leaf = GB_TRUE;
144	146
145		leaf->sequence = leaf->tree_root->sequence_template->dup();
146		leaf->sequence->set(GB_read_char_pntr(gb_data));
147		GB_commit_transaction (GLOBAL_gb_main);
148
149		if (leaf->sequence->real_len() < MIN_SEQUENCE_LENGTH)
150		{
	147	leaf->set_seq(leaf->get_tree_root()->get_seqTemplate()->dup());
	148	GB_ERROR error = leaf->get_seq()->bind_to_species(gb_node);
	149
	150	if (error) {
	151	aw_message(error);
	152	return val;
	153	}
	154
	155	if (leaf->get_seq()->weighted_base_count() < MIN_SEQUENCE_LENGTH) {
151	156	sprintf(AW_ERROR_BUFFER,
152		"Species %s has too short sequence (%i, minimum is %i)",
	157	"Species %s has too short sequence (%f, minimum is %i)",
153	158	key,
154		~~(int)leaf->sequence->real_len~~(),
	159	leaf->get_seq()->weighted_base_count(),
155	160	MIN_SEQUENCE_LENGTH);
156	161	aw_message();
…	…
206	211
207	212	tree->buildBranchList(blist,bsum,AP_TRUE,-1); // get all branches
208		AP_sequence::global_combineCount = 0;
209
210		AP_tree *bestposl = tree->leftson;
211		AP_tree *bestposr = tree->rightson;
	213
	214	#if defined(DEBUG)
	215	long prevCombineCount = AP_sequence::combine_count();
	216	#endif // DEBUG
	217
	218	AP_tree *bestposl = tree->get_leftson();
	219	AP_tree *bestposr = tree->get_rightson();
212	220	leaf->insert(bestposl);
213	221	AP_FLOAT best_parsimony,akt_parsimony;
214		best_parsimony = akt_parsimony = ~~(*ap_main->tree_root~~)->costs();
	222	best_parsimony = akt_parsimony = rootNode()->costs();
215	223
216	224	for (counter = 0; !isits->abort_flag && blist[counter]; counter += 2)
…	…
238	246
239	247	leaf->moveTo(bl,0.5);
240		akt_parsimony = ~~(*ap_main->tree_root~~)->costs();
	248	akt_parsimony = rootNode()->costs();
241	249
242	250	if (akt_parsimony<best_parsimony)
…	…
258	266	{
259	267	AP_tree_nlen fath = ((AP_tree_nlen)bestposl)->Father()->Father();
	268
260	269	char *seq_with_leaf;
261	270	char *seq_without_leaf;
262		long ~~len_with_leaf~~;
263		long len_without_leaf;
264		~~long i;~~
265
266		~~seq_with_leaf = fath->getSequence();~~
267		len_with_leaf = fath->sequence->sequence_len;
268
	271	long i;
	272
	273	// Note: removed sequence length code here,
	274	// cause "sequence_len" is always filter-length (i.e. constant until filter changes)
	275	// ralf 10/2009
	276
	277	seq_with_leaf = fath->getSequenceCopy();
269	278
270	279	ap_main->push();
	280
271	281	leaf->remove();
272
273		seq_without_leaf = fath->getSequence();
274		len_without_leaf = fath->sequence->sequence_len;
275
	282	seq_without_leaf = fath->getSequenceCopy();
276	283
277	284	ap_main->pop();
278	285
279
280		if (len_with_leaf==len_without_leaf) {
281		for (i=0; i<len_with_leaf; i++) {
282		if (seq_with_leaf[i]!=seq_without_leaf[i]) {
283		baseDiff++;
284		}
	286	for (i=0; seq_with_leaf[i]; i++) {
	287	if (seq_with_leaf[i]!=seq_without_leaf[i]) {
	288	baseDiff++;
285	289	}
286		}
287		else {
288		cout << "Laenge der Sequenz hat sich geaendert!!!";
	290
289	291	}
290	292
…	…
295	297	rootEdge()->countSpecies();
296	298
297		// printf("Combines: %i\n",global_combineCount);
	299	#if defined(DEBUG)
	300	printf("Combines: %li\n", AP_sequence::combine_count()-prevCombineCount);
	301	#endif // DEBUG
298	302
299	303	if (!isits->quick_add_flag ) {
…	…
319	323	AP_tree leaf1 = (AP_tree)leaf1_ptr;
320	324
321		AP_FLOAT len0 = leaf0->~~sequence->real_len~~();
322		AP_FLOAT len1 = leaf1->~~sequence->real_len~~();
	325	AP_FLOAT len0 = leaf0->get_seq()->weighted_base_count();
	326	AP_FLOAT len1 = leaf1->get_seq()->weighted_base_count();
323	327
324	328	return len0<len1 ? 1 : (len0>len1 ? -1 : 0); // longest sequence first
325	329	}
326	330
327		static long transform_gbd_to_leaf(const char key,long val, void ) {
	331	static long transform_gbd_to_leaf(const char key, long val, void ) {
328	332	if (!val) return val;
329	333
330		AP_tree tree = (ap_main->tree_root);
331		GBDATA gb_node = (GBDATA )val;
332		GBDATA *gb_data = GBT_read_sequence(gb_node,ap_main->use);
333
334		if (!gb_data) {
335		sprintf(AW_ERROR_BUFFER,"Warning Species '%s' has no sequence '%s'",
336		key,ap_main->use);
337		aw_message();
338		return 0;
339		}
340		AP_tree *leaf = tree->dup();
	334	#if defined(DEVEL_RALF)
	335	#warning use create_linked_leaf() when impl
	336	#endif // DEVEL_RALF
	337
	338	GBDATA gb_node = (GBDATA )val;
	339	AP_tree_root *troot = ap_main->get_tree_root()->tree_static;
	340
	341	AP_tree leaf = DOWNCAST(const AP_tree, troot->get_nodeTemplate())->dup();
341	342	leaf->gb_node = gb_node;
342		leaf->name = strdup(key);
	343	leaf->name = strdup(key);
343	344	leaf->is_leaf = GB_TRUE;
344		leaf->sequence = leaf->tree_root->sequence_template->dup();
345		leaf->sequence->set(GB_read_char_pntr(gb_data));
	345
	346	leaf->set_seq(troot->get_seqTemplate()->dup());
	347	GB_ERROR error = leaf->get_seq()->bind_to_species(gb_node);
	348	if (error) {
	349	aw_message(error);
	350	delete leaf; leaf = 0;
	351	}
346	352	return (long)leaf;
347	353	}
…	…
354	360	if (isits->abort_flag) return leaf;
355	361
356		AP_tree tree = (ap_main->tree_root);
357
358
359		if (leaf->sequence->real_len() < MIN_SEQUENCE_LENGTH) {
360		sprintf(AW_ERROR_BUFFER,"Species %s has too short sequence (%i, minimum is %i)",
361		key, (int)leaf->sequence->real_len(), MIN_SEQUENCE_LENGTH);
	362	AP_tree *tree = rootNode();
	363
	364	if (leaf->get_seq()->weighted_base_count() < MIN_SEQUENCE_LENGTH) {
	365	sprintf(AW_ERROR_BUFFER,
	366	"Species %s has too short sequence (%f, minimum is %i)",
	367	key,
	368	leaf->get_seq()->weighted_base_count(),
	369	MIN_SEQUENCE_LENGTH);
	370
362	371	aw_message();
363	372	delete leaf;
…	…
371	380	aw_openstatus(AW_ERROR_BUFFER);
372	381	}
373		aw_status("Searching best position");
374
375		AP_tree **blist;
376		AP_tree_nlen bl,blf;
377		long bsum = 0;
378		long counter = 0;
379
380		tree->buildBranchList(blist,bsum,AP_TRUE,-1); // get all branches
381		AP_sequence::global_combineCount = 0;
382
383		AP_tree *bestposl = tree->leftson;
384		AP_tree *bestposr = tree->rightson;
385		leaf->insert(bestposl);
386		AP_FLOAT best_parsimony,akt_parsimony;
387		best_parsimony = akt_parsimony = (*ap_main->tree_root)->costs();
388
389		for (counter = 0;!isits->abort_flag && blist[counter];counter += 2) {
390		if (isits->singlestatus && (counter & 0xf) == 0) {
391		isits->abort_flag = (AP_BOOL)aw_status(counter/(bsum*2.0));
392		}
393		bl = (AP_tree_nlen *)blist[counter];
394		blf = (AP_tree_nlen *)blist[counter+1];
395		if (blf->father == bl ) {
396		bl = (AP_tree_nlen *)blist[counter+1];
397		blf = (AP_tree_nlen *)blist[counter];
398		}
399
400		if (bl->father) { //->father
401		bl->set_root();
402		}
403
404		leaf->moveTo(bl,0.5);
405		akt_parsimony = (*ap_main->tree_root)->costs();
406		if (akt_parsimony < best_parsimony) {
407		best_parsimony = akt_parsimony;
408		bestposl = bl;
409		bestposr = blf;
410		}
411
412		}
413		delete blist;blist = 0;
414		if (bestposl->father != bestposr){
415		bestposl = bestposr;
416		}
417		leaf->moveTo(bestposl,0.5);
418
419		if (!isits->quick_add_flag) {
420		int deep = 5;
421		if ( (isits->currentspecies & 0xf ) == 0) deep = -1;
422		aw_status("optimization");
423		((AP_tree_nlen *)bestposl->father)->
424		nn_interchange_rek(AP_FALSE, isits->abort_flag, deep, AP_BL_NNI_ONLY, GB_TRUE);
425		}
426		AP_tree *brother = leaf->brother();
427		if ( brother->is_leaf && // brother is a short sequence
428		brother->sequence->real_len() *2 < leaf->sequence->real_len() &&
429		leaf->father->father){ // There are more than two species
430		brother->remove();
431		leaf->remove();
432		isits->currentspecies--;
433		char *label = GBS_global_string_copy("2:%s",leaf->name);
434		insert_species_in_tree(label, leaf, cd_isits); // reinsert species
435		delete label;
436		isits->currentspecies--;
437		label = GBS_global_string_copy("shortseq:%s",brother->name);
438		insert_species_in_tree(label, brother, cd_isits); // reinsert short sequence
439		delete label;
440		}
441
442		if (!isits->singlestatus) {
443		isits->abort_flag \|= aw_status(isits->currentspecies/(double)isits->maxspecies);
	382
	383	if (!tree) { // no tree yet
	384	static AP_tree *last_inserted = NULL;
	385
	386	if (!last_inserted) { // store 1st leaf
	387	last_inserted = leaf;
	388	}
	389	else { // 2nd leaf -> create initial tree
	390	AP_tree_root *troot = ap_main->get_tree_root()->tree_static;
	391	leaf->insert(last_inserted);
	392	last_inserted = NULL;
	393
	394	AP_tree *initial_tree = leaf->get_father();
	395	troot->change_root(NULL, initial_tree);
	396
	397	ASSERT_VALID_TREE(troot->get_root_node());
	398	}
	399	}
	400	else {
	401	aw_status("Searching best position");
	402
	403	ASSERT_VALID_TREE(tree);
	404
	405	AP_tree **blist;
	406	AP_tree_nlen bl,blf;
	407	long bsum = 0;
	408	long counter = 0;
	409
	410	tree->buildBranchList(blist,bsum,AP_TRUE,-1); // get all branches
	411
	412	AP_tree *bestposl = tree->get_leftson();
	413	AP_tree *bestposr = tree->get_rightson();
	414	leaf->insert(bestposl);
	415
	416	ASSERT_VALID_TREE(rootNode());
	417
	418	AP_FLOAT best_parsimony,akt_parsimony;
	419	best_parsimony = akt_parsimony = rootNode()->costs();
	420
	421	for (counter = 0;!isits->abort_flag && blist[counter];counter += 2) {
	422	if (isits->singlestatus && (counter & 0xf) == 0) {
	423	isits->abort_flag = (AP_BOOL)aw_status(counter/(bsum*2.0));
	424	}
	425	bl = (AP_tree_nlen *)blist[counter];
	426	blf = (AP_tree_nlen *)blist[counter+1];
	427	if (blf->father == bl ) {
	428	bl = (AP_tree_nlen *)blist[counter+1];
	429	blf = (AP_tree_nlen *)blist[counter];
	430	}
	431
	432	if (bl->father) { //->father
	433	bl->set_root();
	434	}
	435
	436	leaf->moveTo(bl,0.5);
	437	akt_parsimony = rootNode()->costs();
	438	if (akt_parsimony < best_parsimony) {
	439	best_parsimony = akt_parsimony;
	440	bestposl = bl;
	441	bestposr = blf;
	442	}
	443
	444	}
	445	delete blist;blist = 0;
	446	if (bestposl->father != bestposr){
	447	bestposl = bestposr;
	448	}
	449	leaf->moveTo(bestposl,0.5);
	450
	451	if (!isits->quick_add_flag) {
	452	int deep = 5;
	453	if ( (isits->currentspecies & 0xf ) == 0) deep = -1;
	454	aw_status("optimization");
	455	((AP_tree_nlen *)bestposl->father)->
	456	nn_interchange_rek(AP_FALSE, isits->abort_flag, deep, AP_BL_NNI_ONLY, GB_TRUE);
	457	}
	458	AP_tree *brother = leaf->get_brother();
	459	if (brother->is_leaf && // brother is a short sequence
	460	2 * brother->get_seq()->weighted_base_count() < leaf->get_seq()->weighted_base_count() &&
	461	leaf->father->father) // There are more than two species
	462	{
	463	brother->remove();
	464	leaf->remove();
	465	isits->currentspecies--;
	466	char *label = GBS_global_string_copy("2:%s",leaf->name);
	467	insert_species_in_tree(label, leaf, cd_isits); // reinsert species
	468	delete label;
	469	isits->currentspecies--;
	470	label = GBS_global_string_copy("shortseq:%s",brother->name);
	471	insert_species_in_tree(label, brother, cd_isits); // reinsert short sequence
	472	delete label;
	473	}
	474
	475	if (!isits->singlestatus) {
	476	isits->abort_flag \|= aw_status(isits->currentspecies/(double)isits->maxspecies);
	477	}
444	478	}
445	479
…	…
459	493	}
460	494
461		static void nt_add(AW_window , AWT_canvas ntw, int what, AP_BOOL quick, int test)
	495	enum AddWhat {
	496	NT_ADD_MARKED,
	497	NT_ADD_SELECTED,
	498	};
	499
	500	static void nt_add(AW_window , AWT_canvas ntw, AddWhat what, AP_BOOL quick, int test)
462	501	{
463		GB_begin_transaction(GLOBAL_gb_main);
	502	GB_ERROR error = 0;
	503
	504	AP_tree *oldrootleft = NULL;
	505	AP_tree *oldrootright = NULL;
	506	{
	507	AP_tree *root = rootNode();
	508	if (root) {
	509	oldrootleft = root->get_leftson();
	510	oldrootright = root->get_rightson();
	511	}
	512	}
	513
	514	aw_openstatus("Search selected species");
	515
464	516	GB_HASH *hash = 0;
465		GB_ERROR error = 0;
466		AP_tree oldrootleft = (ap_main->tree_root)->leftson;
467		AP_tree oldrootright = (ap_main->tree_root)->rightson;
468		aw_openstatus("Search selected species");
469
470		if (what)
471		{
472		char *name = GBT_readOrCreate_string(GLOBAL_gb_main, AWAR_SPECIES_NAME, "");
473		if (name && strlen(name)) {
474		GBDATA *gb_species = GBT_find_species(GLOBAL_gb_main,name);
475		if (gb_species) {
476		hash = GBS_create_hash(10, GB_MIND_CASE);
477		GBS_write_hash(hash,name,(long)gb_species);
	517	{
	518	GB_transaction ta(GLOBAL_gb_main);
	519	switch (what) {
	520	case NT_ADD_SELECTED: {
	521	char *name = GBT_readOrCreate_string(GLOBAL_gb_main, AWAR_SPECIES_NAME, "");
	522	if (name && strlen(name)) {
	523	GBDATA *gb_species = GBT_find_species(GLOBAL_gb_main, name);
	524	if (gb_species) {
	525	hash = GBS_create_hash(10, GB_MIND_CASE);
	526	GBS_write_hash(hash, name, (long)gb_species);
	527	}
	528	else error = GBS_global_string("Selected Species (%s) not found", name);
	529	}
	530	else error = "Please select a species";
	531	free(name);
	532	break;
478	533	}
479		else {
480		error = "Error: Selected Species not found";
	534	case NT_ADD_MARKED: {
	535	hash = GBT_create_marked_species_hash(GLOBAL_gb_main);
	536	break;
481	537	}
482	538	}
483		else {
484		error= "Please select an species"
485		" to select an species: 1. arb_edit: enable global cursor and select sequence"
486		" 2. arb_ntree: species/search and select species";
487		}
488		free(name);
489		}
490		else {
491		hash = GBT_create_marked_species_hash(GLOBAL_gb_main);
492		}
493		GB_commit_transaction(GLOBAL_gb_main);
494
	539	}
	540
	541	ap_assert(hash);
495	542	if (!error) {
496		NT_remove_species_in_tree_from_hash(*ap_main->tree_root,hash);
	543	NT_remove_species_in_tree_from_hash(rootNode(), hash);
497	544
498	545	InsertData isits(quick);
499
500	546	GBS_hash_do_loop(hash, count_hash_elements, &isits);
501
502	547	aw_openstatus(GBS_global_string("Adding %li species", isits.maxspecies));
503	548
…	…
520	565	rootEdge()->nni_rek(AP_FALSE,isits.abort_flag,-1, GB_FALSE ,AP_BL_BL_ONLY);
521	566
522		~~rootNode()->test_tree(~~);
	567	ASSERT_VALID_TREE(rootNode());
523	568	rootNode()->compute_tree(GLOBAL_gb_main);
524	569
525		if (oldrootleft->father == oldrootright) oldrootleft->set_root();
526		else oldrootright->set_root();
	570	if (oldrootleft) {
	571	if (oldrootleft->father == oldrootright) oldrootleft->set_root();
	572	else oldrootright->set_root();
	573	}
	574	else {
	575	ARB_edge innermost = rootNode()->get_tree_root()->find_innermost_edge();
	576	AP_TREE_CAST(innermost.son())->set_root();
	577	}
527	578
528	579	aw_closestatus();
…	…
533	584
534	585	AWT_TREE(ntw)->resort_tree(0);
535		ntw->zoom_reset();
536		if (!error) pars_export_tree();
	586	pars_saveNrefresh_changed_tree(ntw);
537	587	}
538	588
…	…
606	656	long curr_penalty;
607	657
608		leaf_full->~~sequence->partial_match(get_self()->sequence~~, &curr_overlap, &curr_penalty);
	658	leaf_full->get_seq()->partial_match(get_self()->get_seq(), &curr_overlap, &curr_penalty);
609	659
610	660	bool better = false;
…	…
661	711	}
662	712	else {
663		error = nt_best_partial_match_rek(partial, tree->~~leftson~~);
664		if (!error) error = nt_best_partial_match_rek(partial, tree->~~rightson~~);
	713	error = nt_best_partial_match_rek(partial, tree->get_leftson());
	714	if (!error) error = nt_best_partial_match_rek(partial, tree->get_rightson());
665	715	}
666	716	}
…	…
680	730	}
681	731	else {
682		count_partial_and_full(at->~~leftson~~, partial, full, zombies, default_value, define_if_undef);
683		count_partial_and_full(at->~~rightson~~, partial, full, zombies, default_value, define_if_undef);
	732	count_partial_and_full(at->get_leftson(), partial, full, zombies, default_value, define_if_undef);
	733	count_partial_and_full(at->get_rightson(), partial, full, zombies, default_value, define_if_undef);
684	734	}
685	735	}
…	…
698	748	}
699	749
700		AP_tree *left = find_least_deep_leaf(at->~~leftson~~, depth+1, min_depth);
701		AP_tree *right = find_least_deep_leaf(at->~~rightson~~, depth+1, min_depth);
	750	AP_tree *left = find_least_deep_leaf(at->get_leftson(), depth+1, min_depth);
	751	AP_tree *right = find_least_deep_leaf(at->get_rightson(), depth+1, min_depth);
702	752
703	753	return right ? right : left;
…	…
731	781	++marked_found;
732	782
733		if (GBT_read_sequence(gb_marked,ap_main->~~use~~)) { // species has sequence in alignment
	783	if (GBT_read_sequence(gb_marked,ap_main->get_aliname())) { // species has sequence in alignment
734	784	const char *name = GBT_read_name(gb_marked);
735	785
…	…
760	810
761	811	if (!error) {
762		NT_remove_species_in_tree_from_hash(*ap_main->tree_root,partial_hash); // skip all species which are in tree
	812	NT_remove_species_in_tree_from_hash(rootNode(), partial_hash); // skip all species which are in tree
763	813	GBS_hash_do_loop(partial_hash, push_partial, &partial); // build partial list from hash
764	814
765	815	int partials_already_in_tree = partial_marked_sequences - partial.size();
766	816
767		if (no_data>0) aw_message(GBS_global_string("%i marked species have no data in '%s'", no_data, ap_main->~~use~~));
	817	if (no_data>0) aw_message(GBS_global_string("%i marked species have no data in '%s'", no_data, ap_main->get_aliname()));
768	818	if (full_marked_sequences>0) aw_message(GBS_global_string("%i marked species are declared full sequences", full_marked_sequences));
769	819	if (partials_already_in_tree>0) aw_message(GBS_global_string("%i marked species are already in tree", partials_already_in_tree));
…	…
775	825	if (!error) {
776	826	// find best matching full sequence for each partial sequence
777		error = nt_best_partial_match_rek(partial, *ap_main->tree_root);
	827	error = nt_best_partial_match_rek(partial, rootNode());
778	828
779	829	list<PartialSequence>::iterator i = partial.begin();
…	…
797	847	AP_tree *part_leaf = i->release();
798	848	AP_tree full_seq = const_cast<AP_tree>(i->get_best_match());
799		AP_tree *brother = full_seq->brother();
	849	AP_tree *brother = full_seq->get_brother();
800	850	int is_partial = 0;
801	851	AP_tree *target = 0;
…	…
847	897
848	898	// we need to create the sequence of the father node!
849		AP_tree *father = part_leaf->father;
	899	AP_tree_nlen *father = AP_TREE_NLEN_CAST(part_leaf->get_father());
850	900	father->costs();
851	901
…	…
893	943	}
894	944
895		// AWT_TREE(ntw)->resort_tree(0);
896		ntw->zoom_reset();
897		if (!error) pars_export_tree();
	945	// AWT_TREE(ntw)->resort_tree(0);
	946	pars_saveNrefresh_changed_tree(ntw);
898	947	}
899	948
…	…
904	953	// normal versions :
905	954
906		static void NT_add(AW_window * aww, AWT_canvas *ntw, int what) {
907		// what == 0 marked ==1 selected
908		nt_add(aww,ntw,what,AP_FALSE,0);
909		}
910
911		static void NT_quick_add(AW_window * aww, AWT_canvas *ntw, int what) {
912		// what == 0 marked ==1 selected
913		nt_add(aww,ntw,what,AP_TRUE,0);
914		}
	955	static void NT_add (AW_window * aww, AWT_canvas *ntw, AddWhat what){ nt_add(aww, ntw, what, AP_FALSE, 0); }
	956	static void NT_quick_add(AW_window * aww, AWT_canvas *ntw, AddWhat what){ nt_add(aww, ntw, what, AP_TRUE, 0); }
915	957
916	958	// test versions :
917	959
918	960	#if defined(TEST_FUNCTIONS)
919		static void NT_add_test(AW_window * aww, AWT_canvas *ntw, int what) {
920		// what == 0 marked ==1 selected
921		nt_add(aww,ntw,what,AP_FALSE,1);
922		}
923
924		static void NT_quick_add_test(AW_window * aww, AWT_canvas *ntw, int what) {
925		// what == 0 marked ==1 selected
926		nt_add(aww,ntw,what,AP_TRUE,1);
927		}
	961	static void NT_add_test (AW_window * aww, AWT_canvas *ntw, AddWhat what){ nt_add(aww, ntw, what, AP_FALSE, 1); }
	962	static void NT_quick_add_test(AW_window * aww, AWT_canvas *ntw, AddWhat what){ nt_add(aww, ntw, what, AP_TRUE, 1); }
928	963	#endif // TEST_FUNCTIONS
929	964
…	…
932	967	// -----------------------------------------
933	968
934		static void NT_radd_internal(AW_window * aww, AWT_canvas *ntw, int what, AP_BOOL quick, int test) {
935		// what == 0 marked ==1 selected
936
	969	static void NT_radd_internal(AW_window * aww, AWT_canvas *ntw, AddWhat what, AP_BOOL quick, int test) {
937	970	AW_awar *awar_best_pars = aww->get_root()->awar(AWAR_BEST_PARSIMONY);
938	971	int oldparsval = awar_best_pars->read_int();
939	972
940		NT_remove_leafs(0,ntw,AWT_REMOVE_BUT_DONT_FREE \| AWT_REMOVE_MARKED);
	973	AWT_graphic_tree *agt = AWT_TREE(ntw);
	974	if (agt->get_root_node()) {
	975	agt->tree_static->remove_leafs(AWT_REMOVE_BUT_DONT_FREE\|AWT_REMOVE_MARKED);
	976	}
941	977
942	978	// restore old parsimony value (otherwise the state where species were removed would count) :
…	…
948	984	// normal versions :
949	985
950		static void NT_radd(AW_window * aww, AWT_canvas *ntw, int what) {
951		// what == 0 marked ==1 selected
952		NT_radd_internal(aww, ntw, what, AP_FALSE, 0);
953		}
954
955		static void NT_rquick_add(AW_window * aww, AWT_canvas *ntw, int what) {
956		// what == 0 marked ==1 selected
957		NT_radd_internal(aww, ntw, what, AP_TRUE, 0);
958		}
959
960		// static void NT_radd_test_internal(AW_window * aww, AWT_canvas *ntw, int what, AP_BOOL quick) {
961		// // what == 0 marked ==1 selected
962		// NT_remove_leafs(0,ntw,AWT_REMOVE_BUT_DONT_FREE \| AWT_REMOVE_MARKED);
963		// nt_add(aww,ntw,what,quick,1);
964		// }
	986	static void NT_radd (AW_window * aww, AWT_canvas *ntw, AddWhat what){ NT_radd_internal(aww, ntw, what, AP_FALSE, 0); }
	987	static void NT_rquick_add(AW_window * aww, AWT_canvas *ntw, AddWhat what){ NT_radd_internal(aww, ntw, what, AP_TRUE, 0); }
965	988
966	989	// test versions :
967	990
968	991	#if defined(TEST_FUNCTIONS)
969		static void NT_radd_test(AW_window * aww, AWT_canvas *ntw, int what) {
970		// what == 0 marked ==1 selected
971		NT_radd_internal(aww, ntw, what, AP_FALSE, 1);
972		}
973
974		static void NT_rquick_add_test(AW_window * aww, AWT_canvas *ntw, int what) {
975		// what == 0 marked ==1 selected
976		NT_radd_internal(aww, ntw, what, AP_TRUE, 1);
977		}
