source: branches/tree/TOOLS/arb_consensus_tree.cxx

Last change on this file was 18785, checked in by westram, 4 years ago
File size: 26.8 KB
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1// ============================================================= //
2//                                                               //
3//   File      : arb_consensus_tree.cxx                          //
4//   Purpose   : build consensus tree with the same library      //
5//               as ARB-NJ                                       //
6//                                                               //
7//   Coded by Ralf Westram (coder@reallysoft.de) in March 2012   //
8//   Institute of Microbiology (Technical University Munich)     //
9//   http://www.arb-home.de/                                     //
10//                                                               //
11// ============================================================= //
12
13#include <CT_ctree.hxx>
14#include <TreeRead.h>
15#include <TreeWrite.h>
16#include <arb_str.h>
17#include <arb_diff.h>
18#include <arb_defs.h>
19
20using namespace std;
21
22static TreeNode *build_consensus_tree(const CharPtrArray& input_trees, GB_ERROR& error, size_t& different_species, double weight, char *&comment) {
23    // read all input trees, generate and return consensus tree
24    // (Note: the 'weight' used here doesn't matter atm, since all trees are added with the same weight)
25
26    arb_assert(!error);
27    error   = NULp;
28    comment = NULp;
29
30    TreeNode *consense_tree = NULp;
31    if (input_trees.empty()) {
32        error = "no trees given";
33    }
34    else {
35        ConsensusTreeBuilder tree_builder;
36
37        for (size_t i = 0; !error && i<input_trees.size(); ++i) {
38            char *warnings = NULp;
39
40            TreeRoot      *root = new SizeAwareRoot; // will be deleted when tree gets deleted
41            SizeAwareTree *tree = DOWNCAST(SizeAwareTree*, TREE_load(input_trees[i], root, NULp, true, &warnings));
42            if (!tree) {
43                error = GBS_global_string("Failed to load tree '%s' (Reason: %s)", input_trees[i], GB_await_error());
44            }
45            else {
46                if (warnings) {
47                    GB_warningf("while loading tree '%s':\n%s", input_trees[i], warnings);
48                    free(warnings);
49                }
50                tree_builder.add(tree, input_trees[i], weight);
51            }
52        }
53
54        if (!error) consense_tree = tree_builder.get(different_species, error);
55        if (!error) comment = tree_builder.get_tree_remark();
56    }
57    arb_assert(contradicted(consense_tree, error));
58    return consense_tree;
59}
60
61static char *create_tree_name(const char *savename) {
62    // create a DB treename (using savename as hint)
63    char *tree_name;
64    {
65        // as default use part behind '/' and remove file extension
66        const char *lslash   = strrchr(savename, '/');
67        if (lslash) savename = lslash+1;
68
69        const char *ldot = strrchr(savename, '.');
70
71        tree_name = ldot ? ARB_strpartdup(savename, ldot-1) : ARB_strdup(savename);
72        if (tree_name[0] == 0) freedup(tree_name, "tree_consensus");
73    }
74
75    // make sure tree name starts with 'tree_'
76    if (!ARB_strBeginsWith(tree_name, "tree_")) {
77        freeset(tree_name, GBS_global_string_copy("tree_%s", tree_name));
78    }
79    return tree_name;
80}
81
82static GB_ERROR save_tree_as_newick(TreeNode *tree, const char *savename, const char *comment) {
83    // save a tree to a newick file
84
85    // since ARB only saves trees out of a database,
86    // i use a hack here:
87    // - create temp DB
88    // - save tree there
89    // - save to newick as usual
90
91    GB_shell  shell;
92    GBDATA   *gb_main = GB_open("", "crw");
93    GB_ERROR  error   = NULp;
94
95    if (!gb_main) {
96        error = GB_await_error();
97    }
98    else {
99        char *db_tree_name = create_tree_name(savename);
100
101        {
102            GB_transaction ta(gb_main);
103            error = GBT_write_tree_with_remark(gb_main, db_tree_name, tree, comment);
104        }
105        if (!error) {
106            Node_ID_Labeler labels_use_IDs;
107            error = TREE_write_Newick(gb_main, db_tree_name, labels_use_IDs, true, true, true, true, TREE_SINGLE_QUOTES, savename);
108        }
109
110        free(db_tree_name);
111        GB_close(gb_main);
112    }
113
114    if (error) {
115        error = GBS_global_string("Failed to save tree to '%s' (Reason: %s)", savename, error);
116    }
117
118    return error;
119}
120
121int ARB_main(int argc, char *argv[]) {
122    GB_ERROR error = NULp;
123
124    if (argc<2) {
125        printf("Usage: arb_consensus_tree [options] [tree]+\n"
126               "Purpose: Create a consensus tree out of multiple trees\n"
127               "  options:\n"
128               "  -w outfile      write consensus tree to outfile\n");
129
130        // @@@ wanted options
131        // - do not add relative frequency of used subtrees as bootstrap values
132        // - multifurcate branches with bootstrap value below XXX
133        // - eliminate branches with bootstrap value below YYY
134        // - ... ?
