ARB
PARS_dtree.cxx
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1 // =============================================================== //
2 // //
3 // File : PARS_dtree.cxx //
4 // Purpose : //
5 // //
6 // Institute of Microbiology (Technical University Munich) //
7 // http://www.arb-home.de/ //
8 // //
9 // =============================================================== //
10 
11 #include "PerfMeter.h"
12 #include "pars_dtree.hxx"
13 #include "pars_main.hxx"
14 #include "pars_awars.h"
15 #include "ap_tree_nlen.hxx"
16 #include "ap_main.hxx"
17 
18 #include <AP_TreeColors.hxx>
19 #include <AP_seq_dna.hxx>
20 #include <AP_seq_protein.hxx>
21 #include <AP_filter.hxx>
22 
23 #include <TreeCallbacks.hxx>
24 
25 #include <ColumnStat.hxx>
26 #include <awt_sel_boxes.hxx>
27 #include <awt_filter.hxx>
28 
29 #include <gui_aliview.hxx>
30 
31 #include <aw_preset.hxx>
32 #include <aw_awar.hxx>
33 #include <aw_msg.hxx>
34 #include <arb_progress.h>
35 #include <aw_root.hxx>
36 #include <aw_question.hxx>
37 
38 static void AWT_graphic_parsimony_root_changed(void *cd, AP_tree *old, AP_tree *newroot) {
40  UNCOVERED();
41 
42  if (old == agt->get_logical_root()) agt->set_logical_root_to(newroot);
43 }
44 
45 static AliView *pars_generate_aliview(WeightedFilter *pars_weighted_filter) {
46  GBDATA *gb_main = pars_weighted_filter->get_gb_main();
47  char *ali_name;
48  {
49  GB_transaction ta(gb_main);
50  ali_name = GBT_read_string(gb_main, AWAR_ALIGNMENT);
51  }
53  AliView *aliview = pars_weighted_filter->create_aliview(ali_name, error);
54  if (!aliview) aw_popup_exit(error);
55  free(ali_name);
56  return aliview;
57 }
58 
60  ap_assert(agt->get_root_node());
62 
64  GB_transaction ta(gb_main);
65 
66  const char *use = ap_main->get_aliname();
67  long ali_len = GBT_get_alignment_len(gb_main, use);
68  if (ali_len <= 1) {
69  aw_popup_exit("No valid alignment selected! Try again");
70  }
71 
72  agt->get_tree_root()->set_root_changed_callback(AWT_graphic_parsimony_root_changed, agt);
73 }
74 
75 QuadraticThreshold::QuadraticThreshold(KL_DYNAMIC_THRESHOLD_TYPE type, double startx, double maxy, double maxx, double maxDepth, Mutations pars_start) {
76  // set a, b, and c for quadratic equation y = ax^2 + bx + c
77  switch (type) {
78  default:
79  ap_assert(0);
80  // fall-through
81  case AP_QUADRAT_START:
82  c = startx;
83  a = (startx - maxy) / (maxx * maxx);
84  b = -2.0 * a * maxx;
85  break;
86 
87  case AP_QUADRAT_MAX: // unused (experimental)
88  a = - maxy / ((maxDepth - maxx) * (maxDepth - maxx));
89  b = -2.0 * a * maxx;
90  c = maxy + a * maxx * maxx;
91  break;
92  }
93  c += pars_start;
94 }
95 
96 void ArbParsimony::kernighan_optimize_tree(AP_tree_nlen *at, const KL_Settings& settings, const Mutations *pars_global_start, bool dumpPerf) {
97  AP_tree_nlen *oldrootleft = get_root_node()->get_leftson();
98  AP_tree_nlen *oldrootright = get_root_node()->get_rightson();
99  Mutations pars_curr = get_root_node()->costs();
100  const Mutations pars_org = pars_curr;
101 
102  OptiPerfMeter performance("KL-recursion", pars_curr);
103 
104  // setup KL recursion parameters:
105  KL_params KL;
106  {
107  KL.max_rec_depth = settings.maxdepth; ap_assert(KL.max_rec_depth>0);
108  KL.inc_rec_depth = settings.incdepth;
109  KL.thresFunctor = QuadraticThreshold(settings.Dynamic.type, settings.Dynamic.start, settings.Dynamic.maxy, settings.Dynamic.maxx, KL.max_rec_depth, pars_curr);
111 
112  for (int x = 0; x<CUSTOM_DEPTHS; ++x) {