	992	static void NT_radd_test (AW_window * aww, AWT_canvas *ntw, AddWhat what){ NT_radd_internal(aww, ntw, what, AP_FALSE, 1); }
	993	static void NT_rquick_add_test(AW_window * aww, AWT_canvas *ntw, AddWhat what){ NT_radd_internal(aww, ntw, what, AP_TRUE, 1); }
978	994	#endif // TEST_FUNCTIONS
979	995
…	…
998	1014	AWT_TREE(ntw)->resort_tree(0);
999	1015
1000		ntw->zoom_reset();
1001		ntw->refresh();
1002		pars_export_tree();
1003		}
1004
1005		static void NT_bootstrap(AW_window aw,AWT_canvas ntw,AW_CL limit_only)
1006		{
1007		AW_POPUP_HELP(aw, (AW_CL)"pa_bootstrap.hlp");
	1016	pars_saveNrefresh_changed_tree(ntw);
	1017	}
	1018
	1019	static void NT_bootstrap(AW_window , AWT_canvas ntw, AW_CL limit_only) {
1008	1020	aw_openstatus("Calculating Bootstrap Limit");
1009	1021	int abort_flag = AP_FALSE;
1010	1022	rootEdge()->nni_rek(AP_FALSE, abort_flag, -1, GB_FALSE,
1011		~~limit_only ? AP_BL_BOOTSTRAP_LIMIT : AP_BL_BOOTSTRAP_ESTIMATE~~);
	1023	AP_BL_MODE((limit_only ? AP_BL_BOOTSTRAP_LIMIT : AP_BL_BOOTSTRAP_ESTIMATE)\|AP_BL_BL_ONLY));
1012	1024	aw_closestatus();
1013	1025
1014	1026	AWT_TREE(ntw)->resort_tree(0);
1015	1027
1016		AWT_TREE(ntw)->tree_root_display = AWT_TREE(ntw)->tree_root;
1017		ntw->zoom_reset();
1018		ntw->refresh();
1019		pars_export_tree();
	1028	AWT_TREE(ntw)->tree_root_display = AWT_TREE(ntw)->get_root_node();
	1029	pars_saveNrefresh_changed_tree(ntw);
1020	1030	}
1021	1031
…	…
1024	1034	aw_openstatus("Optimize Tree");
1025	1035
1026		PARS_optimizer_cb(~~(*ap_main->tree_root~~));
1027		~~rootNode()->test_tree(~~);
	1036	PARS_optimizer_cb(rootNode());
	1037	ASSERT_VALID_TREE(rootNode());
1028	1038
1029	1039	aw_openstatus("Calculating Branch Lengths");
…	…
1033	1043	rootNode()->compute_tree(GLOBAL_gb_main);
1034	1044	aw_closestatus();
1035		ntw->zoom_reset();
1036		ntw->refresh();
1037		pars_export_tree();
	1045	pars_saveNrefresh_changed_tree(ntw);
1038	1046	}
1039	1047
…	…
1060	1068	rootNode()->compute_tree(GLOBAL_gb_main);
1061	1069	aw_closestatus();
1062		ntw->zoom_reset();
1063		ntw->refresh();
1064		pars_export_tree();
	1070	pars_saveNrefresh_changed_tree(ntw);
1065	1071	}
1066	1072
…	…
1120	1126	ntw->refresh();
1121	1127	}
1122
1123		~~static void testTree(AP_tree_nlen tree,int nodeCount, int *edgeCount)~~
1124		{
1125		~~tree->test();~~
1126		~~(*nodeCount)++;~~
1127
1128		~~if (tree->father) // we do only test edges if were not at root~~
1129		{
1130		~~AP_tree_edge *e =0;~~
1131		~~int skipTest=0;~~
1132
1133		~~if (tree->father->father)~~
1134		{
1135		~~e = tree->edgeTo(tree->Father());~~
1136		}
1137		~~else // son of root!~~
1138		{
1139		~~if (tree->father->leftson==(AP_tree*)tree) // to not test twice~~
1140		{
1141		~~e = tree->edgeTo(tree->Brother());~~
1142		}
1143		~~else~~
1144		{
1145		~~skipTest=1;~~
1146		}
1147		}
1148
1149		~~if (!skipTest)~~
1150		{
1151		~~if (e)~~
1152		{
1153		~~int dist2bord;~~
1154
1155		~~e->test();~~
1156		~~(*edgeCount)++;~~
1157
1158		~~dist2bord = e->distanceToBorder();~~
1159		~~if (dist2bord != e->Distance())~~
1160		{
1161		~~cout << *e << "distance error: should=" << dist2bord << " is=" << e->Distance() << endl;~~
1162		}
1163		}
1164		~~else~~
1165		{
1166		~~cout << *tree << "has no edge to father\n";~~
1167		}
1168		}
1169		}
1170
1171		~~if (!tree->is_leaf)~~
1172		{
1173		~~testTree((AP_tree_nlen*)tree->leftson,nodeCount,edgeCount);~~
1174		~~testTree((AP_tree_nlen*)tree->rightson,nodeCount,edgeCount);~~
1175		}
1176		}
1177
1178		~~static void TEST_testWholeTree(AW_window , AWT_canvas )~~
1179		~~// Tests the whole tree structure (edges and nodes) for consistency~~
1180		{
1181		~~AP_tree_nlen root = (AP_tree_nlen)*ap_main->tree_root;~~
1182		~~int nodes = 0;~~
1183		~~int edges = 0;~~
1184
1185		~~if (root->father)~~
1186		{
1187		~~int m = INT_MAX;~~
1188
1189		~~cout << "OOPS! Root has father:\n" << *root << '\n';~~
1190		~~while (m-- && root->father) root = root->Father();~~
1191
1192		~~if (root->father)~~
1193		{
1194		~~cout << "Root node lost between:\n"~~
1195		~~<< *root << '\n'~~
1196		~~<< *(root->Father()) << '\n';~~
1197		}
1198		~~else~~
1199		{
1200		~~cout << "Found a root:\n" << *root << "\n Let's test from here:\n";~~
1201		}
1202		}
1203
1204		~~root->test_tree();~~
1205		~~testTree(root, &nodes, &edges);~~
1206
1207		~~cout << "Nodes tested: " << nodes << '\n'~~
1208		~~<< "Edges tested: " << edges << '\n';~~
1209		}
1210		~~#endif // TEST_FUNCTIONS~~
1211
1212		~~static int dumpNodes(AP_tree_nlen *node)~~
1213		{
1214		~~int cnt = 1;~~
1215
1216		~~cout << *node~~
1217		~~<< "(llen=" << node->leftlen~~
1218		~~<< ",rlen=" << node->rightlen << ")\n";~~
1219
1220		~~if (!node->is_leaf)~~
1221		{
1222		~~cnt += dumpNodes(node->Leftson());~~
1223		~~cnt += dumpNodes(node->Rightson());~~
1224		}
1225
1226		~~return cnt;~~
1227		}
1228
1229		~~#if defined(TEST_FUNCTIONS)~~
1230		~~static void TEST_dumpNodes(AW_window , AWT_canvas )~~
1231		{
1232		~~AP_tree_nlen root = (AP_tree_nlen)*ap_main->tree_root;~~
1233		~~int cnt;~~
1234
1235		~~cout << "----- Dumping all nodes in tree\n";~~
1236		~~cnt = dumpNodes(root);~~
1237		~~cout << "----- " << cnt << "nodes dumped!\n";~~
1238		}
1239	1128	#endif // TEST_FUNCTIONS
1240	1129
…	…
1252	1141	static void TEST_setBranchlen(AW_window , AWT_canvas ntw)
1253	1142	{
1254		AP_tree_nlen root = ~~(AP_tree_nlen)*ap_main->tree_root~~;
	1143	AP_tree_nlen *root = rootNode();
1255	1144
1256	1145	setBranchlens(root,1.0);
1257	1146	refreshTree(ntw);
1258	1147	}
1259		#endif // TEST_FUNCTIONS
1260
1261		/*
1262		static AP_tree_nlen getRandomSonOf(AP_tree_nlen daddy, int innerNodeAllowed,int rootAllowed)
1263		{
1264		if (daddy->is_leaf) return daddy;
1265		int r = rand() % (innerNodeAllowed && rootAllowed ? 3 : 2);
1266		if (r==2) return daddy;
1267		return getRandomSonOf(r ? daddy->Leftson() : daddy->Rightson(),
1268		innerNodeAllowed, 1);
1269		}
1270		static void TEST_performRandomMoves(AW_window aww,AWT_canvas ntw)
1271		{
1272		AWUSE(aww);
1273
1274		int cnt=10000;
1275
1276		while(cnt)
1277		{
1278		AP_tree_nlen root = (AP_tree_nlen)*ap_main->tree_root;
1279		AP_tree_nlen *source = getRandomSonOf(root,1,0);
1280		AP_tree_nlen *dest = getRandomSonOf(root,1,0);
1281
1282		if (source!=dest && !dest->is_son(source))
1283		{
1284		root->setBranchlen(1.0,1.0);
1285		source->setBranchlen(1.0,1.0);
1286		dest->setBranchlen(1.0,1.0);
1287
1288		char *error = source->move(dest,0.5);
1289
1290		if (error)
1291		{
1292		cout << error << '\n';
1293		break;
1294		}
1295
1296		cnt--;
1297		// cout << "Moves left: " << cnt << '\n';
1298		}
1299		}
1300
1301		cout << "Testing tree\n";
1302		TEST_testWholeTree(aww,ntw);
1303
1304		// cout << "setting branchlens\n";
1305		// TEST_setBranchlen(aww,ntw);
1306
1307		// cout << "dumping nodes\n";
1308		// TEST_dumpNodes(aww,ntw);
1309
1310		cout << "done\n";
1311		// refreshTree(ntw);
1312		}
1313		*/
1314
1315		#if defined(TEST_FUNCTIONS)
	1148
	1149	static void TEST_treeStats(AW_window , AWT_canvas ) {
	1150	ARB_tree_info tinfo;
	1151	AP_tree_nlen *root = rootNode();
	1152
	1153	{
	1154	GB_transaction ta(root->get_tree_root()->get_gb_main());
	1155	root->calcTreeInfo(tinfo);
	1156	}
	1157
	1158	puts("Tree stats:");
	1159
	1160	printf("nodes =%6zu\n", tinfo.nodes());
	1161	printf(" inner =%6zu\n", tinfo.innerNodes);
	1162	printf(" groups =%6zu\n", tinfo.groups);
	1163	printf(" leafs =%6zu\n", tinfo.leafs);
	1164	printf(" unlinked =%6zu (zombies?)\n", tinfo.unlinked);
	1165	printf(" linked =%6zu\n", tinfo.linked());
	1166	printf(" marked =%6zu\n", tinfo.marked);
	1167	}
	1168
1316	1169	static void TEST_mixTree(AW_window , AWT_canvas ntw)
1317	1170	{
…	…
1322	1175	static void TEST_sortTreeByName(AW_window , AWT_canvas ntw)
1323	1176	{
1324		AP_tree_nlen root = ~~(AP_tree_nlen)*ap_main->tree_root~~;
	1177	AP_tree_nlen *root = rootNode();
1325	1178
1326	1179	root->sortByName();
…	…
1330	1183	static void TEST_buildAndDumpChain(AW_window , AWT_canvas )
1331	1184	{
1332		AP_tree_nlen root = ~~(AP_tree_nlen)*ap_main->tree_root~~;
	1185	AP_tree_nlen *root = rootNode();
1333	1186
1334	1187	root->Leftson()->edgeTo(root->Rightson())->testChain(2);
…	…
1349	1202	awm->create_menu("Test[debug]", "T", AWM_ALL );
1350	1203
1351		~~awm->insert_menu_topic(0, "Test edges", "T", "", AWM_ALL, (AW_CB)TEST_testWholeTree, (AW_CL)ntw, 0);~~
1352	1204	awm->insert_menu_topic(0, "Mix tree", "M", "", AWM_ALL, (AW_CB)TEST_mixTree, (AW_CL)ntw, 0);
1353		awm->insert_menu_topic(0, "~~Dump nodes", "D", "", AWM_ALL, (AW_CB)TEST_dumpNode~~s, (AW_CL)ntw, 0);
	1205	awm->insert_menu_topic(0, "Tree statistics", "s", "", AWM_ALL, (AW_CB)TEST_treeStats, (AW_CL)ntw, 0);
1354	1206	awm->insert_menu_topic(0, "Set branchlens", "b", "", AWM_ALL, (AW_CB)TEST_setBranchlen, (AW_CL)ntw, 0);
1355		awm->insert_menu_topic(0, "Sort tree by name", "S", "", AWM_ALL, (AW_CB)TEST_sortTreeByName, (AW_CL)ntw, 0);
	1207	awm->insert_menu_topic(0, "Sort tree by name", "o", "", AWM_ALL, (AW_CB)TEST_sortTreeByName, (AW_CL)ntw, 0);
1356	1208	awm->insert_menu_topic(0, "Build & dump chain", "c", "", AWM_ALL, (AW_CB)TEST_buildAndDumpChain, (AW_CL)ntw, 0);
1357	1209	awm->insert_separator();
1358		awm->insert_menu_topic(0, "Add marked species", "A", "pa_quick.hlp", AWM_ALL, (AW_CB)NT_quick_add_test, (AW_CL)ntw, 0);
1359		awm->insert_menu_topic(0, "Add marked species + NNI", "N", "pa_add.hlp", AWM_ALL, (AW_CB)NT_add_test, (AW_CL)ntw, 0);
1360		awm->insert_menu_topic(0, "Remove & add marked species", "o", "pa_add.hlp", AWM_ALL, (AW_CB)NT_rquick_add_test, (AW_CL)ntw, 0);
1361		awm->insert_menu_topic(0, "Remove & add marked + NNI", "v", "pa_add.hlp", AWM_ALL, (AW_CB)NT_radd_test, (AW_CL)ntw, 0);
	1210	awm->insert_menu_topic(0, "Add marked species", "A", "pa_quick.hlp", AWM_ALL, (AW_CB)NT_quick_add_test, (AW_CL)ntw, NT_ADD_MARKED);
	1211	awm->insert_menu_topic(0, "Add marked species + NNI", "N", "pa_add.hlp", AWM_ALL, (AW_CB)NT_add_test, (AW_CL)ntw, NT_ADD_MARKED);
	1212	awm->insert_menu_topic(0, "Remove & add marked species", "o", "pa_add.hlp", AWM_ALL, (AW_CB)NT_rquick_add_test, (AW_CL)ntw, NT_ADD_MARKED);
	1213	awm->insert_menu_topic(0, "Remove & add marked + NNI", "v", "pa_add.hlp", AWM_ALL, (AW_CB)NT_radd_test, (AW_CL)ntw, NT_ADD_MARKED);
1362	1214	awm->insert_separator();
1363		awm->insert_menu_topic(0, "Add selected species", "l", "pa_quick_sel.hlp", AWM_ALL, (AW_CB)NT_quick_add_test, (AW_CL)ntw, 1);
1364		awm->insert_menu_topic(0, "Add selected species + NNI", "I", "pa_add_sel.hlp", AWM_ALL, (AW_CB)NT_add_test, (AW_CL)ntw, 1);
	1215	awm->insert_menu_topic(0, "Add selected species", "l", "pa_quick_sel.hlp", AWM_ALL, (AW_CB)NT_quick_add_test, (AW_CL)ntw, NT_ADD_SELECTED);
	1216	awm->insert_menu_topic(0, "Add selected species + NNI", "I", "pa_add_sel.hlp", AWM_ALL, (AW_CB)NT_add_test, (AW_CL)ntw, NT_ADD_SELECTED);
1365	1217	}
1366	1218	#endif // TEST_FUNCTIONS
…	…
1408	1260	******************************************************/
1409	1261
1410		static void pars_start_cb(AW_window *aw_parent, AW_CL cd_adfiltercbstruct) {
1411		AW_root *awr = aw_parent->get_root();
	1262
	1263
	1264	static void pars_start_cb(AW_window *aw_parent, AW_CL cd_weightedFilter, AW_CL cl_cmds) {
	1265	WeightedFilter wfilt = (WeightedFilter)cd_weightedFilter;
	1266	PARS_commands cmds = (PARS_commands)cl_cmds;
	1267	AW_root *awr = aw_parent->get_root();
1412	1268	GB_begin_transaction(GLOBAL_gb_main);
1413	1269	{
…	…
1428	1284
1429	1285	AW_gc_manager aw_gc_manager = 0;
1430		GLOBAL_NT->tree = PARS_generate_tree(awr);
	1286
	1287	GLOBAL_PARS->tree = PARS_generate_tree(awr, wfilt);
1431	1288
1432	1289	AWT_canvas *ntw;
1433	1290	{
1434		AP_tree_sort old_sort_type = GLOBAL_NT->tree->tree_sort;
1435		GLOBAL_NT->tree->set_tree_type(AP_LIST_SIMPLE); // avoid NDS warnings during startup
1436		ntw = new AWT_canvas(GLOBAL_gb_main, (AW_window *)awm, GLOBAL_NT->tree, aw_gc_manager, AWAR_TREE);
1437		GLOBAL_NT->tree->set_tree_type(old_sort_type);
1438		}
1439
1440		{
	1291	AP_tree_sort old_sort_type = GLOBAL_PARS->tree->tree_sort;
	1292	GLOBAL_PARS->tree->set_tree_type(AP_LIST_SIMPLE); // avoid NDS warnings during startup
	1293	ntw = new AWT_canvas(GLOBAL_gb_main, (AW_window *)awm, GLOBAL_PARS->tree, aw_gc_manager, AWAR_TREE);
	1294	GLOBAL_PARS->tree->set_tree_type(old_sort_type);
	1295	}
	1296
	1297	{
	1298	GB_ERROR error = 0;
	1299
1441	1300	aw_openstatus("load tree");
1442		NT_reload_tree_event(awr,ntw,GB_TRUE); // load first tree and set delete callbacks
1443		if (!GLOBAL_NT->tree->tree_root) {
1444		aw_closestatus();
1445		aw_popup_exit("I cannot load the selected tree");
1446		}
1447
1448		AP_tree_edge::initialize((AP_tree_nlen)ap_main->tree_root); // builds edges
1449		GLOBAL_NT->tree->tree_root->remove_leafs(ntw->gb_main, AWT_REMOVE_DELETED);
1450
1451		adfiltercbstruct acbs = (adfiltercbstruct)cd_adfiltercbstruct;
1452		NT_tree_init(GLOBAL_NT->tree, acbs);
1453
1454		GLOBAL_NT->tree->tree_root->remove_leafs(ntw->gb_main, AWT_REMOVE_DELETED \| AWT_REMOVE_NO_SEQUENCE);
1455
1456		GB_commit_transaction(ntw->gb_main);
1457		aw_status("Calculating inner nodes");
1458		GLOBAL_NT->tree->tree_root->costs();
1459
	1301	NT_reload_tree_event(awr, ntw); // load first tree
	1302	if (!GLOBAL_PARS->tree->get_root_node()) {
	1303	error = "I cannot load the selected tree";
	1304	}
	1305	else {
	1306	AP_tree_edge::initialize(rootNode()); // builds edges
	1307	GLOBAL_PARS->tree->tree_static->remove_leafs(AWT_REMOVE_DELETED);
	1308
	1309	PARS_tree_init(GLOBAL_PARS->tree);
	1310	GLOBAL_PARS->tree->tree_static->remove_leafs(AWT_REMOVE_DELETED \| AWT_REMOVE_NO_SEQUENCE);
	1311
	1312	if (!GLOBAL_PARS->tree->get_root_node()) {
	1313	const char *aliname = GLOBAL_PARS->tree->tree_static->get_aliview()->get_aliname();
	1314	error = GBS_global_string("Less than 2 species contain data in '%s'\n"
	1315	"Tree vanished", aliname);
	1316	}
	1317
	1318	error = GB_end_transaction(ntw->gb_main, error);
	1319	if (!error) {
	1320	aw_status("Calculating inner nodes");
	1321	AP_TREE_NLEN_CAST(GLOBAL_PARS->tree->get_root_node())->costs();
	1322	}
	1323	}
1460	1324	aw_closestatus();
	1325	if (error) aw_popup_exit(error);
1461	1326	}
1462	1327
1463	1328	awr->awar( AWAR_COLOR_GROUPS_USE)->add_callback( (AW_RCB)NT_recompute_cb, (AW_CL)ntw,0);
1464	1329
1465		if (~~ap_main->commands.add_marked) NT_quick_add(awm,ntw,0~~);
1466		if (~~ap_main->commands.add_selected) NT_quick_add(awm,ntw,1~~);
1467		if (~~ap_main->commands.~~calc_branch_lengths) NT_branch_lengths(awm,ntw);
1468		if (~~ap_main->commands.~~calc_bootstrap) NT_bootstrap(awm,ntw,0);
1469		if (~~ap_main->commands.~~quit) pars_exit(awm);
	1330	if (cmds->add_marked) NT_quick_add(awm,ntw,NT_ADD_MARKED);
	1331	if (cmds->add_selected) NT_quick_add(awm,ntw,NT_ADD_SELECTED);
	1332	if (cmds->calc_branch_lengths) NT_branch_lengths(awm,ntw);
	1333	if (cmds->calc_bootstrap) NT_bootstrap(awm,ntw,0);
	1334	if (cmds->quit) pars_exit(awm);
1470	1335
1471	1336	GB_transaction dummy(ntw->gb_main);
…	…
1517	1382	awm->insert_sub_menu("Add Species to Tree", "A");
1518	1383	{
1519		awm->insert_menu_topic("add_marked", "Add Marked Species", "M", "pa_quick.hlp", AWM_ALL, (AW_CB)NT_quick_add, (AW_CL)ntw, 0);
1520		awm->insert_menu_topic("add_marked_nni", "Add Marked Species + Local Optimization (NNI)", "N", "pa_add.hlp", AWM_ALL, (AW_CB)NT_add, (AW_CL)ntw, 0);
1521		awm->insert_menu_topic("rm_add_marked", "Remove & Add Marked Species", "R", "pa_add.hlp", AWM_ALL, (AW_CB)NT_rquick_add, (AW_CL)ntw, 0);
1522		awm->insert_menu_topic("rm_add_marked_nni\|", "Remove & Add Marked + Local Optimization (NNI)", "L", "pa_add.hlp", AWM_ALL, (AW_CB)NT_radd, (AW_CL)ntw, 0);
	1384	awm->insert_menu_topic("add_marked", "Add Marked Species", "M", "pa_quick.hlp", AWM_ALL, (AW_CB)NT_quick_add, (AW_CL)ntw, NT_ADD_MARKED);
	1385	awm->insert_menu_topic("add_marked_nni", "Add Marked Species + Local Optimization (NNI)", "N", "pa_add.hlp", AWM_ALL, (AW_CB)NT_add, (AW_CL)ntw, NT_ADD_MARKED);
	1386	awm->insert_menu_topic("rm_add_marked", "Remove & Add Marked Species", "R", "pa_add.hlp", AWM_ALL, (AW_CB)NT_rquick_add, (AW_CL)ntw, NT_ADD_MARKED);
	1387	awm->insert_menu_topic("rm_add_marked_nni\|", "Remove & Add Marked + Local Optimization (NNI)", "L", "pa_add.hlp", AWM_ALL, (AW_CB)NT_radd, (AW_CL)ntw, NT_ADD_MARKED);
1523	1388	awm->insert_separator();
1524	1389	awm->insert_menu_topic("add_marked_partial", "Add Marked Partial Species", "P", "pa_partial.hlp", AWM_ALL, NT_partial_add, (AW_CL)ntw, (AW_CL)0);
1525	1390	awm->insert_separator();
1526		awm->insert_menu_topic("add_selected", "Add Selected Species", "S", "pa_quick_sel.hlp", AWM_ALL, (AW_CB)NT_quick_add, (AW_CL)ntw, 1);
1527		awm->insert_menu_topic("add_selected_nni", "Add Selected Species + Local Optimization (NNI)", "O", "pa_add_sel.hlp", AWM_ALL, (AW_CB)NT_add, (AW_CL)ntw, 1);
	1391	awm->insert_menu_topic("add_selected", "Add Selected Species", "S", "pa_quick_sel.hlp", AWM_ALL, (AW_CB)NT_quick_add, (AW_CL)ntw, NT_ADD_SELECTED);
	1392	awm->insert_menu_topic("add_selected_nni", "Add Selected Species + Local Optimization (NNI)", "O", "pa_add_sel.hlp", AWM_ALL, (AW_CB)NT_add, (AW_CL)ntw, NT_ADD_SELECTED);
1528	1393	}
1529	1394	awm->close_sub_menu();
…	…
1682	1547	}
1683	1548
1684		static AW_window create_pars_init_window(AW_root awr)
1685		{
	1549	static AW_window create_pars_init_window(AW_root awr, const PARS_commands *cmds) {
1686	1550	AW_window_simple *aws = new AW_window_simple;
1687	1551	aws->init( awr, "PARS_PROPS", "SET PARSIMONY OPTIONS");
…	…
1699	1563	aws->create_button("HELP","HELP","H");
1700	1564
	1565	WeightedFilter *weighted_filter = // do NOT free (bound to callbacks)
	1566	new WeightedFilter(GLOBAL_gb_main, aws->get_root(), AWAR_FILTER_NAME, AWAR_CSP_NAME);
	1567
1701	1568	aws->at("filter");
1702		adfiltercbstruct *filtercd = awt_create_select_filter(aws->get_root(),GLOBAL_gb_main,AWAR_FILTER_NAME);
1703		aws->callback(AW_POPUP, (AW_CL)awt_create_select_filter_win, (AW_CL)filtercd);
	1569	aws->callback(AW_POPUP, (AW_CL)awt_create_select_filter_win, (AW_CL)weighted_filter->get_adfiltercbstruct());
1704	1570	aws->create_button("SELECT_FILTER",AWAR_FILTER_NAME);
1705	1571
1706		aws->callback(pars_start_cb, (AW_CL)filtercd);
	1572	aws->at("weights");
	1573	aws->callback(AW_POPUP,(AW_CL)create_csp_window,(AW_CL)weighted_filter->get_csp());
	1574	aws->create_button("SELECT_CSP", AWAR_CSP_NAME);
	1575
	1576	aws->at("alignment");
	1577	awt_create_selection_list_on_ad(GLOBAL_gb_main,(AW_window )aws,AWAR_ALIGNMENT,"=");
	1578
	1579	aws->at("tree");
	1580	awt_create_selection_list_on_trees(GLOBAL_gb_main,(AW_window *)aws,AWAR_TREE);
	1581
	1582	aws->callback(pars_start_cb, (AW_CL)weighted_filter, (AW_CL)cmds);
1707	1583	aws->at("go");
1708	1584	aws->create_button("GO","GO","G");
1709	1585
1710		aws->at("alignment");
1711		awt_create_selection_list_on_ad(GLOBAL_gb_main,(AW_window )aws,AWAR_ALIGNMENT,"=");
1712
1713		aws->at("tree");
1714		awt_create_selection_list_on_trees(GLOBAL_gb_main,(AW_window *)aws,AWAR_TREE);
1715
1716		awt_csp = new AWT_csp(GLOBAL_gb_main,awr,"tmp/pars/csp/name");
1717
1718		aws->at("weights");
1719		aws->callback(AW_POPUP,(AW_CL)create_csp_window,(AW_CL)awt_csp);
1720		aws->create_button("SELECT_CSP","tmp/pars/csp/name");
1721
1722		return (AW_window *)aws;
	1586	return aws;
1723	1587	}
1724	1588
…	…
1845	1709	ap_main = new AP_main;
1846	1710
1847		GLOBAL_~~NT = (NT_global *)calloc(sizeof(NT~~_global),1);
1848		GLOBAL_NT->awr = aw_root;
	1711	GLOBAL_PARS = (PARS_global *)calloc(sizeof(PARS_global),1);
	1712	GLOBAL_PARS->awr = aw_root;
1849	1713
1850	1714	const char *db_server = ":";
	1715
	1716	PARS_commands cmds;
1851	1717
1852	1718	while (argc>=2 && argv[1][0] == '-'){
1853	1719	argc--;
1854	1720	argv++;
1855		if (!strcmp(argv[0],"-quit")){
1856		ap_main->commands.quit = 1;
1857		continue;
1858		}
1859		if (!strcmp(argv[0],"-add_marked")){
1860		ap_main->commands.add_marked = 1;
1861		continue;
1862		}
1863		if (!strcmp(argv[0],"-add_selected")){
1864		ap_main->commands.add_selected = 1;
1865		continue;
1866		}
1867		if (!strcmp(argv[0],"-calc_branchlengths")){
1868		ap_main->commands.calc_branch_lengths = 1;
1869		continue;
1870		}
1871		if (!strcmp(argv[0],"-calc_bootstrap")){
1872		ap_main->commands.calc_bootstrap = 1;
1873		continue;
1874		}
1875		GB_export_errorf("Unknown option '%s'",argv[0]);
1876		GB_print_error();
1877		printf(" Options: Meaning:\n"
1878		"\n"
1879		" -add_marked add marked species (without changing topology)\n"
1880		" -add_selected add selected species (without changing topology)\n"
1881		" -calc_branchlengths calculate branch lengths only\n"
1882		" -calc_bootstrap estimate bootstrap values\n"
1883		" -quit quit after performing operations\n"
1884		);
1885
1886		exit(-1);
	1721	if (!strcmp(argv[0],"-quit")) cmds.quit = 1;
	1722	else if (!strcmp(argv[0],"-add_marked")) cmds.add_marked = 1;
	1723	else if (!strcmp(argv[0],"-add_selected")) cmds.add_selected = 1;
	1724	else if (!strcmp(argv[0],"-calc_branchlengths")) cmds.calc_branch_lengths = 1;
	1725	else if (!strcmp(argv[0],"-calc_bootstrap")) cmds.calc_bootstrap = 1;
	1726	else {
	1727	GB_export_errorf("Unknown option '%s'",argv[0]);
	1728	GB_print_error();
	1729	printf(" Options: Meaning:\n"
	1730	"\n"
	1731	" -add_marked add marked species (without changing topology)\n"
	1732	" -add_selected add selected species (without changing topology)\n"
	1733	" -calc_branchlengths calculate branch lengths only\n"
	1734	" -calc_bootstrap estimate bootstrap values\n"
	1735	" -quit quit after performing operations\n"
	1736	);
	1737
	1738	exit(-1);
	1739	}
1887	1740	}
1888	1741
…	…
1901	1754	pars_create_all_awars(aw_root,aw_default);
1902	1755
1903		aww = create_pars_init_window(aw_root);
	1756	aww = create_pars_init_window(aw_root, &cmds);
1904	1757	aww->show();
1905	1758
…	…
1909	1762	}
1910	1763
1911