135    }
136    else {
137        char *savename = NULp;
138
139        ConstStrArray input_tree_names;
140
141        for (int a = 1; a<argc; ++a) {
142            const char *arg = argv[a];
143            if (arg[0] == '-') {
144                switch (arg[1]) {
145                    case 'w': savename = ARB_strdup(argv[++a]); break;
146                    default : error = GBS_global_string("Unknown switch '-%c'", arg[1]); break;
147                }
148            }
149            else {
150                input_tree_names.put(argv[a]);
151            }
152        }
153
154        if (!error && input_tree_names.empty()) error = "no input trees specified";
155
156        if (!error) {
157            size_t    species_count;
158            char     *comment;
159            TreeNode *cons_tree = build_consensus_tree(input_tree_names, error, species_count, 1.0, comment);
160
161            if (!cons_tree) {
162                error = GBS_global_string("Failed to build consensus tree (Reason: %s)", error);
163            }
164            else {
165                size_t leafs   = GBT_count_leafs(cons_tree);
166                double percent = size_t((leafs*1000)/species_count)/10.0;
167
168                printf("Generated tree contains %.1f%% of species (%zu of %zu found in input trees)\n",
169                       percent, leafs, species_count);
170
171                if (savename) {
172                    error = save_tree_as_newick(cons_tree, savename, comment);
173                }
174                else {
175                    printf("successfully created consensus tree\n"
176                           "(no savename specified -> tree not saved)\n");
177                }
178                UNCOVERED();
179                destroy(cons_tree);
180            }
181            free(comment);
182        }
183        free(savename);
184    }
185
186    if (error) {
187        printf("Error in arb_consensus_tree: %s\n", error);
188    }
189
190    return error ? EXIT_FAILURE : EXIT_SUCCESS;
191}
192
193// --------------------------------------------------------------------------------
194
195#ifdef UNIT_TESTS
196#ifndef TEST_UNIT_H
197#include <test_unit.h>
198#endif
199
200#include "command_output.h"
201
202// #define TEST_AUTO_UPDATE // uncomment to update expected trees (if more than date differs)
203
204static char *custom_tree_name(int dir, const char *name) { return GBS_global_string_copy("consense/%i/%s.tree", dir, name); }
205static char *custom_numbered_tree_name(int dir, const char *name, int treeNr) { return GBS_global_string_copy("consense/%i/%s_%i.tree", dir, name, treeNr); }
206
207static void add_inputnames(StrArray& to, int dir, const char *basename, int first_tree, int last_tree) {
208    for (int t = first_tree; t <= last_tree; ++t) {
209        to.put(custom_numbered_tree_name(dir, basename, t));
210    }
211}
212
213static double calc_intree_distance(TreeNode *tree) {
214    if (tree->is_leaf()) return 0.0;
215    return
216        tree->leftlen +
217        tree->rightlen +
218        calc_intree_distance(tree->get_leftson()) +
219        calc_intree_distance(tree->get_rightson());
220}
221
222#define LENSUM_EPSILON .000001
223
224static arb_test::match_expectation consense_tree_generated(TreeNode *tree, GB_ERROR error, size_t species_count, size_t expected_species_count, double expected_intree_distance) {
225    using namespace   arb_test;
226    expectation_group expected;
227
228    expected.add(that(error).is_equal_to_NULL());
229    expected.add(that(tree).does_differ_from_NULL());
230
231    if (tree) {
232        expected.add(that(species_count).is_equal_to(expected_species_count));
