source: tags/arb-6.0-rc1/NTREE/ad_trees.cxx

Last change on this file was 11968, checked in by westram, 11 years ago
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File size: 55.7 KB
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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 "NT_local.h"
12#include "ad_trees.h"
13#include "NT_tree_cmp.h"
14
15#include <CT_ctree.hxx>
16
17#include <TreeAdmin.h>
18#include <TreeRead.h>
19#include <TreeWrite.h>
20#include <TreeCallbacks.hxx>
21
22#include <awt_sel_boxes.hxx>
23#include <awt_modules.hxx>
24#include <awt_TreeAwars.hxx>
25
26#include <aw_awars.hxx>
27#include <aw_edit.hxx>
28#include <aw_file.hxx>
29#include <aw_msg.hxx>
30#include <aw_root.hxx>
31#include <aw_select.hxx>
32
33#include <arb_strbuf.h>
34#include <arb_file.h>
35#include <arb_diff.h>
36
37#include <cctype>
38
39#define AWAR_TREE_SAV "ad_tree/"
40#define AWAR_TREE_TMP "tmp/ad_tree/"
41
42#define AWAR_TREE_SECURITY         AWAR_TREE_TMP "tree_security"
43#define AWAR_TREE_REM              AWAR_TREE_TMP "tree_rem"
44#define AWAR_TREE_IMPORT           AWAR_TREE_TMP "import_tree"
45#define AWAR_NODE_INFO_ONLY_MARKED AWAR_TREE_TMP "import_only_marked_node_info"
46
47#define AWAR_TREE_EXPORT_FILEBASE AWAR_TREE_TMP "export_tree"
48#define AWAR_TREE_EXPORT_FILTER   AWAR_TREE_EXPORT_FILEBASE "/filter"
49#define AWAR_TREE_EXPORT_NAME     AWAR_TREE_EXPORT_FILEBASE "/file_name"
50
51#define AWAR_TREE_EXPORT_SAV AWAR_TREE_SAV "export_tree/"
52
53#define AWAR_TREE_EXPORT_FORMAT             AWAR_TREE_EXPORT_SAV "format"
54#define AWAR_TREE_EXPORT_NDS                AWAR_TREE_EXPORT_SAV "NDS"
55#define AWAR_TREE_EXPORT_INCLUDE_BOOTSTRAPS AWAR_TREE_EXPORT_SAV "bootstraps"
56#define AWAR_TREE_EXPORT_INCLUDE_BRANCHLENS AWAR_TREE_EXPORT_SAV "branchlens"
57#define AWAR_TREE_EXPORT_INCLUDE_GROUPNAMES AWAR_TREE_EXPORT_SAV "groupnames"
58#define AWAR_TREE_EXPORT_HIDE_FOLDED_GROUPS AWAR_TREE_EXPORT_SAV "hide_folded"
59#define AWAR_TREE_EXPORT_QUOTEMODE          AWAR_TREE_EXPORT_SAV "quote_mode"
60#define AWAR_TREE_EXPORT_REPLACE            AWAR_TREE_EXPORT_SAV "replace"
61
62
63#define AWAR_TREE_CONSENSE_TMP AWAR_TREE_TMP "consense/"
64#define AWAR_TREE_CONSENSE_SAV AWAR_TREE_SAV "consense/"
65
66#define AWAR_TREE_CONSENSE_TREE     AWAR_TREE_CONSENSE_SAV "tree"
67#define AWAR_TREE_CONSENSE_SELECTED AWAR_TREE_CONSENSE_TMP "selected"
68
69static void tree_vars_callback(AW_root *aw_root) // Map tree vars to display objects
70{
71    if (GLOBAL.gb_main) {
72        GB_push_transaction(GLOBAL.gb_main);
73        char *treename = aw_root->awar(AWAR_TREE_NAME)->read_string();
74        GBDATA *ali_cont = GBT_find_tree(GLOBAL.gb_main, treename);
75        if (!ali_cont) {
76            aw_root->awar(AWAR_TREE_SECURITY)->unmap();
77            aw_root->awar(AWAR_TREE_REM)->unmap();
78        }
79        else {
80            GBDATA *tree_prot = GB_search(ali_cont, "security", GB_FIND);
81            if (!tree_prot) GBT_readOrCreate_int(ali_cont, "security", GB_read_security_write(ali_cont));
82            tree_prot         = GB_search(ali_cont, "security", GB_INT);
83
84            GBDATA *tree_rem = GB_search(ali_cont, "remark",   GB_STRING);
85            aw_root->awar(AWAR_TREE_SECURITY)->map(tree_prot);
86            aw_root->awar(AWAR_TREE_REM)     ->map(tree_rem);
87        }
88        char *suffix = aw_root->awar(AWAR_TREE_EXPORT_FILTER)->read_string();
89        char *fname  = GBS_string_eval(treename, GBS_global_string("*=*1.%s:tree_*=*1", suffix), 0);
90        aw_root->awar(AWAR_TREE_EXPORT_NAME)->write_string(fname); // create default file name
91        free(fname);
92        free(suffix);
93        GB_pop_transaction(GLOBAL.gb_main);
94        free(treename);
95    }
96}
97//  update import tree name depending on file name
98static void tree_import_callback(AW_root *aw_root) {
99    GB_transaction  ta(GLOBAL.gb_main);
100    char           *treename        = aw_root->awar(AWAR_TREE_IMPORT "/file_name")->read_string();
101    char           *treename_nopath = strrchr(treename, '/');
102
103    if (treename_nopath) {
104        ++treename_nopath;
105    }
106    else {
107        treename_nopath = treename;
108    }
109
110    char *fname = GBS_string_eval(treename_nopath, "*.tree=tree_*1:*.ntree=tree_*1:*.xml=tree_*1:.=", 0);
111    aw_root->awar(AWAR_TREE_IMPORT "/tree_name")->write_string(fname);
112
113    free(fname);
114    free(treename);
115}
116
117
118static void ad_tree_set_security(AW_root *aw_root)
119{
120    if (GLOBAL.gb_main) {
121        GB_transaction ta(GLOBAL.gb_main);
122        char *treename = aw_root->awar(AWAR_TREE_NAME)->read_string();
123        GBDATA *ali_cont = GBT_find_tree(GLOBAL.gb_main, treename);
124        if (ali_cont) {
125            long prot = aw_root->awar(AWAR_TREE_SECURITY)->read_int();
126            long old;
127            old = GB_read_security_delete(ali_cont);
128            GB_ERROR error = 0;
129            if (old != prot) {
130                error = GB_write_security_delete(ali_cont, prot);
131                if (!error)
132                    error = GB_write_security_write(ali_cont, prot);
133            }
134            if (error) aw_message(error);
135        }
136        free(treename);
137    }
138}
139
140enum ExportTreeType {
141    AD_TREE_EXPORT_FORMAT_NEWICK,
142    AD_TREE_EXPORT_FORMAT_XML,
143    AD_TREE_EXPORT_FORMAT_NEWICK_PRETTY,
144};
145
146enum ExportNodeType {
147    AD_TREE_EXPORT_NODE_SPECIES_NAME,
148    AD_TREE_EXPORT_NODE_NDS
149};
150
151static void update_filter_cb(AW_root *root) {
152    const char *filter_type = 0;
153
154    switch (ExportTreeType(root->awar(AWAR_TREE_EXPORT_FORMAT)->read_int())) {
155        case AD_TREE_EXPORT_FORMAT_XML: filter_type = "xml"; break;
156        case AD_TREE_EXPORT_FORMAT_NEWICK:
157        case AD_TREE_EXPORT_FORMAT_NEWICK_PRETTY:
158            switch (ExportNodeType(root->awar(AWAR_TREE_EXPORT_NDS)->read_int())) {
159                case AD_TREE_EXPORT_NODE_SPECIES_NAME:  filter_type = "tree"; break;
160                case AD_TREE_EXPORT_NODE_NDS:           filter_type = "ntree"; break;
161                default: nt_assert(0); break;
162            }
163            break;
164        default: nt_assert(0); break;
165    }
166
167    nt_assert(filter_type);
168    root->awar(AWAR_TREE_EXPORT_FILTER)->write_string(filter_type);
169}
170
171void create_trees_var(AW_root *aw_root, AW_default aw_def) {
172    AW_awar *awar_tree_name = aw_root->awar_string(AWAR_TREE_NAME, 0, aw_def)->set_srt(GBT_TREE_AWAR_SRT);
173
174    TreeAdmin::create_awars(aw_root, aw_def, true);
175
176    aw_root->awar_int   (AWAR_TREE_SECURITY, 0, aw_def);
177    aw_root->awar_string(AWAR_TREE_REM,      0, aw_def);
178
179    AW_create_fileselection_awars(aw_root, AWAR_TREE_EXPORT_FILEBASE, "", ".tree", "treefile");
180    aw_root->awar_int(AWAR_TREE_EXPORT_FORMAT, AD_TREE_EXPORT_FORMAT_NEWICK, aw_def)-> add_callback(update_filter_cb);
181    aw_root->awar_int(AWAR_TREE_EXPORT_NDS,  AD_TREE_EXPORT_NODE_SPECIES_NAME, aw_def)-> add_callback(update_filter_cb);
182
183    aw_root->awar_int(AWAR_TREE_EXPORT_INCLUDE_BOOTSTRAPS,  0, aw_def);
184    aw_root->awar_int(AWAR_TREE_EXPORT_INCLUDE_BRANCHLENS,  1, aw_def);
185    aw_root->awar_int(AWAR_TREE_EXPORT_HIDE_FOLDED_GROUPS,  0, aw_def);
186    aw_root->awar_int(AWAR_TREE_EXPORT_INCLUDE_GROUPNAMES,  1, aw_def);
187    aw_root->awar_int(AWAR_TREE_EXPORT_QUOTEMODE, TREE_SINGLE_QUOTES, aw_def); // old default behavior
188    aw_root->awar_int(AWAR_TREE_EXPORT_REPLACE, 0, aw_def); // old default behavior
189
190    AW_create_fileselection_awars(aw_root, AWAR_TREE_IMPORT, "", ".tree", "treefile");
191
192    aw_root->awar_string(AWAR_TREE_IMPORT "/tree_name", "tree_",    aw_def)->set_srt(GBT_TREE_AWAR_SRT);
193