113  KL.rec_width[x] = settings.Static.depth[x];
114  }
116  }
117 
118  AP_tree_edge *startEdge = NULp;
119  AP_tree_nlen *skipNode = NULp;
120  bool skipStartEdge = true;
121 
122  if (!at->father) {
123  startEdge = rootEdge();
124  skipStartEdge = false;
125  }
126  else if (at->is_son_of_root()) {
127  startEdge = rootEdge();
128  skipNode = startEdge->otherNode(at);
129  }
130  else {
131  skipNode = at->get_father();
132  startEdge = at->edgeTo(skipNode);
133  }
134  ap_assert(startEdge);
135 
136  EdgeChain chain(startEdge, EdgeSpec(SKIP_LEAF_EDGES|settings.whichEdges), true, skipNode, skipStartEdge);
137  arb_progress progress(chain.size());
138 
139  if (pars_global_start) {
140  progress.subtitle(GBS_global_string("best=%li (gain=%li)", pars_curr, *pars_global_start-pars_curr));
141  }
142  else {
143  progress.subtitle(GBS_global_string("best=%li", pars_curr));
144  }
145 
146  if (skipStartEdge) startEdge->set_visited(true); // avoid traversal beyond startEdge
147 
148  while (chain && !progress.aborted()) {
149  AP_tree_edge *edge = *chain; ++chain;
150 
151  ap_assert(!edge->is_leaf_edge());
153 
154  ap_main->remember();
155 
156  bool better_tree_found = edge->kl_rec(KL, 0, pars_curr);
157 
158  if (better_tree_found) {
159  ap_main->accept();
160  Mutations pars_new = get_root_node()->costs();
161  KL.thresFunctor.change_parsimony_start(pars_new-pars_curr);
162  pars_curr = pars_new;
163  if (pars_global_start) {
164  progress.subtitle(GBS_global_string("best=%li (gain=%li, KL=%li)", pars_curr, *pars_global_start-pars_curr, pars_org-pars_curr));
165  }
166  else {
167  progress.subtitle(GBS_global_string("best=%li (gain=%li)", pars_curr, pars_org-pars_curr));
168  }
169  }
170  else {
171  ap_main->revert();
172  }
173  progress.inc();
174  }
175 
176  if (skipStartEdge) startEdge->set_visited(false); // reallow traversal beyond startEdge
177 
178  if (dumpPerf) performance.dump(stdout, pars_curr);
179 
180  if (oldrootleft->father == oldrootright) {
181  oldrootleft->set_root();
182  }
183  else {
184  oldrootright->set_root();
185  }
186 }
187 
188 
189 
190 void ArbParsimony::optimize_tree(AP_tree_nlen *at, const KL_Settings& settings, arb_progress& progress) {
191  AP_tree_nlen *oldrootleft = get_root_node()->get_leftson();
192  AP_tree_nlen *oldrootright = get_root_node()->get_rightson();
193  const Mutations org_pars = get_root_node()->costs();
194  Mutations prev_pars = org_pars;
195 
196  OptiPerfMeter overallPerf("global optimization", org_pars);
197 
198  progress.subtitle(GBS_global_string("best=%li", org_pars));
199 
200  // define available heuristics
201  enum Heuristic {
202  RECURSIVE_NNI,
203  CUSTOM_KL,
204 
205  NO_FURTHER_HEURISTIC,
206  HEURISTIC_COUNT = NO_FURTHER_HEURISTIC,
207  } heuristic = RECURSIVE_NNI;
208 
209  struct H_Settings {
210  const char *name; // name shown in OptiPerfMeter
211  const KL_Settings *kl; // ==NULp -> NNI; else KL with these settings
212  bool repeat; // retry same heuristic when tree improved
213  Heuristic onImprove; // continue with this heuristic if improved (repeated or not)
214  Heuristic onFailure; // continue with this heuristic if NOT improved
215  } heuristic_setting[HEURISTIC_COUNT] = {
216  { "recursive NNIs", NULp, true, CUSTOM_KL, CUSTOM_KL },
217  { "KL-optimizer", &settings, false, RECURSIVE_NNI, NO_FURTHER_HEURISTIC },
218  };
219 
220  Mutations heu_start_pars = prev_pars;
221  OptiPerfMeter *heuPerf = NULp;
222 
223 #if defined(ASSERTION_USED)