233        expected.add(that(GBT_count_leafs(tree)).is_equal_to(expected_species_count));
234        expected.add(that(calc_intree_distance(tree)).fulfills(epsilon_similar(LENSUM_EPSILON), expected_intree_distance));
235    }
236
237    return all().ofgroup(expected);
238}
239
240static arb_test::match_expectation build_expected_consensus_tree(const int treedir, const char *basename, int first_tree, int last_tree, double weight, const char *outbasename, size_t expected_species_count, double expected_intree_distance) {
241    using namespace       arb_test;
242    expectation_group     expected;
243    arb_suppress_progress hideProgress;
244
245    GB_ERROR  error   = NULp;
246    StrArray  input_tree_names;
247    add_inputnames(input_tree_names, treedir, basename, first_tree, last_tree);
248
249    size_t    species_count;
250    char     *comment;
251    TreeNode *tree = build_consensus_tree(input_tree_names, error, species_count, weight, comment);
252    expected.add(consense_tree_generated(tree, error, species_count, expected_species_count, expected_intree_distance));
253
254    char *saveas = custom_tree_name(treedir, outbasename);
255    error        = save_tree_as_newick(tree, saveas, comment);
256    expected.add(that(error).is_equal_to_NULL());
257
258    if (!error) {
259        char *expected_save        = custom_tree_name(treedir, GBS_global_string("%s_expected", outbasename));
260        bool  exported_as_expected = arb_test::textfiles_have_difflines_ignoreDates(saveas, expected_save, 0);
261
262#if defined(TEST_AUTO_UPDATE)
263        if (!exported_as_expected) {
264            TEST_COPY_FILE(saveas, expected_save);
265        }
266#else // !defined(TEST_AUTO_UPDATE)
267        expected.add(that(exported_as_expected).is_equal_to(true));
268#endif
269        TEST_EXPECT_ZERO_OR_SHOW_ERRNO(GB_unlink(saveas));
270        free(expected_save);
271    }
272
273    free(saveas);
274    free(comment);
275    destroy(tree);
276
277    return all().ofgroup(expected);
278}
279
280void TEST_consensus_tree_1() {
281    TEST_EXPECTATION(build_expected_consensus_tree(1, "bootstrapped", 1, 5, 0.7, "consense1", 22, 0.925779));
282    // ../UNIT_TESTER/run/consense/1/consense1.tree
283}
284void TEST_consensus_tree_1_single() {
285    TEST_EXPECTATION(build_expected_consensus_tree(1, "bootstrapped", 1, 1, 0.01, "consense1_single", 22, 0.924610));
286    // ../UNIT_TESTER/run/consense/1/consense1_single.tree
287}
288
289void TEST_consensus_tree_2() {
290    TEST_EXPECTATION(build_expected_consensus_tree(2, "bootstrapped", 1, 4, 2.5, "consense2", 59, 2.849827));
291    // ../UNIT_TESTER/run/consense/2/consense2.tree
292}
293
294void TEST_consensus_tree_3() {
295    TEST_EXPECTATION(build_expected_consensus_tree(3, "bootstrapped", 1, 3, 137.772, "consense3", 128, 2.170685));
296    // ../UNIT_TESTER/run/consense/3/consense3.tree
297}
298
299void TEST_consensus_tree_from_disjunct_trees() {
300    TEST_EXPECTATION(build_expected_consensus_tree(4, "disjunct", 1, 2, 137.772, "disjunct_merged", 15, 2.034290));
301    // ../UNIT_TESTER/run/consense/4/disjunct_merged.tree
302}
303
304void TEST_consensus_tree_from_partly_overlapping_trees() {
305    // tree_disjunct_3 contains 7 species
306    // (3 from upper subtree (tree_disjunct_1) and 4 from lower subtree (tree_disjunct_2))
307
308    TEST_EXPECTATION(build_expected_consensus_tree(4, "disjunct", 1, 3, 137.772, "overlap_merged", 15, 2.596455));
309    // ../UNIT_TESTER/run/consense/4/overlap_merged.tree
310}
311
312void TEST_consensus_tree_from_minimal_overlapping_trees() {
313    // tree_disjunct_0 only contains 2 species (1 from upper and 1 from lower subtree).