194    aw_root->awar(AWAR_TREE_IMPORT "/file_name")->add_callback(tree_import_callback);
195    awar_tree_name->add_callback(tree_vars_callback);
196    awar_tree_name->map(AWAR_TREE);
197    aw_root->awar(AWAR_TREE_SECURITY)->add_callback(ad_tree_set_security);
198
199    aw_root->awar_int(AWAR_NODE_INFO_ONLY_MARKED, 0,    aw_def);
200
201    aw_root->awar_string(AWAR_TREE_CONSENSE_TREE, "tree_consensus", aw_def)->set_srt(GBT_TREE_AWAR_SRT);
202    AW_awar *ctree_awar = aw_root->awar_string(AWAR_TREE_CONSENSE_SELECTED, "", aw_def);
203    AWT_registerTreeAwarSimple(ctree_awar);
204
205    update_filter_cb(aw_root);
206    tree_vars_callback(aw_root);
207}
208
209static void tree_save_cb(AW_window *aww) {
210    AW_root  *aw_root   = aww->get_root();
211    char     *tree_name = aw_root->awar(AWAR_TREE_NAME)->read_string();
212
213    GB_ERROR error = 0;
214
215    if (!tree_name || !strlen(tree_name)) {
216        error = "Please select a tree first";
217    }
218    else {
219        char *fname   = aw_root->awar(AWAR_TREE_EXPORT_NAME)->read_string();
220        char *db_name = aw_root->awar(AWAR_DB_NAME)->read_string();
221
222        bool                use_NDS    = ExportNodeType(aw_root->awar(AWAR_TREE_EXPORT_NDS)->read_int()) == AD_TREE_EXPORT_NODE_NDS;
223        ExportTreeType      exportType = static_cast<ExportTreeType>(aw_root->awar(AWAR_TREE_EXPORT_FORMAT)->read_int());
224        TREE_node_text_gen *node_gen   = use_NDS ? new TREE_node_text_gen(make_node_text_init, make_node_text_nds) : 0;
225
226        switch (exportType) {
227            case AD_TREE_EXPORT_FORMAT_XML:
228                error = TREE_write_XML(GLOBAL.gb_main, db_name, tree_name, node_gen,
229                                       aw_root->awar(AWAR_TREE_EXPORT_HIDE_FOLDED_GROUPS)->read_int(),
230                                       fname);
231                break;
232
233            case AD_TREE_EXPORT_FORMAT_NEWICK:
234            case AD_TREE_EXPORT_FORMAT_NEWICK_PRETTY:
235                TREE_node_quoting quoteMode = TREE_node_quoting(aw_root->awar(AWAR_TREE_EXPORT_QUOTEMODE)->read_int());
236                if (aw_root->awar(AWAR_TREE_EXPORT_REPLACE)->read_int()) {
237                    quoteMode = TREE_node_quoting(quoteMode|TREE_FORCE_REPLACE);
238                }
239
240                error = TREE_write_Newick(GLOBAL.gb_main, tree_name, node_gen,
241                                          aw_root->awar(AWAR_TREE_EXPORT_INCLUDE_BRANCHLENS)->read_int(),
242                                          aw_root->awar(AWAR_TREE_EXPORT_INCLUDE_BOOTSTRAPS)->read_int(),
243                                          aw_root->awar(AWAR_TREE_EXPORT_INCLUDE_GROUPNAMES)->read_int(),
244                                          exportType == AD_TREE_EXPORT_FORMAT_NEWICK_PRETTY,
245                                          quoteMode,
246                                          fname);
247                break;
248        }
249
250        AW_refresh_fileselection(aw_root, AWAR_TREE_EXPORT_FILEBASE);
251
252        delete node_gen;
253        free(db_name);
254        free(fname);
255    }
256
257    aww->hide_or_notify(error);
258    free(tree_name);
259}
260
261static AW_window *create_tree_export_window(AW_root *root)
262{
263    AW_window_simple *aws = new AW_window_simple;
264    aws->init(root, "SAVE_TREE", "TREE SAVE");
265    aws->load_xfig("sel_box_user2.fig");
266
267    aws->callback((AW_CB0)AW_POPDOWN);
268    aws->at("close");
269    aws->create_button("CLOSE", "CLOSE", "C");
270
271    aws->at("help");
272    aws->callback(makeHelpCallback("tr_export.hlp"));
273    aws->create_button("HELP", "HELP", "H");
274
275    aws->at("user");
276    aws->create_option_menu(AWAR_TREE_EXPORT_FORMAT, 0, 0);
277    aws->insert_option("NEWICK TREE FORMAT",                   "N", AD_TREE_EXPORT_FORMAT_NEWICK);
278    aws->insert_option("NEWICK TREE FORMAT (pretty, but big)", "P", AD_TREE_EXPORT_FORMAT_NEWICK_PRETTY);
279    aws->insert_option("ARB_XML TREE FORMAT",                  "X", AD_TREE_EXPORT_FORMAT_XML);
280    aws->update_option_menu();
281
282    AW_create_standard_fileselection(aws, AWAR_TREE_EXPORT_FILEBASE);
283
284    aws->at("user2");
285    aws->auto_space(10, 10);
286    aws->label("Nodetype");
287    aws->create_toggle_field(AWAR_TREE_EXPORT_NDS, 1);
288    aws->insert_default_toggle("Species ID ('name')", "S", 0);
289    aws->insert_toggle("NDS", "N", 1);
290    aws->update_toggle_field();
291
292    aws->at_newline(); aws->label("Save branch lengths"); aws->create_toggle(AWAR_TREE_EXPORT_INCLUDE_BRANCHLENS);
293    aws->at_newline(); aws->label("Save bootstrap values"); aws->create_toggle(AWAR_TREE_EXPORT_INCLUDE_BOOTSTRAPS);
294    aws->at_newline(); aws->label("Save group names"); aws->create_toggle(AWAR_TREE_EXPORT_INCLUDE_GROUPNAMES);
295    aws->at_newline(); aws->label("Hide folded groups (XML only)"); aws->create_toggle(AWAR_TREE_EXPORT_HIDE_FOLDED_GROUPS);
296
297    aws->at_newline(); aws->label("Name quoting (Newick only)");
298    aws->create_option_menu(AWAR_TREE_EXPORT_QUOTEMODE, 0, 0);
299    aws->insert_option("none",            "n", TREE_DISALLOW_QUOTES);
300    aws->insert_option("single",          "s", TREE_SINGLE_QUOTES);
301    aws->insert_option("double",          "d", TREE_DOUBLE_QUOTES);
302    aws->insert_option("single (forced)", "i", TREE_SINGLE_QUOTES|TREE_FORCE_QUOTES);
303    aws->insert_option("double (forced)", "o", TREE_DOUBLE_QUOTES|TREE_FORCE_QUOTES);
304    aws->update_option_menu();
305
306    aws->at_newline(); aws->label("Replace problem chars"); aws->create_toggle(AWAR_TREE_EXPORT_REPLACE);
307
308    aws->at_newline();
309    aws->callback(tree_save_cb);
310    aws->create_button("SAVE", "SAVE", "o");
311
312    aws->callback((AW_CB0)AW_POPDOWN);
313    aws->create_button("CANCEL", "CANCEL", "C");
314
315    aws->window_fit();
316    update_filter_cb(root);
317
318    return aws;
319}
320
321static char *readXmlTree(char *fname) {
322    // create a temp file
323    char tempFile[]  = "newickXXXXXX";
324    int createTempFile = mkstemp(tempFile);
325
326    if (createTempFile) {
327        GBS_strstruct *buf = GBS_stropen(strlen(fname));
328
329        // extract path from fname in order to place a copy of dtd file required to validate xml file
330        {
331            char *tmpFname = strdup(fname);
332            for (char *tok = strtok(tmpFname, "/"); tok;) {
333                char *tmp = tok;
334                tok = strtok(0, "/");
335                if (tok) {
336                    GBS_strcat(buf, "/");
337                    GBS_strcat(buf, tmp);
338                }
339            }
340            free(tmpFname);
341        }
342
343        char *path = GBS_strclose(buf);
344
345        // linking arb_tree.dtd file to the Path from where xml file is loaded
346#if defined(WARN_TODO)
347#warning fix hack
348#endif
349        char *command = GBS_global_string_copy("ln -s %s/lib/dtd/arb_tree.dtd %s/.", GB_getenvARBHOME(), path);
350        GB_xcmd(command, false, true);
351
352        // execute xml2newick to convert xml format tree to newick format tree
353        command = GBS_global_string_copy("xml2newick %s %s", fname, tempFile);
354        GB_xcmd(command, false, true);
355
356        free(command);
357        free(path);
358
359        // return newick format tree file
360        return strdup(tempFile);
361    }
362    else {
363        printf("Failed to create Temporary File to Parse xml file!\n");
364        return 0;
365    }
366}
367
368static void tree_load_cb(AW_window *aww) {
369    GB_ERROR  error     = 0;
370    AW_root  *aw_root   = aww->get_root();
371    char     *tree_name = aw_root->awar(AWAR_TREE_IMPORT "/tree_name")->read_string();
372
373    {
374        char *pcTreeFormat = aw_root->awar(AWAR_TREE_IMPORT "/filter")->read_string();
