1 | // ================================================================ // |
---|
2 | // // |
---|
3 | // File : RootedTree.cxx // |
---|
4 | // Purpose : // |
---|
5 | // // |
---|
6 | // Coded by Ralf Westram (coder@reallysoft.de) in December 2013 // |
---|
7 | // Institute of Microbiology (Technical University Munich) // |
---|
8 | // http://www.arb-home.de/ // |
---|
9 | // // |
---|
10 | // ================================================================ // |
---|
11 | |
---|
12 | #include "RootedTree.h" |
---|
13 | #include <map> |
---|
14 | #include <set> |
---|
15 | #include <cmath> // needed with 4.4.3 (but not with 4.7.3) |
---|
16 | |
---|
17 | // ------------------ |
---|
18 | // TreeRoot |
---|
19 | |
---|
20 | TreeRoot::~TreeRoot() { |
---|
21 | deleteWithNodes = false; // avoid recursive call of ~TreeRoot |
---|
22 | delete rootNode; |
---|
23 | rt_assert(!rootNode); |
---|
24 | delete nodeMaker; |
---|
25 | } |
---|
26 | |
---|
27 | void TreeRoot::change_root(RootedTree *oldroot, RootedTree *newroot) { |
---|
28 | rt_assert(rootNode == oldroot); |
---|
29 | rt_assert(implicated(newroot, !newroot->father)); |
---|
30 | rootNode = newroot; |
---|
31 | |
---|
32 | if (oldroot && oldroot->get_tree_root() && !oldroot->is_inside(newroot)) oldroot->set_tree_root(0); // unlink from this |
---|
33 | if (newroot && newroot->get_tree_root() != this) newroot->set_tree_root(this); // link to this |
---|
34 | } |
---|
35 | |
---|
36 | // -------------------- |
---|
37 | // RootedTree |
---|
38 | |
---|
39 | #if defined(PROVIDE_TREE_STRUCTURE_TESTS) |
---|
40 | |
---|
41 | void RootedTree::assert_valid() const { |
---|
42 | rt_assert(this); |
---|
43 | |
---|
44 | TreeRoot *troot = get_tree_root(); |
---|
45 | if (troot) { |
---|
46 | if (!is_leaf) { |
---|
47 | rt_assert(rightson); |
---|
48 | rt_assert(leftson); |
---|
49 | get_rightson()->assert_valid(); |
---|
50 | get_leftson()->assert_valid(); |
---|
51 | } |
---|
52 | if (father) { |
---|
53 | rt_assert(is_inside(get_father())); |
---|
54 | rt_assert(troot->get_root_node()->is_anchestor_of(this)); |
---|
55 | rt_assert(get_father()->get_tree_root() == troot); |
---|
56 | } |
---|
57 | else { |
---|
58 | rt_assert(troot->get_root_node() == this); |
---|
59 | rt_assert(!is_leaf); // leaf@root (tree has to have at least 2 leafs) |
---|
60 | } |
---|
61 | } |
---|
62 | else { // removed node (may be incomplete) |
---|
63 | if (!is_leaf) { |
---|
64 | if (rightson) get_rightson()->assert_valid(); |
---|
65 | if (leftson) get_leftson()->assert_valid(); |
---|
66 | } |
---|
67 | if (father) { |
---|
68 | rt_assert(is_inside(get_father())); |
---|
69 | rt_assert(!get_father()->get_tree_root()); |
---|
70 | } |
---|
71 | } |
---|
72 | } |
---|
73 | #endif // PROVIDE_TREE_STRUCTURE_TESTS |
---|
74 | |
---|
75 | void RootedTree::set_tree_root(TreeRoot *new_root) { |
---|
76 | if (tree_root != new_root) { |
---|
77 | tree_root = new_root; |
---|
78 | if (leftson) get_leftson()->set_tree_root(new_root); |
---|
79 | if (rightson) get_rightson()->set_tree_root(new_root); |
---|
80 | } |
---|
81 | } |
---|
82 | |
---|