314    TEST_EXPECTATION(build_expected_consensus_tree(4, "disjunct", 0, 2, 137.772, "overlap_mini_merged", 15, 2.750745));
315    // ../UNIT_TESTER/run/consense/4/overlap_mini_merged.tree
316}
317
318void TEST_consensus_tree_described_in_arbhelp() {
319    // see ../HELP_SOURCE/source/consense_algo.hlp
320    TEST_EXPECTATION(build_expected_consensus_tree(5, "help", 1, 2, 2.0, "help_merged", 6, 1.050000));
321    // ../UNIT_TESTER/run/consense/5/help_merged.tree
322}
323
324void TEST_consensus_tree_from_trees_overlapping_by_twothirds() {
325    // These 3 trees where copied from an existing tree.
326    // From each copy one third of all species has been removed
327    // (removed sets were disjunct)
328    TEST_EXPECTATION(build_expected_consensus_tree(6, "overlap_two_thirds", 1, 3, 19.2, "overlap_twothirds_merged", 15, 3.561680));
329    // ../UNIT_TESTER/run/consense/6/overlap_twothirds_merged.tree
330}
331
332void TEST_consensus_tree_from_mostly_overlapping_trees() {
333    // the 3 trees were copied from tree_disjunct_source.
334    // from each tree 2 (different) species were deleted.
335    TEST_EXPECTATION(build_expected_consensus_tree(7, "disjunct_del2", 1, 3, 137.772, "overlap_mostly", 15, 1.820057));
336    // ../UNIT_TESTER/run/consense/7/overlap_mostly.tree
337}
338
339void TEST_consensus_tree_from_mostly_overlapping_trees_2() {
340    // the 3 trees were copied from tree_disjunct1
341    // from each tree 1 (different) species was deleted.
342    TEST_EXPECTATION(build_expected_consensus_tree(8, "overlap2", 1, 3, 137.772, "overlap2_mostly", 8, 0.529109));
343    // ../UNIT_TESTER/run/consense/8/overlap2_mostly.tree
344}
345TEST_PUBLISH(TEST_consensus_tree_from_mostly_overlapping_trees_2);
346
347
348#define REPEATED_TESTS
349
350#if defined(REPEATED_TESTS)
351void TEST_consensus_tree_generation_is_deterministic() {
352    TEST_consensus_tree_described_in_arbhelp();
353    TEST_consensus_tree_from_minimal_overlapping_trees();
354    TEST_consensus_tree_from_partly_overlapping_trees();
355    TEST_consensus_tree_from_disjunct_trees();
356    TEST_consensus_tree_3();
357    TEST_consensus_tree_2();
358    TEST_consensus_tree_1_single();
359    TEST_consensus_tree_1();
360}
361
362void TEST_arb_consensus_tree() {
363    TEST_STDOUT_CONTAINS("(arb_consensus_tree -x || true)", "Unknown switch '-x'");
364    TEST_STDOUT_CONTAINS("(arb_consensus_tree -w sth || true)", "no input trees specified");
365
366    {
367        char *saveas   = custom_tree_name(1, "consense1");
368        char *expected = custom_tree_name(1, "consense1_expected");
369
370        TEST_OUTPUT_CONTAINS("arb_consensus_tree"
371                             " -w consense/1/consense1.tree"
372                             " consense/1/bootstrapped_1.tree"
373                             " consense/1/bootstrapped_2.tree"
374                             " consense/1/bootstrapped_3.tree"
375                             " consense/1/bootstrapped_4.tree"
376                             " consense/1/bootstrapped_5.tree",
377                             (const char *)NULp,
378                             "Created new database \"\"");
379
380        TEST_EXPECT_TEXTFILE_DIFFLINES_IGNORE_DATES(saveas, expected, 0);
381        TEST_EXPECT_ZERO_OR_SHOW_ERRNO(GB_unlink(saveas));
382
383        free(expected);
384        free(saveas);
385    }
386
387    {