375        char *fname        = aw_root->awar(AWAR_TREE_IMPORT "/file_name")->read_string();
376        char *warnings     = 0;
377        char *tree_comment = 0;
378
379        GBT_TREE *tree;
380        if (strcmp(pcTreeFormat, "xml") == 0) {
381            char *tempFname = readXmlTree(fname);
382            tree = TREE_load(tempFname, GBT_TREE_NodeFactory(), &tree_comment, true, &warnings);
383            GB_unlink_or_warn(tempFname, NULL);
384            free(tempFname);
385        }
386        else {
387            tree = TREE_load(fname, GBT_TREE_NodeFactory(), &tree_comment, true, &warnings);
388        }
389
390        if (!tree) error = GB_await_error();
391        else {
392            if (warnings) GBT_message(GLOBAL.gb_main, warnings);
393
394            {
395                GB_transaction ta(GLOBAL.gb_main);
396                error = GBT_write_tree_with_remark(GLOBAL.gb_main, tree_name, tree, tree_comment);
397                error = ta.close(error);
398            }
399
400            if (!error) aw_root->awar(AWAR_TREE)->write_string(tree_name); // show new tree
401
402            delete tree;
403        }
404
405        free(warnings);
406        free(tree_comment);
407        free(fname);
408        free(pcTreeFormat);
409    }
410
411    aww->hide_or_notify(error);
412    free(tree_name);
413}
414
415static AW_window *create_tree_import_window(AW_root *root)
416{
417    AW_window_simple *aws = new AW_window_simple;
418    aws->init(root, "LOAD_TREE", "TREE LOAD");
419    aws->load_xfig("sel_box_tree.fig");
420
421    aws->callback((AW_CB0)AW_POPDOWN);
422    aws->at("close");
423    aws->create_button("CLOSE", "CLOSE", "C");
424
425    aws->at("format");
426    aws->label("Tree Format");
427    aws->create_option_menu(AWAR_TREE_IMPORT "/filter");
428    aws->insert_default_option("Newick", "t", "tree");
429    aws->insert_option("XML", "x", "xml");
430    aws->update_option_menu();
431
432    aws->at("user");
433    aws->label("Tree name");
434    aws->create_input_field(AWAR_TREE_IMPORT "/tree_name", 15);
435
436    AW_create_standard_fileselection(aws, AWAR_TREE_IMPORT);
437
438    aws->at("save2");
439    aws->callback(tree_load_cb);
440    aws->create_button("LOAD", "LOAD", "o");
441
442    aws->callback((AW_CB0)AW_POPDOWN);
443    aws->at("cancel2");
444    aws->create_button("CANCEL", "CANCEL", "C");
445
446    aws->window_fit();
447
448    return (AW_window *)aws;
449}
450
451static void ad_move_tree_info(AW_window *aww, TreeInfoMode mode) {
452    bool nodes_with_marked_only = false;
453
454    char     *log_file = 0;
455    GB_ERROR  error    = 0;
456
457    if (mode == TREE_INFO_COPY || mode == TREE_INFO_ADD) {
458        // move or add node-info writes a log file (containing errors)
459        // compare_node_info only sets remark branches
460        char *log_name       = GB_unique_filename("arb_node", "log");
461        log_file             = GB_create_tempfile(log_name);
462        if (!log_file) error = GB_await_error();
463        free(log_name);
464
465        nodes_with_marked_only = aww->get_root()->awar(AWAR_NODE_INFO_ONLY_MARKED)->read_int();
466    }
467
468    if (!error) {
469        AW_root *awr      = aww->get_root();
470        char    *src_tree = TreeAdmin::source_tree_awar(awr)->read_string();
471        char    *dst_tree = TreeAdmin::dest_tree_awar(awr)->read_string();
472
473        error = AWT_move_info(GLOBAL.gb_main, src_tree, dst_tree, log_file, mode, nodes_with_marked_only);
474        if (log_file) {
475            AW_edit(log_file);
476            GB_remove_on_exit(log_file);
477        }
478
479        free(dst_tree);
480        free(src_tree);
481    }
482
483    if (error) aw_message(error);
484    else aww->hide();
485
486    free(log_file);
487}
488
489static void swap_source_dest_cb(AW_window *aww) {
490    AW_root *root = aww->get_root();
491
492    AW_awar *s = TreeAdmin::source_tree_awar(root);
493    AW_awar *d = TreeAdmin::dest_tree_awar(root);
494
495    char *old_src = s->read_string();
496    s->write_string(d->read_char_pntr());
497    d->write_string(old_src);
498    free(old_src);
499}
500
501static void copy_tree_awar_cb(UNFIXED, AW_awar *aw_source, AW_awar *aw_dest) {
502    const char *tree = aw_source->read_char_pntr();
503    if (tree && tree[0]) aw_dest->write_string(tree);
504}
505
506static AW_window_simple *create_select_two_trees_window(AW_root *root, const char *winId, const char *winTitle, const char *helpFile) {
507    AW_window_simple *aws = new AW_window_simple;
508    aws->init(root, winId, winTitle);
509    aws->load_xfig("ad_two_trees.fig");
510
511    aws->at("close");
512    aws->auto_space(10, 3);
513
514    aws->callback(AW_POPDOWN);
515    aws->create_button("CLOSE", "Close", "C");
516
517    aws->at("help");
518    aws->callback(makeHelpCallback(helpFile));
519    aws->create_button("HELP", "Help", "H");
520
521    aws->at("tree1");
522    awt_create_selection_list_on_trees(GLOBAL.gb_main, aws, TreeAdmin::source_tree_awar(root)->awar_name);
523    aws->at("tree2");
524    awt_create_selection_list_on_trees(GLOBAL.gb_main, aws, TreeAdmin::dest_tree_awar(root)->awar_name);
525
526    AW_awar *awar_displayed_tree = root->awar(AWAR_TREE_NAME);
527
528    aws->at("select1");
529    aws->callback(makeWindowCallback(copy_tree_awar_cb, awar_displayed_tree, TreeAdmin::source_tree_awar(root)));  aws->create_autosize_button("SELECT_DISPLAYED1", "Use");
530    aws->callback(makeWindowCallback(copy_tree_awar_cb, TreeAdmin::source_tree_awar(root), awar_displayed_tree));  aws->create_autosize_button("DISPLAY_SELECTED1", "Display");
531
532    aws->callback(swap_source_dest_cb);
533    aws->create_autosize_button("SWAP", "Swap");
534
535    aws->at("select2");
536    aws->callback(makeWindowCallback(copy_tree_awar_cb, awar_displayed_tree, TreeAdmin::dest_tree_awar(root)));  aws->create_autosize_button("SELECT_DISPLAYED2", "Use");
537    aws->callback(makeWindowCallback(copy_tree_awar_cb, TreeAdmin::dest_tree_awar(root), awar_displayed_tree));  aws->create_autosize_button("DISPLAY_SELECTED2", "Display");
538
539    aws->at("user");
540
541    return aws;
542}
543
544static AW_window_simple *create_select_other_tree_window(AW_root *root, const char *winId, const char *winTitle, const char *helpFile, const char *displayed_tree_awarname) {
545    AW_window_simple *aws = new AW_window_simple;
546    aws->init(root, winId, winTitle);
547    aws->load_xfig("ad_one_tree.fig");
548
549    aws->at("close");
550    aws->auto_space(10, 3);
551
552    aws->callback(AW_POPDOWN);
553    aws->create_button("CLOSE", "Close", "C");
554
555    aws->at("help");
556    aws->callback(makeHelpCallback(helpFile));
557    aws->create_button("HELP", "Help", "H");
558
559    AW_awar *awar_displayed_tree = root->awar(displayed_tree_awarname);
560
561    aws->at("tree");
562    awt_create_selection_list_on_trees(GLOBAL.gb_main, aws, TreeAdmin::source_tree_awar(root)->awar_name);
563
564    aws->at("select");
565    aws->callback(makeWindowCallback(copy_tree_awar_cb, awar_displayed_tree, TreeAdmin::source_tree_awar(root)));  aws->create_autosize_button("SELECT_DISPLAYED", "Use");
566    aws->callback(makeWindowCallback(copy_tree_awar_cb, TreeAdmin::source_tree_awar(root), awar_displayed_tree));  aws->create_autosize_button("DISPLAY_SELECTED", "Display");
567
568    aws->at("user");
569
570    return aws;
571}
572
573static AW_window *create_tree_diff_window(AW_root *root) {
574    AW_window_simple *aws = create_select_two_trees_window(root, "CMP_TOPOLOGY", "Compare tree topologies", "tree_diff.hlp");
575
576    aws->callback(makeWindowCallback(ad_move_tree_info, TREE_INFO_COMPARE));
577    aws->create_autosize_button("CMP_TOPOLOGY", "Compare topologies");
578
579    return aws;
