source: tags/ms_r18q1/TOOLS/arb_consensus_tree.cxx

Last change on this file was 17110, checked in by westram, 6 years ago
File size: 26.4 KB
Line 
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_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) error = TREE_write_Newick(gb_main, db_tree_name, NULp, true, true, true, true, TREE_SINGLE_QUOTES, savename);
106
107        free(db_tree_name);
108        GB_close(gb_main);
109    }
110
111    if (error) {
112        error = GBS_global_string("Failed to save tree to '%s' (Reason: %s)", savename, error);
113    }
114
115    return error;
116}
117
118int ARB_main(int argc, char *argv[]) {
119    GB_ERROR error = NULp;
120
121    if (argc<2) {
122        printf("Usage: arb_consensus_tree [options] [tree]+\n"
123               "Purpose: Create a consensus tree out of multiple trees\n"
124               "  options:\n"
125               "  -w outfile      write consensus tree to outfile\n");
126
127        // @@@ wanted options
128        // - do not add relative frequency of used subtrees as bootstrap values
129        // - multifurcate branches with bootstrap value below XXX
130        // - eliminate branches with bootstrap value below YYY
131        // - ... ?
132    }
133    else {
134        char *savename = NULp;
135
136        ConstStrArray input_tree_names;
137
138        for (int a = 1; a<argc; ++a) {
139            const char *arg = argv[a];
140            if (arg[0] == '-') {
141                switch (arg[1]) {
142                    case 'w': savename = ARB_strdup(argv[++a]); break;
143                    default : error = GBS_global_string("Unknown switch '-%c'", arg[1]); break;
144                }
145            }
146            else {
147                input_tree_names.put(argv[a]);
148            }
149        }
150
151        if (!error && input_tree_names.empty()) error = "no input trees specified";
152
153        if (!error) {
154            size_t    species_count;
155            char     *comment;
156            TreeNode *cons_tree = build_consensus_tree(input_tree_names, error, species_count, 1.0, comment);
157
158            if (!cons_tree) {
159                error = GBS_global_string("Failed to build consensus tree (Reason: %s)", error);
160            }
161            else {
162                size_t leafs   = GBT_count_leafs(cons_tree);
163                double percent = size_t((leafs*1000)/species_count)/10.0;
164
165                printf("Generated tree contains %.1f%% of species (%zu of %zu found in input trees)\n",
166                       percent, leafs, species_count);
167
168                if (savename) {
169                    error = save_tree_as_newick(cons_tree, savename, comment);
170                }
171                else {
172                    printf("successfully created consensus tree\n"
173                           "(no savename specified -> tree not saved)\n");
174                }
175                UNCOVERED();
176                destroy(cons_tree);
177            }
178            free(comment);
179        }
180        free(savename);
181    }
182
183    if (error) {
184        printf("Error in arb_consensus_tree: %s\n", error);
185    }
186
187    return error ? EXIT_FAILURE : EXIT_SUCCESS;
188}
189
190// --------------------------------------------------------------------------------
191
192#ifdef UNIT_TESTS
193#ifndef TEST_UNIT_H
194#include <test_unit.h>
195#endif
196
197#include "command_output.h"
198
199// #define TEST_AUTO_UPDATE // uncomment to update expected trees (if more than date differs)
200
201static char *custom_tree_name(int dir, const char *name) { return GBS_global_string_copy("consense/%i/%s.tree", dir, name); }
202static 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); }
203
204static void add_inputnames(StrArray& to, int dir, const char *basename, int first_tree, int last_tree) {
205    for (int t = first_tree; t <= last_tree; ++t) {
206        to.put(custom_numbered_tree_name(dir, basename, t));
207    }
208}
209
210static double calc_intree_distance(TreeNode *tree) {
211    if (tree->is_leaf()) return 0.0;
212    return
213        tree->leftlen +
214        tree->rightlen +
215        calc_intree_distance(tree->get_leftson()) +
216        calc_intree_distance(tree->get_rightson());
217}
218
219#define LENSUM_EPSILON .000001
220
221static 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) {