224  bool at_is_root = at == rootNode();
225 #endif
226 
227  {
228  arb_suppress_progress quiet; // @@@ use weighted progress (#789) for loop below
229 
230  while (heuristic != NO_FURTHER_HEURISTIC && !progress.aborted()) {
231  const H_Settings& hset = heuristic_setting[heuristic];
232  if (!heuPerf) {
233  ap_assert(heu_start_pars == prev_pars);
234  heuPerf = new OptiPerfMeter(hset.name, heu_start_pars);
235  }
236 
237  Mutations this_pars(-1);
238  if (hset.kl) {
239  kernighan_optimize_tree(at, *hset.kl, &org_pars, false);
240  this_pars = get_root_node()->costs();
241  }
242  else {
243  this_pars = at->nn_interchange_rec(settings.whichEdges, AP_BL_NNI_ONLY);
244  }
245  ap_assert(this_pars>=0); // ensure this_pars was set
246  ap_assert(this_pars<=prev_pars); // otherwise heuristic worsened the tree
247 
248  ap_assert(at_is_root == (at == rootNode()));
249 
250  bool dumpOverall = false;
251  Heuristic nextHeuristic = heuristic;
252  if (this_pars<prev_pars) { // found better tree
253  prev_pars = this_pars;
254  progress.subtitle(GBS_global_string("best=%li (gain=%li)", this_pars, org_pars-this_pars));
255  if (!hset.repeat) {
256  nextHeuristic = hset.onImprove;
257  dumpOverall = heuristic == CUSTOM_KL;
258  }
259  }
260  else { // last step did not find better tree
261  nextHeuristic = this_pars<heu_start_pars ? hset.onImprove : hset.onFailure;
262  }
263 
264  if (nextHeuristic != heuristic) {
265  heuristic = nextHeuristic;
266  heu_start_pars = this_pars;
267 
268  heuPerf->dump(stdout, this_pars);
269  delete heuPerf; heuPerf = NULp;
270  }
271  if (dumpOverall) overallPerf.dumpCustom(stdout, this_pars, "overall (so far)");
272  }
273  }
274 
275  if (oldrootleft->father == oldrootright) {
276  oldrootleft->set_root();
277  }
278  else {
279  oldrootright->set_root();
280  }
281 
282  overallPerf.dump(stdout, prev_pars);
283 }
284 
286  : AWT_graphic_tree(AW_root::SINGLETON, gb_main_, map_viewer_cb_),
287  parsimony(parsimony_)
288 {}
289 
290 AP_tree_root *AWT_graphic_parsimony::create_tree_root(AliView *aliview, AP_sequence *seq_prototype, bool insert_delete_cbs) {
291  return new AP_pars_root(aliview, seq_prototype, insert_delete_cbs, &groupScale);
292 }
293 
294 
295 void ArbParsimony::generate_tree(WeightedFilter *pars_weighted_filter) {
296  AliView *aliview = pars_generate_aliview(pars_weighted_filter);
297  AP_sequence *seq_templ = NULp;
298 
299  GBDATA *gb_main = aliview->get_gb_main();
300  {
301  GB_transaction ta(gb_main);
302  bool is_aa = GBT_is_alignment_protein(gb_main, aliview->get_aliname());
303 
304  if (is_aa) seq_templ = new AP_sequence_protein(aliview);
305  else seq_templ = new AP_sequence_parsimony(aliview);
306  }
307 
308  AWT_graphic_parsimony *new_tree = new AWT_graphic_parsimony(*this, aliview->get_gb_main(), PARS_map_viewer);
309  new_tree->init(aliview, seq_templ, true, false);
310  set_tree(new_tree);
311 }
312 
313 AW_gc_manager *AWT_graphic_parsimony::init_devices(AW_window *aww, AW_device *device, AWT_canvas* ntw) {
314  AW_init_color_group_defaults("arb_ntree");
315 
316  AW_gc_manager *gc_manager =
317  AW_manage_GC(aww,
318  ntw->get_gc_base_name(),
319  device, AWT_GC_MAX, AW_GCM_DATA_AREA,
320  makeGcChangedCallback(TREE_GC_changed_cb, ntw),
321  "#AAAA55",
322 
323  // Important note :
324  // Many gc indices are shared between ABR_NTREE and ARB_PARSIMONY
325  // e.g. the tree drawing routines use same gc's for drawing both trees
326  // (keep in sync with ../SL/TREEDISP/TreeDisplay.cxx@init_devices)