580}
581
582static AW_window *create_tree_cmp_window(AW_root *root) {
583    AW_window_simple *aws = create_select_two_trees_window(root, "COPY_NODE_INFO_OF_TREE", "Move tree node info", "tree_cmp.hlp");
584
585    aws->button_length(11);
586
587    aws->callback(makeWindowCallback(ad_move_tree_info, TREE_INFO_COPY));
588    aws->create_button("COPY_INFO", "Copy info");
589
590    aws->label("copy/add only info containing marked species");
591    aws->create_toggle(AWAR_NODE_INFO_ONLY_MARKED);
592
593    aws->at_newline();
594
595    aws->callback(makeWindowCallback(ad_move_tree_info, TREE_INFO_ADD));
596    aws->create_button("ADD_INFO", "Add info");
597
598    return aws;
599}
600
601static void reorder_trees_cb(AW_window *aww, awt_reorder_mode dest, AW_CL) {
602    // moves the tree in the list of trees
603
604    char     *tree_name = aww->get_root()->awar(AWAR_TREE_NAME)->read_string();
605    GB_ERROR  error     = NULL;
606
607    GB_transaction ta(GLOBAL.gb_main);
608    GBDATA *gb_treedata   = GBT_get_tree_data(GLOBAL.gb_main);
609    GBDATA *gb_moved_tree = GB_entry(gb_treedata, tree_name);
610
611    if (!gb_moved_tree) {
612        error = "No tree selected";
613    }
614    else {
615        GBT_ORDER_MODE  move_mode;
616        GBDATA         *gb_target_tree = NULL;
617
618        switch (dest) {
619            case ARM_UP:
620                move_mode      = GBT_INFRONTOF;
621                gb_target_tree = GBT_tree_infrontof(gb_moved_tree);
622                if (gb_target_tree) break;
623                // fall-through (move top-tree up = move to bottom)
624            case ARM_BOTTOM:
625                move_mode      = GBT_BEHIND;
626                gb_target_tree = GBT_find_bottom_tree(GLOBAL.gb_main);
627                break;
628
629            case ARM_DOWN:
630                move_mode      = GBT_BEHIND;
631                gb_target_tree = GBT_tree_behind(gb_moved_tree);
632                if (gb_target_tree) break;
633                // fall-through (move bottom-tree down = move to top)
634            case ARM_TOP:
635                move_mode      = GBT_INFRONTOF;
636                gb_target_tree = GBT_find_top_tree(GLOBAL.gb_main);
637                break;
638        }
639
640        if (gb_target_tree && gb_target_tree != gb_moved_tree) {
641            error = GBT_move_tree(gb_moved_tree, move_mode, gb_target_tree);
642        }
643    }
644
645    if (error) aw_message(error);
646    free(tree_name);
647}
648
649void popup_tree_admin_window(AW_window *aws) {
650    popup_tree_admin_window(aws->get_root());
651}
652void popup_tree_admin_window(AW_root *aw_root) {
653    static AW_window_simple *aws = 0;
654    if (!aws) {
655        aws = new AW_window_simple;
656        aws->init(aw_root, "TREE_ADMIN", "TREE ADMIN");
657        aws->load_xfig("ad_tree.fig");
658
659        aws->callback(AW_POPDOWN);
660        aws->at("close");
661        aws->create_button("CLOSE", "CLOSE", "C");
662
663        aws->callback(makeHelpCallback("treeadm.hlp"));
664        aws->at("help");
665        aws->create_button("HELP", "HELP", "H");
666
667        aws->button_length(40);
668
669        aws->at("sel");
670        aws->create_button(0, AWAR_TREE_NAME, 0, "+");
671
672        aws->at("security");
673        aws->create_option_menu(AWAR_TREE_SECURITY);
674        aws->insert_option("0", "0", 0);
675        aws->insert_option("1", "1", 1);
676        aws->insert_option("2", "2", 2);
677        aws->insert_option("3", "3", 3);
678        aws->insert_option("4", "4", 4);
679        aws->insert_option("5", "5", 5);
680        aws->insert_default_option("6", "6", 6);
681        aws->update_option_menu();
682
683        aws->at("rem");
684        aws->create_text_field(AWAR_TREE_REM);
685
686
687        aws->button_length(20);
688
689        static TreeAdmin::Spec spec(GLOBAL.gb_main, AWAR_TREE_NAME);
690
691        aws->at("delete");
692        aws->callback(makeWindowCallback(TreeAdmin::delete_tree_cb, &spec));
693        aws->create_button("DELETE", "Delete", "D");
694
695        aws->at("rename");
696        aws->callback(makeCreateWindowCallback(TreeAdmin::create_rename_window, &spec));
697        aws->create_button("RENAME", "Rename", "R");
698
699        aws->at("copy");
700        aws->callback(makeCreateWindowCallback(TreeAdmin::create_copy_window, &spec));
701        aws->create_button("COPY", "Copy", "C");
702
703        aws->at("move");
704        aws->callback(create_tree_cmp_window);
705        aws->create_button("MOVE_NODE_INFO", "Move node info", "C");
706
707        aws->at("cmp");
708        aws->callback(create_tree_diff_window);
709        aws->sens_mask(AWM_EXP);
710        aws->create_button("CMP_TOPOLOGY", "Compare topology", "T");
711        aws->sens_mask(AWM_ALL);
712
713        aws->at("export");
714        aws->callback(AW_POPUP, (AW_CL)create_tree_export_window, 0);
715        aws->create_button("EXPORT", "Export", "E");
716
717        aws->at("import");
718        aws->callback(AW_POPUP, (AW_CL)create_tree_import_window, 0);
719        aws->create_button("IMPORT", "Import", "I");
720
721        aws->button_length(0);
722
723        aws->at("list");
724        awt_create_selection_list_on_trees(GLOBAL.gb_main, aws, AWAR_TREE_NAME);
725
726        aws->at("sort");
727        awt_create_order_buttons(aws, reorder_trees_cb, 0);
728    }
729
730    aws->activate();
731}
732
733// -----------------------
734//      consense tree
735
736
737static void create_consense_tree_cb(AW_window *aww, AW_CL cl_selected_trees) {
738    AW_root  *aw_root = aww->get_root();
739    GB_ERROR  error   = NULL;
740
741    const char *cons_tree_name = aw_root->awar(AWAR_TREE_CONSENSE_TREE)->read_char_pntr();
742    if (!cons_tree_name || !cons_tree_name[0]) {
743        error = "No name specified for the consensus tree";
744    }
745    else {
746        AW_selection *selected_trees = (AW_selection*)cl_selected_trees;
747
748        StrArray tree_names;
749        selected_trees->get_values(tree_names);
750
751        if (tree_names.size()<2) {
752            error = "Not enough trees selected (at least 2 needed)";
753        }
754        else {
755            GBDATA *gb_main = GLOBAL.gb_main;
756            GB_transaction ta(gb_main);
757
758            {
759                arb_progress progress("Building consensus tree", 2); // 2 steps: deconstruct, reconstruct
760                ConsensusTreeBuilder tree_builder;
761
762                progress.subtitle("loading input trees");
763                for (size_t t = 0; t<tree_names.size() && !error; ++t) {
764                    TreeRoot      *root = new TreeRoot(new SizeAwareNodeFactory, true); // will be deleted when tree gets deleted
765                    SizeAwareTree *tree = DOWNCAST(SizeAwareTree*, GBT_read_tree(gb_main, tree_names[t], *root));
766                    if (!tree) {
767                        error = GB_await_error();
768                    }
769                    else {
770                        tree_builder.add(tree, tree_names[t], 1.0);
771                    }
772                }
773
774                size_t    species_count;
775                GBT_TREE *cons_tree = tree_builder.get(species_count, error); // triggers 2 implicit progress increments
776
777                if (!error && progress.aborted()) {
778                    error = "user abort";
779                }
780
781                arb_assert(contradicted(cons_tree, error));
782                if (cons_tree) {
783                    char *comment = tree_builder.get_remark();
784                    error         = GBT_write_tree_with_remark(gb_main, cons_tree_name, cons_tree, comment);
785                    free(comment);
786                    delete cons_tree;
787                }
