source: tags/arb_5.1/PROBE/pt_prototypes.h

Last change on this file was 5968, checked in by westram, 17 years ago
  • new flag -w to aisc_mkpt (add include wrapper)
  • uniform style for several include wrappers
  • removed duplicated includes
  • removed useless nt_concatenate.hxx
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 5.9 KB
Line 
1/*
2 * This file is generated by aisc_mkpt.
3 * Any changes you make here will be overwritten later!
4 *
5 */
6
7#ifndef PT_PROTOTYPES_H
8#define PT_PROTOTYPES_H
9
10#ifndef P_
11# if defined(__STDC__) || defined(__cplusplus)
12#  define P_(s) s
13# else
14#  define P_(s) ()
15# endif
16#else
17# error P_ already defined elsewhere
18#endif
19
20
21/* PT_new_design.cxx */
22int ptnd_check_pure P_((char *probe));
23double ptnd_check_split P_((PT_pdc *pdc, char *probe, int pos, char ref));
24extern "C" char *get_design_info P_((PT_tprobes *tprobe));
25extern "C" char *get_design_hinfo P_((PT_tprobes *tprobe));
26extern "C" int PT_start_design P_((PT_pdc *pdc, int dummy_1x));
27void ptnd_new_match P_((PT_local *locs, char *probestring));
28
29/* PT_family.cxx */
30extern "C" int ff_find_family P_((PT_local *locs, bytestring *species));
31
32/* PT_prefixtree.cxx */
33void PT_init_count_bits P_((void));
34char *PTM_get_mem P_((int size));
35int PTM_destroy_mem P_((void));
36void PTM_free_mem P_((char *data, int size));
37void PTM_debug_mem P_((void));
38PTM2 *PT_init P_((int base_count));
39int PTD P_((POS_TREE *node));
40void PT_change_father P_((POS_TREE *father, POS_TREE *source, POS_TREE *dest));
41POS_TREE *PT_add_to_chain P_((PTM2 *ptmain, POS_TREE *node, int name, int apos, int rpos));
42POS_TREE *PT_change_leaf_to_node P_((PTM2 *, POS_TREE *node));
43POS_TREE *PT_leaf_to_chain P_((PTM2 *ptmain, POS_TREE *node));
44POS_TREE *PT_create_leaf P_((PTM2 *ptmain, POS_TREE **pfather, PT_BASES base, int rpos, int apos, int name));
45void PTD_clear_fathers P_((PTM2 *ptmain, POS_TREE *node));
46void PTD_put_longlong P_((FILE *out, ULONG i));
47void PTD_put_int P_((FILE *out, ULONG i));
48void PTD_put_short P_((FILE *out, ULONG i));
49void PTD_set_object_to_saved_status P_((POS_TREE *node, long pos, int size));
50long PTD_write_tip_to_disk P_((FILE *out, PTM2 *, POS_TREE *node, long pos));
51int ptd_count_chain_entries P_((char *entry));
52void ptd_set_chain_references P_((char *entry, char **entry_tab));
53void ptd_write_chain_entries P_((FILE *out, long *ppos, PTM2 *, char **entry_tab, int n_entries, int mainapos));
54long PTD_write_chain_to_disk P_((FILE *out, PTM2 *ptmain, POS_TREE *node, long pos));
55void PTD_debug_nodes P_((void));
56long PTD_write_node_to_disk P_((FILE *out, PTM2 *ptmain, POS_TREE *node, long *r_poss, long pos));
57long PTD_write_leafs_to_disk P_((FILE *out, PTM2 *ptmain, POS_TREE *node, long pos, long *pnodepos, int *pblock));
58void PTD_read_leafs_from_disk P_((char *fname, PTM2 *ptmain, POS_TREE **pnode));
59
60/* PT_main.cxx */
61char *pt_init_main_struct P_((PT_main *main, char *filename));
62extern "C" int server_shutdown P_((PT_main *pm, aisc_string passwd));
63extern "C" int broadcast P_((PT_main *main, int dummy));
64void PT_init_psg P_((void));
65void PT_init_map P_((void));
66
67/* PT_io.cxx */
68int compress_data P_((char *probestring));
69void PT_base_2_string P_((char *id_string, long len));
70void probe_read_data_base P_((char *name));
