source: tags/arb-6.0/TOOLS/arb_consensus_tree.cxx

Last change on this file was 12267, checked in by westram, 8 years ago
File size: 26.4 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 GBT_TREE *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   = NULL;
28    comment = NULL;
29
30    GBT_TREE *consense_tree = NULL;
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 = NULL;
39
40            TreeRoot      *root = new TreeRoot(new SizeAwareNodeFactory, true); // will be deleted when tree gets deleted
41            SizeAwareTree *tree = DOWNCAST(SizeAwareTree*, TREE_load(input_trees[i], *root, NULL, 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 ? GB_strpartdup(savename, ldot-1) : 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(GBT_TREE *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   = NULL;
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, NULL, 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 = NULL;
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 = NULL;
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 = 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            GBT_TREE *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("sucessfully created consensus tree\n"
173                           "(no savename specified -> tree not saved)\n");
174                }
175                delete cons_tree;
176            }
177            free(comment);
178        }
179        free(savename);
180    }
181
182    if (error) {
183        printf("Error in arb_consensus_tree: %s\n", error);
184    }
185
186    return error ? EXIT_FAILURE : EXIT_SUCCESS;
187}
188
189// --------------------------------------------------------------------------------
190
191#ifdef UNIT_TESTS
192#ifndef TEST_UNIT_H
193#include <test_unit.h>
194#endif
195
196#include "command_output.h"
197
198// #define TEST_AUTO_UPDATE // uncomment to update expected trees (if more than date differs)
199
200static char *custom_tree_name(int dir, const char *name) { return GBS_global_string_copy("consense/%i/%s.tree", dir, name); }
201static 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); }
202
203static void add_inputnames(StrArray& to, int dir, const char *basename, int first_tree, int last_tree) {
204    for (int t = first_tree; t <= last_tree; ++t) {
205        to.put(custom_numbered_tree_name(dir, basename, t));
206    }
207}
208
209static double calc_intree_distance(GBT_TREE *tree) {
210    if (tree->is_leaf) return 0.0;
211    return
212        tree->leftlen +
213        tree->rightlen +
214        calc_intree_distance(tree->leftson) +
215        calc_intree_distance(tree->rightson);
216}
217
218#define LENSUM_EPSILON .000001
219
220static arb_test::match_expectation consense_tree_generated(GBT_TREE *tree, GB_ERROR error, size_t species_count, size_t expected_species_count, double expected_intree_distance) {
221    using namespace   arb_test;
222    expectation_group expected;
223
224    expected.add(that(error).is_equal_to_NULL());
225    expected.add(that(tree).does_differ_from_NULL());
226
227    if (tree) {
228        expected.add(that(species_count).is_equal_to(expected_species_count));
229        expected.add(that(GBT_count_leafs(tree)).is_equal_to(expected_species_count));
230        expected.add(that(calc_intree_distance(tree)).fulfills(epsilon_similar(LENSUM_EPSILON), expected_intree_distance));
231    }
232
233    return all().ofgroup(expected);
234}
235
236static 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) {
237    using namespace       arb_test;
238    expectation_group     expected;
239    arb_suppress_progress hideProgress;
240
241    GB_ERROR  error   = NULL;
242    StrArray  input_tree_names;
243    add_inputnames(input_tree_names, treedir, basename, first_tree, last_tree);
244
245    size_t    species_count;
246    char     *comment;
247    GBT_TREE *tree = build_consensus_tree(input_tree_names, error, species_count, weight, comment);
248    expected.add(consense_tree_generated(tree, error, species_count, expected_species_count, expected_intree_distance));
249