788                if (error) progress.done();
789            }
790            error = ta.close(error);
791        }
792    }
793
794    if (!error) {
795        aw_root->awar(AWAR_TREE_NAME)->write_string(cons_tree_name); // show in main window
796    }
797
798    aw_message_if(error);
799}
800
801static void use_selected_as_target_cb(AW_window *aww) {
802    AW_root *aw_root = aww->get_root();
803    aw_root->awar(AWAR_TREE_CONSENSE_TREE)->write_string(aw_root->awar(AWAR_TREE_CONSENSE_SELECTED)->read_char_pntr());
804}
805
806AW_window *NT_create_consense_window(AW_root *aw_root) {
807    static AW_window_simple *aws = 0;
808    if (!aws) {
809        aws = new AW_window_simple;
810        aws->init(aw_root, "CONSENSE_TREE", "Consensus Tree");
811        aws->load_xfig("ad_cons_tree.fig");
812
813        aws->auto_space(10, 10);
814
815        aws->callback(AW_POPDOWN);
816        aws->at("close");
817        aws->create_button("CLOSE", "CLOSE", "C");
818
819        aws->callback(makeHelpCallback("consense_tree.hlp"));
820        aws->at("help");
821        aws->create_button("HELP", "HELP", "H");
822
823        aws->at("list");
824        AW_DB_selection *all_trees      = awt_create_selection_list_on_trees(GLOBAL.gb_main, aws, AWAR_TREE_CONSENSE_SELECTED);
825        AW_selection    *selected_trees = awt_create_subset_selection_list(aws, all_trees->get_sellist(), "selected", "add", "sort");
826
827        aws->at("name");
828        aws->create_input_field(AWAR_TREE_CONSENSE_TREE);
829
830        aws->callback(use_selected_as_target_cb);
831        aws->create_button("USE_AS_TARGET", "#moveLeft.xpm", 0);
832
833        aws->at("build");
834        aws->callback(create_consense_tree_cb, AW_CL(selected_trees));
835        aws->create_autosize_button("BUILD", "Build consensus tree", "B");
836    }
837    return aws;
838}
839
840
841class SortByTopo {
842    typedef std::map<std::string, unsigned> SpeciesPosition;
843
844    SpeciesPosition spos;
845    unsigned        maxSpec;
846
847    unsigned storeSpeciesPosition(const GBT_TREE *node, unsigned specLeftOf) {
848        if (node->is_leaf) {
849            spos[node->name] = specLeftOf;
850            return 1;
851        }
852        unsigned leftsize  = storeSpeciesPosition(node->get_leftson(), specLeftOf);
853        return storeSpeciesPosition(node->get_rightson(), specLeftOf+leftsize) + leftsize;
854    }
855
856public:
857
858    SortByTopo(const GBT_TREE *by) {
859        maxSpec = storeSpeciesPosition(by, 0);
860    }
861
862    double relativePos(const char *name) {
863        SpeciesPosition::iterator found = spos.find(name);
864        double res = (found == spos.end()) ? 0.5 : (found->second/double(maxSpec-1));
865        arb_assert(res>=0.0 && res<=1.0);
866        return res;
867    }
868
869    double reorder_subtree(RootedTree *node) { // similar to ../SL/ROOTED_TREE/RootedTree.cxx@reorder_subtree
870        static const char *smallest_leafname; // has to be set to the alphabetically smallest name (when function exits)
871
872        if (node->is_leaf) {
873            smallest_leafname = node->name;
874            return relativePos(smallest_leafname);
875        }
876
877        double      leftRelSum              = reorder_subtree(node->get_leftson());
878        const char *smallest_leafname_left  = smallest_leafname;
879        double      rightRelSum             = reorder_subtree(node->get_rightson());
880        const char *smallest_leafname_right = smallest_leafname;
881
882        bool left_leafname_bigger = strcmp(smallest_leafname_left, smallest_leafname_right)>0;
883        {
884            double leftRelPos  = leftRelSum  / node->get_leftson() ->get_leaf_count();
885            double rightRelPos = rightRelSum / node->get_rightson()->get_leaf_count();
886
887            if (leftRelPos>=rightRelPos) {
888                if (leftRelPos>rightRelPos || left_leafname_bigger) { // equal -> use leafname
889                    node->swap_sons();
890                }
891            }
892        }
893
894        smallest_leafname = left_leafname_bigger ? smallest_leafname_right : smallest_leafname_left;
895
896        return leftRelSum+rightRelSum;
897    }
898};
899
900static GB_ERROR sort_tree_by_other_tree(GBDATA *gb_main, RootedTree *tree, const char *other_tree) {
901    GB_ERROR       error = NULL;
902    GB_transaction ta(gb_main);
903
904    GBT_TREE *otherTree   = GBT_read_tree(gb_main, other_tree, GBT_TREE_NodeFactory());
905    if (!otherTree) error = GB_await_error();
906    else {
907        SortByTopo sorter(otherTree);
908        delete otherTree;
909        sorter.reorder_subtree(tree);
910    }
911    return error;
912}
913
914static bool sort_dtree_by_other_tree_cb(RootedTree *tree, GB_ERROR& error) {
915    const char *other_tree = TreeAdmin::source_tree_awar(AW_root::SINGLETON)->read_char_pntr();
916    error = sort_tree_by_other_tree(GLOBAL.gb_main, tree, other_tree);
917    return !error;
918}
919
920static void sort_tree_by_other_tree_cb(UNFIXED, AWT_canvas *ntw) {
921    GB_ERROR error = NT_with_displayed_tree_do(ntw, sort_dtree_by_other_tree_cb);
922    aw_message_if(error);
923}
924
925AW_window *NT_create_sort_tree_by_other_tree_window(AW_root *aw_root, AWT_canvas *ntw) {
926    AW_window_simple *aws = create_select_other_tree_window(aw_root, ntw->aww->local_id("SORT_BY_OTHER"), "Sort tree by other tree", "resortbyother.hlp", ntw->user_awar);
927
928    aws->callback(makeWindowCallback(sort_tree_by_other_tree_cb, ntw));
929    aws->create_autosize_button("RESORT", "Sort according to source tree");
930
931    return aws;
932}
933
934// ---------------------------
935//      multifurcate tree
936
937#define AWAR_MFURC                    "tree/multifurc/"
938#define AWAR_MFURC_CONSIDER_BOOTSTRAP AWAR_MFURC "use_bs"
939#define AWAR_MFURC_CONSIDER_LENGTH    AWAR_MFURC "use_len"
940#define AWAR_MFURC_CONSIDER_TERMINALS AWAR_MFURC "terminals"
941#define AWAR_MFURC_LENGTH_LIMIT       AWAR_MFURC "len"
942#define AWAR_MFURC_BOOTSTRAP_LIMIT    AWAR_MFURC "bs"
943
944void NT_create_multifurcate_tree_awars(AW_root *aw_root, AW_default props) {
945    aw_root->awar_int  (AWAR_MFURC_CONSIDER_BOOTSTRAP, 0,   props);
946    aw_root->awar_int  (AWAR_MFURC_CONSIDER_LENGTH,    1,   props);
947    aw_root->awar_int  (AWAR_MFURC_CONSIDER_TERMINALS, 0,   props);
948    aw_root->awar_float(AWAR_MFURC_LENGTH_LIMIT,       0.1, props);
949    aw_root->awar_float(AWAR_MFURC_BOOTSTRAP_LIMIT,    50,  props);
950}
951static void multifurcation_cb(UNFIXED, AWT_canvas *ntw) {
952    AW_root *aw_root = ntw->aww->get_root();
953
954    double below_bootstrap = 101.0;
955    double below_length    = 1000000.0;
956    bool   applyAtLeafs    = aw_root->awar(AWAR_MFURC_CONSIDER_TERMINALS)->read_int();
957
958    if (aw_root->awar(AWAR_MFURC_CONSIDER_BOOTSTRAP)->read_int()) below_bootstrap = aw_root->awar(AWAR_MFURC_BOOTSTRAP_LIMIT)->read_float();
959    if (aw_root->awar(AWAR_MFURC_CONSIDER_LENGTH)   ->read_int()) below_length    = aw_root->awar(AWAR_MFURC_LENGTH_LIMIT)   ->read_float();
960
961    NT_multifurcate_tree(ntw, RootedTree::multifurc_limits(below_bootstrap, below_length, applyAtLeafs));
962}
963AW_window *NT_create_multifurcate_tree_window(AW_root *aw_root, AWT_canvas *ntw) {
964    AW_window_simple *aws = new AW_window_simple;
965
966    aws->init(aw_root, ntw->aww->local_id("multifurcate"), "Multifurcate tree");
967    aws->at(10, 10);
968    aws->auto_space(10, 10);
969
970    aws->callback((AW_CB0) AW_POPDOWN);
971    aws->create_button("CLOSE", "CLOSE", "C");
972
973    aws->callback(makeHelpCallback("multifurcate.hlp"));
974    aws->create_button("HELP", "HELP", "H");
975
976    const int LABEL_LENGTH = 46;
977    aws->label_length(LABEL_LENGTH);
978
979    aws->at_newline();