71int probe_compress_sequence P_((char *seq, int seqsize));
72char *probe_read_alignment P_((int j, int *psize));
73void probe_read_alignments P_((void));
74void PT_build_species_hash P_((void));
75long PT_abs_2_rel P_((long pos));
76long PT_rel_2_abs P_((long pos));
77
78/* PT_etc.cxx */
79void set_table_for_PT_N_mis P_((void));
80void pt_export_error P_((PT_local *locs, const char *error));
81extern "C" const char *virt_name P_((PT_probematch *ml));
82extern "C" const char *virt_fullname P_((PT_probematch *ml));
83int *table_copy P_((int *mis_table, int length));
84void table_add P_((int *mis_tabled, int *mis_tables, int length));
85char *ptpd_read_names P_((PT_local *locs, const char *names_list, const char *checksums, const char *&error));
86extern "C" bytestring *PT_unknown_names P_((struct_PT_pdc *pdc));
87int get_clip_max_from_length P_((int length));
88void PT_init_base_string_counter P_((char *str, char initval, int size));
89void PT_inc_base_string_count P_((char *str, char initval, char maxval, int size));
90
91/* PT_buildtree.cxx */
92POS_TREE *build_pos_tree P_((POS_TREE *pt, int anfangs_pos, int apos, int RNS_nr, unsigned int end));
93long PTD_save_partial_tree P_((FILE *out, PTM2 *ptmain, POS_TREE *node, char *partstring, int partsize, long pos, long *ppos));
94void enter_stage_1_build_tree P_((PT_main *main, char *tname));
95void enter_stage_3_load_tree P_((PT_main *main, char *tname));
96void PT_analyse_tree P_((POS_TREE *pt, int height));
97void PT_debug_tree P_((void));
98
99/* PT_match.cxx */
100int read_names_and_pos P_((PT_local *locs, POS_TREE *pt));
101int get_info_about_probe P_((PT_local *locs, char *probe, POS_TREE *pt, int mismatches, double wmismatches, int N_mismatches, int height));
102void pt_sort_match_list P_((PT_local *locs));
103char *reverse_probe P_((char *probe, int probe_length));
104int PT_complement P_((int base));
105void complement_probe P_((char *probe, int probe_length));
106void pt_build_pos_to_weight P_((PT_MATCH_TYPE type, const char *sequence));
107extern "C" int probe_match P_((PT_local *locs, aisc_string probestring));
108extern "C" bytestring *match_string P_((PT_local *locs));
109extern "C" bytestring *MP_match_string P_((PT_local *locs));
110extern "C" bytestring *MP_all_species_string P_((PT_local *));
111extern "C" int MP_count_all_species P_((PT_local *));
112
113/* PT_findEx.cxx */
114extern "C" int PT_find_exProb P_((PT_exProb *pep));
115
116/* probe_tree.hxx */
117GB_INLINE const char *PT_READ_CHAIN_ENTRY P_((const char *ptr, int mainapos, int *name, int *apos, int *rpos));
118GB_INLINE char *PT_WRITE_CHAIN_ENTRY P_((const char *const ptr, const int mainapos, int name, const int apos, const int rpos));
119GB_INLINE POS_TREE *PT_read_son P_((PTM2 *ptmain, POS_TREE *node, PT_BASES base));
120GB_INLINE POS_TREE *PT_read_son_stage_1 P_((PTM2 *ptmain, POS_TREE *node, PT_BASES base));
121GB_INLINE PT_NODE_TYPE PT_read_type P_((POS_TREE *node));
122GB_INLINE int PT_read_name P_((PTM2 *ptmain, POS_TREE *node));
123GB_INLINE int PT_read_rpos P_((PTM2 *ptmain, POS_TREE *node));
124GB_INLINE int PT_read_apos P_((PTM2 *ptmain, POS_TREE *node));
125template <typename T >int PT_read_chain P_((PTM2 *ptmain, POS_TREE *node, T func));
126
127#undef P_
128
129#else
130#error pt_prototypes.h included twice
131#endif /* PT_PROTOTYPES_H */
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