327 
328  "Cursor$#FFFFFF",
329  "Branch remarks$#DBE994",
330  "+-Bootstrap$#DBE994", "-B.(limited)$white",
331  "!1", // reserve GC-number used for "IRS group box" in arb_ntree
332  "Marked$#FFFF00",
333  "Some marked$#eeee88",
334  "Not marked$black",
335  "Zombies etc.$#cc5924",
336 
337  "!14", // reserve 14 GC-numbers which are used for probe colors in ARB_NTREE
338  // (namely 'None', 'All' and 'P1' up to 'P12')
339 
340  "&color_groups", // use color groups
341 
342  NULp);
343  return gc_manager;
344 }
345 
346 void AWT_graphic_parsimony::show(AW_device *device) {
347  AP_tree_nlen *root_node = parsimony.get_root_node();
348  AW_awar *awar_pars = get_root()->awar(AWAR_PARSIMONY);
349  AW_awar *awar_best = get_root()->awar(AWAR_BEST_PARSIMONY);
350 
351  long parsval = root_node ? root_node->costs() : 0;
352  awar_pars->write_int(parsval);
353 
354  long best_pars = awar_best->read_int();
355  if (parsval < best_pars || 0==best_pars) awar_best->write_int(parsval);
356 
357  AWT_graphic_tree::show(device);
358 }
359 
360 void AWT_graphic_parsimony::handle_command(AW_device *device, AWT_graphic_event& event) {
361  ClickedTarget clicked(this, event.best_click());
362  bool recalc_branchlengths_on_structure_change = true;
363 
364  switch (event.cmd()) {
365  case AWT_MODE_NNI:
366  case AWT_MODE_KERNINGHAN:
367  case AWT_MODE_OPTIMIZE: {
368  const char *what = NULp;
369  const char *where = NULp;
370 
371  switch (event.cmd()) {
372  case AWT_MODE_NNI: what = "Recursive NNI on"; break;
373  case AWT_MODE_KERNINGHAN: what = "K.L. optimize"; break;
374  case AWT_MODE_OPTIMIZE: what = "Global optimize"; break;
375  default: break;
376  }
377 
378  AP_tree_nlen *startNode = NULp;
379  bool repeatOpti = true;
380 
381  if (event.type() == AW_Mouse_Press) {
382  switch (event.button()) {
383  case AW_BUTTON_LEFT:
384  repeatOpti = false;
385  // fall-through
386  case AW_BUTTON_RIGHT:
387  startNode = DOWNCAST(AP_tree_nlen*, clicked.node());
388  where = (startNode == get_root_node()) ? "tree" : "subtree";
389  break;
390 
391  default:
392  break;
393  }
394  }
395 
396  if (what && where) {
397  arb_progress progress(GBS_global_string("%s %s", what, where));
398 
399  Mutations start_pars = get_root_node()->costs();
400  Mutations curr_pars = start_pars;
401 
402  KL_Settings KL(get_root());
403 
404  do {
405  Mutations prev_pars = curr_pars;
406 
407  switch (event.cmd()) {
408  case AWT_MODE_NNI:
409  startNode->nn_interchange_rec(KL.whichEdges, AP_BL_NNI_ONLY);
410  break;
411  case AWT_MODE_KERNINGHAN:
412  parsimony.kernighan_optimize_tree(startNode, KL, &start_pars, true);
413  break;
414  case AWT_MODE_OPTIMIZE:
415  parsimony.optimize_tree(startNode, KL, progress);
416  repeatOpti = false; // never loop here (optimize_tree already loops until no further improvement)
417  break;
418  default:
419  repeatOpti = false;
420  break;
421  }
422 
423  curr_pars = get_root_node()->costs();
424  repeatOpti = repeatOpti && curr_pars<prev_pars;
425  } while (repeatOpti);
426 
429  }
430  break;
431  }
432 
433  default:
434  recalc_branchlengths_on_structure_change = false;
435  FALLTHROUGH; // unlisted modes trigger branchlength calculation internally when needed
436  case AWT_MODE_MOVE:
437  AWT_graphic_tree::handle_command(device, event);
438  break;
439  }
440 
441  if (exports.needs_save() && recalc_branchlengths_on_structure_change) {
442  arb_progress progress("Recalculating branch lengths");