980    aws->label("Multifurcate branches with branchlength below");
981    aws->create_toggle(AWAR_MFURC_CONSIDER_LENGTH);
982    aws->create_input_field(AWAR_MFURC_LENGTH_LIMIT, 10);
983
984    aws->at_newline();
985    aws->label("                          AND bootstrap below");
986    aws->create_toggle(AWAR_MFURC_CONSIDER_BOOTSTRAP);
987    aws->create_input_field(AWAR_MFURC_BOOTSTRAP_LIMIT, 10);
988
989    aws->label_length(0);
990    aws->at_newline();
991    aws->label("Also apply to terminal branches");
992    aws->create_toggle(AWAR_MFURC_CONSIDER_TERMINALS);
993
994    aws->at_newline();
995    aws->callback(makeWindowCallback(multifurcation_cb, ntw));
996    aws->create_autosize_button("MULTIFURCATE", "Multifurcate", "M");
997
998    return aws;
999}
1000
1001// --------------------------------------------------------------------------------
1002
1003#ifdef UNIT_TESTS
1004#ifndef TEST_UNIT_H
1005#include <test_unit.h>
1006#endif
1007
1008static GB_ERROR sort_namedtree_by_other_tree(GBDATA *gb_main, const char *tree, const char *other_tree) {
1009    GB_ERROR       error = NULL;
1010    GB_transaction ta(gb_main);
1011    SizeAwareTree *Tree = DOWNCAST(SizeAwareTree*, GBT_read_tree(gb_main, tree, *new TreeRoot(new SizeAwareNodeFactory, true)));
1012    if (!Tree) error = GB_await_error();
1013    else {
1014        Tree->compute_tree();
1015        error             = sort_tree_by_other_tree(gb_main, Tree, other_tree);
1016        if (!error) error = GBT_write_tree(gb_main, tree, Tree);
1017    }
1018    delete Tree;
1019    return error;
1020}
1021
1022void TEST_sort_tree_by_other_tree() {
1023    GB_shell  shell;
1024    GBDATA   *gb_main = GB_open("TEST_trees.arb", "rw");
1025    TEST_REJECT_NULL(gb_main);
1026
1027    const char *topo_test   = "(((((((CloTyro3:1.046,CloTyro4:0.061):0.026,CloTyro2:0.017):0.017,CloTyrob:0.009):0.274,CloInnoc:0.371):0.057,CloBifer:0.388):0.124,(((CloButy2:0.009,CloButyr:0.000):0.564,CloCarni:0.120):0.010,CloPaste:0.179):0.131):0.081,((((CorAquat:0.084,CurCitre:0.058):0.103,CorGluta:0.522):0.053,CelBiazo:0.059):0.207,CytAquat:0.711):0.081);";
1028    const char *topo_center = "(((CloPaste:0.179,((CloButy2:0.009,CloButyr:0.000):0.564,CloCarni:0.120):0.010):0.131,((CloInnoc:0.371,((CloTyro2:0.017,(CloTyro3:1.046,CloTyro4:0.061):0.026):0.017,CloTyrob:0.009):0.274):0.057,CloBifer:0.388):0.124):0.081,((CelBiazo:0.059,((CorAquat:0.084,CurCitre:0.058):0.103,CorGluta:0.522):0.053):0.207,CytAquat:0.711):0.081);";
1029    const char *topo_bottom = "((CytAquat:0.711,(CelBiazo:0.059,(CorGluta:0.522,(CorAquat:0.084,CurCitre:0.058):0.103):0.053):0.207):0.081,((CloPaste:0.179,(CloCarni:0.120,(CloButy2:0.009,CloButyr:0.000):0.564):0.010):0.131,(CloBifer:0.388,(CloInnoc:0.371,(CloTyrob:0.009,(CloTyro2:0.017,(CloTyro3:1.046,CloTyro4:0.061):0.026):0.017):0.274):0.057):0.124):0.081);";
1030
1031    TEST_EXPECT_DIFFERENT(topo_test,   topo_center);
1032    TEST_EXPECT_DIFFERENT(topo_test,   topo_bottom);
1033    TEST_EXPECT_DIFFERENT(topo_center, topo_bottom);
1034
1035    // create sorted copies of tree_test
1036    {
1037        GB_transaction  ta(gb_main);
1038        SizeAwareTree  *tree = DOWNCAST(SizeAwareTree*, GBT_read_tree(gb_main, "tree_test", *new TreeRoot(new SizeAwareNodeFactory, true)));
1039        TEST_REJECT_NULL(tree);
1040        TEST_EXPECT_NEWICK(nLENGTH, tree, topo_test);
1041
1042        tree->reorder_tree(BIG_BRANCHES_TO_CENTER); TEST_EXPECT_NO_ERROR(GBT_write_tree(gb_main, "tree_sorted_center", tree)); TEST_EXPECT_NEWICK(nLENGTH, tree, topo_center);
1043        tree->reorder_tree(BIG_BRANCHES_TO_BOTTOM); TEST_EXPECT_NO_ERROR(GBT_write_tree(gb_main, "tree_sorted_bottom", tree)); TEST_EXPECT_NEWICK(nLENGTH, tree, topo_bottom);
1044
1045        // test SortByTopo
1046        {
1047            SortByTopo   sbt(tree);
1048            const double EPSILON = 0.0001;
1049
1050            TEST_EXPECT_SIMILAR(sbt.relativePos("CytAquat"), 0.0, EPSILON); // leftmost species (in topo_bottom)
1051            TEST_EXPECT_SIMILAR(sbt.relativePos("CloTyro4"), 1.0, EPSILON); // rightmost species
1052
1053            TEST_EXPECT_SIMILAR(sbt.relativePos("CurCitre"), 0.2857, EPSILON); // (5 of 15)
1054            TEST_EXPECT_SIMILAR(sbt.relativePos("CloButy2"), 0.5,    EPSILON); // center species (8 of 15)
1055            TEST_EXPECT_SIMILAR(sbt.relativePos("CloTyrob"), 0.7857, EPSILON); // (12 of 15)
1056        }
1057
1058        tree->reorder_tree(BIG_BRANCHES_TO_EDGE); TEST_EXPECT_NO_ERROR(GBT_write_tree(gb_main, "tree_work", tree));
1059
1060        delete tree;
1061    }
1062
1063
1064    TEST_EXPECT_NO_ERROR(sort_namedtree_by_other_tree(gb_main, "tree_work", "tree_sorted_center")); TEST_EXPECT_SAVED_NEWICK(nLENGTH, gb_main, "tree_work", topo_center);
1065    TEST_EXPECT_NO_ERROR(sort_namedtree_by_other_tree(gb_main, "tree_work", "tree_sorted_bottom")); TEST_EXPECT_SAVED_NEWICK(nLENGTH, gb_main, "tree_work", topo_bottom);
1066    TEST_EXPECT_NO_ERROR(sort_namedtree_by_other_tree(gb_main, "tree_work", "tree_test"));          TEST_EXPECT_SAVED_NEWICK(nLENGTH, gb_main, "tree_work", topo_test);
1067
1068    GB_close(gb_main);
1069}
1070
1071void TEST_move_node_info() {
1072    GB_shell  shell;
1073    GBDATA   *gb_main = GB_open("TEST_trees.arb", "r");
1074
1075#define GROUP_TEST "(CloTyrob,(CloTyro2,(CloTyro3,CloTyro4)))"
1076
1077#define NAMED_GROUP_TEST       GROUP_TEST "'test'"
1078#define OVERWRITTEN_GROUP_TEST GROUP_TEST "'g2 [was: test]'"
1079
1080    const char *org_topo = "((CloInnoc," GROUP_TEST "),(CloBifer,((CloCarni,CurCitre),((CloPaste,(Zombie1,(CloButy2,CloButyr))),(CytAquat,(CelBiazo,(CorGluta,(CorAquat,Zombie2))))))));";
1081
1082    const char *unwanted_topo1 = "((CytAquat,(CelBiazo,(CorGluta,(CorAquat,Zombie2)))),((CloPaste,(Zombie1,(CloButy2,CloButyr))),((CloCarni,CurCitre),(CloBifer,(CloInnoc," NAMED_GROUP_TEST ")))));";
1083    const char *unwanted_topo2 = "((CloButy2,CloButyr),(Zombie1,(CloPaste,((((CloInnoc," OVERWRITTEN_GROUP_TEST "),CloBifer),(CloCarni,CurCitre)),(CytAquat,(CelBiazo,(CorGluta,(CorAquat,Zombie2)))))))'outer');";
1084
1085    const char *sorted_topo1 = "(((((CloInnoc," NAMED_GROUP_TEST "),CloBifer),(CloCarni,CurCitre)),(CloPaste,(Zombie1,(CloButy2,CloButyr)))),(CytAquat,(CelBiazo,(CorGluta,(CorAquat,Zombie2)))));";
1086    const char *sorted_topo2 = "(((((((CloInnoc," OVERWRITTEN_GROUP_TEST "),CloBifer),(CloCarni,CurCitre)),(CytAquat,(CelBiazo,(CorGluta,(CorAquat,Zombie2))))),CloPaste),Zombie1)'outer',(CloButy2,CloButyr));";
1087
1088    const char *compared_topo = "(((((((CloInnoc,(CloTyrob,(CloTyro2,(CloTyro3,CloTyro4)))),CloBifer),(CloCarni,CurCitre)'# 2')'# 2',(CytAquat,(CelBiazo,(CorGluta,(CorAquat,Zombie2)'# 1')'# 1')'# 1')'# 1')'# 1',CloPaste),Zombie1),(CloButy2,CloButyr));";
1089
1090    const char *LOG = "move_node_info.log";
1091
1092    // create copy of 'tree_removal'
1093    {
1094        GB_transaction  ta(gb_main);
1095        GBT_TREE       *tree = GBT_read_tree(gb_main, "tree_removal", GBT_TREE_NodeFactory());
1096
1097        TEST_EXPECT_NEWICK(nSIMPLE, tree, org_topo);
1098        TEST_EXPECT_NO_ERROR(GBT_write_tree(gb_main, "tree_removal_copy", tree));
1099        delete tree;
1100    }
1101
1102    // move node info
1103    {
1104        TEST_EXPECT_NO_ERROR(AWT_move_info(gb_main, "tree_test", "tree_removal", LOG, TREE_INFO_COPY, false));
1105
1106        TEST_EXPECT_SAVED_NEWICK__BROKEN(nSIMPLE, gb_main, "tree_removal", org_topo); // @@@ moving node info modifies topology (might be necessary to insert groups)
1107        TEST_EXPECT_SAVED_NEWICK(nGROUP, gb_main, "tree_removal", unwanted_topo1);
1108
1109        // @@@ when we have a function to set the root according to another tree (#449),
1110        // use that function here. sorting tree after that, should again result in 'org_topo'!