388        char *saveas   = custom_tree_name(2, "consense2");
389        char *expected = custom_tree_name(2, "consense2_expected");
390
391        TEST_OUTPUT_CONTAINS("arb_consensus_tree"
392                             " -w consense/2/consense2.tree"
393                             " consense/2/bootstrapped_1.tree"
394                             " consense/2/bootstrapped_2.tree"
395                             " consense/2/bootstrapped_3.tree"
396                             " consense/2/bootstrapped_4.tree",
397                             (const char *)NULp,
398                             "Created new database \"\"");
399
400        TEST_EXPECT_TEXTFILE_DIFFLINES_IGNORE_DATES(saveas, expected, 0);
401        TEST_EXPECT_ZERO_OR_SHOW_ERRNO(GB_unlink(saveas));
402
403        free(expected);
404        free(saveas);
405    }
406}
407#endif // REPEATED_TESTS
408
409// #define TREEIO_AUTO_UPDATE // uncomment to auto-update expected test-results
410// #define TREEIO_AUTO_UPDATE_IF_EXPORT_DIFFERS // uncomment to auto-update expected test-results
411// #define TREEIO_AUTO_UPDATE_IF_REEXPORT_DIFFERS // uncomment to auto-update expected test-results
412
413static const char *findFirstNameContaining(TreeNode *tree, const char *part) {
414    const char *found = NULp;
415    if (tree->name && strstr(tree->name, part)) {
416        found = tree->name;
417    }
418    else if (!tree->is_leaf()) {
419        found             = findFirstNameContaining(tree->get_leftson(), part);
420        if (!found) found = findFirstNameContaining(tree->get_rightson(), part);
421    }
422    return found;
423}
424
425void TEST_SLOW_treeIO_stable() {
426    const char *dbname   = "trees/bootstrap_groups.arb";
427    const char *treename = "tree_bootstrap_and_groups";
428    const char *savename = "bg";
429
430    GB_shell  shell;
431    GBDATA   *gb_main = GB_open(dbname, "rw");
432
433    TEST_REJECT_NULL(gb_main);
434
435    char *outfile = GBS_global_string_copy("trees/%s.tree", savename);
436
437    for (int save_branchlengths = 0; save_branchlengths <= 1; ++save_branchlengths) {
438        for (int save_bootstraps = 0; save_bootstraps <= 1; ++save_bootstraps) {
439            for (int save_groupnames = 0; save_groupnames <= 1; ++save_groupnames) {
440                bool quoting_occurs = save_bootstraps && save_groupnames;
441                for (int pretty = 0; pretty <= 1; ++pretty) {
442
443                    for (int quoting = TREE_DISALLOW_QUOTES; quoting <= (quoting_occurs ? TREE_DOUBLE_QUOTES : TREE_DISALLOW_QUOTES); ++quoting) {
444                        TREE_node_quoting quoteMode = TREE_node_quoting(quoting);
445
446                        char *paramID = GBS_global_string_copy("%s_%s%s%s_%i",
447                                                               pretty ? "p" : "s",
448                                                               save_bootstraps ? "Bs" : "",
449                                                               save_groupnames ? "Grp" : "",
450                                                               save_branchlengths ? "Len" : "",
451                                                               quoteMode);
452
453                        TEST_ANNOTATE(GBS_global_string("for paramID='%s'", paramID));
454
455                        {
456                            Node_ID_Labeler labels_use_IDs;