443  rootEdge()->calc_branchlengths();
444  reorderTree(BIG_BRANCHES_TO_TOP); // beautify after recalc_branch_lengths
445  }
446 }
447 
448 
449 // --------------------------------------------------------------------------------
450 
451 #ifdef UNIT_TESTS
452 #include <arb_diff.h>
453 #include <test_unit.h>
454 #include "test_env.h"
455 
456 template<typename SEQTYPE>
457 PARSIMONY_testenv<SEQTYPE>::PARSIMONY_testenv(const char *dbname, const char *aliName)
458  : parsimony(),
459  klSettings(NULp)
460 {
461  common_init(dbname);
463  GB_transaction ta(gb_main);
464  size_t aliLength = GBT_get_alignment_len(gb_main, aliName);
465 
466  klSettings = new KL_Settings();
467 
468  AP_filter filter(aliLength);
469  if (!filter.is_invalid()) {
470  AP_weights weights(&filter);
471  agt->init(new AliView(gb_main, filter, weights, aliName));
472  }
473 }
474 
475 template PARSIMONY_testenv<AP_sequence_protein>::PARSIMONY_testenv(const char *dbname, const char *aliName); // explicit instanciation (otherwise link error in unittest)
476 template PARSIMONY_testenv<AP_sequence_parsimony>::PARSIMONY_testenv(const char *dbname, const char *aliName); // explicit instanciation (as above, but only happens with gcc 4.6.3/NDEBUG)
477 
478 
479 void TEST_basic_tree_modifications() {
480  PARSIMONY_testenv<AP_sequence_parsimony> env("TEST_trees.arb");
481  TEST_EXPECT_NO_ERROR(env.load_tree("tree_test"));
482 
483  {
484  AP_tree_nlen *root = env.root_node();
485 
486  // first check initial state:
487  {
488  AP_tree_members& root_info = root->gr;
489 
490  TEST_EXPECT_EQUAL(root_info.grouped, false);
491  TEST_EXPECT_EQUAL(root_info.hidden, false);
492  TEST_EXPECT_EQUAL(root_info.mark_sum, 6);
493  TEST_EXPECT_EQUAL(root_info.leaf_sum, 15);
494 
495  TEST_EXPECT_SIMILAR(root_info.max_tree_depth, 1.624975, 0.000001);
496  TEST_EXPECT_SIMILAR(root_info.min_tree_depth, 0.341681, 0.000001);
497 
498  GB_transaction ta(env.gbmain());
499  GBT_mark_all(env.gbmain(), 0); // unmark all species
500  root->compute_tree();
501  TEST_EXPECT_EQUAL(root_info.mark_sum, 0);
502  }
503 
504 
505 #define B1_TOP "(((((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"
506 #define B1_BOT "(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"
507 #define B2_TOP "(((CloButy2:0.009,CloButyr:0.000):0.564,CloCarni:0.120):0.010,CloPaste:0.179):0.131"
508 #define B2_BOT "(CloPaste:0.179,(CloCarni:0.120,(CloButy2:0.009,CloButyr:0.000):0.564):0.010):0.131"
509 
510 
511 #define B3_LEFT_TOP_SONS "(((CorAquat:0.084,CurCitre:0.058):0.103,CorGluta:0.522):0.053,CelBiazo:0.059)"
512 #define B3_TOP_SONS B3_LEFT_TOP_SONS ":0.207,CytAquat:0.711"
513 #define B3_TOP_SONS_CCR "((CorAquat:0.187,CorGluta:0.522):0.053,CelBiazo:0.059):0.207,CytAquat:0.711" // CCR = CurCitre removed
514 #define B3_TOP "(" B3_TOP_SONS "):0.081"
515 #define B3_BOT "(CytAquat:0.711,(CelBiazo:0.059,(CorGluta:0.522,(CorAquat:0.084,CurCitre:0.058):0.103):0.053):0.207):0.081"
516 
517 
518  const char *top_topo = "((" B1_TOP "," B2_TOP "):0.081," B3_TOP ");";
519  const char *edge_topo = "((" B1_TOP "," B2_BOT "):0.081," B3_BOT ");";
520  const char *bottom_topo = "(" B3_BOT ",(" B2_BOT "," B1_BOT "):0.081);";
521 
522  const char *radial_topo =
523  "(((CloPaste:0.179,((CloButy2:0.009,CloButyr:0.000):0.564,CloCarni:0.120):0.010):0.131,"
524  "((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,"
525  "((CelBiazo:0.059,((CorAquat:0.084,CurCitre:0.058):0.103,CorGluta:0.522):0.053):0.207,CytAquat:0.711):0.081);";