trunk/PARSIMONY/ap_tree_nlen.hxx

r6141	r6280
	1	// =============================================================== //
	2	// //
	3	// File : ap_tree_nlen.hxx //
	4	// Purpose : //
	5	// //
	6	// Coded by Ralf Westram (coder@reallysoft.de) in Summer 1995 //
	7	// Institute of Microbiology (Technical University Munich) //
	8	// http://www.arb-home.de/ //
	9	// //
	10	// =============================================================== //
	11
	12	#ifndef AP_TREE_NLEN_HXX
	13	#define AP_TREE_NLEN_HXX
	14
	15	#ifndef _CPP_IOSTREAM
1	16	#include <iostream>
2		#include <limits.h>
3
4		#define ap_assert(x) arb_assert(x)
	17	#endif
	18	#ifndef _CPP_CLIMITS
	19	#include <climits>
	20	#endif
	21	#ifndef ARBDBT_H
	22	#include <arbdbt.h>
	23	#endif
	24	#ifndef AP_TREE_HXX
	25	#include <AP_Tree.hxx>
	26	#endif
	27	#ifndef AP_BUFFER_HXX
	28	#include "AP_buffer.hxx"
	29	#endif
	30	#ifndef AP_MAIN_HXX
	31	#include <ap_main.hxx>
	32	#endif
	33
	34	// ---------------------------------------------
	35	// downcasts for AP_tree_nlen
	36
	37	#ifndef DOWNCAST_H
	38	#include <downcast.h>
	39	#endif
	40
	41	#define AP_TREE_NLEN_CAST(arb_tree) DOWNCAST(AP_tree_nlen*, arb_tree)
	42	#define AP_TREE_NLEN_CONST_CAST(arb_tree) DOWNCAST(const AP_tree_nlen*, arb_tree)
	43
	44
5	45
6	46	class AP_tree_nlen;
…	…
30	70	AP_BL_NNI_BL = 3, // better tree & branch lengths
31	71	AP_BL_BOOTSTRAP_LIMIT = 4, // calculate upper bootstrap limits
32		AP_BL_BOOTSTRAP_ESTIMATE = 12 // calculate estimate of bootstrap
	72	AP_BL_BOOTSTRAP_ESTIMATE = 12 // calculate estimate of bootstrap (includes AP_BL_BOOTSTRAP_LIMIT)
33	73	} AP_BL_MODE;
34	74
35	75	class AP_tree_edge;
36	76
37		class AP_tree_nlen : public AP_tree { /* tree that is independent of branch lengths and root */
38		AP_tree *dup(void);
39
40		AP_BOOL clear(unsigned long stack_update,unsigned long user_push_counter);
41		void unhash_sequence(void);
42		void createListRekUp(AP_CO_LIST list,int cn);
43		void createListRekSide(AP_CO_LIST list,int cn);
44
	77	class AP_tree_nlen : public AP_tree {
	78	/* tree that is independent of branch lengths and root */
45	79
46	80	AP_TREE_SIDE kernighan; // Flag zum markieren
…	…
52	86	int index[3]; // index to node[] in AP_tree_edge
53	87
54		protected:
	88	AP_FLOAT mutation_rate;
	89
	90
	91
	92	AP_tree_nlen *dup() const;
	93
	94	void createListRekUp(AP_CO_LIST list,int cn);
	95	void createListRekSide(AP_CO_LIST list,int cn);
55	96
56	97	public:
57		~~AP_FLOAT costs(void); /* cost of a tree (number of changes ..)*/~~
58		~~AP_BOOL push(AP_STACK_MODE, unsigned long); /* push state of costs */~~
59		~~void pop(unsigned long); /* pop old tree costs */~~
60
61		~~virtual AP_UPDATE_FLAGS check_update(); // disable load !!!!~~
62
63
64	98	AP_tree_nlen(AP_tree_root *tree_root);
65	99	virtual ~AP_tree_nlen() {}
66	100
	101	void unhash_sequence();
	102	AP_FLOAT costs(char mutPerSite = NULL); / cost of a tree (number of changes ..)*/
	103
	104	AP_BOOL push(AP_STACK_MODE, unsigned long); /* push state of costs */
	105	void pop(unsigned long); /* pop old tree costs */
	106	AP_BOOL clear(unsigned long stack_update,unsigned long user_push_counter);
	107
	108	virtual AP_UPDATE_FLAGS check_update(); // disable load !!!!
	109
67	110	void copy(AP_tree_nlen *tree);
68	111	int Distance();
…	…
70	113	// tree reconstruction methods:
71	114	void insert(AP_tree *new_brother);
72		void remove(~~void~~);
	115	void remove();
73	116	void swap_assymetric(AP_TREE_SIDE mode);
74	117	void moveTo(AP_tree *new_brother, AP_FLOAT rel_pos); // if unsure, use cantMoveTo to test if possible
…	…
76	119
77	120	// tree optimization methods:
78		void parsimony_rek();
	121	void parsimony_rek(char *mutPerSite = NULL);
79	122
80	123	AP_FLOAT nn_interchange_rek(AP_BOOL openclosestatus,
…	…
109	152	void setBranchlen(double leftLen,double rightLen) { leftlen = leftLen; rightlen = rightLen; }
110	153
111		~~int test() const;~~
112	154	const char* fullname() const;
113
114	155	const char* sortByName();
115	156
116	157	// casted access to neighbours:
117	158
118		AP_tree_nlen Father() const { return (AP_tree_nlen)father; }
119		AP_tree_nlen Brother() const { return (AP_tree_nlen)brother(); }
120		AP_tree_nlen Leftson() const { return (AP_tree_nlen)leftson; }
121		AP_tree_nlen Rightson() const { return (AP_tree_nlen)rightson; }
	159	AP_tree_nlen *Father() { return AP_TREE_NLEN_CAST(get_father()); }
	160	AP_tree_nlen *Brother() { return AP_TREE_NLEN_CAST(get_brother()); }
	161	AP_tree_nlen *Leftson() { return AP_TREE_NLEN_CAST(get_leftson()); }
	162	AP_tree_nlen *Rightson() { return AP_TREE_NLEN_CAST(get_rightson()); }
	163	const AP_tree_nlen *Father() const { return AP_TREE_NLEN_CONST_CAST(get_father()); }
	164	const AP_tree_nlen *Brother() const { return AP_TREE_NLEN_CONST_CAST(get_brother()); }
	165	const AP_tree_nlen *Leftson() const { return AP_TREE_NLEN_CONST_CAST(get_leftson()); }
	166	const AP_tree_nlen *Rightson() const { return AP_TREE_NLEN_CONST_CAST(get_rightson()); }
122	167
123	168	// AP_tree_edge access functions:
…	…
134	179	void unlinkAllEdges(AP_tree_edge edgePtr1, AP_tree_edge edgePtr2, AP_tree_edge **edgePtr3);
135	180
136		//void destroyAllEdges();
137
138		// test stuff:
139
140		char *getSequence();
141
	181	char *getSequenceCopy();
	182
	183	#if defined(CHECK_TREE_STRUCTURE)
	184	void assert_edges_valid() const;
	185	void assert_valid() const;
	186	#endif // CHECK_TREE_STRUCTURE
	187
	188
142	189	friend class AP_tree_edge;
143	190	friend std::ostream& operator<<(std::ostream&,const AP_tree_nlen&);
…	…
146	193
147	194	/********** AP_tree_edge **********/
	195
	196	class MutationsPerSite;
	197
148	198	class AP_tree_edge
149	199	{
…	…
175	225	AP_tree_edge *comesFrom = NULL);
176	226
177		long sizeofChain(~~void~~);
	227	long sizeofChain();
178	228	void calcDistance();
179	229	void tailDistance(AP_tree_nlen*);
…	…
223	273	AP_tree_nlen *skipNode = NULL);
224	274
225		AP_FLOAT nni(AP_FLOAT pars_one, AP_BL_MODE mode);
	275	AP_FLOAT nni_mutPerSite(AP_FLOAT pars_one, AP_BL_MODE mode, MutationsPerSite *mps);
	276	AP_FLOAT nni(AP_FLOAT pars_one, AP_BL_MODE mode) { return nni_mutPerSite(pars_one, mode, NULL); }
226	277
227	278	// test methods:
…	…
233	284
234	285	int Distance() const { ap_assert(distanceOK()); return (node[0]->distance+node[1]->distance) >> 1; }
235		int distanceToBorder(int maxsearch=INT_MAX,AP_tree_nlen *skip=NULL) const; // obsolete
	286	int distanceToBorder(int maxsearch=INT_MAX,AP_tree_nlen *skip=NULL) const; // obsolete
236	287
237	288	static int dumpNNI; // should NNI dump its values?
…	…
242	293	void countSpecies(int deep=-1,const AP_tree_nlen* skip=NULL);
243	294
244		static int speciesInTree; // no of species (leafs) in tree
245		static int nodesInTree; // no of nodes in tree
	295	static int speciesInTree; // no of species (leafs) in tree (updated by countSpecies)
	296	static int nodesInTree; // no of nodes in tree - including leafs, but w/o rootnode (updated by countSpecies)
	297
	298	static int edgesInTree() { return nodesInTree-1; } // (updated by countSpecies)
246	299	};
247	300
…	…
251	304
252	305	inline AP_tree_nlen *rootNode() {
253		return ~~((AP_tree_nlen)ap_main->tree_root~~);
	306	return ap_main->get_root_node();
254	307	}
255	308
…	…
259	312
260	313	/**************************************************/
	314
	315	#else
	316	#error ap_tree_nlen.hxx included twice
	317	#endif // AP_TREE_NLEN_HXX