83 | void RootedTree::reorder_subtree(TreeOrder mode) { |
---|
84 | static const char *smallest_leafname; // has to be set to the alphabetically smallest name (when function exits) |
---|
85 | |
---|
86 | if (is_leaf) { |
---|
87 | smallest_leafname = name; |
---|
88 | } |
---|
89 | else { |
---|
90 | int leftsize = get_leftson() ->get_leaf_count(); |
---|
91 | int rightsize = get_rightson()->get_leaf_count(); |
---|
92 | |
---|
93 | { |
---|
94 | bool big_at_top = leftsize>rightsize; |
---|
95 | bool big_at_bottom = leftsize<rightsize; |
---|
96 | bool swap_branches = (mode&ORDER_BIG_DOWN) ? big_at_top : big_at_bottom; |
---|
97 | if (swap_branches) swap_sons(); |
---|
98 | } |
---|
99 | |
---|
100 | TreeOrder lmode, rmode; |
---|
101 | if (mode & (ORDER_BIG_TO_EDGE|ORDER_BIG_TO_CENTER)) { // symmetric |
---|
102 | if (mode & ORDER_ALTERNATING) mode = TreeOrder(mode^(ORDER_BIG_TO_EDGE|ORDER_BIG_TO_CENTER)); |
---|
103 | |
---|
104 | if (mode & ORDER_BIG_TO_CENTER) { |
---|
105 | lmode = TreeOrder(mode | ORDER_BIG_DOWN); |
---|
106 | rmode = TreeOrder(mode & ~ORDER_BIG_DOWN); |
---|
107 | } |
---|
108 | else { |
---|
109 | lmode = TreeOrder(mode & ~ORDER_BIG_DOWN); |
---|
110 | rmode = TreeOrder(mode | ORDER_BIG_DOWN); |
---|
111 | } |
---|
112 | } |
---|
113 | else { // asymmetric |
---|
114 | if (mode & ORDER_ALTERNATING) mode = TreeOrder(mode^ORDER_BIG_DOWN); |
---|
115 | |
---|
116 | lmode = mode; |
---|
117 | rmode = mode; |
---|
118 | } |
---|
119 | |
---|
120 | get_leftson()->reorder_subtree(lmode); |
---|
121 | const char *leftleafname = smallest_leafname; |
---|
122 | |
---|
123 | get_rightson()->reorder_subtree(rmode); |
---|
124 | const char *rightleafname = smallest_leafname; |
---|
125 | |
---|
126 | if (leftleafname && rightleafname) { |
---|
127 | int name_cmp = strcmp(leftleafname, rightleafname); |
---|
128 | if (name_cmp <= 0) { |
---|
129 | smallest_leafname = leftleafname; |
---|
130 | } |
---|
131 | else { |
---|
132 | smallest_leafname = rightleafname; |
---|
133 | if (leftsize == rightsize) { // if sizes of subtrees are equal and rightleafname<leftleafname -> swap branches |
---|
134 | const char *smallest_leafname_save = smallest_leafname; |
---|
135 | |
---|
136 | swap_sons(); |
---|
137 | get_leftson ()->reorder_subtree(lmode); rt_assert(strcmp(smallest_leafname, rightleafname)== 0); |
---|
138 | get_rightson()->reorder_subtree(rmode); rt_assert(strcmp(smallest_leafname, leftleafname) == 0); |
---|
139 | |
---|
140 | smallest_leafname = smallest_leafname_save; |
---|
141 | } |
---|
142 | } |
---|
143 | } |
---|
144 | } |
---|
145 | rt_assert(smallest_leafname); |
---|
146 | } |
---|
147 | |
---|
148 | void RootedTree::reorder_tree(TreeOrder mode) { |
---|
149 | /*! beautify tree (does not change topology, only swaps branches) |
---|
150 | */ |
---|
151 | compute_tree(); |
---|
152 | reorder_subtree(mode); |
---|
153 | } |
---|
154 | |
---|
155 | void RootedTree::rotate_subtree() { |
---|
156 | if (!is_leaf) { |
---|
157 | swap_sons(); |
---|
158 | get_leftson()->rotate_subtree(); |
---|
159 | get_rightson()->rotate_subtree(); |
---|
160 | } |
---|
161 | } |
---|
162 | |
---|