250    char *saveas = custom_tree_name(treedir, outbasename);
251    error        = save_tree_as_newick(tree, saveas, comment);
252    expected.add(that(error).is_equal_to_NULL());
253
254    if (!error) {
255        char *expected_save        = custom_tree_name(treedir, GBS_global_string("%s_expected", outbasename));
256        bool  exported_as_expected = arb_test::textfiles_have_difflines_ignoreDates(expected_save, saveas, 0);
257
258#if defined(TEST_AUTO_UPDATE)
259        if (!exported_as_expected) {
260            ASSERT_RESULT(int, 0, system(GBS_global_string("cp %s %s", saveas, expected_save)));
261        }
262#else // !defined(TEST_AUTO_UPDATE)
263        expected.add(that(exported_as_expected).is_equal_to(true));
264#endif
265        TEST_EXPECT_ZERO_OR_SHOW_ERRNO(GB_unlink(saveas));
266        free(expected_save);
267    }
268
269    free(saveas);
270    free(comment);
271    delete tree;
272
273    return all().ofgroup(expected);
274}
275
276void TEST_consensus_tree_1() {
277    TEST_EXPECTATION(build_expected_consensus_tree(1, "bootstrapped", 1, 5, 0.7, "consense1", 22, 0.925779));
278    // ../UNIT_TESTER/run/consense/1/consense1.tree
279}
280void TEST_consensus_tree_1_single() {
281    TEST_EXPECTATION(build_expected_consensus_tree(1, "bootstrapped", 1, 1, 0.01, "consense1_single", 22, 0.924610));
282    // ../UNIT_TESTER/run/consense/1/consense1_single.tree
283}
284
285void TEST_consensus_tree_2() {
286    TEST_EXPECTATION(build_expected_consensus_tree(2, "bootstrapped", 1, 4, 2.5, "consense2", 59, 2.849827));
287    // ../UNIT_TESTER/run/consense/2/consense2.tree
288}
289
290void TEST_consensus_tree_3() {
291    TEST_EXPECTATION(build_expected_consensus_tree(3, "bootstrapped", 1, 3, 137.772, "consense3", 128, 2.170685));
292    // ../UNIT_TESTER/run/consense/3/consense3.tree
293}
294
295void TEST_consensus_tree_from_disjunct_trees() {
296    TEST_EXPECTATION(build_expected_consensus_tree(4, "disjunct", 1, 2, 137.772, "disjunct_merged", 15, 2.034290));
297    // ../UNIT_TESTER/run/consense/4/disjunct_merged.tree
298}
299
300void TEST_consensus_tree_from_partly_overlapping_trees() {
301    // tree_disjunct_3 contains 7 species
302    // (3 from upper subtree (tree_disjunct_1) and 4 from lower subtree (tree_disjunct_2))
303
304    TEST_EXPECTATION(build_expected_consensus_tree(4, "disjunct", 1, 3, 137.772, "overlap_merged", 15, 2.596455));
305    // ../UNIT_TESTER/run/consense/4/overlap_merged.tree
306}
307
308void TEST_consensus_tree_from_minimal_overlapping_trees() {
309    // tree_disjunct_0 only contains 2 species (1 from upper and 1 from lower subtree).
310    TEST_EXPECTATION(build_expected_consensus_tree(4, "disjunct", 0, 2, 137.772, "overlap_mini_merged", 15, 2.750745));
311    // ../UNIT_TESTER/run/consense/4/overlap_mini_merged.tree
312}
313
314void TEST_consensus_tree_described_in_arbhelp() {
315    // see ../HELP_SOURCE/oldhelp/consense_algo.hlp
316    TEST_EXPECTATION(build_expected_consensus_tree(5, "help", 1, 2, 2.0, "help_merged", 6, 1.050000));
317    // ../UNIT_TESTER/run/consense/5/help_merged.tree
318}
319
320void TEST_consensus_tree_from_trees_overlapping_by_twothirds() {
321    // These 3 trees where copied from an existing tree.
322    // From each copy one third of all species has been removed
323    // (removed sets were disjunct)
324    TEST_EXPECTATION(build_expected_consensus_tree(6, "overlap_two_thirds", 1, 3, 19.2, "overlap_twothirds_merged", 15, 3.561680));
325    // ../UNIT_TESTER/run/consense/6/overlap_twothirds_merged.tree
326}
327
328void TEST_consensus_tree_from_mostly_overlapping_trees() {
329    // the 3 trees were copied from tree_disjunct_source.
330    // from each tree 2 (different) species were deleted.
331    TEST_EXPECTATION(build_expected_consensus_tree(7, "disjunct_del2", 1, 3, 137.772, "overlap_mostly", 15, 1.820057));
332    // ../UNIT_TESTER/run/consense/7/overlap_mostly.tree
333}
334
335void TEST_consensus_tree_from_mostly_overlapping_trees_2() {
336    // the 3 trees were copied from tree_disjunct1
337    // from each tree 1 (different) species was deleted.