526  const char *radial_topo2 =
527  "(((CloBifer:0.388,(CloInnoc:0.371,(((CloTyro3:1.046,CloTyro4:0.061):0.026,CloTyro2:0.017):0.017,CloTyrob:0.009):0.274):0.057):0.124," B2_TOP "):0.081,"
528  "(CytAquat:0.711," B3_LEFT_TOP_SONS ":0.207):0.081);";
529 
530  // expect that no mode reproduces another mode:
531  TEST_EXPECT_DIFFERENT(top_topo, edge_topo);
532  TEST_EXPECT_DIFFERENT(top_topo, bottom_topo);
533  TEST_EXPECT_DIFFERENT(top_topo, radial_topo);
534  TEST_EXPECT_DIFFERENT(top_topo, radial_topo2);
535  TEST_EXPECT_DIFFERENT(edge_topo, bottom_topo);
536  TEST_EXPECT_DIFFERENT(edge_topo, radial_topo);
537  TEST_EXPECT_DIFFERENT(edge_topo, radial_topo2);
538  TEST_EXPECT_DIFFERENT(bottom_topo, radial_topo);
539  TEST_EXPECT_DIFFERENT(bottom_topo, radial_topo2);
540  TEST_EXPECT_DIFFERENT(radial_topo, radial_topo2);
541 
542  env.push(); // 1st stack level (=top_topo)
543 
545 
546  TEST_EXPECT_NEWICK(nLENGTH, root, top_topo);
547  // test reorder_tree:
548  root->reorder_tree(BIG_BRANCHES_TO_EDGE); TEST_EXPECT_NEWICK(nLENGTH, root, edge_topo); env.push(); // 2nd stack level (=edge_topo)
549  root->reorder_tree(BIG_BRANCHES_TO_BOTTOM); TEST_EXPECT_NEWICK(nLENGTH, root, bottom_topo); env.push(); // 3rd stack level (=bottom_topo)
550  root->reorder_tree(BIG_BRANCHES_TO_CENTER); TEST_EXPECT_NEWICK(nLENGTH, root, radial_topo);
551  root->reorder_tree(BIG_BRANCHES_ALTERNATING); TEST_EXPECT_NEWICK(nLENGTH, root, radial_topo2);
552  root->reorder_tree(BIG_BRANCHES_TO_TOP); TEST_EXPECT_NEWICK(nLENGTH, root, top_topo);
553 
555 
556  // test set root:
557  AP_tree_nlen *CloTyrob = root->findLeafNamed("CloTyrob");
558  TEST_REJECT_NULL(CloTyrob);
559 
560  ARB_edge rootEdge(root->get_leftson(), root->get_rightson());
561  CloTyrob->set_root();
562 
564 
565  const char *rootAtCloTyrob_topo =
566  "(CloTyrob:0.004,"
567  "(((CloTyro3:1.046,CloTyro4:0.061):0.026,CloTyro2:0.017):0.017,"
568  "((((" B3_TOP_SONS "):0.162," B2_TOP "):0.124,CloBifer:0.388):0.057,CloInnoc:0.371):0.274):0.004);";
569 
570  TEST_EXPECT_NEWICK(nLENGTH, root, rootAtCloTyrob_topo);
571  env.push(); // 4th stack level (=rootAtCloTyrob_topo)
572 
574 
575  AP_tree_nlen *CelBiazoFather = root->findLeafNamed("CelBiazo")->get_father();
576  TEST_REJECT_NULL(CelBiazoFather);
577  CelBiazoFather->set_root();
578 
579  const char *rootAtCelBiazoFather_topo = "(" B3_LEFT_TOP_SONS ":0.104,((" B1_TOP "," B2_TOP "):0.162,CytAquat:0.711):0.104);";
580  TEST_EXPECT_NEWICK(nLENGTH, root, rootAtCelBiazoFather_topo);
581 
583 
584  ARB_edge oldRootEdge(rootEdge.source(), rootEdge.dest());
585  DOWNCAST(AP_tree_nlen*,oldRootEdge.son())->set_root();
586 
587  const char *rootSetBack_topo = top_topo;
588  TEST_EXPECT_NEWICK(nLENGTH, root, rootSetBack_topo);
589  env.push(); // 5th stack level (=rootSetBack_topo)
590 
592 
593  // test remove:
594  AP_tree_nlen *CurCitre = root->findLeafNamed("CurCitre");
595  TEST_REJECT_NULL(CurCitre);
596  TEST_REJECT_NULL(CurCitre->get_father());
597 
598  CurCitre->REMOVE();
599  const char *CurCitre_removed_topo = "((" B1_TOP "," B2_TOP "):0.081,(" B3_TOP_SONS_CCR "):0.081);";
600  // ------------------------------------------------------------------- ^^^ = B3_TOP_SONS minus CurCitre
601  TEST_EXPECT_NEWICK(nLENGTH, root, CurCitre_removed_topo);
602 
604  TEST_EXPECT_VALID_TREE(CurCitre);
605 
606  TEST_EXPECT_EQUAL(root->gr.leaf_sum, 15); // out of date
607  root->compute_tree();
608  TEST_EXPECT_EQUAL(root->gr.leaf_sum, 14);
609 