457                            GB_ERROR        export_error = TREE_write_Newick(gb_main, treename, labels_use_IDs, save_branchlengths, save_bootstraps, save_groupnames, pretty, quoteMode, outfile);
458                            TEST_EXPECT_NULL(export_error);
459                        }
460
461                        char *expectedfile = GBS_global_string_copy("trees/%s_exp_%s.tree", savename, paramID);
462
463#if defined(TREEIO_AUTO_UPDATE)
464                        system(GBS_global_string("cp %s %s", outfile, expectedfile));
465#else // !defined(TREEIO_AUTO_UPDATE)
466                        bool exported_as_expected = arb_test::textfiles_have_difflines_ignoreDates(expectedfile, outfile, 0);
467#if defined(TREEIO_AUTO_UPDATE_IF_EXPORT_DIFFERS)
468                        if (!exported_as_expected) {
469                            system(GBS_global_string("cp %s %s", outfile, expectedfile));
470                        }
471#else // !defined(TREEIO_AUTO_UPDATE_IF_EXPORT_DIFFERS)
472                        TEST_EXPECT(exported_as_expected);
473#endif
474
475                        // reimport exported tree
476                        const char *reloaded_treename = "tree_reloaded";
477                        {
478                            char     *comment    = NULp;
479                            TreeNode *tree       = TREE_load(expectedfile, new SimpleRoot, &comment, true, NULp);
480                            GB_ERROR  load_error = tree ? NULp : GB_await_error();
481
482                            TEST_EXPECTATION(all().of(that(tree).does_differ_from_NULL(),
483                                                      that(load_error).is_equal_to_NULL()));
484                            // store tree in DB
485                            {
486                                GB_transaction ta(gb_main);
487                                GB_ERROR       store_error = GBT_write_tree_with_remark(gb_main, reloaded_treename, tree, comment);
488                                TEST_EXPECT_NULL(store_error);
489                            }
490                            free(comment);
491
492                            if (save_groupnames) {
493                                const char *quotedGroup     = findFirstNameContaining(tree, "quoted");
494                                const char *underscoreGroup = findFirstNameContaining(tree, "bs100");
495                                TEST_EXPECT_EQUAL(quotedGroup, "quoted");
496                                TEST_EXPECT_EQUAL(underscoreGroup, "__bs100");
497                            }
498                            const char *capsLeaf = findFirstNameContaining(tree, "Caps");
499                            TEST_EXPECT_EQUAL(capsLeaf, "_MhuCaps");
500
501                            destroy(tree);
502                        }
503
504                        // export again
505                        {
506                            Node_ID_Labeler labels_use_IDs;
507                            GB_ERROR        reexport_error = TREE_write_Newick(gb_main, reloaded_treename, labels_use_IDs, save_branchlengths, save_bootstraps, save_groupnames, pretty, quoteMode, outfile);
508                            TEST_EXPECT_NULL(reexport_error);
509                        }
510
511                        // eliminate comments added by loading/saving
512                        char *outfile2 = GBS_global_string_copy("trees/%s2.tree", savename);