338    TEST_EXPECTATION(build_expected_consensus_tree(8, "overlap2", 1, 3, 137.772, "overlap2_mostly", 8, 0.529109));
339    // ../UNIT_TESTER/run/consense/8/overlap2_mostly.tree
340}
341
342
343
344#define REPEATED_TESTS
345
346#if defined(REPEATED_TESTS)
347void TEST_consensus_tree_generation_is_deterministic() {
348    TEST_consensus_tree_described_in_arbhelp();
349    TEST_consensus_tree_from_minimal_overlapping_trees();
350    TEST_consensus_tree_from_partly_overlapping_trees();
351    TEST_consensus_tree_from_disjunct_trees();
352    TEST_consensus_tree_3();
353    TEST_consensus_tree_2();
354    TEST_consensus_tree_1_single();
355    TEST_consensus_tree_1();
356}
357
358void TEST_arb_consensus_tree() {
359    TEST_STDOUT_CONTAINS("(arb_consensus_tree -x || true)", "Unknown switch '-x'");
360    TEST_STDOUT_CONTAINS("(arb_consensus_tree -w sth || true)", "no input trees specified");
361
362    {
363        char *saveas   = custom_tree_name(1, "consense1");
364        char *expected = custom_tree_name(1, "consense1_expected");
365   
366        TEST_STDOUT_CONTAINS("arb_consensus_tree"
367                             " -w consense/1/consense1.tree"
368                             " consense/1/bootstrapped_1.tree"
369                             " consense/1/bootstrapped_2.tree"
370                             " consense/1/bootstrapped_3.tree"
371                             " consense/1/bootstrapped_4.tree"
372                             " consense/1/bootstrapped_5.tree"
373                             ,
374                             "database  created");
375
376        TEST_EXPECT_TEXTFILE_DIFFLINES_IGNORE_DATES(saveas, expected, 0);
377        TEST_EXPECT_ZERO_OR_SHOW_ERRNO(GB_unlink(saveas));
378
379        free(expected);
380        free(saveas);
381    }
382
383    {
384        char *saveas   = custom_tree_name(2, "consense2");
385        char *expected = custom_tree_name(2, "consense2_expected");
386   
387        TEST_STDOUT_CONTAINS("arb_consensus_tree"
388                             " -w consense/2/consense2.tree"
389                             " consense/2/bootstrapped_1.tree"
390                             " consense/2/bootstrapped_2.tree"
391                             " consense/2/bootstrapped_3.tree"
392                             " consense/2/bootstrapped_4.tree"
393                             ,
394                             "database  created");
395
396        TEST_EXPECT_TEXTFILE_DIFFLINES_IGNORE_DATES(saveas, expected, 0);
397        TEST_EXPECT_ZERO_OR_SHOW_ERRNO(GB_unlink(saveas));
398
399        free(expected);
400        free(saveas);
401    }
402}
403#endif // REPEATED_TESTS
404
405// #define TREEIO_AUTO_UPDATE // uncomment to auto-update expected test-results
406// #define TREEIO_AUTO_UPDATE_IF_EXPORT_DIFFERS // uncomment to auto-update expected test-results
407// #define TREEIO_AUTO_UPDATE_IF_REEXPORT_DIFFERS // uncomment to auto-update expected test-results
408
409static const char *findFirstNameContaining(GBT_TREE *tree, const char *part) {
410    const char *found = NULL;
411    if (tree->name && strstr(tree->name, part)) {
412        found = tree->name;
413    }
414    else if (!tree->is_leaf) {
415        found             = findFirstNameContaining(tree->leftson, part);
416        if (!found) found = findFirstNameContaining(tree->rightson, part);
417    }
418    return found;
419}
420
421void TEST_SLOW_treeIO_stable() {
422    const char *dbname   = "trees/bootstrap_groups.arb";
423    const char *treename = "tree_bootstrap_and_groups";
424    const char *savename = "bg";
425
426    GB_shell  shell;
427    GBDATA   *gb_main = GB_open(dbname, "rw");
428
429    TEST_REJECT_NULL(gb_main);
430
431    GBT_TREE_NodeFactory nodeMaker;