trunk/PARSIMONY/pars_dtree.hxx

r5827	r6280
	1	// =============================================================== //
	2	// //
	3	// File : pars_dtree.hxx //
	4	// Purpose : //
	5	// //
	6	// Institute of Microbiology (Technical University Munich) //
	7	// http://www.arb-home.de/ //
	8	// //
	9	// =============================================================== //
	10
	11	#ifndef PARS_DTREE_HXX
	12	#define PARS_DTREE_HXX
	13
	14	#ifndef TREEDISPLAY_HXX
	15	#include <TreeDisplay.hxx>
	16	#endif
	17
	18
1	19	class AWT_graphic_parsimony: public AWT_graphic_tree {
2	20	virtual AW_gc_manager init_devices(AW_window ,AW_device , AWT_canvas *ntw,AW_CL cd2);
…	…
16	34	};
17	35
18		struct adfiltercbstruct;
19		void NT_tree_init(AWT_graphic_tree agt, adfiltercbstruct pars_global_filter);
	36	void PARS_tree_init(AWT_graphic_tree *agt);
20	37	void PARS_optimizer_cb(AP_tree *tree);
	38
	39	#else
	40	#error pars_dtree.hxx included twice
	41	#endif // PARS_DTREE_HXX

trunk/PARSIMONY/pars_main.hxx

r5827	r6280
1		#define MIN_SEQUENCE_LENGTH 20
	1	// =============================================================== //
	2	// //
	3	// File : pars_main.hxx //
	4	// Purpose : //
	5	// //
	6	// Institute of Microbiology (Technical University Munich) //
	7	// http://www.arb-home.de/ //
	8	// //
	9	// =============================================================== //
2	10
3		extern struct NT_global {
4		AW_root *awr;
	11	#ifndef PARS_MAIN_HXX
	12	#define PARS_MAIN_HXX
	13
	14	#define MIN_SEQUENCE_LENGTH 20
	15
	16	class AW_root;
	17	class AWT_graphic_tree;
	18	class WeightedFilter;
	19
	20	extern struct PARS_global {
	21	AW_root *awr;
5	22	AWT_graphic_tree *tree;
6		} *GLOBAL_NT;
	23	} *GLOBAL_PARS;
7	24
8		AWT_graphic_tree PARS_generate_tree(AW_root root);
	25	AWT_graphic_tree PARS_generate_tree(AW_root root, WeightedFilter *pars_weighted_filter);
9	26
	27
	28	#else
	29	#error pars_main.hxx included twice
	30	#endif // PARS_MAIN_HXX

trunk/PHYLO/Makefile

r6277	r6280
37	37	PH_data.o: $(ARBHOME)/INCLUDE/ad_prot.h
38	38	PH_data.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
	39	PH_data.o: $(ARBHOME)/INCLUDE/AP_matrix.hxx
39	40	PH_data.o: $(ARBHOME)/INCLUDE/arb_assert.h
40	41	PH_data.o: $(ARBHOME)/INCLUDE/arb_error.h
…	…
44	45	PH_data.o: $(ARBHOME)/INCLUDE/arbtools.h
45	46	PH_data.o: $(ARBHOME)/INCLUDE/attributes.h
46		~~PH_data.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx~~
47	47	PH_data.o: $(ARBHOME)/INCLUDE/aw_device.hxx
48	48	PH_data.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
…	…
50	50	PH_data.o: $(ARBHOME)/INCLUDE/aw_root.hxx
51	51	PH_data.o: $(ARBHOME)/INCLUDE/aw_window.hxx
52		~~PH_data.o: $(ARBHOME)/INCLUDE/awt_pro_a_nucs.hxx~~
53		~~PH_data.o: $(ARBHOME)/INCLUDE/awt_tree.hxx~~
54	52	PH_data.o: $(ARBHOME)/INCLUDE/smartptr.h
55	53
…	…
61	59	PH_display.o: $(ARBHOME)/INCLUDE/ad_prot.h
62	60	PH_display.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
	61	PH_display.o: $(ARBHOME)/INCLUDE/AP_matrix.hxx
63	62	PH_display.o: $(ARBHOME)/INCLUDE/arb_assert.h
64	63	PH_display.o: $(ARBHOME)/INCLUDE/arb_error.h
…	…
68	67	PH_display.o: $(ARBHOME)/INCLUDE/arbtools.h
69	68	PH_display.o: $(ARBHOME)/INCLUDE/attributes.h
70		~~PH_display.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx~~
71	69	PH_display.o: $(ARBHOME)/INCLUDE/aw_device.hxx
72	70	PH_display.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
…	…
74	72	PH_display.o: $(ARBHOME)/INCLUDE/aw_root.hxx
75	73	PH_display.o: $(ARBHOME)/INCLUDE/aw_window.hxx
76		~~PH_display.o: $(ARBHOME)/INCLUDE/awt_pro_a_nucs.hxx~~
77		~~PH_display.o: $(ARBHOME)/INCLUDE/awt_tree.hxx~~
78	74	PH_display.o: $(ARBHOME)/INCLUDE/smartptr.h
79	75
…	…
84	80	PH_filt.o: $(ARBHOME)/INCLUDE/ad_prot.h
85	81	PH_filt.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
	82	PH_filt.o: $(ARBHOME)/INCLUDE/AP_matrix.hxx
86	83	PH_filt.o: $(ARBHOME)/INCLUDE/arb_assert.h
87	84	PH_filt.o: $(ARBHOME)/INCLUDE/arb_error.h
…	…
91	88	PH_filt.o: $(ARBHOME)/INCLUDE/arbtools.h
92	89	PH_filt.o: $(ARBHOME)/INCLUDE/attributes.h
93		~~PH_filt.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx~~
94	90	PH_filt.o: $(ARBHOME)/INCLUDE/aw_device.hxx
95	91	PH_filt.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
…	…
97	93	PH_filt.o: $(ARBHOME)/INCLUDE/aw_root.hxx
98	94	PH_filt.o: $(ARBHOME)/INCLUDE/aw_window.hxx
99		~~PH_filt.o: $(ARBHOME)/INCLUDE/awt_pro_a_nucs.hxx~~
100		~~PH_filt.o: $(ARBHOME)/INCLUDE/awt_tree.hxx~~
101	95	PH_filt.o: $(ARBHOME)/INCLUDE/smartptr.h
102	96
…	…
108	102	PH_main.o: $(ARBHOME)/INCLUDE/ad_prot.h
109	103	PH_main.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
	104	PH_main.o: $(ARBHOME)/INCLUDE/AP_matrix.hxx
110	105	PH_main.o: $(ARBHOME)/INCLUDE/arb_assert.h
111	106	PH_main.o: $(ARBHOME)/INCLUDE/arb_error.h
…	…
115	110	PH_main.o: $(ARBHOME)/INCLUDE/arbtools.h
116	111	PH_main.o: $(ARBHOME)/INCLUDE/attributes.h
117		~~PH_main.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx~~
118	112	PH_main.o: $(ARBHOME)/INCLUDE/aw_device.hxx
119	113	PH_main.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
…	…
123	117	PH_main.o: $(ARBHOME)/INCLUDE/aw_window.hxx
124	118	PH_main.o: $(ARBHOME)/INCLUDE/awt.hxx
125		~~PH_main.o: $(ARBHOME)/INCLUDE/awt_pro_a_nucs.hxx~~
126	119	PH_main.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx
127		~~PH_main.o: $(ARBHOME)/INCLUDE/awt_tree.hxx~~
128	120	PH_main.o: $(ARBHOME)/INCLUDE/smartptr.h
129	121
…	…
133	125	PH_matr.o: $(ARBHOME)/INCLUDE/ad_prot.h
134	126	PH_matr.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
	127	PH_matr.o: $(ARBHOME)/INCLUDE/AP_matrix.hxx
	128	PH_matr.o: $(ARBHOME)/INCLUDE/AP_pro_a_nucs.hxx
135	129	PH_matr.o: $(ARBHOME)/INCLUDE/arb_assert.h
136	130	PH_matr.o: $(ARBHOME)/INCLUDE/arb_error.h
…	…
140	134	PH_matr.o: $(ARBHOME)/INCLUDE/arbtools.h
141	135	PH_matr.o: $(ARBHOME)/INCLUDE/attributes.h
142		~~PH_matr.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx~~
143	136	PH_matr.o: $(ARBHOME)/INCLUDE/aw_device.hxx
144	137	PH_matr.o: $(ARBHOME)/INCLUDE/aw_global.hxx
…	…
148	141	PH_matr.o: $(ARBHOME)/INCLUDE/aw_window.hxx
149	142	PH_matr.o: $(ARBHOME)/INCLUDE/awt.hxx
150		~~PH_matr.o: $(ARBHOME)/INCLUDE/awt_pro_a_nucs.hxx~~
151		~~PH_matr.o: $(ARBHOME)/INCLUDE/awt_tree.hxx~~
152	143	PH_matr.o: $(ARBHOME)/INCLUDE/smartptr.h
153	144
…	…
157	148	PH_root.o: $(ARBHOME)/INCLUDE/ad_prot.h
158	149	PH_root.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
	150	PH_root.o: $(ARBHOME)/INCLUDE/AP_matrix.hxx
159	151	PH_root.o: $(ARBHOME)/INCLUDE/arb_assert.h
160	152	PH_root.o: $(ARBHOME)/INCLUDE/arb_error.h
…	…
164	156	PH_root.o: $(ARBHOME)/INCLUDE/arbtools.h
165	157	PH_root.o: $(ARBHOME)/INCLUDE/attributes.h
166		~~PH_root.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx~~
167	158	PH_root.o: $(ARBHOME)/INCLUDE/aw_root.hxx
168		~~PH_root.o: $(ARBHOME)/INCLUDE/awt_pro_a_nucs.hxx~~
169		~~PH_root.o: $(ARBHOME)/INCLUDE/awt_tree.hxx~~
170	159	PH_root.o: $(ARBHOME)/INCLUDE/smartptr.h

trunk/PHYLO/PH_matr.cxx

r5625	r6280
4	4	#include <awt.hxx>
5	5
	6	#include <AP_pro_a_nucs.hxx>
	7
6	8	#include <cstring>
7	9	#include <cstdlib>
	10
8	11
9	12	#warning module completely unused

trunk/PHYLO/phylo.hxx

r5901	r6280
1		/////////////////////////////////////////////////////////////////
2		/////////////////////////////////////////////////////////////////
3		// //
4		// FILENAME: phylo.hxx //
5		// //
6		/////////////////////////////////////////////////////////////////
7		// //
8		// contains: abstract classes and //
9		// global needed definitions,declarations and //
10		// functions //
11		// //
12		/////////////////////////////////////////////////////////////////
13		/////////////////////////////////////////////////////////////////
	1	// =============================================================== //
	2	// //
	3	// File : phylo.hxx //
	4	// Purpose : //
	5	// //
	6	// Institute of Microbiology (Technical University Munich) //
	7	// http://www.arb-home.de/ //
	8	// //
	9	// =============================================================== //
14	10
	11	#ifndef PHYLO_HXX
	12	#define PHYLO_HXX
15	13
16	14	#ifndef _CPP_CSTDIO
…	…
23	21	#include <arbdbt.h>
24	22	#endif
25		#ifndef AW~~T_TREE~~_HXX
26		#include <aw~~t_tree~~.hxx>
	23	#ifndef AW_ROOT_HXX
	24	#include <aw_root.hxx>
27	25	#endif
28
	26	#ifndef AP_MATRIX_HXX
	27	#include <AP_matrix.hxx>
	28	#endif
29	29	#ifndef ARB_ASSERT_H
30	30	#include <arb_assert.h>
31	31	#endif
32
33	32	#ifndef PH_FILTER_HXX
34	33	#include "PH_filter.hxx"
…	…
132	131	long AP_timer(void);
133	132
134		~~GBT_TREE neighbourjoining(char names, AP_FLOAT *m, long size, size_t structure_size);~~
135
136	133	/////////////////////////////////////////////////////////////////
137	134	// //
…	…
192	189	};
193	190
194
	191	#else
	192	#error phylo.hxx included twice
	193	#endif // PHYLO_HXX

trunk/PROBE_DESIGN/Makefile

r6277	r6280
34	34	probe_design.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
35	35	probe_design.o: $(ARBHOME)/INCLUDE/adGene.h
	36	probe_design.o: $(ARBHOME)/INCLUDE/AliView.hxx
	37	probe_design.o: $(ARBHOME)/INCLUDE/AP_sequence.hxx
	38	probe_design.o: $(ARBHOME)/INCLUDE/AP_Tree.hxx
36	39	probe_design.o: $(ARBHOME)/INCLUDE/arb_assert.h
37	40	probe_design.o: $(ARBHOME)/INCLUDE/arb_error.h
	41	probe_design.o: $(ARBHOME)/INCLUDE/ARB_Tree.hxx
38	42	probe_design.o: $(ARBHOME)/INCLUDE/arbdb.h
39	43	probe_design.o: $(ARBHOME)/INCLUDE/arbdb_base.h
…	…
52	56	probe_design.o: $(ARBHOME)/INCLUDE/awt_canvas.hxx
53	57	probe_design.o: $(ARBHOME)/INCLUDE/awt_config_manager.hxx
54		~~probe_design.o: $(ARBHOME)/INCLUDE/awt_dtree.hxx~~
55	58	probe_design.o: $(ARBHOME)/INCLUDE/awt_iupac.hxx
56		~~probe_design.o: $(ARBHOME)/INCLUDE/awt_pro_a_nucs.hxx~~
57	59	probe_design.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx
58		~~probe_design.o: $(ARBHOME)/INCLUDE/awt_tree.hxx~~
59		~~probe_design.o: $(ARBHOME)/INCLUDE/awt_tree_cb.hxx~~
60	60	probe_design.o: $(ARBHOME)/INCLUDE/client.h
	61	probe_design.o: $(ARBHOME)/INCLUDE/downcast.h
61	62	probe_design.o: $(ARBHOME)/INCLUDE/GEN.hxx
62	63	probe_design.o: $(ARBHOME)/INCLUDE/PT_com.h
63	64	probe_design.o: $(ARBHOME)/INCLUDE/servercntrl.h
64	65	probe_design.o: $(ARBHOME)/INCLUDE/smartptr.h
	66	probe_design.o: $(ARBHOME)/INCLUDE/TreeCallbacks.hxx
	67	probe_design.o: $(ARBHOME)/INCLUDE/TreeDisplay.hxx
65	68
66	69	probe_match_parser.o: probe_match_parser.hxx
…	…
88	91	SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/attributes.h
89	92	SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/aw_awars.hxx
90		~~SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx~~
91	93	SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/aw_device.hxx
92	94	SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
…	…
98	100	SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/awt_canvas.hxx
99	101	SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/awt_config_manager.hxx
100		~~SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/awt_dtree.hxx~~
101	102	SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/awt_nds.hxx
102		~~SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/awt_pro_a_nucs.hxx~~
103	103	SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx
104		~~SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/awt_tree.hxx~~
105		~~SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/awt_tree_cb.hxx~~
106	104	SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/smartptr.h

trunk/PROBE_DESIGN/SaiProbeVisualization.cxx

r6188	r6280
18	18
19	19	#include <awt_canvas.hxx>
20		~~#include <awt_tree.hxx>~~
21		~~#include <awt_dtree.hxx>~~
22		~~#include <awt_tree_cb.hxx>~~
23	20	#include <awt_config_manager.hxx>
24	21

trunk/PROBE_DESIGN/probe_design.cxx

r6141	r6280
18	18
19	19	#include <awt_canvas.hxx>
20		~~#include <awt_tree.hxx>~~
21		~~#include <awt_dtree.hxx>~~
22		~~#include <awt_tree_cb.hxx>~~
23	20	#include <awt_config_manager.hxx>
24	21	#include <awt_canvas.hxx>
…	…
34	31	#include "probe_match_parser.hxx"
35	32
36		void NT_group_not_marked_cb(void dummy, AWT_canvas ntw); // real prototype is in awt_tree_cb.hxx
	33	#include <TreeCallbacks.hxx>
37	34
38	35	// general awars

trunk/SECEDIT/SEC_graphic.cxx

r6141	r6280
310	310	break;
311	311	}
312		case AWT_MODE_~~MOD~~: // edit constraints
	312	case AWT_MODE_EDIT: // edit constraints
313	313	if (button==AWT_M_LEFT && event==AW_Mouse_Press) {
314	314	error = change_constraints(elem);
…	…
489	489	AW_clicked_line cl, AW_clicked_text ct)
490	490	{
491		if (cmd != AWT_MODE_~~MOD~~ && cmd != AWT_MODE_STRETCH) sec_root->set_show_constraints(SEC_NO_TYPE);
	491	if (cmd != AWT_MODE_EDIT && cmd != AWT_MODE_STRETCH) sec_root->set_show_constraints(SEC_NO_TYPE);
492	492
493	493	GB_ERROR error = 0;

trunk/SECEDIT/SEC_main.cxx

r6188	r6280
219	219	break;
220	220	}
221		case AWT_MODE_~~MOD~~: {
	221	case AWT_MODE_EDIT: {
222	222	text="CONSTRAINT MODE LEFT: modify constraint";
223	223	sec_root->set_show_constraints(SEC_ANY_TYPE);
…	…
756	756	awm->create_mode("rot.bitmap", "sec_mode.hlp", AWM_ALL, sec_mode_event, (AW_CL)root, (AW_CL)AWT_MODE_ROT);
757	757	awm->create_mode("stretch.bitmap", "sec_mode.hlp", AWM_ALL, sec_mode_event, (AW_CL)root, (AW_CL)AWT_MODE_STRETCH);
758		awm->create_mode("info.bitmap", "sec_mode.hlp", AWM_ALL, sec_mode_event, (AW_CL)root, (AW_CL)AWT_MODE_~~MOD~~);
	758	awm->create_mode("info.bitmap", "sec_mode.hlp", AWM_ALL, sec_mode_event, (AW_CL)root, (AW_CL)AWT_MODE_EDIT);
759	759	awm->create_mode("sec_setcurs.bitmap", "sec_mode.hlp", AWM_ALL, sec_mode_event, (AW_CL)root, (AW_CL)AWT_MODE_LINE);
760	760	awm->create_mode("probeInfo.bitmap", "sec_mode.hlp", AWM_ALL, sec_mode_event, (AW_CL)root, (AW_CL)AWT_MODE_PROINFO);

trunk/SEQ_QUALITY/Makefile

r6277	r6280
38	38	SQ_functions.o: $(ARBHOME)/INCLUDE/ad_prot.h
39	39	SQ_functions.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
	40	SQ_functions.o: $(ARBHOME)/INCLUDE/AP_filter.hxx
40	41	SQ_functions.o: $(ARBHOME)/INCLUDE/arb_assert.h
41	42	SQ_functions.o: $(ARBHOME)/INCLUDE/arb_error.h
…	…
45	46	SQ_functions.o: $(ARBHOME)/INCLUDE/arbtools.h
46	47	SQ_functions.o: $(ARBHOME)/INCLUDE/attributes.h
47		~~SQ_functions.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx~~
48	48	SQ_functions.o: $(ARBHOME)/INCLUDE/aw_device.hxx
49	49	SQ_functions.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
…	…
54	54	SQ_functions.o: $(ARBHOME)/INCLUDE/awt.hxx
55	55	SQ_functions.o: $(ARBHOME)/INCLUDE/awt_iupac.hxx
56		~~SQ_functions.o: $(ARBHOME)/INCLUDE/awt_pro_a_nucs.hxx~~
57		~~SQ_functions.o: $(ARBHOME)/INCLUDE/awt_tree.hxx~~
58	56	SQ_functions.o: $(ARBHOME)/INCLUDE/BI_helix.hxx
59	57	SQ_functions.o: $(ARBHOME)/INCLUDE/smartptr.h
…	…
65	63	SQ_GroupData.o: $(ARBHOME)/INCLUDE/attributes.h
66	64
67		~~SQ_main.o: ../AWT/awtfilter.hxx~~
68	65	SQ_main.o: seq_quality.h
69	66	SQ_main.o: SQ_functions.h
…	…
80	77	SQ_main.o: $(ARBHOME)/INCLUDE/attributes.h
81	78	SQ_main.o: $(ARBHOME)/INCLUDE/aw_awars.hxx
82		~~SQ_main.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx~~
83	79	SQ_main.o: $(ARBHOME)/INCLUDE/aw_device.hxx
84	80	SQ_main.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
…	…
87	83	SQ_main.o: $(ARBHOME)/INCLUDE/aw_window.hxx
88	84	SQ_main.o: $(ARBHOME)/INCLUDE/awt.hxx
89		SQ_main.o: $(ARBHOME)/INCLUDE/awt_~~pro_a_nucs~~.hxx
	85	SQ_main.o: $(ARBHOME)/INCLUDE/awt_filter.hxx
90	86	SQ_main.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx
91		~~SQ_main.o: $(ARBHOME)/INCLUDE/awt_tree.hxx~~
92	87	SQ_main.o: $(ARBHOME)/INCLUDE/smartptr.h

trunk/SEQ_QUALITY/SQ_functions.cxx

r6141	r6280
26	26	#include <aw_preset.hxx>
27	27	#include <awt.hxx>
28		~~#include <awt_tree.hxx>~~
29	28
30	29	#include "SQ_GroupData.h"
…	…
411	410
412	411	char SQ_fetch_filtered_sequence(GBDATA read_sequence, AP_filter * filter) {
413		if (!read_sequence)
414		return 0;
415
416		const char *rawSequence = GB_read_char_pntr(read_sequence);
417		int filteredLength = filter->real_len;
418
419		if (filter->filterpos_2_seqpos == 0)
420		filter->calc_filter_2_seq();
421
422		char filteredSequence = (char ) malloc(filteredLength * sizeof(char));
423
424		if (filteredSequence) {
425		for (int i = 0; i < filteredLength; ++i) {
426		filteredSequence[i] = rawSequence[filter->filterpos_2_seqpos[i]];
427		}
428		}
429
	412	char *filteredSequence = 0;
	413	if (read_sequence) {
	414	const char *rawSequence = GB_read_char_pntr(read_sequence);
	415	int filteredLength = filter->get_filtered_length();
	416	const size_t *filterpos_2_seqpos = filter->get_filterpos_2_seqpos();
	417
	418	filteredSequence = (char)malloc(filteredLength sizeof(char));
	419	if (filteredSequence) {
	420	for (int i = 0; i < filteredLength; ++i) {
	421	filteredSequence[i] = rawSequence[filterpos_2_seqpos[i]];
	422	}
	423	}
	424	}
430	425	return filteredSequence;
431	426	}
…	…
473	468	char *rawSequence = SQ_fetch_filtered_sequence(read_sequence,
474	469	filter);
475		int sequenceLength = filter->~~real_len~~;
	470	int sequenceLength = filter->get_filtered_length();
476	471
477	472	/calculate physical layout of sequence /
…	…
576	571	char *rawSequence = SQ_fetch_filtered_sequence(
577	572	read_sequence, filter);
578		int sequenceLength = filter->~~real_len~~;
	573	int sequenceLength = filter->get_filtered_length();
579	574
580	575	/calculate physical layout of sequence /