610  env.push(); // 6th stack level (=CurCitre_removed_topo)
611 
613 
614  // test insert:
615  AP_tree_nlen *CloCarni = root->findLeafNamed("CloCarni");
616  TEST_REJECT_NULL(CloCarni);
617  CurCitre->insert(CloCarni); // this creates two extra edges (not destroyed by destroy() below) and one extra node
618 
619  const char *CurCitre_inserted_topo = "((" B1_TOP ",(((CloButy2:0.009,CloButyr:0.000):0.564,(CurCitre:0.060,CloCarni:0.060):0.060):0.010,CloPaste:0.179):0.131):0.081,(" B3_TOP_SONS_CCR "):0.081);";
620  TEST_EXPECT_NEWICK(nLENGTH, root, CurCitre_inserted_topo);
621 
623 
624  // now check pops:
625  env.pop(); TEST_EXPECT_NEWICK(nLENGTH, root, CurCitre_removed_topo); TEST_EXPECT_VALID_TREE(root);
626  env.pop(); TEST_EXPECT_NEWICK(nLENGTH, root, rootSetBack_topo); TEST_EXPECT_VALID_TREE(root);
627  env.pop(); TEST_EXPECT_NEWICK(nLENGTH, root, rootAtCloTyrob_topo); TEST_EXPECT_VALID_TREE(root);
628  env.pop(); TEST_EXPECT_NEWICK(nLENGTH, root, bottom_topo); TEST_EXPECT_VALID_TREE(root);
629  env.pop(); TEST_EXPECT_NEWICK(nLENGTH, root, edge_topo); TEST_EXPECT_VALID_TREE(root);
630  env.pop(); TEST_EXPECT_NEWICK(nLENGTH, root, top_topo); TEST_EXPECT_VALID_TREE(root);
631  }
632 }
633 
634 void TEST_calc_bootstraps() {
635  PARSIMONY_testenv<AP_sequence_parsimony> env("TEST_trees.arb", "ali_5s");
636  TEST_EXPECT_NO_ERROR(env.load_tree("tree_test"));
637 
638  const char *bs_origi_topo = "(((((((CloTyro3,CloTyro4)'40%',CloTyro2)'0%',CloTyrob)'97%',CloInnoc)'0%',CloBifer)'53%',(((CloButy2,CloButyr),CloCarni)'33%',CloPaste)'97%'),((((CorAquat,CurCitre),CorGluta)'17%',CelBiazo)'40%',CytAquat));";
639  const char *bs_limit_topo = "(((((((CloTyro3,CloTyro4)'87%',CloTyro2)'0%',CloTyrob)'100%',CloInnoc)'87%',CloBifer)'83%',(((CloButy2,CloButyr)'99%',CloCarni)'17%',CloPaste)'56%')'61%',((((CorAquat,CurCitre)'78%',CorGluta)'0%',CelBiazo)'59%',CytAquat)'61%');";
640  const char *bs_estim_topo = "(((((((CloTyro3,CloTyro4)'75%',CloTyro2)'0%',CloTyrob)'100%',CloInnoc)'75%',CloBifer)'78%',(((CloButy2,CloButyr)'99%',CloCarni)'13%',CloPaste)'32%')'53%',((((CorAquat,CurCitre)'74%',CorGluta)'0%',CelBiazo)'56%',CytAquat)'53%');";
641 
642  {
643  AP_tree_nlen *root = env.root_node();
644  AP_tree_edge *root_edge = rootEdge();
645 
646  TEST_EXPECT(root && root_edge);
647 
648  root->reorder_tree(BIG_BRANCHES_TO_TOP); TEST_EXPECT_NEWICK(nREMARK, root, bs_origi_topo);
649 
651 
653  root->reorder_tree(BIG_BRANCHES_TO_TOP);
654  TEST_EXPECT_NEWICK(nREMARK, root, bs_limit_topo);
656 
658  root->reorder_tree(BIG_BRANCHES_TO_TOP);
659  TEST_EXPECT_NEWICK(nREMARK, root, bs_estim_topo);
661 
662  TEST_EXPECT_EQUAL(env.root_node(), root);
663  }
664 
665 }
666 
667 void TEST_tree_remove_add_all() {
668  // reproduces crash as described in #527
669  PARSIMONY_testenv<AP_sequence_parsimony> env("TEST_trees.arb", "ali_5s");
670  TEST_EXPECT_NO_ERROR(env.load_tree("tree_nj"));
671 
672  const int LEAFS = 6;
673  AP_tree_nlen *leaf[LEAFS];
674  const char *name[LEAFS] = {
675  "CloButy2",
676  "CloButyr",
677  "CytAquat",
678  "CorAquat",
679  "CurCitre",
680  "CorGluta",
681  };
682 
683  AP_tree_nlen *root = env.root_node();
684 
685  for (int i = 0; i<LEAFS; ++i) {
686  leaf[i] = root->findLeafNamed(name[i]);
687  TEST_REJECT_NULL(leaf[i]);
688  }
689 
691 
692  AP_pars_root *troot = leaf[0]->get_tree_root();
693  TEST_REJECT_NULL(troot);
694 
695  for (int i = 0; i<LEAFS-1; ++i) {
696  // Note: removing the second to last leaf, "removes" both remaining
697  // leafs (but only destroys their father node)