163 | void RootedTree::set_root() { |
---|
164 | /*! set the root at parent edge of this |
---|
165 | * pointers to tree-nodes remain valid, but all parent-nodes of this change their meaning |
---|
166 | * (afterwards they will point to [father+brother] instead of [this+brother]) |
---|
167 | * esp. pointers to the root-node will still point to the root-node (which only changed children) |
---|
168 | */ |
---|
169 | |
---|
170 | if (at_root()) return; // already root |
---|
171 | |
---|
172 | RootedTree *old_root = get_root_node(); |
---|
173 | RootedTree *old_brother = is_inside(old_root->get_leftson()) ? old_root->get_rightson() : old_root->get_leftson(); |
---|
174 | |
---|
175 | // move remark branches to top |
---|
176 | { |
---|
177 | char *remark = nulldup(get_remark()); |
---|
178 | for (RootedTree *node = this; node->father; node = node->get_father()) { |
---|
179 | remark = node->swap_remark(remark); |
---|
180 | } |
---|
181 | free(remark); |
---|
182 | } |
---|
183 | |
---|
184 | GBT_LEN old_root_len = old_root->leftlen + old_root->rightlen; |
---|
185 | |
---|
186 | // new node & this init |
---|
187 | old_root->leftson = this; |
---|
188 | old_root->rightson = father; // will be set later |
---|
189 | |
---|
190 | if (father->leftson == this) { |
---|
191 | old_root->leftlen = old_root->rightlen = father->leftlen*.5; |
---|
192 | } |
---|
193 | else { |
---|
194 | old_root->leftlen = old_root->rightlen = father->rightlen*.5; |
---|
195 | } |
---|
196 | |
---|
197 | RootedTree *next = get_father()->get_father(); |
---|
198 | RootedTree *prev = old_root; |
---|
199 | RootedTree *pntr = get_father(); |
---|
200 | |
---|
201 | if (father->leftson == this) father->leftson = old_root; // to set the flag correctly |
---|
202 | |
---|
203 | // loop from father to son of root, rotate tree |
---|
204 | while (next->father) { |
---|
205 | double len = (next->leftson == pntr) ? next->leftlen : next->rightlen; |
---|
206 | |
---|
207 | if (pntr->leftson == prev) { |
---|
208 | pntr->leftson = next; |
---|
209 | pntr->leftlen = len; |
---|
210 | } |
---|
211 | else { |
---|
212 | pntr->rightson = next; |
---|
213 | pntr->rightlen = len; |
---|
214 | } |
---|
215 | |
---|
216 | pntr->father = prev; |
---|
217 | prev = pntr; |
---|
218 | pntr = next; |
---|
219 | next = next->get_father(); |
---|
220 | } |
---|
221 | // now next points to the old root, which has been destroyed above |
---|
222 | // |
---|
223 | // pointer at oldroot |
---|
224 | // pntr == brother before old root == next |
---|
225 | |
---|
226 | if (pntr->leftson == prev) { |
---|
227 | pntr->leftlen = old_root_len; |
---|
228 | pntr->leftson = old_brother; |
---|
229 | } |
---|
230 | else { |
---|
231 | pntr->rightlen = old_root_len; |
---|
232 | pntr->rightson = old_brother; |
---|
233 | } |
---|
234 | |
---|
235 | old_brother->father = pntr; |
---|
236 | pntr->father = prev; |
---|
237 | father = old_root; |
---|
238 | |
---|
239 | rt_assert(get_root_node() == old_root); |
---|
240 | } |
---|
241 | |
---|
242 | RootedTree *RootedTree::findLeafNamed(const char *wantedName) { |
---|
243 | RootedTree *found = NULL; |
---|