513                        {
514                            char *cmd = GBS_global_string_copy("cat %s"
515                                                               " | grep -v 'Loaded from trees/.*_exp_'"
516                                                               " | grep -v 'tree_reloaded saved to'"
517                                                               " > %s", outfile, outfile2);
518                            TEST_EXPECT_NO_ERROR(GBK_system(cmd));
519                            free(cmd);
520                        }
521
522                        bool reexported_as_expected = arb_test::textfiles_have_difflines(expectedfile, outfile2, 0);
523
524#if defined(TREEIO_AUTO_UPDATE_IF_REEXPORT_DIFFERS)
525                        if (!reexported_as_expected) {
526                            system(GBS_global_string("cp %s %s", outfile2, expectedfile));
527                        }
528#else // !defined(TREEIO_AUTO_UPDATE_IF_REEXPORT_DIFFERS)
529                        TEST_EXPECT(reexported_as_expected);
530#endif
531
532                        TEST_EXPECT_ZERO_OR_SHOW_ERRNO(unlink(outfile2));
533                        free(outfile2);
534#endif
535                        free(expectedfile);
536                        free(paramID);
537                    }
538                }
539            }
540        }
541    }
542    TEST_ANNOTATE(NULp);
543
544    TEST_EXPECT_ZERO_OR_SHOW_ERRNO(unlink(outfile));
545    free(outfile);
546
547    GB_close(gb_main);
548}
549
550void TEST_CONSENSUS_TREE_functionality() {
551    // functionality wanted in TreeNode (for use in library CONSENSUS_TREE)
552
553    char *comment = NULp;
554
555    SizeAwareTree *tree = DOWNCAST(SizeAwareTree*, TREE_load("trees/bg_exp_p_GrpLen_0.tree",
556                                                             new SizeAwareRoot,
557                                                             &comment, false, NULp));
558    // -> ../UNIT_TESTER/run/trees/bg_exp_p_GrpLen_0.tree
559
560#define ORG_1111 "(AticSea6,(RblAerol,RblMesop))"
561#define TOP_1111 "((RblAerol,RblMesop),AticSea6)"
562#define BOT_1111 ORG_1111
563
564#define ORG_11121 "((DnrShiba,RsbElon4),MmbAlkal)"
565#define TOP_11121 ORG_11121
566#define BOT_11121 "(MmbAlkal,(DnrShiba,RsbElon4))"
567
568#define ORG_11122 "((MabPelag,MabSalin),PaoMaris)"
569#define TOP_11122 ORG_11122
570#define BOT_11122 "(PaoMaris,(MabPelag,MabSalin))"
571
572#define ORG_1112 "(" ORG_11121 "," ORG_11122 ")"
573#define TOP_1112 "(" TOP_11121 "," TOP_11122 ")"
574#define BOT_1112 "(" BOT_11121 "," BOT_11122 ")"
575#define EDG_1112 "(" TOP_11121 "," BOT_11122 ")"
576
577#define ORG_111 "(" ORG_1111 "," ORG_1112 ")"
578#define TOP_111 "(" TOP_1112 "," TOP_1111 ")"
579#define BOT_111 "(" BOT_1111 "," BOT_1112 ")"
580#define EDG_111 "(" EDG_1112 "," BOT_1111 ")"
581
582#define ORG_112 "(OnlGran2,RsnAnta2)"
583#define TOP_112 ORG_112
584#define BOT_112 ORG_112
585
586#define ORG_11 "(" ORG_111 "," ORG_112 ")"
587#define TOP_11 "(" TOP_111 "," TOP_112 ")"
588#define BOT_11 "(" BOT_112 "," BOT_111 ")"
589#define EDG_11 "(" EDG_111 "," BOT_112 ")"
590
591#define ORG_12 "(_MhuCaps,ThtNivea)"
592#define TOP_12 "(ThtNivea,_MhuCaps)"
593#define BOT_12 TOP_12
594
595#define ORG_1 "(" ORG_11 "," ORG_12 ")"
596#define TOP_1 "(" TOP_11 "," TOP_12 ")"