222    using namespace   arb_test;
223    expectation_group expected;
224
225    expected.add(that(error).is_equal_to_NULL());
226    expected.add(that(tree).does_differ_from_NULL());
227
228    if (tree) {
229        expected.add(that(species_count).is_equal_to(expected_species_count));
230        expected.add(that(GBT_count_leafs(tree)).is_equal_to(expected_species_count));
231        expected.add(that(calc_intree_distance(tree)).fulfills(epsilon_similar(LENSUM_EPSILON), expected_intree_distance));
232    }
233
234    return all().ofgroup(expected);
235}
236
237static 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) {
238    using namespace       arb_test;
239    expectation_group     expected;
240    arb_suppress_progress hideProgress;
241
242    GB_ERROR  error   = NULp;
243    StrArray  input_tree_names;
244    add_inputnames(input_tree_names, treedir, basename, first_tree, last_tree);
245
246    size_t    species_count;
247    char     *comment;
248    TreeNode *tree = build_consensus_tree(input_tree_names, error, species_count, weight, comment);
249    expected.add(consense_tree_generated(tree, error, species_count, expected_species_count, expected_intree_distance));
250
251    char *saveas = custom_tree_name(treedir, outbasename);
252    error        = save_tree_as_newick(tree, saveas, comment);
253    expected.add(that(error).is_equal_to_NULL());
254
255    if (!error) {
256        char *expected_save        = custom_tree_name(treedir, GBS_global_string("%s_expected", outbasename));
257        bool  exported_as_expected = arb_test::textfiles_have_difflines_ignoreDates(expected_save, saveas, 0);
258
259#if defined(TEST_AUTO_UPDATE)
260        if (!exported_as_expected) {
261            TEST_COPY_FILE(saveas, expected_save);
262        }
263#else // !defined(TEST_AUTO_UPDATE)
264        expected.add(that(exported_as_expected).is_equal_to(true));
265#endif
266        TEST_EXPECT_ZERO_OR_SHOW_ERRNO(GB_unlink(saveas));
267        free(expected_save);
268    }
269
270    free(saveas);
271    free(comment);
272    destroy(tree);
273
274    return all().ofgroup(expected);
275}
276
277void TEST_consensus_tree_1() {
278    TEST_EXPECTATION(build_expected_consensus_tree(1, "bootstrapped", 1, 5, 0.7, "consense1", 22, 0.925779));
279    // ../UNIT_TESTER/run/consense/1/consense1.tree
280}
281void TEST_consensus_tree_1_single() {
282    TEST_EXPECTATION(build_expected_consensus_tree(1, "bootstrapped", 1, 1, 0.01, "consense1_single", 22, 0.924610));
283    // ../UNIT_TESTER/run/consense/1/consense1_single.tree
284}
285
286void TEST_consensus_tree_2() {
287    TEST_EXPECTATION(build_expected_consensus_tree(2, "bootstrapped", 1, 4, 2.5, "consense2", 59, 2.849827));
288    // ../UNIT_TESTER/run/consense/2/consense2.tree
289}
290
291void TEST_consensus_tree_3() {
292    TEST_EXPECTATION(build_expected_consensus_tree(3, "bootstrapped", 1, 3, 137.772, "consense3", 128, 2.170685));
293    // ../UNIT_TESTER/run/consense/3/consense3.tree
294}
295
296void TEST_consensus_tree_from_disjunct_trees() {
297    TEST_EXPECTATION(build_expected_consensus_tree(4, "disjunct", 1, 2, 137.772, "disjunct_merged", 15, 2.034290));
298    // ../UNIT_TESTER/run/consense/4/disjunct_merged.tree
299}
300
301void TEST_consensus_tree_from_partly_overlapping_trees() {
302    // tree_disjunct_3 contains 7 species
303    // (3 from upper subtree (tree_disjunct_1) and 4 from lower subtree (tree_disjunct_2))
304
305    TEST_EXPECTATION(build_expected_consensus_tree(4, "disjunct", 1, 3, 137.772, "overlap_merged", 15, 2.596455));
306    // ../UNIT_TESTER/run/consense/4/overlap_merged.tree
307}
308
309void TEST_consensus_tree_from_minimal_overlapping_trees() {
310    // tree_disjunct_0 only contains 2 species (1 from upper and 1 from lower subtree).
311    TEST_EXPECTATION(build_expected_consensus_tree(4, "disjunct", 0, 2, 137.772, "overlap_mini_merged", 15, 2.750745));
312    // ../UNIT_TESTER/run/consense/4/overlap_mini_merged.tree
313}
314
315void TEST_consensus_tree_described_in_arbhelp() {
316    // see ../HELP_SOURCE/oldhelp/consense_algo.hlp
317    TEST_EXPECTATION(build_expected_consensus_tree(5, "help", 1, 2, 2.0, "help_merged", 6, 1.050000));
318    // ../UNIT_TESTER/run/consense/5/help_merged.tree
319}
320
321void TEST_consensus_tree_from_trees_overlapping_by_twothirds() {
322    // These 3 trees where copied from an existing tree.