698 
700  leaf[i]->REMOVE();
701  TEST_EXPECT_VALID_TREE(leaf[i]);
702  }
703 
704  leaf[0]->initial_insert(leaf[1], troot);
705  for (int i = 2; i<LEAFS; ++i) {
706  TEST_EXPECT_VALID_TREE(leaf[i-1]);
707  TEST_EXPECT_VALID_TREE(leaf[i]);
708  leaf[i]->insert(leaf[i-1]);
709  }
710 }
711 
712 #endif // UNIT_TESTS
713 
714 // --------------------------------------------------------------------------------
void reorderTree(TreeOrder mode)
#define TEST_EXPECT_COMBINES_PERFORMED(env, expComb)
Definition: test_env.h:150
const char * GB_ERROR
Definition: arb_core.h:25
GB_TYPES type
AP_tree * get_logical_root()
const char * get_aliname() const
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#define TEST_EXPECT_SIMILAR(expr, want, epsilon)
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static int maxDepth
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unsigned mark_sum
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int maxdepth
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AP_tree_nlen * get_root_node()
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GBDATA * get_gb_main() const
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void TREE_GC_changed_cb(GcChange whatChanged, AWT_canvas *ntw)
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bool GBT_is_alignment_protein(GBDATA *gb_main, const char *alignment_name)
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AW_gc_manager * AW_manage_GC(AW_window *aww, const char *gc_base_name, AW_device *device, int base_drag, AW_GCM_AREA area, const GcChangedCallback &changecb, const char *default_background_color,...)
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void set_visited(bool vis)
size_t size() const
int rec_width[CUSTOM_DEPTHS]
void AW_init_color_group_defaults(const char *for_program)
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#define DOWNCAST(totype, expr)
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void change_parsimony_start(Mutations offset)
KL_DYNAMIC_THRESHOLD_TYPE
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void(* AD_map_viewer_cb)(GBDATA *gbd, AD_MAP_VIEWER_TYPE type)
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#define AWAR_PARSIMONY
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bool needs_save() const
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#define TEST_EXPECT(cond)
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char * GBT_read_string(GBDATA *gb_container, const char *fieldpath)
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#define TEST_EXPECT_NEWICK(format, tree, expected_newick)
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const char * get_gc_base_name() const
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AW_root * get_root() const
static SearchSettings * settings[SEARCH_PATTERNS]
Definition: ED4_search.cxx:628
bool aborted()
Definition: arb_progress.h:277
static int weights[MAX_BASETYPES][MAX_BASETYPES]
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bool is_leaf_edge() const
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#define TEST_REJECT_NULL(n)
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long Mutations
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static void error(const char *msg)
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#define ap_assert(cond)
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KL_RECURSION_TYPE rec_type
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