244 | if (is_leaf) { |
---|
245 | if (name && strcmp(name, wantedName) == 0) found = this; |
---|
246 | } |
---|
247 | else { |
---|
248 | found = get_leftson()->findLeafNamed(wantedName); |
---|
249 | if (!found) found = get_rightson()->findLeafNamed(wantedName); |
---|
250 | } |
---|
251 | return found; |
---|
252 | } |
---|
253 | |
---|
254 | // ---------------------------- |
---|
255 | // find_innermost_edge |
---|
256 | |
---|
257 | class NodeLeafDistance { |
---|
258 | GBT_LEN downdist, updist; |
---|
259 | enum { NLD_NODIST = 0, NLD_DOWNDIST, NLD_BOTHDIST } state; |
---|
260 | |
---|
261 | public: |
---|
262 | |
---|
263 | NodeLeafDistance() |
---|
264 | : downdist(-1.0), |
---|
265 | updist(-1.0), |
---|
266 | state(NLD_NODIST) |
---|
267 | {} |
---|
268 | |
---|
269 | GBT_LEN get_downdist() const { rt_assert(state >= NLD_DOWNDIST); return downdist; } |
---|
270 | void set_downdist(GBT_LEN DownDist) { |
---|
271 | if (state < NLD_DOWNDIST) state = NLD_DOWNDIST; |
---|
272 | downdist = DownDist; |
---|
273 | } |
---|
274 | |
---|
275 | GBT_LEN get_updist() const { rt_assert(state >= NLD_BOTHDIST); return updist; } |
---|
276 | void set_updist(GBT_LEN UpDist) { |
---|
277 | if (state < NLD_BOTHDIST) state = NLD_BOTHDIST; |
---|
278 | updist = UpDist; |
---|
279 | } |
---|
280 | |
---|
281 | }; |
---|
282 | |
---|
283 | class EdgeFinder { |
---|
284 | std::map<RootedTree*, NodeLeafDistance> data; // maximum distance to farthest leaf |
---|
285 | |
---|
286 | ARB_edge innermost; |
---|
287 | double min_distdiff; // abs diff between up- and downdiff |
---|
288 | |
---|
289 | GBT_LEN calc_distdiff(GBT_LEN d1, GBT_LEN d2) { return fabs(d1-d2); } |
---|
290 | |
---|
291 | void insert_tree(RootedTree *node) { |
---|
292 | if (node->is_leaf) { |
---|
293 | data[node].set_downdist(0.0); |
---|
294 | } |
---|
295 | else { |
---|
296 | insert_tree(node->get_leftson()); |
---|
297 | insert_tree(node->get_rightson()); |
---|
298 | |
---|
299 | data[node].set_downdist(std::max(data[node->get_leftson()].get_downdist()+node->leftlen, |
---|
300 | data[node->get_rightson()].get_downdist()+node->rightlen)); |
---|
301 | } |
---|
302 | } |
---|
303 | |
---|
304 | void findBetterEdge_sub(RootedTree *node) { |
---|
305 | RootedTree *father = node->get_father(); |
---|
306 | RootedTree *brother = node->get_brother(); |
---|
307 | |
---|
308 | GBT_LEN len = node->get_branchlength(); |
---|
309 | GBT_LEN brothLen = brother->get_branchlength(); |
---|
310 | |
---|
311 | GBT_LEN upDist = std::max(data[father].get_updist(), data[brother].get_downdist()+brothLen); |
---|
312 | GBT_LEN downDist = data[node].get_downdist(); |
---|
313 | |
---|
314 | { |
---|
315 | GBT_LEN edge_dd = calc_distdiff(upDist, downDist); |
---|
316 | if (edge_dd<min_distdiff) { // found better edge |
---|
317 | innermost = ARB_edge(node, father); |
---|
318 | min_distdiff = edge_dd; |
---|
319 | } |
---|
320 | } |
---|
321 | |
---|
322 | data[node].set_updist(upDist+len); |
---|
323 | |
---|
324 | if (!node->is_leaf) { |
---|
325 | findBetterEdge_sub(node->get_leftson()); |
---|
326 | findBetterEdge_sub(node->get_rightson()); |