323    // From each copy one third of all species has been removed
324    // (removed sets were disjunct)
325    TEST_EXPECTATION(build_expected_consensus_tree(6, "overlap_two_thirds", 1, 3, 19.2, "overlap_twothirds_merged", 15, 3.561680));
326    // ../UNIT_TESTER/run/consense/6/overlap_twothirds_merged.tree
327}
328
329void TEST_consensus_tree_from_mostly_overlapping_trees() {
330    // the 3 trees were copied from tree_disjunct_source.
331    // from each tree 2 (different) species were deleted.
332    TEST_EXPECTATION(build_expected_consensus_tree(7, "disjunct_del2", 1, 3, 137.772, "overlap_mostly", 15, 1.820057));
333    // ../UNIT_TESTER/run/consense/7/overlap_mostly.tree
334}
335
336void TEST_consensus_tree_from_mostly_overlapping_trees_2() {
337    // the 3 trees were copied from tree_disjunct1
338    // from each tree 1 (different) species was deleted.
339    TEST_EXPECTATION(build_expected_consensus_tree(8, "overlap2", 1, 3, 137.772, "overlap2_mostly", 8, 0.529109));
340    // ../UNIT_TESTER/run/consense/8/overlap2_mostly.tree
341}
342TEST_PUBLISH(TEST_consensus_tree_from_mostly_overlapping_trees_2);
343
344
345#define REPEATED_TESTS
346
347#if defined(REPEATED_TESTS)
348void TEST_consensus_tree_generation_is_deterministic() {
349    TEST_consensus_tree_described_in_arbhelp();
350    TEST_consensus_tree_from_minimal_overlapping_trees();
351    TEST_consensus_tree_from_partly_overlapping_trees();
352    TEST_consensus_tree_from_disjunct_trees();
353    TEST_consensus_tree_3();
354    TEST_consensus_tree_2();
355    TEST_consensus_tree_1_single();
356    TEST_consensus_tree_1();
357}
358
359void TEST_arb_consensus_tree() {
360    TEST_STDOUT_CONTAINS("(arb_consensus_tree -x || true)", "Unknown switch '-x'");
361    TEST_STDOUT_CONTAINS("(arb_consensus_tree -w sth || true)", "no input trees specified");
362
363    {
364        char *saveas   = custom_tree_name(1, "consense1");
365        char *expected = custom_tree_name(1, "consense1_expected");
366   
367        TEST_OUTPUT_CONTAINS("arb_consensus_tree"
368                             " -w consense/1/consense1.tree"
369                             " consense/1/bootstrapped_1.tree"
370                             " consense/1/bootstrapped_2.tree"
371                             " consense/1/bootstrapped_3.tree"
372                             " consense/1/bootstrapped_4.tree"
373                             " consense/1/bootstrapped_5.tree"
374                             ,"",
375                             "Created new database \"\"");
376
377        TEST_EXPECT_TEXTFILE_DIFFLINES_IGNORE_DATES(saveas, expected, 0);
378        TEST_EXPECT_ZERO_OR_SHOW_ERRNO(GB_unlink(saveas));
379
380        free(expected);
381        free(saveas);
382    }
383
384    {
385        char *saveas   = custom_tree_name(2, "consense2");
386        char *expected = custom_tree_name(2, "consense2_expected");
387   
388        TEST_OUTPUT_CONTAINS("arb_consensus_tree"
389                             " -w consense/2/consense2.tree"
390                             " consense/2/bootstrapped_1.tree"
391                             " consense/2/bootstrapped_2.tree"
392                             " consense/2/bootstrapped_3.tree"
393                             " consense/2/bootstrapped_4.tree"
394                             ,"",
395                             "Created new database \"\"");
396
397        TEST_EXPECT_TEXTFILE_DIFFLINES_IGNORE_DATES(saveas, expected, 0);
398        TEST_EXPECT_ZERO_OR_SHOW_ERRNO(GB_unlink(saveas));
399
400        free(expected);
401        free(saveas);
402    }
403}
404#endif // REPEATED_TESTS
405
406// #define TREEIO_AUTO_UPDATE // uncomment to auto-update expected test-results
407// #define TREEIO_AUTO_UPDATE_IF_EXPORT_DIFFERS // uncomment to auto-update expected test-results
408// #define TREEIO_AUTO_UPDATE_IF_REEXPORT_DIFFERS // uncomment to auto-update expected test-results
409