trunk/SEQ_QUALITY/SQ_helix.h

r5675	r6280
23	23	#include <BI_helix.hxx>
24	24	#endif
	25	#ifndef AP_FILTER_HXX
	26	#include <AP_filter.hxx>
	27	#endif
	28
25	29
26	30	class SQ_helix {
…	…
86	90
87	91	void SQ_helix::SQ_calc_helix_layout(const char seq, GBDATA gb_main,
88		char alignment_name, GBDATA gb_quality, AP_filter * filter) {
	92	char alignment_name, GBDATA gb_quality, AP_filter * filter) {
89	93	getHelix(gb_main, alignment_name);
	94
	95	size_t filterLen = filter->get_filtered_length();
	96	const size_t *filterpos_2_seqpos = filter->get_filterpos_2_seqpos();
90	97
91	98	// one call should be enough here (alignment does not change during the whole evaluation)
…	…
93	100	filterMap.clear();
94	101
95		for (int filter_pos = 0; filter_pos < filter~~->real_l~~en; filter_pos++) {
96		filterMap[filter~~->filter~~pos_2_seqpos[filter_pos]] = filter_pos;
	102	for (int filter_pos = 0; filter_pos < filterLen; filter_pos++) {
	103	filterMap[filterpos_2_seqpos[filter_pos]] = filter_pos;
97	104	}
98	105
…	…
108	115	std::map<int,int>::iterator it;
109	116
110		for (int filter_pos = 0; filter_pos < filter~~->real_l~~en; filter_pos++) {
111		int seq_pos = filter~~->filter~~pos_2_seqpos[filter_pos];
	117	for (int filter_pos = 0; filter_pos < filterLen; filter_pos++) {
	118	int seq_pos = filterpos_2_seqpos[filter_pos];
112	119
113	120	BI_PAIR_TYPE pair_type = helix->pairtype(seq_pos);

trunk/SEQ_QUALITY/SQ_main.cxx

r6141	r6280
23	23	#include <aw_window.hxx>
24	24	#include <awt.hxx>
25		#include <awt_tree.hxx>
26		#include "../AWT/awtfilter.hxx"
	25	#include <awt_filter.hxx>
27	26	#include <awt_sel_boxes.hxx>
28	27	#include <aw_awars.hxx>

trunk/SL/AP_TREE/Makefile

r6238	r6280
44	44	AP_Tree.o: $(ARBHOME)/INCLUDE/AP_sequence.hxx
45	45	AP_Tree.o: $(ARBHOME)/INCLUDE/arb_assert.h
	46	AP_Tree.o: $(ARBHOME)/INCLUDE/arb_error.h
46	47	AP_Tree.o: $(ARBHOME)/INCLUDE/ARB_Tree.hxx
47	48	AP_Tree.o: $(ARBHOME)/INCLUDE/arbdb.h
…	…
54	55	AP_Tree.o: $(ARBHOME)/INCLUDE/awt_attributes.hxx
55	56	AP_Tree.o: $(ARBHOME)/INCLUDE/downcast.h
	57	AP_Tree.o: $(ARBHOME)/INCLUDE/smartptr.h

trunk/SL/GUI_ALIVIEW/Makefile

r6253	r6280
46	46	AWT_csp.o: $(ARBHOME)/INCLUDE/AP_filter.hxx
47	47	AWT_csp.o: $(ARBHOME)/INCLUDE/arb_assert.h
	48	AWT_csp.o: $(ARBHOME)/INCLUDE/arb_error.h
48	49	AWT_csp.o: $(ARBHOME)/INCLUDE/arbdb.h
49	50	AWT_csp.o: $(ARBHOME)/INCLUDE/arbdb_base.h
…	…
58	59	AWT_csp.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx
59	60	AWT_csp.o: $(ARBHOME)/INCLUDE/BI_helix.hxx
	61	AWT_csp.o: $(ARBHOME)/INCLUDE/smartptr.h
60	62
61	63	AWT_filter.o: awt_filter.hxx
…	…
65	67	AWT_filter.o: $(ARBHOME)/INCLUDE/AP_filter.hxx
66	68	AWT_filter.o: $(ARBHOME)/INCLUDE/arb_assert.h
	69	AWT_filter.o: $(ARBHOME)/INCLUDE/arb_error.h
67	70	AWT_filter.o: $(ARBHOME)/INCLUDE/arbdb.h
68	71	AWT_filter.o: $(ARBHOME)/INCLUDE/arbdb_base.h
…	…
78	81	AWT_filter.o: $(ARBHOME)/INCLUDE/awt.hxx
79	82	AWT_filter.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx
	83	AWT_filter.o: $(ARBHOME)/INCLUDE/smartptr.h
80	84
81	85	GUI_aliview.o: awt_csp.hxx

trunk/SL/MATRIX/Makefile

r6225	r6280
41	41	AP_matrix.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
42	42	AP_matrix.o: $(ARBHOME)/INCLUDE/arb_assert.h
	43	AP_matrix.o: $(ARBHOME)/INCLUDE/arb_error.h
43	44	AP_matrix.o: $(ARBHOME)/INCLUDE/arbdb.h
44	45	AP_matrix.o: $(ARBHOME)/INCLUDE/arbdb_base.h
…	…
51	52	AP_matrix.o: $(ARBHOME)/INCLUDE/aw_root.hxx
52	53	AP_matrix.o: $(ARBHOME)/INCLUDE/aw_window.hxx
	54	AP_matrix.o: $(ARBHOME)/INCLUDE/smartptr.h

trunk/SL/Makefile

r6023	r6280
1	1
2	2	ARCHS_ALL = \
3		~~TREE_READ/TREE_READ~~.dummy \
4		~~TREE_WRITE/TREE_WRIT~~E.dummy \
5		~~HELIX/HELIX~~.dummy \
	3	ALIVIEW/ALIVIEW.dummy \
	4	AP_TREE/AP_TREE.dummy \
	5	ARB_TREE/ARB_TREE.dummy \
6	6	AW_HELIX/AW_HELIX.dummy \
7	7	AW_NAME/AW_NAME.dummy \
8	8	DB_SCANNER/DB_SCANNER.dummy \
	9	FAST_ALIGNER/FAST_ALIGNER.dummy \
9	10	FILE_BUFFER/FILE_BUFFER.dummy \
	11	FILTER/FILTER.dummy \
	12	GUI_ALIVIEW/GUI_ALIVIEW.dummy \
	13	HELIX/HELIX.dummy \
	14	MATRIX/MATRIX.dummy \
	15	NEIGHBOURJOIN/NEIGHBOURJOIN.dummy \
	16	PRONUC/PRONUC.dummy \
10	17	REGEXPR/REGEXPR.dummy \
11		FAST_ALIGNER/FAST_ALIGNER.dummy \
	18	SEQUENCE/SEQUENCE.dummy \
	19	TREE_READ/TREE_READ.dummy \
	20	TREE_WRITE/TREE_WRITE.dummy \
12	21
13	22	# --------------------------------------------------------------------------------
…	…
44	53	clean: $(ARCHS:.dummy=.clean)
45	54
	55	proto: TREEDISP/TREEDISP.proto
	56
46	57	%.depend:
47	58	@cp -p $(@D)/Makefile $(@D)/Makefile.old # save old Makefile
…	…
65	76	clean
66	77
	78	%.proto:
	79	@$(MAKE) -C $(@D) \
	80	proto
	81
67	82	# the end of the above command avoids that the output of parallel make calls gets mixed up
68	83

trunk/SL/PRONUC/Makefile

r6225	r6280
43	43	AP_codon_table.o: $(ARBHOME)/INCLUDE/ad_prot.h
44	44	AP_codon_table.o: $(ARBHOME)/INCLUDE/arb_assert.h
	45	AP_codon_table.o: $(ARBHOME)/INCLUDE/arb_error.h
45	46	AP_codon_table.o: $(ARBHOME)/INCLUDE/arbdb.h
46	47	AP_codon_table.o: $(ARBHOME)/INCLUDE/arbdb_base.h
…	…
54	55	AP_codon_table.o: $(ARBHOME)/INCLUDE/awt.hxx
55	56	AP_codon_table.o: $(ARBHOME)/INCLUDE/awt_iupac.hxx
	57	AP_codon_table.o: $(ARBHOME)/INCLUDE/smartptr.h
56	58
57	59	AP_pro_a_nucs.o: AP_codon_table.hxx
…	…
61	63	AP_pro_a_nucs.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
62	64	AP_pro_a_nucs.o: $(ARBHOME)/INCLUDE/arb_assert.h
	65	AP_pro_a_nucs.o: $(ARBHOME)/INCLUDE/arb_error.h
63	66	AP_pro_a_nucs.o: $(ARBHOME)/INCLUDE/arbdb.h
64	67	AP_pro_a_nucs.o: $(ARBHOME)/INCLUDE/arbdb_base.h
…	…
73	76	AP_pro_a_nucs.o: $(ARBHOME)/INCLUDE/awt.hxx
74	77	AP_pro_a_nucs.o: $(ARBHOME)/INCLUDE/inline.h
	78	AP_pro_a_nucs.o: $(ARBHOME)/INCLUDE/smartptr.h

trunk/SL/TREE_WRITE/TreeWrite.h

r6066	r6280
11	11	#ifndef TREEWRITE_H
12	12	#define TREEWRITE_H
	13
	14	#ifndef ARBDBT_H
	15	#include <arbdbt.h>
	16	#endif
13	17
14	18	typedef void (TREE_make_node_text_init)(GBDATA gb_main);

trunk/SOURCE_TOOLS/generate_all_links.sh

r6277	r6280
4	4
5	5	finderr() {
6		FOUND=`grep -Hn "$1" $SELF`
7		if [ -z ~~$FOUND~~ ]; then
	6	FOUND=`grep -Hn "$1" $SELF \| perl -ne '/^[^:]+:[^:]+:/; print $&."\n";'`
	7	if [ -z "$FOUND" ]; then
8	8	echo "$SELF:8: $2 ($1 not located -- search manually)"
9	9	else
…	…
35	35	(test -e $DIR/$1 \|\| finderr $1 "Target '$DIR/$1 does not exists (anymore)" ) &&
36	36	(test -e $2 \|\| (test -h $2 &&
37		(finderr $2 "~~Warning Symlink '$2' points~~ to nowhere -- removing wrong link";ls -al $2;rm $2;true)
	37	(finderr $2 "Note: Symlink '$2' pointed to nowhere -- removing wrong link";ls -al $2;rm $2;true)
38	38	) \|\| true) &&
39	39	symlink_maybe_no_target $1 $2
…	…
121	121	symlink ../TEMPLATES/attributes.h INCLUDE/attributes.h &&
122	122	symlink ../TEMPLATES/config_parser.h INCLUDE/config_parser.h &&
	123	symlink ../TEMPLATES/downcast.h INCLUDE/downcast.h &&
123	124	symlink ../TEMPLATES/inline.h INCLUDE/inline.h &&
124	125	symlink ../TEMPLATES/output.h INCLUDE/output.h &&
…	…
140	141
141	142	symlink ../AISC_COM/C/aisc_func_types.h INCLUDE/aisc_func_types.h &&
	143	symlink ../AISC_COM/C/aisc_global.h INCLUDE/aisc_global.h &&
142	144	symlink ../AISC_COM/C/client.h INCLUDE/client.h &&
143	145	symlink ../AISC_COM/C/client_privat.h INCLUDE/client_privat.h &&
144	146	symlink ../AISC_COM/C/server.h INCLUDE/server.h &&
145	147	symlink ../AISC_COM/C/struct_man.h INCLUDE/struct_man.h &&
146		~~symlink ../AISC_COM/C/aisc_global.h INCLUDE/aisc_global.h &&~~
147	148	symlink ../ARBDB/adGene.h INCLUDE/adGene.h &&
	149	symlink ../ARBDB/ad_config.h INCLUDE/ad_config.h &&
	150	symlink ../ARBDB/ad_k_prot.h INCLUDE/ad_k_prot.h &&
148	151	symlink ../ARBDB/ad_prot.h INCLUDE/ad_prot.h &&
149		~~symlink ../ARBDB/ad_config.h INCLUDE/ad_config.h &&~~
150	152	symlink ../ARBDB/ad_t_prot.h INCLUDE/ad_t_prot.h &&
151		~~symlink ../ARBDB/ad_k_prot.h INCLUDE/ad_k_prot.h &&~~
152	153	symlink ../ARBDB/arb_assert.h INCLUDE/arb_assert.h &&
153	154	symlink ../ARBDB/arbdb.h INCLUDE/arbdb.h &&
…	…
162	163	symlink ../AWT/awt_attributes.hxx INCLUDE/awt_attributes.hxx &&
163	164	symlink ../AWT/awt_canvas.hxx INCLUDE/awt_canvas.hxx &&
164		~~symlink ../AWT/awt_codon_table.hxx INCLUDE/awt_codon_table.hxx &&~~
165	165	symlink ../AWT/awt_config_manager.hxx INCLUDE/awt_config_manager.hxx &&
166		~~symlink ../AWT/awt_csp.hxx INCLUDE/awt_csp.hxx &&~~
167		~~symlink ../AWT/awt_dtree.hxx INCLUDE/awt_dtree.hxx &&~~
168	166	symlink ../AWT/awt_hotkeys.hxx INCLUDE/awt_hotkeys.hxx &&
169	167	symlink ../AWT/awt_input_mask.hxx INCLUDE/awt_input_mask.hxx &&
…	…
174	172	symlink ../AWT/awt_nds.hxx INCLUDE/awt_nds.hxx &&
175	173	symlink ../AWT/awt_preset.hxx INCLUDE/awt_preset.hxx &&
176		~~symlink ../AWT/awt_pro_a_nucs.hxx INCLUDE/awt_pro_a_nucs.hxx &&~~
177	174	symlink ../AWT/awt_sel_boxes.hxx INCLUDE/awt_sel_boxes.hxx &&
178	175	symlink ../AWT/awt_seq_colors.hxx INCLUDE/awt_seq_colors.hxx &&
179		~~symlink ../AWT/awt_seq_dna.hxx INCLUDE/awt_seq_dna.hxx &&~~
180		~~symlink ../AWT/awt_seq_protein.hxx INCLUDE/awt_seq_protein.hxx &&~~
181		~~symlink ../AWT/awt_seq_simple_pro.hxx INCLUDE/awt_seq_simple_pro.hxx &&~~
182		~~symlink ../AWT/awt_translate.hxx INCLUDE/awt_translate.hxx &&~~
183		~~symlink ../AWT/awt_tree.hxx INCLUDE/awt_tree.hxx &&~~
184		~~symlink ../AWT/awt_tree_cb.hxx INCLUDE/awt_tree_cb.hxx &&~~
185		~~symlink ../AWT/awt_tree_cmp.hxx INCLUDE/awt_tree_cmp.hxx &&~~
186	176	symlink ../AWT/awt_www.hxx INCLUDE/awt_www.hxx &&
187	177	symlink ../AWT/awtlocal.hxx INCLUDE/awtlocal.hxx &&
…	…
204	194	symlink ../PROBE_DESIGN/probe_design.hxx INCLUDE/probe_design.hxx &&
205	195	symlink ../SECEDIT/secedit_extern.hxx INCLUDE/secedit_extern.hxx &&
	196	symlink ../SEQ_QUALITY/seq_quality.h INCLUDE/seq_quality.h &&
206	197	symlink ../SERVERCNTRL/servercntrl.h INCLUDE/servercntrl.h &&
207		symlink ../SEQ_QUALITY/seq_quality.h INCLUDE/seq_quality.h &&
	198	symlink ../SL/ALIVIEW/AliView.hxx INCLUDE/AliView.hxx &&
	199	symlink ../SL/AP_TREE/AP_Tree.hxx INCLUDE/AP_Tree.hxx &&
	200	symlink ../SL/ARB_TREE/ARB_Tree.hxx INCLUDE/ARB_Tree.hxx &&
208	201	symlink ../SL/AW_HELIX/AW_helix.hxx INCLUDE/AW_helix.hxx &&
209	202	symlink ../SL/AW_NAME/AW_rename.hxx INCLUDE/AW_rename.hxx &&
…	…
211	204	symlink ../SL/FAST_ALIGNER/fast_aligner.hxx INCLUDE/fast_aligner.hxx &&
212	205	symlink ../SL/FILE_BUFFER/FileBuffer.h INCLUDE/FileBuffer.h &&
	206	symlink ../SL/FILTER/AP_filter.hxx INCLUDE/AP_filter.hxx &&
	207	symlink ../SL/GUI_ALIVIEW/awt_csp.hxx INCLUDE/awt_csp.hxx &&
	208	symlink ../SL/GUI_ALIVIEW/awt_filter.hxx INCLUDE/awt_filter.hxx &&
	209	symlink ../SL/GUI_ALIVIEW/gui_aliview.hxx INCLUDE/gui_aliview.hxx &&
213	210	symlink ../SL/HELIX/BI_helix.hxx INCLUDE/BI_helix.hxx &&
	211	symlink ../SL/MATRIX/AP_matrix.hxx INCLUDE/AP_matrix.hxx &&
	212	symlink ../SL/NEIGHBOURJOIN/neighbourjoin.hxx INCLUDE/neighbourjoin.hxx &&
	213	symlink ../SL/PRONUC/AP_codon_table.hxx INCLUDE/AP_codon_table.hxx &&
	214	symlink ../SL/PRONUC/AP_pro_a_nucs.hxx INCLUDE/AP_pro_a_nucs.hxx &&
214	215	symlink ../SL/REGEXPR/RegExpr.hxx INCLUDE/RegExpr.hxx &&
	216	symlink ../SL/SEQUENCE/AP_seq_dna.hxx INCLUDE/AP_seq_dna.hxx &&
	217	symlink ../SL/SEQUENCE/AP_seq_protein.hxx INCLUDE/AP_seq_protein.hxx &&
	218	symlink ../SL/SEQUENCE/AP_seq_simple_pro.hxx INCLUDE/AP_seq_simple_pro.hxx &&
	219	symlink ../SL/SEQUENCE/AP_sequence.hxx INCLUDE/AP_sequence.hxx &&
	220	symlink ../SL/TRANSLATE/Translate.hxx INCLUDE/Translate.hxx &&
	221	symlink ../SL/TREEDISP/TreeCallbacks.hxx INCLUDE/TreeCallbacks.hxx &&
	222	symlink ../SL/TREEDISP/TreeDisplay.hxx INCLUDE/TreeDisplay.hxx &&
215	223	symlink ../SL/TREE_READ/TreeRead.h INCLUDE/TreeRead.h &&
216	224	symlink ../SL/TREE_WRITE/TreeWrite.h INCLUDE/TreeWrite.h &&
…	…
219	227	symlink ../WINDOW/aw_color_groups.hxx INCLUDE/aw_color_groups.hxx &&
220	228	symlink ../WINDOW/aw_device.hxx INCLUDE/aw_device.hxx &&
	229	symlink ../WINDOW/aw_font_group.hxx INCLUDE/aw_font_group.hxx &&
	230	symlink ../WINDOW/aw_global.hxx INCLUDE/aw_global.hxx &&
221	231	symlink ../WINDOW/aw_global_awars.hxx INCLUDE/aw_global_awars.hxx &&
222	232	symlink ../WINDOW/aw_keysym.hxx INCLUDE/aw_keysym.hxx &&
…	…
226	236	symlink ../WINDOW/aw_root.hxx INCLUDE/aw_root.hxx &&
227	237	symlink ../WINDOW/aw_window.hxx INCLUDE/aw_window.hxx &&
228		~~symlink ../WINDOW/aw_global.hxx INCLUDE/aw_global.hxx &&~~
229	238	symlink ../WINDOW/aw_window_Xm_interface.hxx INCLUDE/aw_window_Xm_interface.hxx &&
230		~~symlink ../WINDOW/aw_font_group.hxx INCLUDE/aw_font_group.hxx &&~~
231	239	symlink ../XML/xml.hxx INCLUDE/xml.hxx &&
232	240

trunk/SOURCE_TOOLS/touch_modified.pl

r5952	r6280
32	32
33	33	if ($touch==1) {
34		if (not -f $file) { die "File '$file' not found (statusline='$line')" }
	34	if (-d $file) {
	35	$handled = 1;
	36	}
	37	else {
	38	if (not -f $file) { die "File '$file' not found (statusline='$line')" }
35	39
36		my $touch_cmd = "touch '$file'";
37		print '['.$touch_cmd."]\n";
38		system($touch_cmd);
39		$handled = 1;
	40	my $touch_cmd = "touch '$file'";
	41	print '['.$touch_cmd."]\n";
	42	system($touch_cmd);
	43	$handled = 1;
	44	}
40	45	}
41	46	}