---|
327 | } |
---|
328 | } |
---|
329 | |
---|
330 | void findBetterEdge(RootedTree *node) { |
---|
331 | if (!node->is_leaf) { |
---|
332 | findBetterEdge_sub(node->get_leftson()); |
---|
333 | findBetterEdge_sub(node->get_rightson()); |
---|
334 | } |
---|
335 | } |
---|
336 | |
---|
337 | public: |
---|
338 | EdgeFinder(RootedTree *rootNode) |
---|
339 | : innermost(rootNode->get_leftson(), rootNode->get_rightson()) // root-edge |
---|
340 | { |
---|
341 | insert_tree(rootNode); |
---|
342 | |
---|
343 | RootedTree *lson = rootNode->get_leftson(); |
---|
344 | RootedTree *rson = rootNode->get_rightson(); |
---|
345 | |
---|
346 | GBT_LEN rootEdgeLen = rootNode->leftlen + rootNode->rightlen; |
---|
347 | |
---|
348 | GBT_LEN lddist = data[lson].get_downdist(); |
---|
349 | GBT_LEN rddist = data[rson].get_downdist(); |
---|
350 | |
---|
351 | data[lson].set_updist(rddist+rootEdgeLen); |
---|
352 | data[rson].set_updist(lddist+rootEdgeLen); |
---|
353 | |
---|
354 | min_distdiff = calc_distdiff(lddist, rddist); |
---|
355 | |
---|
356 | findBetterEdge(lson); |
---|
357 | findBetterEdge(rson); |
---|
358 | } |
---|
359 | |
---|
360 | const ARB_edge& innermost_edge() const { return innermost; } |
---|
361 | }; |
---|
362 | |
---|
363 | ARB_edge TreeRoot::find_innermost_edge() { |
---|
364 | EdgeFinder edgeFinder(get_root_node()); |
---|
365 | return edgeFinder.innermost_edge(); |
---|
366 | } |
---|
367 | |
---|
368 | // ------------------------ |
---|
369 | // multifurcation |
---|
370 | |
---|
371 | class RootedTree::LengthCollector { |
---|
372 | typedef std::map<RootedTree*,GBT_LEN> LengthMap; |
---|
373 | typedef std::set<RootedTree*> NodeSet; |
---|
374 | |
---|
375 | LengthMap eliminatedParentLength; |
---|
376 | LengthMap addedParentLength; |
---|
377 | |
---|
378 | public: |
---|
379 | void eliminate_parent_edge(RootedTree *node) { |
---|
380 | rt_assert(!node->is_root_node()); |
---|
381 | eliminatedParentLength[node] += parentEdge(node).eliminate(); |
---|
382 | } |
---|
383 | |
---|
384 | void add_parent_length(RootedTree *node, GBT_LEN addLen) { |
---|
385 | rt_assert(!node->is_root_node()); |
---|
386 | addedParentLength[node] += addLen; |
---|
387 | } |
---|
388 | |
---|
389 | void independent_distribution() { |
---|
390 | // step 2: (see caller) |
---|
391 | while (!eliminatedParentLength.empty()) { // got eliminated lengths which need to be distributed |
---|
392 | for (LengthMap::iterator from = eliminatedParentLength.begin(); from != eliminatedParentLength.end(); ++from) { |
---|
393 | ARB_edge elimEdge = parentEdge(from->first); |
---|
394 | GBT_LEN elimLen = from->second; |
---|
395 | |
---|
396 | elimEdge.virtually_distribute_length(elimLen, *this); |
---|
397 | } |
---|
398 | eliminatedParentLength.clear(); // all distributed! |
---|
399 | |
---|
400 | // handle special cases where distributed length is negative and results in negative destination branches. |
---|
401 | // Avoid generating negative dest. branchlengths by |
---|
402 | // - eliminating the dest. branch |
---|
403 | // - redistributing the additional (negative) length (may cause additional negative lengths on other dest. branches) |