410static const char *findFirstNameContaining(TreeNode *tree, const char *part) {
411    const char *found = NULp;
412    if (tree->name && strstr(tree->name, part)) {
413        found = tree->name;
414    }
415    else if (!tree->is_leaf()) {
416        found             = findFirstNameContaining(tree->get_leftson(), part);
417        if (!found) found = findFirstNameContaining(tree->get_rightson(), part);
418    }
419    return found;
420}
421
422void TEST_SLOW_treeIO_stable() {
423    const char *dbname   = "trees/bootstrap_groups.arb";
424    const char *treename = "tree_bootstrap_and_groups";
425    const char *savename = "bg";
426
427    GB_shell  shell;
428    GBDATA   *gb_main = GB_open(dbname, "rw");
429
430    TEST_REJECT_NULL(gb_main);
431
432    char *outfile = GBS_global_string_copy("trees/%s.tree", savename);
433
434    for (int save_branchlengths = 0; save_branchlengths <= 1; ++save_branchlengths) {
435        for (int save_bootstraps = 0; save_bootstraps <= 1; ++save_bootstraps) {
436            for (int save_groupnames = 0; save_groupnames <= 1; ++save_groupnames) {
437                bool quoting_occurs = save_bootstraps && save_groupnames;
438                for (int pretty = 0; pretty <= 1; ++pretty) {
439
440                    for (int quoting = TREE_DISALLOW_QUOTES; quoting <= (quoting_occurs ? TREE_DOUBLE_QUOTES : TREE_DISALLOW_QUOTES); ++quoting) {
441                        TREE_node_quoting quoteMode = TREE_node_quoting(quoting);
442
443                        char *paramID = GBS_global_string_copy("%s_%s%s%s_%i",
444                                                               pretty ? "p" : "s",
445                                                               save_bootstraps ? "Bs" : "",
446                                                               save_groupnames ? "Grp" : "",
447                                                               save_branchlengths ? "Len" : "",
448                                                               quoteMode);
449
450                        TEST_ANNOTATE(GBS_global_string("for paramID='%s'", paramID));
451
452                        GB_ERROR export_error = TREE_write_Newick(gb_main, treename, NULp, save_branchlengths, save_bootstraps, save_groupnames, pretty, quoteMode, outfile);
453                        TEST_EXPECT_NULL(export_error);
454
455                        char *expectedfile = GBS_global_string_copy("trees/%s_exp_%s.tree", savename, paramID);
456
457#if defined(TREEIO_AUTO_UPDATE)
458                        system(GBS_global_string("cp %s %s", outfile, expectedfile));
459#else // !defined(TREEIO_AUTO_UPDATE)
460                        bool exported_as_expected = arb_test::textfiles_have_difflines_ignoreDates(expectedfile, outfile, 0);
461#if defined(TREEIO_AUTO_UPDATE_IF_EXPORT_DIFFERS)
462                        if (!exported_as_expected) {
463                            system(GBS_global_string("cp %s %s", outfile, expectedfile));
464                        }
465#else // !defined(TREEIO_AUTO_UPDATE_IF_EXPORT_DIFFERS)
466                        TEST_EXPECT(exported_as_expected);
467#endif
468
469                        // reimport exported tree
470                        const char *reloaded_treename = "tree_reloaded";
471                        {
472                            char     *comment    = NULp;
473                            TreeNode *tree       = TREE_load(expectedfile, new SimpleRoot, &comment, true, NULp);
474                            GB_ERROR  load_error = tree ? NULp : GB_await_error();
475
476                            TEST_EXPECTATION(all().of(that(tree).does_differ_from_NULL(),
477                                                      that(load_error).is_equal_to_NULL()));
478                            // store tree in DB
479                            {
480                                GB_transaction ta(gb_main);
481                                GB_ERROR       store_error = GBT_write_tree_with_remark(gb_main, reloaded_treename, tree, comment);