trunk/STAT/Makefile

r6277	r6280
35	35	ST_ml.o: $(ARBHOME)/INCLUDE/ad_prot.h
36	36	ST_ml.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
	37	ST_ml.o: $(ARBHOME)/INCLUDE/AliView.hxx
	38	ST_ml.o: $(ARBHOME)/INCLUDE/AP_filter.hxx
	39	ST_ml.o: $(ARBHOME)/INCLUDE/AP_sequence.hxx
	40	ST_ml.o: $(ARBHOME)/INCLUDE/AP_Tree.hxx
37	41	ST_ml.o: $(ARBHOME)/INCLUDE/arb_assert.h
38	42	ST_ml.o: $(ARBHOME)/INCLUDE/arb_error.h
	43	ST_ml.o: $(ARBHOME)/INCLUDE/ARB_Tree.hxx
39	44	ST_ml.o: $(ARBHOME)/INCLUDE/arbdb.h
40	45	ST_ml.o: $(ARBHOME)/INCLUDE/arbdb_base.h
…	…
42	47	ST_ml.o: $(ARBHOME)/INCLUDE/arbtools.h
43	48	ST_ml.o: $(ARBHOME)/INCLUDE/attributes.h
44		~~ST_ml.o: $(ARBHOME)/INCLUDE/aw_awars.hxx~~
45	49	ST_ml.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx
46	50	ST_ml.o: $(ARBHOME)/INCLUDE/aw_root.hxx
47	51	ST_ml.o: $(ARBHOME)/INCLUDE/awt_csp.hxx
48		ST_ml.o: $(ARBHOME)/INCLUDE/awt_pro_a_nucs.hxx
49		ST_ml.o: $(ARBHOME)/INCLUDE/awt_tree.hxx
	52	ST_ml.o: $(ARBHOME)/INCLUDE/downcast.h
50	53	ST_ml.o: $(ARBHOME)/INCLUDE/smartptr.h
51	54
…	…
56	59	ST_quality.o: $(ARBHOME)/INCLUDE/ad_prot.h
57	60	ST_quality.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
	61	ST_quality.o: $(ARBHOME)/INCLUDE/AliView.hxx
	62	ST_quality.o: $(ARBHOME)/INCLUDE/AP_filter.hxx
	63	ST_quality.o: $(ARBHOME)/INCLUDE/AP_sequence.hxx
	64	ST_quality.o: $(ARBHOME)/INCLUDE/AP_Tree.hxx
58	65	ST_quality.o: $(ARBHOME)/INCLUDE/arb_assert.h
59	66	ST_quality.o: $(ARBHOME)/INCLUDE/arb_error.h
	67	ST_quality.o: $(ARBHOME)/INCLUDE/ARB_Tree.hxx
60	68	ST_quality.o: $(ARBHOME)/INCLUDE/arbdb.h
61	69	ST_quality.o: $(ARBHOME)/INCLUDE/arbdb_base.h
…	…
65	73	ST_quality.o: $(ARBHOME)/INCLUDE/aw_awars.hxx
66	74	ST_quality.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx
	75	ST_quality.o: $(ARBHOME)/INCLUDE/aw_device.hxx
	76	ST_quality.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
	77	ST_quality.o: $(ARBHOME)/INCLUDE/aw_position.hxx
67	78	ST_quality.o: $(ARBHOME)/INCLUDE/aw_root.hxx
	79	ST_quality.o: $(ARBHOME)/INCLUDE/aw_window.hxx
68	80	ST_quality.o: $(ARBHOME)/INCLUDE/awt_csp.hxx
69		~~ST_quality.o: $(ARBHOME)/INCLUDE/awt_pro_a_nucs.hxx~~
70		~~ST_quality.o: $(ARBHOME)/INCLUDE/awt_tree.hxx~~
71	81	ST_quality.o: $(ARBHOME)/INCLUDE/BI_helix.hxx
	82	ST_quality.o: $(ARBHOME)/INCLUDE/downcast.h
72	83	ST_quality.o: $(ARBHOME)/INCLUDE/smartptr.h
73	84
74	85	ST_window.o: st_ml.hxx
75		~~ST_window.o: st_quality.hxx~~
76	86	ST_window.o: st_window.hxx
77	87	ST_window.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
78	88	ST_window.o: $(ARBHOME)/INCLUDE/ad_prot.h
79	89	ST_window.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
	90	ST_window.o: $(ARBHOME)/INCLUDE/AliView.hxx
	91	ST_window.o: $(ARBHOME)/INCLUDE/AP_sequence.hxx
	92	ST_window.o: $(ARBHOME)/INCLUDE/AP_Tree.hxx
80	93	ST_window.o: $(ARBHOME)/INCLUDE/arb_assert.h
81	94	ST_window.o: $(ARBHOME)/INCLUDE/arb_error.h
	95	ST_window.o: $(ARBHOME)/INCLUDE/ARB_Tree.hxx
82	96	ST_window.o: $(ARBHOME)/INCLUDE/arbdb.h
83	97	ST_window.o: $(ARBHOME)/INCLUDE/arbdb_base.h
…	…
94	108	ST_window.o: $(ARBHOME)/INCLUDE/awt.hxx
95	109	ST_window.o: $(ARBHOME)/INCLUDE/awt_csp.hxx
	110	ST_window.o: $(ARBHOME)/INCLUDE/awt_filter.hxx
96	111	ST_window.o: $(ARBHOME)/INCLUDE/awt_item_sel_list.hxx
97		ST_window.o: $(ARBHOME)/INCLUDE/awt_pro_a_nucs.hxx
98		ST_window.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx
99		ST_window.o: $(ARBHOME)/INCLUDE/awt_tree.hxx
	112	ST_window.o: $(ARBHOME)/INCLUDE/downcast.h
100	113	ST_window.o: $(ARBHOME)/INCLUDE/smartptr.h

trunk/STAT/ST_ml.cxx

r6141	r6280
1		#include <stdio.h>
2		#include <stdlib.h>
3		#include <string.h>
4		#include <math.h>
5		#include <memory.h>
6		// #include <malloc.h>
7		#include <ctype.h>
8		#include <arbdb.h>
9		#include <arbdbt.h>
10		#include <aw_awars.hxx>
11		#include <awt_tree.hxx>
	1	#include "st_ml.hxx"
	2
12	3	#include <awt_csp.hxx>
13		#include "st_ml.hxx"
	4	#include <AP_filter.hxx>
	5
	6	#include <cctype>
	7	#include <cmath>
	8
14	9
15	10	#define st_assert(bed) arb_assert(bed)
…	…
152	147	#endif
153	148
154		ST_sequence_ml::ST_sequence_ml(AP_tree_root * rooti, ST_ML * st_mli) :
155		AP_sequence(rooti) {
156		gb_data = 0;
157		st_ml = st_mli;
158		sequence = new ST_base_vector[ST_MAX_SEQ_PART];
159		color_out = NULL;
160		color_out_valid_till = NULL;
161		last_updated = 0;
162		}
163
164		void st_sequence_callback(GBDATA , int cl, gb_call_back_type) {
	149	ST_sequence_ml::ST_sequence_ml(const AliView aliview, ST_ML st_ml_)
	150	: AP_sequence(aliview)
	151	, st_ml(st_ml_)
	152	, sequence(new ST_base_vector[ST_MAX_SEQ_PART])
	153	, last_updated(0)
	154	, color_out(NULL)
	155	, color_out_valid_till(NULL)
	156	{
	157	}
	158
	159	ST_sequence_ml::~ST_sequence_ml() {
	160	delete [] sequence;
	161	delete color_out;
	162	delete color_out_valid_till;
	163
	164	unbind_from_species(true);
	165	}
	166
	167	static void st_sequence_callback(GBDATA , int cl, gb_call_back_type) {
165	168	ST_sequence_ml seq = (ST_sequence_ml ) cl;
166	169	seq->sequence_change();
167	170	}
168	171
169		void st_sequence_del_callback(GBDATA , int cl, gb_call_back_type) {
	172	static void st_sequence_del_callback(GBDATA , int cl, gb_call_back_type) {
170	173	ST_sequence_ml seq = (ST_sequence_ml ) cl;
171		seq->delete_sequence();
172		}
173
174		void ST_sequence_ml::delete_sequence() {
175		if (gb_data)
176		GB_remove_callback(gb_data, GB_CB_CHANGED, st_sequence_callback,
177		(int *) this);
178		if (gb_data)
179		GB_remove_callback(gb_data, GB_CB_DELETE, st_sequence_del_callback,
180		(int *) this);
181		gb_data = 0;
	174	seq->unbind_from_species(false);
	175	}
	176
	177
	178	GB_ERROR ST_sequence_ml::bind_to_species(GBDATA *gb_species) {
	179	GB_ERROR error = AP_sequence::bind_to_species(gb_species);
	180	if (!error) {
	181	GBDATA *gb_seq = get_bound_species_data();
	182	st_assert(gb_seq);
	183
	184	error = GB_add_callback(gb_seq, GB_CB_CHANGED, st_sequence_callback, (int *) this);
	185	if (!error) error = GB_add_callback(gb_seq, GB_CB_DELETE, st_sequence_del_callback, (int *) this);
	186	}
	187	return error;
	188	}
	189	void ST_sequence_ml::unbind_from_species(bool remove_callbacks) {
	190	if (remove_callbacks) {
	191	GBDATA *gb_seq = get_bound_species_data();
	192	st_assert(gb_seq);
	193	GB_remove_callback(gb_seq, GB_CB_CHANGED, st_sequence_callback, (int *) this);
	194	GB_remove_callback(gb_seq, GB_CB_DELETE, st_sequence_del_callback, (int *) this);
	195	}
	196	AP_sequence::unbind_from_species();
182	197	}
183	198
184	199	void ST_sequence_ml::sequence_change() {
185	200	st_ml->clear_all();
186
187		}
188
189		ST_sequence_ml::~ST_sequence_ml() {
190		delete[]sequence;
191		delete color_out;
192		delete color_out_valid_till;
193
194		delete_sequence();
195		}
196
197		AP_sequence *ST_sequence_ml::dup() {
198		return new ST_sequence_ml(root, st_ml);
199		}
200
201		void ST_sequence_ml::set_gb(GBDATA * gbd) {
202		delete_sequence();
203		gb_data = gbd;
204		GB_add_callback(gb_data, GB_CB_CHANGED, st_sequence_callback, (int *) this);
205		GB_add_callback(gb_data, GB_CB_DELETE, st_sequence_del_callback,
206		(int *) this);
	201	}
	202
	203	AP_sequence *ST_sequence_ml::dup() const {
	204	return new ST_sequence_ml(get_aliview(), st_ml);
207	205	}
208	206
209	207	void ST_sequence_ml::set(const char *) {
210		st_assert(0); // function does nothing, so i assert it wont be called -- ralf may 2008
	208	st_assert(0); // hmm why not perform set_sequence() here ?
	209	}
	210
	211	void ST_sequence_ml::unset() {
211	212	}
212	213
…	…
218	219	int source_sequence_len = 0;
219	220
	221	GBDATA *gb_data = get_bound_species_data();
220	222	if (gb_data) {
221	223	source_sequence_len = (int) GB_read_string_count(gb_data);
…	…
243	245	}
244	246
245		AP_FLOAT ST_sequence_ml::combine(const AP_sequence , const AP_sequence ) {
246		return 0.0;
	247	AP_FLOAT ST_sequence_ml::combine(const AP_sequence , const AP_sequence , char *) {
	248	st_assert(0);
	249	return -1.0;
247	250	}
248	251
…	…
349	352
350	353	void ST_sequence_ml::print() {
351		~~int i~~;
352		for (i = 0; i < ST_MAX_SEQ_PART; i++) {
353		printf("POS %3i %c ", i, ~~GB_read_char_pntr(gb_data)~~[i]);
	354	const char *data = GB_read_char_pntr(get_bound_species_data());
	355	for (int i = 0; i < ST_MAX_SEQ_PART; i++) {
	356	printf("POS %3i %c ", i, data[i]);
354	357	printf("\n");
355	358	}
	359	}
	360
	361	AP_FLOAT ST_sequence_ml::count_weighted_bases() const {
	362	st_assert(0);
	363	return -1.0;
356	364	}
357	365
…	…
362	370
363	371	ST_ML::~ST_ML() {
364		if (tree_root) {
365		delete tree_root->tree;
366		tree_root->tree = 0;
367		delete tree_root;
368		}
	372	delete tree_root;
369	373	free(alignment_name);
370	374	if (hash_2_ap_tree) GBS_free_hash(hash_2_ap_tree);
…	…
373	377	delete[]inv_base_frequencies;
374	378	delete[]rate_matrices;
375		if (!awt_csp) {
	379	if (!awt_csp) { // rates and ttratio have been allocated (see ST_ML::init)
376	380	delete rates;
377	381	delete ttratio;
…	…
384	388	}
385	389
386		~~/** Translate characters to base frequencies */~~
387	390	void ST_ML::create_frequencies() {
388		ST_base_vector *out = new ST_base_vector[alignment_len];
389		int i, j;
390		float **frequency = 0;
391
392		base_frequencies = out;
	391	// Translate characters to base frequencies
	392
	393	base_frequencies = new ST_base_vector[alignment_len];
393	394	inv_base_frequencies = new ST_base_vector[alignment_len];
394	395
395		if (awt_csp)
396		frequency = awt_csp->frequency;
397
398		if (!frequency) {
399		for (i = 0; i < alignment_len; i++) {
400		for (j = ST_A; j < ST_MAX_BASE; j++) {
401		out[i].b[j] = 1.0;
	396	if (!awt_csp) {
	397	for (int i = 0; i < alignment_len; i++) {
	398	for (int j = ST_A; j < ST_MAX_BASE; j++) {
	399	base_frequencies[i].b[j] = 1.0;
402	400	inv_base_frequencies[i].b[j] = 1.0;
403	401	}
404		~~out[i].lik~~ = 1.0;
	402	base_frequencies[i].lik = 1.0;
405	403	inv_base_frequencies[i].lik = 1.0;
406	404	}
407		return;
408		}
409
410		for (i = 0; i < alignment_len; i++) {
411		for (j = ST_A; j < ST_MAX_BASE; j++) {
412		out[i].b[j] = 0.01; // minimal frequency
413		}
414
415		if (frequency['A'])
416		out[i].b[ST_A] += frequency['A'][i];
417		if (frequency['a'])
418		out[i].b[ST_A] += frequency['a'][i];
419
420		if (frequency['C'])
421		out[i].b[ST_C] += frequency['C'][i];
422		if (frequency['c'])
423		out[i].b[ST_C] += frequency['c'][i];
424
425		if (frequency['G'])
426		out[i].b[ST_G] += frequency['G'][i];
427		if (frequency['g'])
428		out[i].b[ST_G] += frequency['g'][i];
429
430		if (frequency['T'])
431		out[i].b[ST_T] += frequency['T'][i];
432		if (frequency['t'])
433		out[i].b[ST_T] += frequency['t'][i];
434		if (frequency['U'])
435		out[i].b[ST_T] += frequency['U'][i];
436		if (frequency['u'])
437		out[i].b[ST_T] += frequency['u'][i];
438
439		if (frequency['-'])
440		out[i].b[ST_GAP] += frequency['-'][i];
441
442		double sum = 0.0;
443
444		for (j = ST_A; j < ST_MAX_BASE; j++)
445		sum += out[i].b[j];
446		for (j = ST_A; j < ST_MAX_BASE; j++)
447		out[i].b[j] += sum * .01; // smoothen frequencies to avoid crazy values
448		double min = out[i].b[ST_A];
449		for (sum = 0, j = ST_A; j < ST_MAX_BASE; j++) {
450		sum += out[i].b[j];
451		if (out[i].b[j] < min)
452		min = out[i].b[j];
453		}
454		for (j = ST_A; j < ST_MAX_BASE; j++) {
455		if (sum > 0.01) { // valid column ??
456		out[i].b[j] *= ST_MAX_BASE / sum;
457		} else {
458		out[i].b[j] = 1.0; // no
459		}
460		inv_base_frequencies[i].b[j] = min / out[i].b[j];
461		}
462		out[i].lik = 1.0;
463		inv_base_frequencies[i].lik = 1.0;
464
	405	}
	406	else {
	407	for (int i = 0; i < alignment_len; i++) {
	408	for (int j = ST_A; j < ST_MAX_BASE; j++) {
	409	base_frequencies[i].b[j] = 0.01; // minimal frequency
	410	}
	411
	412	static struct {
	413	unsigned char c;
	414	AWT_dna_base b;
	415	} toCount[] = {
	416	{ 'A', ST_A }, { 'a', ST_A },
	417	{ 'C', ST_C }, { 'c', ST_C },
	418	{ 'G', ST_G }, { 'g', ST_G },
	419	{ 'T', ST_T }, { 't', ST_T },
	420	{ 'U', ST_T }, { 'u', ST_T },
	421	{ '-', ST_GAP },
	422	{ 0, ST_UNKNOWN },
	423	};
	424
	425	for (int j = 0; toCount[j].c; ++j) {
	426	const float *freq = awt_csp->get_frequencies(toCount[j].c);
	427	if (freq) base_frequencies[i].b[toCount[j].b] += freq[i];
	428	}
	429
	430	double sum = 0.0;
	431
	432	for (int j = ST_A; j < ST_MAX_BASE; j++) sum += base_frequencies[i].b[j];
	433	for (int j = ST_A; j < ST_MAX_BASE; j++) base_frequencies[i].b[j] += sum * .01; // smoothen frequencies to avoid crazy values
	434
	435	double min = base_frequencies[i].b[ST_A];
	436	sum = 0.0;
	437	for (int j = ST_A; j < ST_MAX_BASE; j++) {
	438	sum += base_frequencies[i].b[j];
	439	if (base_frequencies[i].b[j] < min) min = base_frequencies[i].b[j];
	440	}
	441	for (int j = ST_A; j < ST_MAX_BASE; j++) {
	442	if (sum > 0.01) { // valid column ??
	443	base_frequencies[i].b[j] *= ST_MAX_BASE / sum;
	444	}
	445	else {
	446	base_frequencies[i].b[j] = 1.0; // no
	447	}
	448	inv_base_frequencies[i].b[j] = min / base_frequencies[i].b[j];
	449	}
	450	base_frequencies[i].lik = 1.0;
	451	inv_base_frequencies[i].lik = 1.0;
	452	}
465	453	}
466	454	}
…	…
470	458	if (node->is_leaf) {
471	459	GBS_write_hash(hash_2_ap_tree, node->name, (long) node);
472		} else {
473		insert_tree_into_hash_rek(node->leftson);
474		insert_tree_into_hash_rek(node->rightson);
	460	}
	461	else {
	462	insert_tree_into_hash_rek(node->get_leftson());
	463	insert_tree_into_hash_rek(node->get_rightson());
475	464	}
476	465	}
…	…
497	486	else {
498	487	AP_tree leaf = (AP_tree ) val;
499		AP_tree *father = leaf->~~father~~;
	488	AP_tree *father = leaf->get_father();
500	489	leaf->remove();
501	490	delete father; // deletes me also
…	…
508	497	GB_ERROR error = NULL;
509	498
510		~~if (!tree_root->tree \|\| tree_root->tree->is_leaf) {~~
511		~~const char *tree_name = tree_root->tree_name;~~
512
	499	AP_tree *root = tree_root->get_root_node();
	500	if (!root \|\| root->is_leaf) {
	501	const char *tree_name = tree_root->get_tree_name();
513	502	error = GBS_global_string("Too few species remained in tree '%s'", tree_name);
514	503	}
…	…
519	508	GB_ERROR ST_ML::init(const char tree_name, const char alignment_namei,
520	509	const char *species_names, int marked_only,
521		const char * /filter_string /, AWT_csp * awt_cspi) {
522
523		GB_transaction ta(gb_main);
	510	AWT_csp *awt_cspi, bool show_status)
	511	{
524	512	GB_ERROR error = 0;
	513
525	514	if (is_inited) {
526		return GB_export_error("Sorry, once you selected a column statistic you cannot change parameters");
527		}
528		GB_ERROR awt_csp_error = 0;
529		awt_csp = awt_cspi;
530		awt_csp_error = awt_csp->go();
531		if (awt_csp_error) {
532		fprintf(stderr, "%s\n", awt_csp_error);
533		}
534		alignment_name = strdup(alignment_namei);
535		alignment_len = GBT_get_alignment_len(gb_main, alignment_name);
536		if (alignment_len < 10) {
537		free(alignment_name);
538		return GB_await_error();
539		}
540		AP_tree *tree = new AP_tree(0);
541		tree_root = new AP_tree_root(gb_main, tree, tree_name);
542		error = tree->load(tree_root, 0, GB_FALSE, GB_FALSE, 0, 0); // tree is not linked !!!
543		if (error) {
544		delete tree; tree = 0;
545		delete tree_root; tree_root = 0;
546		return error;
547		}
548		tree_root->tree = tree;
549
550		// aw_openstatus("Initializing Online Statistic");
551		/* send species into hash table */
552		hash_2_ap_tree = GBS_create_hash(1000, GB_MIND_CASE);
553		// aw_status("Loading Tree");
554		/* delete species */
555		if (species_names) { // keep names
556		tree_root->tree->remove_leafs(gb_main, AWT_REMOVE_DELETED);
557
558		error = tree_size_ok(tree_root);
559		if (error) return ta.close(error);
560
561		char l, n;
562		keep_species_hash = GBS_create_hash(GBT_get_species_hash_size(gb_main), GB_MIND_CASE);
563		for (l = (char *) species_names; l; l = n) {
564		n = strchr(l, 1);
565		if (n) *n = 0;
566		GBS_write_hash(keep_species_hash, l, 1);
567		if (n) *(n++) = 1;
568		}
569
570		insert_tree_into_hash_rek(tree_root->tree);
571		GBS_hash_do_loop(hash_2_ap_tree, delete_species, this);
572		GBS_free_hash(keep_species_hash);
573		keep_species_hash = 0;
574		GBT_link_tree((GBT_TREE *) tree_root->tree, gb_main, GB_FALSE, 0, 0);
575		}
576		else { // keep marked
577		GBT_link_tree((GBT_TREE *) tree_root->tree, gb_main, GB_FALSE, 0, 0);
578		tree_root->tree->remove_leafs(gb_main, (marked_only ? AWT_REMOVE_NOT_MARKED : 0)\|AWT_REMOVE_DELETED);
	515	error = "Column statistic can't be re-initialized";
	516	}
	517	else {
	518	GB_transaction ta(gb_main);
	519	GB_ERROR awt_csp_error = 0;
	520
	521	if (show_status) aw_openstatus("Activating column statistic");
	522
	523	awt_csp = awt_cspi;
	524	awt_csp_error = awt_csp->go(NULL);
	525
	526	if (awt_csp_error) fprintf(stderr, "%s\n", awt_csp_error);
	527
	528	alignment_name = strdup(alignment_namei);
	529	alignment_len = GBT_get_alignment_len(gb_main, alignment_name);
	530
	531	if (alignment_len < 10) {
	532	error = GB_await_error();
	533	}
	534	else {
	535	{
	536	AP_filter filter(alignment_len); // unfiltered
	537	AP_weights weights(&filter);
	538	AliView *aliview = new AliView(gb_main, filter, weights, alignment_name);
	539	ST_sequence_ml *seq_templ = new ST_sequence_ml(aliview, this);
	540
	541	tree_root = new AP_tree_root(aliview, AP_tree(0), seq_templ, false);
	542	// do not delete 'aliview' or 'seq_templ' (they belong to 'tree_root' now)
	543	}
	544
	545	if (show_status) aw_status("load tree");
	546	tree_root->loadFromDB(tree_name); // tree is not linked!
	547
	548	if (show_status) aw_status("link tree");
	549	hash_2_ap_tree = GBS_create_hash(1000, GB_MIND_CASE); // send species into hash table
	550
	551	/* delete species */
	552	if (species_names) { // keep names
	553	tree_root->remove_leafs(AWT_REMOVE_DELETED);
	554
	555	error = tree_size_ok(tree_root);
	556	if (!error) {
	557	char l, n;
	558	keep_species_hash = GBS_create_hash(GBT_get_species_hash_size(gb_main), GB_MIND_CASE);
	559	for (l = (char *) species_names; l; l = n) {
	560	n = strchr(l, 1);
	561	if (n) *n = 0;
	562	GBS_write_hash(keep_species_hash, l, 1);
	563	if (n) *(n++) = 1;
	564	}
	565
	566	insert_tree_into_hash_rek(tree_root->get_root_node());
	567	GBS_hash_do_loop(hash_2_ap_tree, delete_species, this);
	568	GBS_free_hash(keep_species_hash);
	569	keep_species_hash = 0;
	570	GBT_link_tree(tree_root->get_root_node()->get_gbt_tree(), gb_main, GB_BOOL(show_status), 0, 0);
	571	}
	572	}
	573	else { // keep marked
	574	GBT_link_tree(tree_root->get_root_node()->get_gbt_tree(), gb_main, GB_BOOL(show_status), 0, 0);
	575	tree_root->remove_leafs((marked_only ? AWT_REMOVE_NOT_MARKED : 0)\|AWT_REMOVE_DELETED);
579	576
580		error = tree_size_ok(tree_root);
581		if (error) return ta.close(error);
582
583		insert_tree_into_hash_rek(tree_root->tree);
584		}
585
586		/* calc frequencies */
587
588		if (!awt_csp_error) {
589		rates = awt_csp->rates;
590		ttratio = awt_csp->ttratio;
591		}
592		else {
593		rates = new float[alignment_len];
594		ttratio = new float[alignment_len];
595		for (int i = 0; i < alignment_len; i++) {
596		rates[i] = 1.0;
597		ttratio[i] = 2.0;
598		}
599		awt_csp = 0;
600		}
601		// aw_status("build frequencies");
602		create_frequencies();
603
604		/* set update time */
605
606		latest_modification = GB_read_clock(gb_main);
607
608		/* load sequences */
609		// aw_status("load sequences");
610		tree_root->sequence_template = new ST_sequence_ml(tree_root, this);
611		tree_root->tree->load_sequences_rek(alignment_name, GB_TRUE, GB_TRUE);
612
613		/* create matrices */
614		create_matrices(2.0, 1000);
615
616		ST_sequence_ml::tmp_out = new ST_base_vector[alignment_len];
617		is_inited = 1;
618		// aw_closestatus();
619		return 0;
	577	error = tree_size_ok(tree_root);
	578	if (!error) insert_tree_into_hash_rek(tree_root->get_root_node());
	579	}
	580
	581	if (!error) {
	582	/* calc frequencies */
	583	if (show_status) aw_status("calculating frequencies");
	584
	585	if (!awt_csp_error) {
	586	rates = awt_csp->get_rates();
	587	ttratio = awt_csp->get_ttratio();
	588	}
	589	else {
	590	float *alloc_rates = new float[alignment_len];
	591	float *alloc_ttratio = new float[alignment_len];
	592
	593	for (int i = 0; i < alignment_len; i++) {
	594	alloc_rates[i] = 1.0;
	595	alloc_ttratio[i] = 2.0;
	596	}
	597	rates = alloc_rates;
	598	ttratio = alloc_ttratio;
	599
	600	awt_csp = 0; // mark rates and ttratio as "allocated"
	601	}
	602	create_frequencies();
	603
	604	/* set update time */
	605
	606	latest_modification = GB_read_clock(gb_main);
	607
	608	/* create matrices */
	609	create_matrices(2.0, 1000);
	610
	611	ST_sequence_ml::tmp_out = new ST_base_vector[alignment_len];
	612	is_inited = 1;
	613	}
	614	if (error) {
	615	delete tree_root; tree_root = NULL;
	616	GBS_free_hash(hash_2_ap_tree); hash_2_ap_tree = NULL;
	617	}
	618	}
	619
	620	if (error) {
	621	free(alignment_name);
	622	error = ta.close(error);
	623	}
	624
	625	if (show_status) aw_closestatus();
	626	}
	627	return error;
	628	}
	629
	630	ST_sequence_ml ST_ML::getOrCreate_seq(AP_tree node) {
	631	ST_sequence_ml seq = DOWNCAST(ST_sequence_ml, node->get_seq());
	632	if (!seq) {
	633	seq = new ST_sequence_ml(tree_root->get_aliview(), this); // @@@ why not use dup() ?
	634
	635	node->set_seq(seq);
	636	if (node->is_leaf) {
	637	st_assert(node->gb_node);
	638	seq->bind_to_species(node->gb_node);
	639	}
	640	}
	641	return seq;
620	642	}
621	643
622	644	/** go through the tree and calculate the ST_base_vector from bottom to top */
623	645	ST_sequence_ml ST_ML::do_tree(AP_tree node) {
624		ST_sequence_ml seq = static_cast<ST_sequence_ml>(node->sequence);
625		if (!seq) {
626		seq = new ST_sequence_ml(tree_root, this);
627		node->sequence = (AP_sequence *) seq;
628		}
629
630		if (seq->last_updated)
631		return seq; // already valid !!!
632
633		if (node->is_leaf) {
634		seq->set_sequence();
635		} else {
636		ST_sequence_ml *ls = do_tree(node->leftson);
637		ST_sequence_ml *rs = do_tree(node->rightson);
638		seq->go(ls, node->leftlen, rs, node->rightlen);
639		}
640		seq->last_updated = 1;
	646	ST_sequence_ml *seq = getOrCreate_seq(node);
	647	if (!seq->last_updated) {
	648	if (node->is_leaf) {
	649	seq->set_sequence();
	650	}
	651	else {
	652	ST_sequence_ml *ls = do_tree(node->get_leftson());
	653	ST_sequence_ml *rs = do_tree(node->get_rightson());
	654	seq->go(ls, node->leftlen, rs, node->rightlen);
	655	}
	656
	657	seq->last_updated = 1;
	658	}
	659
641	660	return seq;
642	661	}
…	…
644	663	void ST_ML::clear_all() {
645	664	GB_transaction dummy(gb_main);
646		undo_tree(tree_root->~~tree~~);
	665	undo_tree(tree_root->get_root_node());
647	666	latest_modification = GB_read_clock(gb_main);
648	667	}
649	668
650	669	void ST_ML::undo_tree(AP_tree * node) {
651		ST_sequence_ml seq = static_cast<ST_sequence_ml>(node->sequence);
652		if (!seq) {
653		seq = new ST_sequence_ml(tree_root, this);
654		node->sequence = (AP_sequence *) seq;
655		}
	670	ST_sequence_ml *seq = getOrCreate_seq(node);
656	671	seq->ungo();
657	672	if (!node->is_leaf) {
658		undo_tree(node->~~leftson~~);
659		undo_tree(node->~~rightson~~);
	673	undo_tree(node->get_leftson());
	674	undo_tree(node->get_rightson());
660	675	}
661	676	}
…	…
677	692	st_assert((end_ali_pos - start_ali_pos + 1) <= ST_MAX_SEQ_PART);
678	693
679		ST_sequence_ml seq = ~~(ST_sequence_ml ) node->sequence~~;
	694	ST_sequence_ml *seq = getOrCreate_seq(node);
680	695
681	696	if (start_ali_pos != base \|\| end_ali_pos > to) {
682		undo_tree(tree_root->~~tree~~); // undo everything
	697	undo_tree(tree_root->get_root_node()); // undo everything
683	698	base = start_ali_pos;
684	699	to = end_ali_pos;
…	…
686	701
687	702	AP_tree *pntr;
688		for (pntr = node->father; pntr; pntr = pntr->father) {
689		ST_sequence_ml sequ = (ST_sequence_ml ) pntr->sequence;
690		if (sequ)
691		sequ->ungo();
	703	for (pntr = node->get_father(); pntr; pntr = pntr->get_father()) {
	704	ST_sequence_ml *sequ = getOrCreate_seq(pntr);
	705	if (sequ) sequ->ungo();
692	706	}
693	707
…	…
695	709
696	710	// get the sequence of my brother
697		AP_tree *brother = node->brother();
	711	AP_tree *brother = node->get_brother();
698	712	ST_sequence_ml *seq_of_brother = do_tree(brother);
699	713
700		seq->calc_out(seq_of_brother, node->father->leftlen
701		+ node->father->rightlen);
	714	seq->calc_out(seq_of_brother, node->father->leftlen + node->father->rightlen);
702	715	return seq;
703	716	}
…	…
743	756	}
744	757
745		ST_sequence_ml seq = ~~(ST_sequence_ml ) node->sequence~~;
	758	ST_sequence_ml *seq = getOrCreate_seq(node);
746	759
747	760	for (int pos = 0; pos < alignment_len; pos++) {
…	…
769	782	ST_ML_Color ST_ML::get_color_string(char species_name, AP_tree * node,
770	783	int start_ali_pos, int end_ali_pos)
771		~~// (Re-)Calculates the color string of a given node for sequence positions start_ali_pos..end_ali_pos~~
772	784	{
773
774		// if node isn't given search it using species name:
	785	// (Re-)Calculates the color string of a given node for sequence positions start_ali_pos..end_ali_pos
775	786	if (!node) {
776		~~if (!hash_2_ap_tree)~~
777		return 0;
	787	// if node isn't given, search it using species name:
	788	if (!hash_2_ap_tree) return 0;
778	789	node = (AP_tree *) GBS_read_hash(hash_2_ap_tree, species_name);
779		if (!node)
780		~~return 0;~~
781		}
	790	if (!node) return 0;
	791	}
	792
782	793	// align start_ali_pos/end_ali_pos to previous/next pos divisible by ST_BUCKET_SIZE:
783	794	start_ali_pos &= ~(ST_BUCKET_SIZE - 1);
784		end_ali_pos = (end_ali_pos & ~(ST_BUCKET_SIZE - 1)) + ST_BUCKET_SIZE - 1;
785		~~if (end_ali_pos > alignment_len)~~
786		end_ali_pos = alignment_len;
	795	end_ali_pos = (end_ali_pos & ~(ST_BUCKET_SIZE - 1)) + ST_BUCKET_SIZE - 1;
	796
	797	if (end_ali_pos > alignment_len) end_ali_pos = alignment_len;
787	798
788	799	double val;
789		ST_sequence_ml seq = ~~(ST_sequence_ml ) node->sequence~~;
	800	ST_sequence_ml *seq = getOrCreate_seq(node);
790	801	int pos;
791	802
…	…
820	831	int source_sequence_len = 0;
821	832
822		if (seq->gb_data) {
823		source_sequence_len = GB_read_string_count(seq->gb_data);
824		source_sequence = GB_read_char_pntr(seq->gb_data);
	833	GBDATA *gb_data = seq->get_bound_species_data();
	834	if (gb_data) {
	835	source_sequence_len = GB_read_string_count(gb_data);
	836	source_sequence = GB_read_char_pntr(gb_data);
825	837	}
826	838	// create color string in 'outs':
…	…
860	872	return seq->color_out;
861	873	}
	874