432
433    char *outfile = GBS_global_string_copy("trees/%s.tree", savename);
434
435    for (int save_branchlengths = 0; save_branchlengths <= 1; ++save_branchlengths) {
436        for (int save_bootstraps = 0; save_bootstraps <= 1; ++save_bootstraps) {
437            for (int save_groupnames = 0; save_groupnames <= 1; ++save_groupnames) {
438                bool quoting_occurs = save_bootstraps && save_groupnames;
439                for (int pretty = 0; pretty <= 1; ++pretty) {
440
441                    for (int quoting = TREE_DISALLOW_QUOTES; quoting <= (quoting_occurs ? TREE_DOUBLE_QUOTES : TREE_DISALLOW_QUOTES); ++quoting) {
442                        TREE_node_quoting quoteMode = TREE_node_quoting(quoting);
443
444                        char *paramID = GBS_global_string_copy("%s_%s%s%s_%i",
445                                                               pretty ? "p" : "s",
446                                                               save_bootstraps ? "Bs" : "",
447                                                               save_groupnames ? "Grp" : "",
448                                                               save_branchlengths ? "Len" : "",
449                                                               quoteMode);
450
451                        TEST_ANNOTATE(GBS_global_string("for paramID='%s'", paramID));
452
453                        GB_ERROR export_error = TREE_write_Newick(gb_main, treename, NULL, save_branchlengths, save_bootstraps, save_groupnames, pretty, quoteMode, outfile);
454                        TEST_EXPECT_NULL(export_error);
455
456                        char *expectedfile = GBS_global_string_copy("trees/%s_exp_%s.tree", savename, paramID);
457
458#if defined(TREEIO_AUTO_UPDATE)
459                        system(GBS_global_string("cp %s %s", outfile, expectedfile));
460#else // !defined(TREEIO_AUTO_UPDATE)
461                        bool exported_as_expected = arb_test::textfiles_have_difflines_ignoreDates(expectedfile, outfile, 0);
462#if defined(TREEIO_AUTO_UPDATE_IF_EXPORT_DIFFERS)
463                        if (!exported_as_expected) {
464                            system(GBS_global_string("cp %s %s", outfile, expectedfile));
465                        }
466#else // !defined(TREEIO_AUTO_UPDATE_IF_EXPORT_DIFFERS)
467                        TEST_EXPECT(exported_as_expected);
468#endif
469
470                        // reimport exported tree
471                        const char *reloaded_treename = "tree_reloaded";
472                        {
473                            char     *comment    = NULL;
474                            GBT_TREE *tree       = TREE_load(expectedfile, nodeMaker, &comment, true, NULL);
475                            GB_ERROR  load_error = tree ? NULL : GB_await_error();
476
477                            TEST_EXPECTATION(all().of(that(tree).does_differ_from_NULL(),
478                                                      that(load_error).is_equal_to_NULL()));
479                            // store tree in DB
480                            {
481                                GB_transaction ta(gb_main);
482                                GB_ERROR       store_error = GBT_write_tree_with_remark(gb_main, reloaded_treename, tree, comment);
483                                TEST_EXPECT_NULL(store_error);
484                            }
485                            free(comment);
486
487                            if (save_groupnames) {
488                                const char *quotedGroup     = findFirstNameContaining(tree, "quoted");
489                                const char *underscoreGroup = findFirstNameContaining(tree, "bs100");