482                                TEST_EXPECT_NULL(store_error);
483                            }
484                            free(comment);
485
486                            if (save_groupnames) {
487                                const char *quotedGroup     = findFirstNameContaining(tree, "quoted");
488                                const char *underscoreGroup = findFirstNameContaining(tree, "bs100");
489                                TEST_EXPECT_EQUAL(quotedGroup, "quoted");
490                                TEST_EXPECT_EQUAL(underscoreGroup, "__bs100");
491                            }
492                            const char *capsLeaf = findFirstNameContaining(tree, "Caps");
493                            TEST_EXPECT_EQUAL(capsLeaf, "_MhuCaps");
494
495                            destroy(tree);
496                        }
497
498                        // export again
499                        GB_ERROR reexport_error = TREE_write_Newick(gb_main, reloaded_treename, NULp, save_branchlengths, save_bootstraps, save_groupnames, pretty, quoteMode, outfile);
500                        TEST_EXPECT_NULL(reexport_error);
501
502                        // eliminate comments added by loading/saving
503                        char *outfile2 = GBS_global_string_copy("trees/%s2.tree", savename);
504                        {
505                            char *cmd = GBS_global_string_copy("cat %s"
506                                                               " | grep -v 'Loaded from trees/.*_exp_'"
507                                                               " | grep -v 'tree_reloaded saved to'"
508                                                               " > %s", outfile, outfile2);
509                            TEST_EXPECT_NO_ERROR(GBK_system(cmd));
510                            free(cmd);
511                        }
512
513                        bool reexported_as_expected = arb_test::textfiles_have_difflines(expectedfile, outfile2, 0);
514
515#if defined(TREEIO_AUTO_UPDATE_IF_REEXPORT_DIFFERS)
516                        if (!reexported_as_expected) {
517                            system(GBS_global_string("cp %s %s", outfile2, expectedfile));
518                        }
519#else // !defined(TREEIO_AUTO_UPDATE_IF_REEXPORT_DIFFERS)
520                        TEST_EXPECT(reexported_as_expected);
521#endif
522
523                        TEST_EXPECT_ZERO_OR_SHOW_ERRNO(unlink(outfile2));
524                        free(outfile2);
525#endif
526                        free(expectedfile);
527                        free(paramID);
528                    }
529                }
530            }
531        }
532    }
533    TEST_ANNOTATE(NULp);
534
535    TEST_EXPECT_ZERO_OR_SHOW_ERRNO(unlink(outfile));
536    free(outfile);
537
538    GB_close(gb_main);
539}
540
541void TEST_CONSENSUS_TREE_functionality() {
542    // functionality wanted in TreeNode (for use in library CONSENSUS_TREE)
543
544    char *comment = NULp;
545
546    SizeAwareTree *tree = DOWNCAST(SizeAwareTree*, TREE_load("trees/bg_exp_p_GrpLen_0.tree",
547                                                             new SizeAwareRoot,
548                                                             &comment, false, NULp));
549    // -> ../UNIT_TESTER/run/trees/bg_exp_p_GrpLen_0.tree
550
551#define ORG_1111 "(AticSea6,(RblAerol,RblMesop))"
552#define TOP_1111 "((RblAerol,RblMesop),AticSea6)"
553#define BOT_1111 ORG_1111
554
555#define ORG_11121 "((DnrShiba,RsbElon4),MmbAlkal)"
556#define TOP_11121 ORG_11121
557#define BOT_11121 "(MmbAlkal,(DnrShiba,RsbElon4))"
558
559#define ORG_11122 "((MabPelag,MabSalin),PaoMaris)"
560#define TOP_11122 ORG_11122
561#define BOT_11122 "(PaoMaris,(MabPelag,MabSalin))"
562
563#define ORG_1112 "(" ORG_11121 "," ORG_11122 ")"
564#define TOP_1112 "(" TOP_11121 "," TOP_11122 ")"
565#define BOT_1112 "(" BOT_11121 "," BOT_11122 ")"