1111
1112        TEST_EXPECT_NO_ERROR(sort_namedtree_by_other_tree(gb_main, "tree_removal", "tree_removal_copy"));
1113        TEST_EXPECT_SAVED_NEWICK(nGROUP, gb_main, "tree_removal", sorted_topo1);
1114    }
1115
1116    // add node info
1117    {
1118        TEST_EXPECT_NO_ERROR(AWT_move_info(gb_main, "tree_tree2", "tree_removal", LOG, TREE_INFO_ADD, false));
1119
1120        TEST_EXPECT_SAVED_NEWICK__BROKEN(nSIMPLE, gb_main, "tree_removal", org_topo); // @@@ moving node info modifies topology (might be necessary to insert groups)
1121        TEST_EXPECT_SAVED_NEWICK(nGROUP, gb_main, "tree_removal", unwanted_topo2);
1122
1123        // @@@ when we have a function to set the root according to another tree (#449),
1124        // use that function here. sorting tree after that, should again result in 'org_topo'!
1125
1126        TEST_EXPECT_NO_ERROR(sort_namedtree_by_other_tree(gb_main, "tree_removal", "tree_removal_copy"));
1127        TEST_EXPECT_SAVED_NEWICK(nGROUP, gb_main, "tree_removal", sorted_topo2);
1128    }
1129
1130    // compare node info
1131    {
1132        TEST_EXPECT_NO_ERROR(AWT_move_info(gb_main, "tree_test", "tree_removal", NULL, TREE_INFO_COMPARE, false));
1133        TEST_EXPECT_SAVED_NEWICK(nREMARK, gb_main, "tree_removal", compared_topo);
1134    }
1135
1136    GB_unlink(LOG);
1137    GB_close(gb_main);
1138}
1139
1140void TEST_edges() {
1141    GB_shell  shell;
1142    GBDATA   *gb_main = GB_open("TEST_trees.arb", "rw");
1143    TEST_REJECT_NULL(gb_main);
1144
1145    {
1146        GB_transaction  ta(gb_main);
1147        RootedTree     *tree = DOWNCAST(RootedTree*, GBT_read_tree(gb_main, "tree_test", *new TreeRoot(new SizeAwareNodeFactory, true)));
1148
1149        RootedTree *left  = tree->findLeafNamed("CloTyro3"); TEST_REJECT_NULL(left);
1150        RootedTree *node  = left->get_father();              TEST_REJECT_NULL(node);
1151        RootedTree *right = node->findLeafNamed("CloTyro4"); TEST_REJECT_NULL(right);
1152
1153        TEST_EXPECT(node == right->get_father());
1154        TEST_EXPECT(node->get_leftson()  == left);
1155        TEST_EXPECT(node->get_rightson() == right);
1156
1157        RootedTree *parent  = node->get_father();                TEST_REJECT_NULL(parent);
1158        RootedTree *brother = parent->findLeafNamed("CloTyro2"); TEST_REJECT_NULL(brother);
1159
1160        TEST_EXPECT(node->get_brother() == brother);
1161
1162        RootedTree *grandpa  = parent->get_father(); TEST_REJECT_NULL(grandpa);
1163
1164        // topology:
1165        //
1166        //            grandpa
1167        //              /
1168        //             /
1169        //            /
1170        //          parent
1171        //           /\              .
1172        //          /  \             .
1173        //         /    \            .
1174        //       node  brother
1175        //        /\                 .
1176        //       /  \                .
1177        //      /    \               .
1178        //    left right
1179
1180        // test next() and otherNext() for inner edge 'node->parent'
1181        {
1182            ARB_edge nodeUp = parentEdge(node);
1183
1184            TEST_EXPECT(node->is_leftson()); // if child is left son..
1185            TEST_EXPECT(nodeUp.next().dest()      == grandpa); // .. next() continues rootwards
1186            TEST_EXPECT(nodeUp.otherNext().dest() == brother);
1187
1188            ARB_edge brotherUp = parentEdge(brother);
1189
1190            TEST_EXPECT(brother->is_rightson());               // if child is right son..
1191            TEST_EXPECT(brotherUp.next().dest()      == node); // .. next() continues with other son
1192            TEST_EXPECT(brotherUp.otherNext().dest() == grandpa);
1193
1194            ARB_edge down = nodeUp.inverse();
1195
1196            TEST_EXPECT(down.next().dest()      == right); // next descends into right son
1197            TEST_EXPECT(down.otherNext().dest() == left);
1198
1199            ARB_edge toLeaf(node, left);
1200            TEST_EXPECT(toLeaf.at_leaf());
1201
1202            // both iterators should turn around at leaf:
1203            TEST_EXPECT(toLeaf.next().dest()      == node);
1204            TEST_EXPECT(toLeaf.otherNext().dest() == node);
1205
1206            // test adjacent_distance
1207            const double EPSILON = 0.000001;
1208
1209            const double NLEN = 0.025806;
1210            const double BLEN = 0.017316;
1211            const double PLEN = 0.017167;
1212            const double LLEN = 1.045690;
1213            const double RLEN = 0.060606;
1214
1215            TEST_EXPECT_SIMILAR(node->get_branchlength(),             NLEN, EPSILON);
1216            TEST_EXPECT_SIMILAR(nodeUp.length(),                      NLEN, EPSILON);
1217            TEST_EXPECT_SIMILAR(down.length(),                        NLEN, EPSILON);
1218            TEST_EXPECT_SIMILAR(nodeUp.length_or_adjacent_distance(), NLEN, EPSILON);
1219            TEST_EXPECT_SIMILAR(down.length_or_adjacent_distance(),   NLEN, EPSILON);
1220
1221            TEST_EXPECT_SIMILAR(brother->get_branchlength(), BLEN,      EPSILON);
1222            TEST_EXPECT_SIMILAR(parent ->get_branchlength(), PLEN,      EPSILON);
1223            TEST_EXPECT_SIMILAR(nodeUp.adjacent_distance(),  BLEN+PLEN, EPSILON);
1224
1225            TEST_EXPECT_SIMILAR(left ->get_branchlength(), LLEN,      EPSILON);
1226            TEST_EXPECT_SIMILAR(right->get_branchlength(), RLEN,      EPSILON);
1227            TEST_EXPECT_SIMILAR(down.adjacent_distance(),  LLEN+RLEN, EPSILON);
1228
1229            // modify lengths
1230            const double MOD_NLEN = 0.123456;
1231            const double MOD_LLEN = 0.246802;
1232
1233            toLeaf.set_length(MOD_LLEN);
1234            nodeUp.set_length(MOD_NLEN);
1235
1236            TEST_EXPECT_SIMILAR(toLeaf.length(), MOD_LLEN, EPSILON);
1237            TEST_EXPECT_SIMILAR(nodeUp.length(), MOD_NLEN, EPSILON);
1238            TEST_EXPECT_SIMILAR(down.length(),   MOD_NLEN, EPSILON);
1239        }
1240
1241        delete tree;
1242    }
1243
1244    GB_close(gb_main);
1245}
1246
1247void TEST_toggle_bootstraps100() {
1248    GB_shell  shell;
1249    GBDATA   *gb_main = GB_open("TEST_trees.arb", "rw");
1250    TEST_REJECT_NULL(gb_main);
1251
1252    {
1253        GB_transaction  ta(gb_main);
1254        RootedTree     *tree = DOWNCAST(RootedTree*, GBT_read_tree(gb_main, "tree_test", *new TreeRoot(new SizeAwareNodeFactory, true)));
1255        TEST_REJECT_NULL(tree);
1256
1257        const char *topo_org   = "(((((((CloTyro3,CloTyro4)'40%',CloTyro2)'0%',CloTyrob)'97%',CloInnoc)'0%',CloBifer)'53%',(((CloButy2,CloButyr)'100%',CloCarni)'33%',CloPaste)'97%')'100%',((((CorAquat,CurCitre)'100%',CorGluta)'17%',CelBiazo)'40%',CytAquat)'100%');";
1258        const char *topo_no100 = "(((((((CloTyro3,CloTyro4)'40%',CloTyro2)'0%',CloTyrob)'97%',CloInnoc)'0%',CloBifer)'53%',(((CloButy2,CloButyr)"    ",CloCarni)'33%',CloPaste)'97%')"    ",((((CorAquat,CurCitre)"    ",CorGluta)'17%',CelBiazo)'40%',CytAquat)"    ");";