trunk/STAT/ST_quality.cxx

r6141	r6280
10	10	#include <aw_awars.hxx>
11	11	#include <BI_helix.hxx>
	12	#include <AP_filter.hxx>
12	13
13	14	#include <aw_root.hxx>
14		~~#include <awt_tree.hxx>~~
15	15	#include <awt_csp.hxx>
16	16	#include "st_ml.hxx"
…	…
91	91
92	92	void st_ml_add_sequence_part_to_stat(ST_ML * st_ml, AWT_csp * /awt_csp /,
93		const char *species_name, int seq_len, int bucket_size,
94		~~GB_HASH * species_to_info_hash, int start, int end) {~~
95
	93	const char *species_name, int seq_len, int bucket_size,
	94	GB_HASH * species_to_info_hash, int start, int end)
	95	{
96	96	AP_tree *node = st_ml_convert_species_name_to_node(st_ml, species_name);
97		if (!node)
98		return;
99		ST_sequence_ml *sml = st_ml->get_ml_vectors(0, node, start, end);
100		if (!sml)
101		return; // no statistic available
102		st_cq_info *info;
103		if (start > 0) {
104		info = (st_cq_info *) GBS_read_hash(species_to_info_hash, species_name);
105		} else {
106		info = new st_cq_info(seq_len, bucket_size);
107		GBS_write_hash(species_to_info_hash, species_name, long (info));
108		}
109		int pos;
110		const char *source_sequence = 0;
111		int source_sequence_len = 0;
112
113		if (sml->gb_data) {
114		source_sequence_len = GB_read_string_count(sml->gb_data);
115		source_sequence = GB_read_char_pntr(sml->gb_data);
116		}
117		if (end > source_sequence_len) {
118		end = source_sequence_len;
119		}
120
121		ST_base_vector *vec = sml->tmp_out + start;
122		for (pos = start; pos < end; vec++, pos++) {
123		double max = 0;
124		double v;
125		int b;
	97	if (node) {
	98	ST_sequence_ml *sml = st_ml->get_ml_vectors(0, node, start, end);
	99	if (sml) {
	100	st_cq_info *info;
	101	if (start > 0) {
	102	info = (st_cq_info *) GBS_read_hash(species_to_info_hash, species_name);
	103	}
	104	else {
	105	info = new st_cq_info(seq_len, bucket_size);
	106	GBS_write_hash(species_to_info_hash, species_name, long (info));
	107	}
	108
	109	int pos;
	110	const char *source_sequence = 0;
	111	int source_sequence_len = 0;
	112
	113	// if (sml->gb_data) {
	114	GBDATA *gb_data = sml->get_bound_species_data();
	115	if (gb_data) {
	116	source_sequence_len = GB_read_string_count(gb_data);
	117	source_sequence = GB_read_char_pntr(gb_data);
	118	}
	119	if (end > source_sequence_len) {
	120	end = source_sequence_len;
	121	}
	122
	123	ST_base_vector *vec = sml->tmp_out + start;
	124	for (pos = start; pos < end; vec++, pos++) {
	125	double max = 0;
	126	double v;
	127	int b;
126	128
127		for (b = ST_A; b < ST_MAX_BASE; b++) {
128		v = vec->b[b];
129		if (v > max)
130		max = v;
131		}
132		AWT_dna_base base = awt_dna_table.char_to_enum(source_sequence[pos]);
133		if (base != ST_UNKNOWN && base != ST_GAP) { // don't count gaps
134		double val = max / (0.0001 + vec->b[base]);
135		double log_val = log(val);
136		info->ss2.add(pos * 2 / seq_len, log_val);
137		info->ss5.add(pos * 5 / seq_len, log_val);
138		info->ssu.add(pos * info->ssu.size / seq_len, log_val);
	129	for (b = ST_A; b < ST_MAX_BASE; b++) {
	130	v = vec->b[b];
	131	if (v > max)
	132	max = v;
	133	}
	134	AWT_dna_base base = awt_dna_table.char_to_enum(source_sequence[pos]);
	135	if (base != ST_UNKNOWN && base != ST_GAP) { // don't count gaps
	136	double val = max / (0.0001 + vec->b[base]);
	137	double log_val = log(val);
	138	info->ss2.add(pos * 2 / seq_len, log_val);
	139	info->ss5.add(pos * 5 / seq_len, log_val);
	140	info->ssu.add(pos * info->ssu.size / seq_len, log_val);
	141	}
	142	}
139	143	}
140	144	}
…	…
193	197
194	198	GB_ERROR st_ml_check_sequence_quality(GBDATA * gb_main, const char *tree_name,
195		const char alignment_name, AWT_csp awt_csp, int bucket_size,
196		int marked_only, st_report_enum report, const char *filter_string,
197		const char *dest_field) {
198		AP_filter filter;
199		int seq_len = GBT_get_alignment_len(gb_main, alignment_name);
200		filter.init(filter_string, "0 ", seq_len);
201		ST_ML st_ml(gb_main);
202		GB_ERROR error = st_ml.init(tree_name, alignment_name, 0, marked_only,
203		filter_string, awt_csp);
204		if (error) {
205		return error;
206		}
207
208		GB_HASH *species_to_info_hash = GBS_create_hash(GBT_get_species_count(gb_main), GB_IGNORE_CASE);
209		GB_CSTR snames = GBT_get_species_names_of_tree((GBT_TREE ) st_ml.tree_root->tree);
210
211		int pos;
212		aw_openstatus("Sequence Quality Check");
213		for (pos = 0; pos < seq_len; pos += ST_MAX_SEQ_PART) {
214		int end = pos + ST_MAX_SEQ_PART - 1;
215		if (end > seq_len)
216		end = seq_len;
217		if (aw_status(pos / double (seq_len))) {
218		return "aborted";
219		}
	199	const char alignment_name, AWT_csp awt_csp, int bucket_size,
	200	int marked_only, st_report_enum report, const char *dest_field)
	201	{
	202	int seq_len = GBT_get_alignment_len(gb_main, alignment_name);
	203	ST_ML st_ml(gb_main);
	204	GB_ERROR error = st_ml.init(tree_name, alignment_name, 0, marked_only, awt_csp, true);
	205
	206	if (!error) {
	207	GB_HASH *species_to_info_hash = GBS_create_hash(GBT_get_species_count(gb_main), GB_IGNORE_CASE);
	208	GB_CSTR *snames = GBT_get_species_names_of_tree(st_ml.tree_root->get_root_node()->get_gbt_tree());
	209
	210	int pos;
	211	aw_openstatus("Sequence Quality Check");
	212	for (pos = 0; pos < seq_len; pos += ST_MAX_SEQ_PART) {
	213	int end = pos + ST_MAX_SEQ_PART - 1;
	214	if (end > seq_len)
	215	end = seq_len;
	216	if (aw_status(pos / double (seq_len))) {
	217	return "aborted";
	218	}
	219	const char **pspecies_name;
	220	for (pspecies_name = snames; *pspecies_name; pspecies_name++) {
	221	st_ml_add_sequence_part_to_stat(&st_ml, awt_csp, *pspecies_name,
	222	seq_len, bucket_size, species_to_info_hash, pos, end);
	223	}
	224	}
	225	aw_status("Generating Result String");
220	226	const char **pspecies_name;
221	227	for (pspecies_name = snames; *pspecies_name; pspecies_name++) {
222		st_ml_add_sequence_part_to_stat(&st_ml, awt_csp, *pspecies_name,
223		seq_len, bucket_size, species_to_info_hash, pos, end);
224		}
225		}
226		aw_status("Generating Result String");
227		const char **pspecies_name;
228		for (pspecies_name = snames; *pspecies_name; pspecies_name++) {
229		st_ml_add_quality_string_to_species(gb_main, alignment_name,
230		*pspecies_name, seq_len, bucket_size, species_to_info_hash,
231		report, dest_field);
232		}
233		aw_closestatus();
234		free(snames);
235		GBS_free_hash(species_to_info_hash);
236		return NULL;
237		}
	228	st_ml_add_quality_string_to_species(gb_main, alignment_name,
	229	*pspecies_name, seq_len, bucket_size, species_to_info_hash,
	230	report, dest_field);
	231	}
	232	aw_closestatus();
	233
	234	free(snames);
	235	GBS_free_hash(species_to_info_hash);
	236	}
	237
	238	return error;
	239	}

trunk/STAT/ST_window.cxx

r5953	r6280
1		#include <stdio.h>
2		#include <stdlib.h>
3		#include <arbdb.h>
4		#include <arbdbt.h>
5		#include <aw_root.hxx>
6		#include <aw_window.hxx>
	1	// ================================================================ //
	2	// //
	3	// File : ST_window.cxx //
	4	// Purpose : //
	5	// //
	6	// Institute of Microbiology (Technical University Munich) //
	7	// http://www.arb-home.de/ //
	8	// //
	9	// ================================================================ //
	10
	11	#include "st_window.hxx"
	12	#include "st_ml.hxx"
	13
7	14	#include <aw_awars.hxx>
8	15	#include <awt.hxx>
9		#include <awt_~~tree~~.hxx>
	16	#include <awt_item_sel_list.hxx>
10	17	#include <awt_csp.hxx>
11		#include <awt_item_sel_list.hxx>
12		#include <awt_sel_boxes.hxx>
13		#include "st_window.hxx"
14		#include "st_ml.hxx"
15		#include "st_quality.hxx"
	18	#include <awt_filter.hxx>
16	19
17	20	void st_ok_cb(AW_window aww, ST_ML st_ml) {
…	…
22	25
23	26	GB_ERROR error = GB_push_transaction(st_ml->gb_main);
24		if (!error) error = st_ml->init(tree_name, alignment_name, ~~(char ) 0, marked_only, (char ) 0, st_ml->awt_csp~~);
	27	if (!error) error = st_ml->init(tree_name, alignment_name, NULL, marked_only, st_ml->awt_csp, true);
25	28	if (!error && st_ml->refresh_func) st_ml->refresh_func(st_ml->aw_window);
26	29
…	…
34	37	AW_window st_create_main_window(AW_root root, ST_ML * st_ml, AW_CB0 refresh_func, AW_window * win) {
35	38	AW_window_simple *aws = new AW_window_simple;
36		aws->init(root, "~~ENABLE_ONLINE_STATISTIC", "ACTIVATE ONLINE~~ STATISTIC");
	39	aws->init(root, "COLUMN_STATISTIC", "COLUMN STATISTIC");
37	40
38	41	aws->load_xfig("stat_main.fig");
…	…
107	110
108	111	void st_check_cb(AW_window * aww, GBDATA * gb_main, AWT_csp * awt_csp) {
109		GB_begin_transaction(gb_main);
	112	GB_transaction ta(gb_main);
	113
110	114	AW_root *r = aww->get_root();
	115
111	116	char *alignment_name = r->awar(ST_ML_AWAR_ALIGNMENT)->read_string();
112		int ~~bucket_size~~ = r->awar(ST_ML_AWAR_CQ_BUCKET_SIZE)->read_int();
113		char *tree_name = r->awar(AWAR_TREE)->read_string();
114		char *dest_field = r->awar(ST_ML_AWAR_CQ_DEST_FIELD)->read_string();
115		int ~~marked_only~~ = r->awar(ST_ML_AWAR_CQ_MARKED_ONLY)->read_int();
116		~~char *filter_string = r->awar(ST_ML_AWAR_CQ_FILTER_FILTER)->read_string();~~
	117	int bucket_size = r->awar(ST_ML_AWAR_CQ_BUCKET_SIZE)->read_int();
	118	char *tree_name = r->awar(AWAR_TREE)->read_string();
	119	char *dest_field = r->awar(ST_ML_AWAR_CQ_DEST_FIELD)->read_string();
	120	int marked_only = r->awar(ST_ML_AWAR_CQ_MARKED_ONLY)->read_int();
	121
117	122	st_report_enum report = (st_report_enum) r->awar(ST_ML_AWAR_CQ_REPORT)->read_int();
118		GB_ERROR error = st_ml_check_sequence_quality(gb_main, tree_name,
119		alignment_name, awt_csp, bucket_size, marked_only, report,
120		filter_string, dest_field);
121		free(filter_string);
	123	GB_ERROR error = st_ml_check_sequence_quality(gb_main, tree_name, alignment_name,
	124	awt_csp, bucket_size, marked_only,
	125	report, dest_field);
122	126	free(dest_field);
123	127	free(alignment_name);
124	128	free(tree_name);
125		if (error) {
126		aw_message(error);
127		GB_abort_transaction(gb_main);
128		} else {
129		GB_commit_transaction(gb_main);
130		}
	129
	130	error = ta.close(error);
	131	if (error) aw_message(error);
131	132	}
132	133
…	…
159	160	root->awar_int(ST_ML_AWAR_CQ_REPORT, 0);
160	161
161		~~root->awar_string(ST_ML_AWAR_CQ_FILTER_NAME, "ECOLI");~~
162		~~root->awar_string(ST_ML_AWAR_CQ_FILTER_ALIGNMENT);~~
163		~~root->awar_string(ST_ML_AWAR_CQ_FILTER_FILTER);~~
164
165	162	root->awar_string(ST_ML_AWAR_ALIGNMENT)->map(AWAR_DEFAULT_ALIGNMENT);
166		~~root->awar_string(ST_ML_AWAR_CQ_FILTER_ALIGNMENT)->~~
167		~~map(AWAR_DEFAULT_ALIGNMENT);~~
168	163
169	164	awt_csp = new AWT_csp(gb_main, root, ST_ML_AWAR_CSP);
170		~~//AW_CL filter_cl =~~
171		~~awt_create_select_filter(root, gb_main, ST_ML_AWAR_CQ_FILTER_NAME);~~
172	165
173	166	aws->at("which");