566#define EDG_1112 "(" TOP_11121 "," BOT_11122 ")"
567
568#define ORG_111 "(" ORG_1111 "," ORG_1112 ")"
569#define TOP_111 "(" TOP_1112 "," TOP_1111 ")"
570#define BOT_111 "(" BOT_1111 "," BOT_1112 ")"
571#define EDG_111 "(" EDG_1112 "," BOT_1111 ")"
572
573#define ORG_112 "(OnlGran2,RsnAnta2)"
574#define TOP_112 ORG_112
575#define BOT_112 ORG_112
576
577#define ORG_11 "(" ORG_111 "," ORG_112 ")"
578#define TOP_11 "(" TOP_111 "," TOP_112 ")"
579#define BOT_11 "(" BOT_112 "," BOT_111 ")"
580#define EDG_11 "(" EDG_111 "," BOT_112 ")"
581
582#define ORG_12 "(_MhuCaps,ThtNivea)"
583#define TOP_12 "(ThtNivea,_MhuCaps)"
584#define BOT_12 TOP_12
585
586#define ORG_1 "(" ORG_11 "," ORG_12 ")"
587#define TOP_1 "(" TOP_11 "," TOP_12 ")"
588#define BOT_1 "(" BOT_12 "," BOT_11 ")"
589#define EDG_1 "(" EDG_11 "," BOT_12 ")"
590
591#define ORG_2 "((LbnMarin,LbnzAlb4),LbnAlexa)"
592#define TOP_2 ORG_2
593#define BOT_2 "(LbnAlexa,(LbnMarin,LbnzAlb4))"
594
595    // test swap_sons
596    TEST_EXPECT_VALID_TREE(tree);
597    TEST_EXPECT_NEWICK(nSIMPLE, tree, "(" ORG_1 "," ORG_2 ");");
598    tree->swap_sons();
599    TEST_EXPECT_NEWICK(nSIMPLE, tree, "(" ORG_2 "," ORG_1 ");");
600
601    // test reorder_tree
602    TEST_EXPECT_VALID_TREE(tree);
603    TreeOrder order[] = { BIG_BRANCHES_TO_TOP, BIG_BRANCHES_TO_BOTTOM, BIG_BRANCHES_TO_EDGE };
604
605    for (size_t o1 = 0; o1<ARRAY_ELEMS(order); ++o1) {
606        TreeOrder to_order = order[o1];
607        for (size_t o2 = 0; o2<ARRAY_ELEMS(order); ++o2) {
608            TreeOrder from_order = order[o2];
609
610            for (int rotate = 0; rotate<=1; ++rotate) {
611                tree->reorder_tree(from_order);
612                if (rotate) tree->rotate_subtree();
613                tree->reorder_tree(to_order);
614
615                switch (to_order) {
616                    case BIG_BRANCHES_TO_TOP:    TEST_EXPECT_NEWICK(nSIMPLE, tree, "(" TOP_1 "," TOP_2 ");"); break;
617                    case BIG_BRANCHES_TO_EDGE:   TEST_EXPECT_NEWICK(nSIMPLE, tree, "(" EDG_1 "," BOT_2 ");"); break;
618                    case BIG_BRANCHES_TO_BOTTOM: TEST_EXPECT_NEWICK(nSIMPLE, tree, "(" BOT_2 "," BOT_1 ");"); break;
619                    default: TEST_REJECT(true); break;
620                }
621
622            }
623        }
624    }
625
626    // test rotate_subtree
627    TEST_EXPECT_VALID_TREE(tree);
628    tree->reorder_tree(BIG_BRANCHES_TO_TOP);
629    tree->rotate_subtree(); TEST_EXPECT_NEWICK(nSIMPLE, tree, "((LbnAlexa,(LbnzAlb4,LbnMarin)),((_MhuCaps,ThtNivea),((RsnAnta2,OnlGran2),((AticSea6,(RblMesop,RblAerol)),((PaoMaris,(MabSalin,MabPelag)),(MmbAlkal,(RsbElon4,DnrShiba)))))));");
630    tree->rotate_subtree(); TEST_EXPECT_NEWICK(nSIMPLE, tree, "(" TOP_1 "," TOP_2 ");");
631
632
633    // test set_root
634    TEST_EXPECT_VALID_TREE(tree);
635    TreeNode *AticSea6Grandpa = tree->findLeafNamed("AticSea6")->get_father()->get_father();
636    TEST_REJECT_NULL(AticSea6Grandpa);
637    TEST_EXPECT_VALID_TREE(AticSea6Grandpa);
638
639    AticSea6Grandpa->set_root();
640    TEST_EXPECT_NEWICK(nSIMPLE, tree,
641                             "((" ORG_1112 "," TOP_1111 ")," // AticSea6 is direct son of TOP_1111
642                             "((" ORG_2 "," TOP_12 ")," ORG_112 "));");
643
644    // test auto-detection of "best" root
645    TEST_EXPECT_VALID_TREE(tree);
646    tree->get_tree_root()->find_innermost_edge().set_root();
647    TEST_EXPECT_NEWICK(nLENGTH, tree,
648                       "((((LbnMarin:0.019,LbnzAlb4:0.003):0.016,LbnAlexa:0.032):0.122,(ThtNivea:0.230,_MhuCaps:0.194):0.427):0.076,"
649                       "(((((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);");
650
651    TEST_EXPECT_VALID_TREE(tree);
652    destroy(tree);
653    free(comment);
654}
655
656#endif // UNIT_TESTS
657
658// --------------------------------------------------------------------------------
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