1259        const char *topo_rem   = "(((((((CloTyro3,CloTyro4),CloTyro2),CloTyrob),CloInnoc),CloBifer),(((CloButy2,CloButyr),CloCarni),CloPaste)),((((CorAquat,CurCitre),CorGluta),CelBiazo),CytAquat));";
1260
1261        TEST_EXPECT_NEWICK(nREMARK, tree, topo_org);
1262
1263        tree->toggle_bootstrap100();
1264        TEST_EXPECT_NEWICK(nREMARK, tree, topo_no100);
1265
1266        tree->toggle_bootstrap100();
1267        TEST_EXPECT_NEWICK(nREMARK, tree, topo_org);
1268
1269        tree->remove_bootstrap();
1270        TEST_EXPECT_NEWICK(nREMARK, tree, topo_rem);
1271
1272        delete tree;
1273    }
1274
1275    GB_close(gb_main);
1276}
1277
1278void TEST_multifurcate_tree() {
1279    GB_shell  shell;
1280    GBDATA   *gb_main = GB_open("TEST_trees.arb", "rw");
1281    TEST_REJECT_NULL(gb_main);
1282
1283    const char *topo_test               = "(((((((CloTyro3:1.046,CloTyro4:0.061)'40%':0.026,CloTyro2:0.017)'0%':0.017,CloTyrob:0.009)'97%:test':0.274,CloInnoc:0.371)'0%':0.057,CloBifer:0.388)'53%':0.124,(((CloButy2:0.009,CloButyr:0.000)'100%':0.564,CloCarni:0.120)'33%':0.010,CloPaste:0.179)'97%':0.131)'100%':0.081,((((CorAquat:0.084,CurCitre:0.058)'100%':0.103,CorGluta:0.522)'17%':0.053,CelBiazo:0.059)'40%':0.207,CytAquat:0.711)'100%':0.081);";
1284    // changes                          = "                                                                                                    +0.307         -0.371     +0.064 "
1285    const char *topo_single             = "(((((((CloTyro3:1.046,CloTyro4:0.061)'40%':0.026,CloTyro2:0.017)'0%':0.017,CloTyrob:0.009)'97%:test':0.581,CloInnoc:0.000)'0%':0.121,CloBifer:0.388)'53%':0.124,(((CloButy2:0.009,CloButyr:0.000)'100%':0.564,CloCarni:0.120)'33%':0.010,CloPaste:0.179)'97%':0.131)'100%':0.081,((((CorAquat:0.084,CurCitre:0.058)'100%':0.103,CorGluta:0.522)'17%':0.053,CelBiazo:0.059)'40%':0.207,CytAquat:0.711)'100%':0.081);";
1286    const char *topo_bs_less_101_005    = "(((((((CloTyro3:1.098,CloTyro4:0.064)"   ":0.000,CloTyro2:0.000)"  ":0.000,CloTyrob:0.000)'97%:test':0.287,CloInnoc:0.371)'0%':0.057,CloBifer:0.388)'53%':0.124,(((CloButy2:0.000,CloButyr:0.000)'100%':0.578,CloCarni:0.121)"   ":0.000,CloPaste:0.181)'97%':0.132)'100%':0.081,((((CorAquat:0.084,CurCitre:0.058)'100%':0.103,CorGluta:0.522)'17%':0.053,CelBiazo:0.059)'40%':0.207,CytAquat:0.711)'100%':0.081);";
1287    const char *topo_bs_less_101_005_NT = "(((((((CloTyro3:1.078,CloTyro4:0.062)"   ":0.000,CloTyro2:0.018)"  ":0.000,CloTyrob:0.009)'97%:test':0.282,CloInnoc:0.371)'0%':0.057,CloBifer:0.388)'53%':0.124,(((CloButy2:0.009,CloButyr:0.000)'100%':0.570,CloCarni:0.121)"   ":0.000,CloPaste:0.181)'97%':0.132)'100%':0.081,((((CorAquat:0.084,CurCitre:0.058)'100%':0.103,CorGluta:0.522)'17%':0.053,CelBiazo:0.059)'40%':0.207,CytAquat:0.711)'100%':0.081);";
1288    const char *topo_bs_less_30_005     = "(((((((CloTyro3:1.046,CloTyro4:0.061)'40%':0.027,CloTyro2:0.018)"  ":0.000,CloTyrob:0.009)'97%:test':0.288,CloInnoc:0.371)'0%':0.057,CloBifer:0.388)'53%':0.124,(((CloButy2:0.009,CloButyr:0.000)'100%':0.564,CloCarni:0.120)'33%':0.010,CloPaste:0.179)'97%':0.131)'100%':0.081,((((CorAquat:0.084,CurCitre:0.058)'100%':0.103,CorGluta:0.522)'17%':0.053,CelBiazo:0.059)'40%':0.207,CytAquat:0.711)'100%':0.081);";
1289    const char *topo_bs_less_30         = "(((((((CloTyro3:1.046,CloTyro4:0.061)'40%':0.027,CloTyro2:0.018)"  ":0.000,CloTyrob:0.009)'97%:test':0.302,CloInnoc:0.390)"  ":0.000,CloBifer:0.407)'53%':0.131,(((CloButy2:0.009,CloButyr:0.000)'100%':0.564,CloCarni:0.120)'33%':0.010,CloPaste:0.179)'97%':0.131)'100%':0.081,((((CorAquat:0.084,CurCitre:0.058)'100%':0.109,CorGluta:0.554)"   ":0.000,CelBiazo:0.062)'40%':0.220,CytAquat:0.711)'100%':0.081);";
1290    const char *topo_all                = "(((((((CloTyro3:0.000,CloTyro4:0.000)"   ":0.000,CloTyro2:0.000)"  ":0.000,CloTyrob:0.000)'"  "test':0.000,CloInnoc:0.000)"  ":0.000,CloBifer:0.000)"   ":0.000,(((CloButy2:0.000,CloButyr:0.000)"    ":0.000,CloCarni:0.000)"   ":0.000,CloPaste:0.000)"   ":0.000)"    ":0.000,((((CorAquat:0.000,CurCitre:0.000)"    ":0.000,CorGluta:0.000)"   ":0.000,CelBiazo:0.000)"   ":0.000,CytAquat:0.000)"    ":0.000);";
1291
1292    const double STABLE_LENGTH = 5.362750;
1293    const double EPSILON       = 0.000001;
1294
1295    for (int test = 1; test<=6; ++test) {
1296        GB_transaction  ta(gb_main);
1297        RootedTree     *tree = DOWNCAST(RootedTree*, GBT_read_tree(gb_main, "tree_test", *new TreeRoot(new SizeAwareNodeFactory, true)));
1298
1299        TEST_REJECT_NULL(tree);
1300        if (test == 1) {
1301            TEST_EXPECT_NEWICK(nALL, tree, topo_test);
1302            TEST_EXPECT_SIMILAR(tree->sum_child_lengths(), STABLE_LENGTH, EPSILON);
1303        }
1304
1305        switch (test) {
1306            case 1:
1307                tree->multifurcate_whole_tree(RootedTree::multifurc_limits(101, 0.05, true));
1308                TEST_EXPECT_NEWICK(nALL, tree, topo_bs_less_101_005);
1309                TEST_EXPECT_SIMILAR(tree->sum_child_lengths(), STABLE_LENGTH, EPSILON);
1310                break;
1311            case 6:
1312                tree->multifurcate_whole_tree(RootedTree::multifurc_limits(101, 0.05, false));
1313                TEST_EXPECT_NEWICK(nALL, tree, topo_bs_less_101_005_NT);
1314                TEST_EXPECT_SIMILAR(tree->sum_child_lengths(), STABLE_LENGTH, EPSILON);
1315                break;
1316            case 2:
1317                tree->multifurcate_whole_tree(RootedTree::multifurc_limits(30, 0.05, true));
1318                TEST_EXPECT_NEWICK(nALL, tree, topo_bs_less_30_005);
1319                TEST_EXPECT_SIMILAR(tree->sum_child_lengths(), STABLE_LENGTH, EPSILON);
1320                break;
1321            case 3:
1322                tree->multifurcate_whole_tree(RootedTree::multifurc_limits(30, 1000, true));
1323                TEST_EXPECT_NEWICK(nALL, tree, topo_bs_less_30);
1324                TEST_EXPECT_SIMILAR(tree->sum_child_lengths(), STABLE_LENGTH, EPSILON);
1325                break;
1326            case 4:
1327                tree->multifurcate_whole_tree(RootedTree::multifurc_limits(101, 1000, true)); // multifurcate all
1328                TEST_EXPECT_NEWICK(nALL, tree, topo_all);
1329                TEST_EXPECT_SIMILAR(tree->sum_child_lengths(), 0.0, EPSILON);
1330                break;
1331            case 5: {
1332                RootedTree *CloInnoc = tree->findLeafNamed("CloInnoc");
1333                TEST_REJECT_NULL(CloInnoc);
1334
1335                parentEdge(CloInnoc).multifurcate();
1336                TEST_EXPECT_NEWICK(nALL, tree, topo_single);
1337
1338                TEST_EXPECT_SIMILAR(tree->sum_child_lengths(), STABLE_LENGTH, EPSILON);
1339                break;
1340            }
1341            default:
1342                nt_assert(0);
1343                break;
1344        }
1345
1346        delete tree;
1347    }
1348
1349    GB_close(gb_main);
1350}
1351
1352#endif // UNIT_TESTS
1353
1354// --------------------------------------------------------------------------------
1355
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