trunk/STAT/st_ml.hxx

r6141	r6280
	1	// =============================================================== //
	2	// //
	3	// File : st_ml.hxx //
	4	// Purpose : //
	5	// //
	6	// Institute of Microbiology (Technical University Munich) //
	7	// http://www.arb-home.de/ //
	8	// //
	9	// =============================================================== //
	10
	11	#ifndef ST_ML_HXX
	12	#define ST_ML_HXX
	13
	14	#ifndef AP_SEQUENCE_HXX
	15	#include <AP_sequence.hxx>
	16	#endif
	17	#ifndef AP_TREE_HXX
	18	#include <AP_Tree.hxx>
	19	#endif
	20
	21
1	22	#ifndef ARB_ASSERT_H
2	23	#include <arb_assert.h>
3	24	#endif
	25
4	26	#define st_assert(bed) arb_assert(bed)
5	27
…	…
55	77
56	78	/** Note: Because we have only limited memory we split the
57		sequence into ST_MAX_SEQ_PART long parts */
58		class ST_sequence_ml : private AP_sequence {
	79	sequence into ST_MAX_SEQ_PART long parts */
	80
	81
	82	class ST_sequence_ml : public AP_sequence {
59	83	friend class ST_ML;
	84
	85	AP_FLOAT count_weighted_bases() const;
	86
60	87	public:
61	88
62		~~GBDATA *gb_data; // the sequence~~
63	89	static ST_base_vector *tmp_out; // len = alignment length
64	90
65	91	protected:
66	92
67		ST_ML *st_ml; // link to a global ST object
68		ST_base_vector *sequence; // A part of the sequence
69		int last_updated;
70		ST_ML_Color *color_out;
71		int *color_out_valid_till; // color_out is valid up to
	93	ST_ML *st_ml; // link to a global ST object
	94	ST_base_vector *sequence; // A part of the sequence
	95	int last_updated;
	96	ST_ML_Color *color_out;
	97	int *color_out_valid_till; // color_out is valid up to
	98
	99	void set(const char *sequence);
	100	void unset();
72	101
73	102	public:
74		void delete_sequence(); // remove link to database
75		void sequence_change(); // sequence has changed in db
76		AP_FLOAT combine(const AP_sequence* lefts, const AP_sequence *rights);
	103
	104	ST_sequence_ml(const AliView aliview, ST_ML st_ml_);
	105	virtual ~ST_sequence_ml();
	106
	107	AP_sequence *dup(void) const;
	108	AP_FLOAT combine(const AP_sequence* lefts, const AP_sequence rights, char mutation_per_site = 0);
77	109	void partial_match(const AP_sequence* part, long overlap, long penalty) const;
78		~~ST_sequence_ml(AP_tree_root rooti, ST_ML st_ml);~~
79		~~~ST_sequence_ml();~~
80		~~AP_sequence *dup(void);~~
81	110
82		void set(const char *sequence);
83		void set_gb(GBDATA *gbd);
	111	GB_ERROR bind_to_species(GBDATA *gb_species);
	112	void unbind_from_species(bool remove_callbacks);
	113	GBDATA *get_bound_species_data() const { return AP_sequence::get_bound_species_data(); }
84	114
85		void set_sequence(); // start at st_ml->base
	115	void sequence_change(); // sequence has changed in db
	116	void set_sequence(); // start at st_ml->base
86	117
87		void go(const ST_sequence_ml *lefts, double leftl,
88		const ST_sequence_ml *rights, double rightl);
	118	void go(const ST_sequence_ml lefts, double leftl, const ST_sequence_ml rights, double rightl);
89	119	void ungo(); // undo go
90	120
…	…
97	127
98	128	class ST_ML {
99		char *alignment_name;
100		friend AP_tree st_ml_convert_species_name_to_node(ST_ML st_ml,
101		const char *species_name);
102		GB_HASH *hash_2_ap_tree; // hash table to get from name to tree_node
103		GB_HASH *keep_species_hash; // temporary hash to find
104		int refresh_n;
105		int *not_valid; // which columns are valid
	129	friend AP_tree st_ml_convert_species_name_to_node(ST_ML st_ml, const char *species_name);
	130
	131	char *alignment_name;
	132	GB_HASH *hash_2_ap_tree; // hash table to get from name to tree_node
	133	GB_HASH *keep_species_hash; // temporary hash to find
	134	int refresh_n;
	135	int *not_valid; // which columns are valid
	136
	137	ST_sequence_ml getOrCreate_seq(AP_tree node);
106	138
107	139	ST_sequence_ml do_tree(AP_tree node);
108		void undo_tree(AP_tree *node); //opposite of do_tree
109		void insert_tree_into_hash_rek(AP_tree *node);
110		void create_matrices(double max_disti, int nmatrices);
111		void create_frequencies();
112		static long delete_species(const char key, long val, void cd_st_ml);
	140	void undo_tree(AP_tree *node); //opposite of do_tree
	141	void insert_tree_into_hash_rek(AP_tree *node);
	142	void create_matrices(double max_disti, int nmatrices);
	143	void create_frequencies();
	144	static long delete_species(const char key, long val, void cd_st_ml);
	145
113	146	public:
114	147	AP_tree_root *tree_root;
115		int ~~latest_modification;~~ // last mod;
116		int base;
117		int to;
118		AW_CB0 refresh_func;
119		AW_window *aw_window;
	148	int latest_modification; // last mod;
	149	int base;
	150	int to;
	151	AW_CB0 refresh_func;
	152	AW_window *aw_window;
120	153
121		GBDATA *gb_main;
122		float *ttratio; // column independent
123		ST_base_vector *base_frequencies; // column independent
124		ST_base_vector *inv_base_frequencies; // column independent
125		float *rates; // column independent
126		double max_dist; // max_dist for rate_matrices
127		double step_size; // max_dist/step_size matrices
128		int max_matr;
129		ST_rate_matrix *rate_matrices; // for each distance a new matrix
130		long alignment_len;
131		AWT_csp *awt_csp;
	154	GBDATA *gb_main;
	155	const float *ttratio; // column independent
	156	ST_base_vector *base_frequencies; // column independent
	157	ST_base_vector *inv_base_frequencies; // column independent
	158	const float *rates; // column independent
	159	double max_dist; // max_dist for rate_matrices
	160	double step_size; // max_dist/step_size matrices
	161	int max_matr;
	162	ST_rate_matrix *rate_matrices; // for each distance a new matrix
	163	long alignment_len;
	164	AWT_csp *awt_csp;
	165
132	166	void set_modified(int *what = 0);
133		void set_refresh(); // set flag for refresh
	167	void set_refresh(); // set flag for refresh
134	168
135	169	~ST_ML();
…	…
138	172	int is_inited;
139	173
140		GB_ERROR init(const char tree_name, const char alignment_name,
141		const char *species_names, int marked_only,
142		const char filter_string, AWT_csp awt_csp);
143		// species_names is 0 -> all [marked] species (else species_names is a (char)1 separated list of species)
144		// filter_string==0 -> no filter
	174	GB_ERROR init(const char *tree_name,
	175	const char *alignment_name,
	176	const char *species_names, // 0 -> all [marked] species (else species_names is a (char)1 separated list of species)
	177	int marked_only,
	178	AWT_csp *awt_csp,
	179	bool show_status) __ATTR__USERESULT;
145	180
146		void clear_all(); // delete all caches
	181	void clear_all(); // delete all caches
147	182
	183	ST_sequence_ml get_ml_vectors(char species_name, AP_tree *node, int start_ali_pos, int end_ali_pos);
	184	ST_ML_Color get_color_string(char species_name, AP_tree *node, int start_ali_pos, int end_ali_pos);
148	185
149		ST_sequence_ml get_ml_vectors(char species_name, AP_tree *node,
150		int start_ali_pos, int end_ali_pos);
151		ST_ML_Color get_color_string(char species_name, AP_tree *node,
152		int start_ali_pos, int end_ali_pos);
153
154		int update_ml_likelihood(char result[4], int latest_update,
155		char species_name, AP_tree node);
	186	int update_ml_likelihood(char result[4], int latest_update, char species_name, AP_tree node);
156	187
157	188	int refresh_needed();
158	189	};
	190
	191	#else
	192	#error st_ml.hxx included twice
	193	#endif // ST_ML_HXX

trunk/STAT/st_window.hxx

r5968	r6280
12	12	#define ST_WINDOW_HXX
13	13
	14	#ifndef ARBDBT_H
	15	#include <arbdbt.h>
	16	#endif
	17	#ifndef AW_WINDOW_HXX
	18	#include <aw_window.hxx>
	19	#endif
14	20
15	21	#define ST_ML_AWAR "tmp/st_ml/"
…	…
18	24	#define ST_ML_AWAR_CQ_BUCKET_SIZE ST_ML_AWAR "bucket_size"
19	25
20		~~#define ST_ML_AWAR_CQ_FILTER_NAME ST_ML_AWAR "filter/name"~~
21		~~#define ST_ML_AWAR_CQ_FILTER_ALIGNMENT ST_ML_AWAR "filter/alignment"~~
22		~~#define ST_ML_AWAR_CQ_FILTER_FILTER ST_ML_AWAR "filter/filter"~~
23	26	#define ST_ML_AWAR_CQ_MARKED_ONLY ST_ML_AWAR "marked_only"
24	27	#define ST_ML_AWAR_CQ_DEST_FIELD ST_ML_AWAR "dest_field"
…	…
53	56	GB_ERROR st_ml_check_sequence_quality(GBDATA * gb_main, const char *tree_name,
54	57	const char alignment_name, AWT_csp awt_csp, int bucket_size,
55		int marked_only, st_report_enum report, const char *filter_string,
56		const char *dest_field);
	58	int marked_only, st_report_enum report, const char *dest_field);
57	59
58	60

trunk/WINDOW/AW_window.cxx

r6223	r6280
1379	1379
1380	1380	static int aw_status_dummy2(const char *val) {
1381		return aw_status(~~(char *)~~val);
	1381	return aw_status(val);
1382	1382	}
1383	1383

trunk/lib/pictures/di_ge_ma.fig

r6141	r6280
8	8	-2
9	9	1200 2
10		6 12825 7245 13905 7875
11		4 0 -1 0 0 18 12 0.0000 4 135 1125 12825 7380 No. of trees:\001
12		4 0 -1 0 0 18 12 0.0000 4 165 705 12825 7830 $bcount\001
13		-6
14		6 12645 1530 13815 2205
15		4 2 -1 0 0 18 12 0.0000 4 180 1155 13815 2160 $mark_upper\001
16		4 2 -1 0 0 18 12 0.0000 4 180 1155 13815 1710 $mark_lower\001
17		-6
18		6 8145 2430 14490 4050
19		2 1 0 2 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
20		8175 4020 14475 4020
21		4 0 -1 0 0 18 12 0.0000 4 135 1620 8175 2595 Trees in Database\001
22		4 0 -1 0 0 18 12 0.0000 4 180 840 9975 2745 $tree_list\001
23		4 2 -1 0 0 18 12 0.0000 4 180 1260 14310 3870 $to:X:tree_list\001
24		-6
25		6 8145 4275 14490 6165
26		2 1 0 2 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
27		8175 6150 14475 6150
28		4 0 -1 0 0 18 12 0.0000 4 165 900 8175 4575 $calculate\001
29		4 0 -1 0 0 18 12 0.0000 4 180 1215 12825 4425 $view_matrix\001
30		4 0 -1 0 0 18 12 0.0000 4 180 975 10425 4575 $compress\001
31		4 0 -1 0 0 18 13 0.0000 4 210 1350 12825 4875 $save_matrix\001
32		4 0 -1 0 0 18 13 0.0000 4 210 1560 8175 5850 $use_sort_tree\001
33		4 0 -1 0 0 18 13 0.0000 4 210 1800 8175 5400 $use_compr_tree\001
34		4 0 -1 0 0 18 12 0.0000 4 180 1710 11100 5400 $compr_tree_name\001
35		4 0 -1 0 0 18 12 0.0000 4 180 1515 11100 5850 $sort_tree_name\001
36		4 2 -1 0 0 18 12 0.0000 4 180 2130 14325 5550 $to:X:compr_tree_name\001
37		4 2 -1 0 0 18 12 0.0000 4 180 1935 14325 6000 $to:X:sort_tree_name\001
	10	6 12285 1530 13680 2205
	11	4 0 -1 0 0 18 12 0.0000 4 225 1365 12285 2160 $mark_upper\001
	12	4 0 -1 0 0 18 12 0.0000 4 225 1305 12285 1710 $mark_lower\001
38	13	-6
39	14	2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 1
…	…
44	19	1275 5700 7500 5700
45	20	2 1 0 2 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
46		7800 1500 7800 ~~796~~5
	21	7800 1500 7800 9045
47	22	2 1 0 2 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
48		8175 2295 14475 2295
	23	8175 5190 14760 5190
	24	2 1 0 2 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
	25	8175 7320 14760 7320
49	26	2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 1
50		14625 8010
51		4 0 -1 0 0 18 12 0.0000 4 165 570 1200 1125 $close\001
52		4 2 -1 0 0 18 12 0.0000 4 180 465 14475 1125 $help\001
53		4 0 -1 0 0 18 12 0.0000 4 180 1170 3975 3675 $filter_select\001
54		4 0 -1 0 0 18 12 0.0000 4 180 1455 3975 4275 $weights_select\001
55		4 0 -1 0 0 18 13 0.0000 4 210 1515 3975 4875 $which_cancel\001
56		4 0 -1 0 0 18 12 0.0000 4 135 2565 1275 5400 User defined distance matrix\001
57		4 0 -1 0 0 18 12 0.0000 4 180 1410 3975 5475 $change_matrix\001
58		4 2 -1 0 0 18 12 0.0000 4 180 1650 5700 5475 $to:change_matrix\001
59		4 0 -1 0 0 18 12 0.0000 4 135 570 6000 5400 enable\001
60		4 0 -1 0 0 18 12 0.0000 4 135 1395 1275 4800 Exclude Column\001
61		4 0 -1 0 0 18 12 0.0000 4 180 1845 1275 4200 Weights/Rates/GC ...\001
62		4 0 -1 0 0 18 12 0.0000 4 135 450 1275 3600 Filter\001
63		4 0 -1 0 0 18 12 0.0000 4 165 1065 3975 6750 $autodetect\001
64		4 0 -1 0 0 18 12 0.0000 4 135 915 1275 6150 Correction\001
65		4 0 -1 0 0 18 12 0.0000 4 180 1635 3975 6225 $which_correction\001
66		4 0 -1 0 0 18 12 0.0000 4 180 1275 1275 1800 Which Species\001
67		4 2 -1 0 0 18 12 0.0000 4 180 1650 7575 6225 $correction_select\001
68		4 2 -1 0 0 18 12 0.0000 4 180 1410 7575 3675 $to:filter_select\001
69		4 2 -1 0 0 18 12 0.0000 4 180 1695 7575 4275 $to:weights_select\001
70		4 2 -1 0 0 18 12 0.0000 4 180 1320 7575 4875 $cancel_select\001
71		4 0 -1 0 0 18 12 0.0000 4 165 675 6825 5475 $enable\001
72		4 0 -1 0 0 18 12 0.0000 4 180 1410 1500 2325 $which_species\001
73		4 0 -1 0 0 18 12 0.0000 4 180 870 3150 1800 Alignment\001
74		4 0 -1 0 0 18 12 0.0000 4 180 1590 4350 1800 $which_alignment\001
75		4 2 -1 0 0 18 12 0.0000 4 180 1830 7575 3075 $to:which_alignment\001
76		4 0 -1 0 0 18 12 0.0000 4 180 1410 8235 1755 $mark_distance\001
77		4 0 -1 0 0 18 13 0.0000 4 210 1425 8175 6765 $use_existing\001
78		4 0 -1 0 0 18 12 0.0000 4 180 1515 11100 6765 $calc_tree_name\001
79		4 2 -1 0 0 18 12 0.0000 4 180 1935 14325 6915 $to:X:calc_tree_name\001
80		4 0 -1 0 0 18 12 0.0000 4 180 1080 8175 7515 $t_calculate\001
81		4 0 -1 0 0 18 12 0.0000 4 180 960 10425 7515 $bootstrap\001
82		4 0 -1 0 0 18 12 0.0000 4 135 3255 8505 2070 where distance to selected is inside:\001
	27	14895 9180
	28	2 1 0 2 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
	29	8175 2295 14760 2295
	30	4 0 -1 0 0 18 12 0.0000 4 210 675 1200 1125 $close\001
	31	4 0 -1 0 0 18 12 0.0000 4 225 1320 3975 3675 $filter_select\001
	32	4 0 -1 0 0 18 12 0.0000 4 225 1650 3975 4275 $weights_select\001
	33	4 0 -1 0 0 18 13 0.0000 4 225 1515 3975 4875 $which_cancel\001
	34	4 0 -1 0 0 18 12 0.0000 4 165 2955 1275 5400 User defined distance matrix\001
	35	4 0 -1 0 0 18 12 0.0000 4 225 1635 3975 5475 $change_matrix\001
	36	4 2 -1 0 0 18 12 0.0000 4 225 1920 5700 5475 $to:change_matrix\001
	37	4 0 -1 0 0 18 12 0.0000 4 165 690 6000 5400 enable\001
	38	4 0 -1 0 0 18 12 0.0000 4 165 1680 1275 4800 Exclude Column\001
	39	4 0 -1 0 0 18 12 0.0000 4 210 2145 1275 4200 Weights/Rates/GC ...\001
	40	4 0 -1 0 0 18 12 0.0000 4 165 540 1275 3600 Filter\001
	41	4 0 -1 0 0 18 12 0.0000 4 210 1230 3975 6750 $autodetect\001
	42	4 0 -1 0 0 18 12 0.0000 4 165 1125 1275 6150 Correction\001
	43	4 0 -1 0 0 18 12 0.0000 4 225 1920 3975 6225 $which_correction\001
	44	4 0 -1 0 0 18 12 0.0000 4 210 1545 1275 1800 Which Species\001
	45	4 2 -1 0 0 18 12 0.0000 4 225 1935 7575 6225 $correction_select\001
	46	4 2 -1 0 0 18 12 0.0000 4 225 1605 7575 3675 $to:filter_select\001
	47	4 2 -1 0 0 18 12 0.0000 4 225 1935 7575 4275 $to:weights_select\001
	48	4 2 -1 0 0 18 12 0.0000 4 225 1530 7575 4875 $cancel_select\001
	49	4 0 -1 0 0 18 12 0.0000 4 210 810 6825 5475 $enable\001
	50	4 0 -1 0 0 18 12 0.0000 4 225 1635 1500 2325 $which_species\001
	51	4 0 -1 0 0 18 12 0.0000 4 210 1050 3150 1800 Alignment\001
	52	4 0 -1 0 0 18 12 0.0000 4 225 1860 4350 1800 $which_alignment\001
	53	4 2 -1 0 0 18 12 0.0000 4 225 2145 7575 3075 $to:which_alignment\001
	54	4 0 -1 0 0 18 12 0.0000 4 165 3765 8505 2070 where distance to selected is inside:\001
	55	4 2 -1 0 0 18 12 0.0000 4 225 570 14745 1125 $help\001
	56	4 0 -1 0 0 18 12 0.0000 4 225 1740 11100 7935 $calc_tree_name\001
	57	4 0 -1 0 0 18 12 0.0000 4 225 1980 11100 6570 $compr_tree_name\001
	58	4 0 -1 0 0 18 12 0.0000 4 225 1740 11100 7020 $sort_tree_name\001
	59	4 2 -1 0 0 18 12 0.0000 4 225 1455 14580 4590 $to:X:tree_list\001
	60	4 2 -1 0 0 18 12 0.0000 4 225 2235 14595 8085 $to:X:calc_tree_name\001
	61	4 2 -1 0 0 18 12 0.0000 4 225 2475 14595 6720 $to:X:compr_tree_name\001
	62	4 2 -1 0 0 18 12 0.0000 4 225 2235 14595 7170 $to:X:sort_tree_name\001
	63	4 0 -1 0 0 18 13 0.0000 4 225 1350 13095 5985 $save_matrix\001
	64	4 0 -1 0 0 18 12 0.0000 4 165 1275 13095 8550 No. of trees:\001
	65	4 0 -1 0 0 18 12 0.0000 4 210 855 13095 9000 $bcount\001
	66	4 0 -1 0 0 18 12 0.0000 4 225 1140 10665 8685 $bootstrap\001
	67	4 0 -1 0 0 18 12 0.0000 4 210 1050 8175 5625 $calculate\001
	68	4 0 -1 0 0 18 12 0.0000 4 225 1320 13095 5625 $view_matrix\001
	69	4 0 -1 0 0 18 12 0.0000 4 225 1140 10665 5625 $compress\001
	70	4 0 -1 0 0 18 12 0.0000 4 225 1635 8145 1755 $mark_distance\001
	71	4 0 -1 0 0 18 12 0.0000 4 165 1860 8145 2595 Trees in Database\001
	72	4 0 -1 0 0 18 12 0.0000 4 225 960 8145 2970 $tree_list\001
	73	4 0 -1 0 0 18 13 0.0000 4 225 1425 8145 7935 $use_existing\001
	74	4 0 -1 0 0 18 12 0.0000 4 225 1245 8145 8685 $t_calculate\001
	75	4 0 -1 0 0 18 13 0.0000 4 225 1560 8145 7020 $use_sort_tree\001
	76	4 0 -1 0 0 18 13 0.0000 4 225 1800 8145 6570 $use_compr_tree\001
	77	4 0 -1 0 0 18 12 0.0000 4 225 1725 8145 4995 $detect_clusters\001

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