490                                TEST_EXPECT_EQUAL(quotedGroup, "quoted");
491                                TEST_EXPECT_EQUAL(underscoreGroup, "__bs100");
492                            }
493                            const char *capsLeaf = findFirstNameContaining(tree, "Caps");
494                            TEST_EXPECT_EQUAL(capsLeaf, "_MhuCaps");
495
496                            delete tree;
497                        }
498
499                        // export again
500                        GB_ERROR reexport_error = TREE_write_Newick(gb_main, reloaded_treename, NULL, save_branchlengths, save_bootstraps, save_groupnames, pretty, quoteMode, outfile);
501                        TEST_EXPECT_NULL(reexport_error);
502
503                        // eliminate comments added by loading/saving
504                        char *outfile2 = GBS_global_string_copy("trees/%s2.tree", savename);
505                        {
506                            char *cmd = GBS_global_string_copy("cat %s"
507                                                               " | grep -v 'Loaded from trees/.*_exp_'"
508                                                               " | grep -v 'tree_reloaded saved to'"
509                                                               " > %s", outfile, outfile2);
510                            TEST_EXPECT_NO_ERROR(GBK_system(cmd));
511                            free(cmd);
512                        }
513
514                        bool reexported_as_expected = arb_test::textfiles_have_difflines(expectedfile, outfile2, 0);
515
516#if defined(TREEIO_AUTO_UPDATE_IF_REEXPORT_DIFFERS)
517                        if (!reexported_as_expected) {
518                            system(GBS_global_string("cp %s %s", outfile2, expectedfile));
519                        }
520#else // !defined(TREEIO_AUTO_UPDATE_IF_REEXPORT_DIFFERS)
521                        TEST_EXPECT(reexported_as_expected);
522#endif
523
524                        TEST_EXPECT_ZERO_OR_SHOW_ERRNO(unlink(outfile2));
525                        free(outfile2);
526#endif
527                        free(expectedfile);
528                        free(paramID);
529                    }
530                }
531            }
532        }
533    }
534    TEST_ANNOTATE(NULL);
535
536    TEST_EXPECT_ZERO_OR_SHOW_ERRNO(unlink(outfile));
537    free(outfile);
538
539    GB_close(gb_main);
540}
541
542void TEST_CONSENSUS_TREE_functionality() {
543    // functionality wanted in RootedTree (for use in library CONSENSUS_TREE)
544
545    char *comment = NULL;
546
547    SizeAwareTree *tree = DOWNCAST(SizeAwareTree*, TREE_load("trees/bg_exp_p_GrpLen_0.tree",
548                                                             *new TreeRoot(new SizeAwareNodeFactory, true),
549                                                             &comment, false, NULL));
550    // -> ../UNIT_TESTER/run/trees/bg_exp_p_GrpLen_0.tree
551
552#define ORG_1111 "(AticSea6,(RblAerol,RblMesop))"
553#define TOP_1111 "((RblAerol,RblMesop),AticSea6)"
554#define BOT_1111 ORG_1111
555
556#define ORG_11121 "((DnrShiba,RsbElon4),MmbAlkal)"
557#define TOP_11121 ORG_11121
558#define BOT_11121 "(MmbAlkal,(DnrShiba,RsbElon4))"
559
560#define ORG_11122 "((MabPelag,MabSalin),PaoMaris)"
561#define TOP_11122 ORG_11122
562#define BOT_11122 "(PaoMaris,(MabPelag,MabSalin))"
563
564#define ORG_1112 "(" ORG_11121 "," ORG_11122 ")"
565#define TOP_1112 "(" TOP_11121 "," TOP_11122 ")"
566#define BOT_1112 "(" BOT_11121 "," BOT_11122 ")"
567#define EDG_1112 "(" TOP_11121 "," BOT_11122 ")"
568
569#define ORG_111 "(" ORG_1111 "," ORG_1112 ")"
570#define TOP_111 "(" TOP_1112 "," TOP_1111 ")"
571#define BOT_111 "(" BOT_1111 "," BOT_1112 ")"
572#define EDG_111 "(" EDG_1112 "," BOT_1111 ")"