597#define BOT_1 "(" BOT_12 "," BOT_11 ")"
598#define EDG_1 "(" EDG_11 "," BOT_12 ")"
599
600#define ORG_2 "((LbnMarin,LbnzAlb4),LbnAlexa)"
601#define TOP_2 ORG_2
602#define BOT_2 "(LbnAlexa,(LbnMarin,LbnzAlb4))"
603
604    // test swap_sons
605    TEST_EXPECT_VALID_TREE(tree);
606    TEST_EXPECT_NEWICK(nSIMPLE, tree, "(" ORG_1 "," ORG_2 ");");
607    tree->swap_sons();
608    TEST_EXPECT_NEWICK(nSIMPLE, tree, "(" ORG_2 "," ORG_1 ");");
609
610    // test reorder_tree
611    TEST_EXPECT_VALID_TREE(tree);
612    TreeOrder order[] = { BIG_BRANCHES_TO_TOP, BIG_BRANCHES_TO_BOTTOM, BIG_BRANCHES_TO_EDGE };
613
614    for (size_t o1 = 0; o1<ARRAY_ELEMS(order); ++o1) {
615        TreeOrder to_order = order[o1];
616        for (size_t o2 = 0; o2<ARRAY_ELEMS(order); ++o2) {
617            TreeOrder from_order = order[o2];
618
619            for (int rotate = 0; rotate<=1; ++rotate) {
620                tree->reorder_tree(from_order);
621                if (rotate) tree->rotate_subtree();
622                tree->reorder_tree(to_order);
623
624                switch (to_order) {
625                    case BIG_BRANCHES_TO_TOP:    TEST_EXPECT_NEWICK(nSIMPLE, tree, "(" TOP_1 "," TOP_2 ");"); break;
626                    case BIG_BRANCHES_TO_EDGE:   TEST_EXPECT_NEWICK(nSIMPLE, tree, "(" EDG_1 "," BOT_2 ");"); break;
627                    case BIG_BRANCHES_TO_BOTTOM: TEST_EXPECT_NEWICK(nSIMPLE, tree, "(" BOT_2 "," BOT_1 ");"); break;
628                    default: TEST_REJECT(true); break;
629                }
630
631            }
632        }
633    }
634
635    // test rotate_subtree
636    TEST_EXPECT_VALID_TREE(tree);
637    tree->reorder_tree(BIG_BRANCHES_TO_TOP);
638    tree->rotate_subtree(); TEST_EXPECT_NEWICK(nSIMPLE, tree, "((LbnAlexa,(LbnzAlb4,LbnMarin)),((_MhuCaps,ThtNivea),((RsnAnta2,OnlGran2),((AticSea6,(RblMesop,RblAerol)),((PaoMaris,(MabSalin,MabPelag)),(MmbAlkal,(RsbElon4,DnrShiba)))))));");
639    tree->rotate_subtree(); TEST_EXPECT_NEWICK(nSIMPLE, tree, "(" TOP_1 "," TOP_2 ");");
640
641
642    // test set_root
643    TEST_EXPECT_VALID_TREE(tree);
644    TreeNode *AticSea6Grandpa = tree->findLeafNamed("AticSea6")->get_father()->get_father();
645    TEST_REJECT_NULL(AticSea6Grandpa);
646    TEST_EXPECT_VALID_TREE(AticSea6Grandpa);
647
648    AticSea6Grandpa->set_root();
649    TEST_EXPECT_NEWICK(nSIMPLE, tree,
650                             "((" ORG_1112 "," TOP_1111 ")," // AticSea6 is direct son of TOP_1111
651                             "((" ORG_2 "," TOP_12 ")," ORG_112 "));");
652
653    // test auto-detection of "best" root
654    TEST_EXPECT_VALID_TREE(tree);
655    tree->get_tree_root()->find_innermost_edge().set_root();
656    TEST_EXPECT_NEWICK(nLENGTH, tree,
657                       "((((LbnMarin:0.019,LbnzAlb4:0.003):0.016,LbnAlexa:0.032):0.122,(ThtNivea:0.230,_MhuCaps:0.194):0.427):0.076,"
658                       "(((((DnrShiba:0.076,RsbElon4:0.053):0.034,MmbAlkal:0.069):0.016,((MabPelag:0.001,MabSalin:0.009):0.095,PaoMaris:0.092):0.036):0.030,((RblAerol:0.085,RblMesop:0.042):0.238,AticSea6:0.111):0.018):0.036,(OnlGran2:0.057,RsnAnta2:0.060):0.021):0.076);");
659
660    TEST_EXPECT_VALID_TREE(tree);
661    destroy(tree);
662    free(comment);
663}
664
665#endif // UNIT_TESTS
666
667// --------------------------------------------------------------------------------
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