573
574#define ORG_112 "(OnlGran2,RsnAnta2)"
575#define TOP_112 ORG_112
576#define BOT_112 ORG_112
577
578#define ORG_11 "(" ORG_111 "," ORG_112 ")"
579#define TOP_11 "(" TOP_111 "," TOP_112 ")"
580#define BOT_11 "(" BOT_112 "," BOT_111 ")"
581#define EDG_11 "(" EDG_111 "," BOT_112 ")"
582
583#define ORG_12 "(_MhuCaps,ThtNivea)"
584#define TOP_12 "(ThtNivea,_MhuCaps)"
585#define BOT_12 TOP_12
586
587#define ORG_1 "(" ORG_11 "," ORG_12 ")"
588#define TOP_1 "(" TOP_11 "," TOP_12 ")"
589#define BOT_1 "(" BOT_12 "," BOT_11 ")"
590#define EDG_1 "(" EDG_11 "," BOT_12 ")"
591
592#define ORG_2 "((LbnMarin,LbnzAlb4),LbnAlexa)"
593#define TOP_2 ORG_2
594#define BOT_2 "(LbnAlexa,(LbnMarin,LbnzAlb4))"
595
596    // test swap_sons
597    TEST_ASSERT_VALID_TREE(tree);
598    TEST_EXPECT_NEWICK(nSIMPLE, tree, "(" ORG_1 "," ORG_2 ");");
599    tree->swap_sons();
600    TEST_EXPECT_NEWICK(nSIMPLE, tree, "(" ORG_2 "," ORG_1 ");");
601
602    // test reorder_tree
603    TEST_ASSERT_VALID_TREE(tree);
604    TreeOrder order[] = { BIG_BRANCHES_TO_TOP, BIG_BRANCHES_TO_BOTTOM, BIG_BRANCHES_TO_EDGE };
605
606    for (size_t o1 = 0; o1<ARRAY_ELEMS(order); ++o1) {
607        TreeOrder to_order = order[o1];
608        for (size_t o2 = 0; o2<ARRAY_ELEMS(order); ++o2) {
609            TreeOrder from_order = order[o2];
610
611            for (int rotate = 0; rotate<=1; ++rotate) {
612                tree->reorder_tree(from_order);
613                if (rotate) tree->rotate_subtree();
614                tree->reorder_tree(to_order);
615
616                switch (to_order) {
617                    case BIG_BRANCHES_TO_TOP:    TEST_EXPECT_NEWICK(nSIMPLE, tree, "(" TOP_1 "," TOP_2 ");"); break;
618                    case BIG_BRANCHES_TO_EDGE:   TEST_EXPECT_NEWICK(nSIMPLE, tree, "(" EDG_1 "," BOT_2 ");"); break;
619                    case BIG_BRANCHES_TO_BOTTOM: TEST_EXPECT_NEWICK(nSIMPLE, tree, "(" BOT_2 "," BOT_1 ");"); break;
620                    default: TEST_REJECT(true); break;
621                }
622
623            }
624        }
625    }
626
627    // test rotate_subtree
628    TEST_ASSERT_VALID_TREE(tree);
629    tree->reorder_tree(BIG_BRANCHES_TO_TOP);
630    tree->rotate_subtree(); TEST_EXPECT_NEWICK(nSIMPLE, tree, "((LbnAlexa,(LbnzAlb4,LbnMarin)),((_MhuCaps,ThtNivea),((RsnAnta2,OnlGran2),((AticSea6,(RblMesop,RblAerol)),((PaoMaris,(MabSalin,MabPelag)),(MmbAlkal,(RsbElon4,DnrShiba)))))));");
631    tree->rotate_subtree(); TEST_EXPECT_NEWICK(nSIMPLE, tree, "(" TOP_1 "," TOP_2 ");");
632
633
634    // test set_root
635    TEST_ASSERT_VALID_TREE(tree);
636    RootedTree *AticSea6Grandpa = tree->findLeafNamed("AticSea6")->get_father()->get_father();
637    TEST_REJECT_NULL(AticSea6Grandpa);
638    TEST_ASSERT_VALID_TREE(AticSea6Grandpa);
639
640    AticSea6Grandpa->set_root();
641    TEST_EXPECT_NEWICK(nSIMPLE, tree,
642                             "((" ORG_1112 "," TOP_1111 ")," // AticSea6 is direct son of TOP_1111
643                             "((" ORG_2 "," TOP_12 ")," ORG_112 "));");
644
645    // test auto-detection of "best" root
646    TEST_ASSERT_VALID_TREE(tree);
647    tree->get_tree_root()->find_innermost_edge().set_root();
648    TEST_EXPECT_NEWICK(nLENGTH, tree,
649                             "((((LbnMarin:0.019,LbnzAlb4:0.003):0.016,LbnAlexa:0.032):0.122,(ThtNivea:0.230,_MhuCaps:0.194):0.427):0.076,"
650                             "(((((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);");
651
652    TEST_ASSERT_VALID_TREE(tree);
653    delete tree;
654    free(comment);
655}
656
657#endif // UNIT_TESTS
658
659// --------------------------------------------------------------------------------
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