---|
404 | |
---|
405 | NodeSet handled; |
---|
406 | for (LengthMap::iterator to = addedParentLength.begin(); to != addedParentLength.end(); ++to) { |
---|
407 | ARB_edge affectedEdge = parentEdge(to->first); |
---|
408 | GBT_LEN additionalLen = to->second; |
---|
409 | double effective_length = affectedEdge.length() + additionalLen; |
---|
410 | |
---|
411 | if (effective_length<=0.0) { // negative or zero |
---|
412 | affectedEdge.set_length(effective_length); |
---|
413 | eliminate_parent_edge(to->first); // adds entry to eliminatedParentLength and causes another additional loop |
---|
414 | handled.insert(to->first); |
---|
415 | } |
---|
416 | } |
---|
417 | |
---|
418 | // remove all redistributed nodes |
---|
419 | for (NodeSet::iterator del = handled.begin(); del != handled.end(); ++del) { |
---|
420 | addedParentLength.erase(*del); |
---|
421 | } |
---|
422 | } |
---|
423 | |
---|
424 | // step 3: |
---|
425 | for (LengthMap::iterator to = addedParentLength.begin(); to != addedParentLength.end(); ++to) { |
---|
426 | ARB_edge affectedEdge = parentEdge(to->first); |
---|
427 | GBT_LEN additionalLen = to->second; |
---|
428 | double effective_length = affectedEdge.length() + additionalLen; |
---|
429 | |
---|
430 | affectedEdge.set_length(effective_length); |
---|
431 | } |
---|
432 | } |
---|
433 | }; |
---|
434 | |
---|
435 | GBT_LEN ARB_edge::adjacent_distance() const { |
---|
436 | //! return length of edges starting from this->dest() |
---|
437 | |
---|
438 | if (at_leaf()) return 0.0; |
---|
439 | return next().length_or_adjacent_distance() + otherNext().length_or_adjacent_distance(); |
---|
440 | } |
---|
441 | |
---|
442 | void ARB_edge::virtually_add_or_distribute_length_forward(GBT_LEN len, RootedTree::LengthCollector& collect) const { |
---|
443 | rt_assert(!is_nan_or_inf(len)); |
---|
444 | if (length() > 0.0) { |
---|
445 | collect.add_parent_length(son(), len); |
---|
446 | } |
---|
447 | else { |
---|
448 | if (len != 0.0) virtually_distribute_length_forward(len, collect); |
---|
449 | } |
---|
450 | } |
---|
451 | |
---|
452 | |
---|
453 | void ARB_edge::virtually_distribute_length_forward(GBT_LEN len, RootedTree::LengthCollector& collect) const { |
---|
454 | /*! distribute length to edges adjacent in edge direction (i.e. edges starting from this->dest()) |
---|
455 | * Split 'len' proportional to adjacent edges lengths. |
---|
456 | * |
---|
457 | * Note: length will not be distributed to tree-struction itself (yet), but collected in 'collect' |
---|
458 | */ |
---|
459 | |
---|
460 | rt_assert(is_normal(len)); |
---|
461 | rt_assert(!at_leaf()); // cannot forward anything (nothing beyond leafs) |
---|
462 | |
---|
463 | ARB_edge e1 = next(); |
---|
464 | ARB_edge e2 = otherNext(); |
---|
465 | |
---|
466 | GBT_LEN d1 = e1.length_or_adjacent_distance(); |
---|
467 | GBT_LEN d2 = e2.length_or_adjacent_distance(); |
---|
468 | |
---|
469 | len = len/(d1+d2); |
---|
470 | |
---|
471 | e1.virtually_add_or_distribute_length_forward(len*d1, collect); |
---|
472 | e2.virtually_add_or_distribute_length_forward(len*d2, collect); |
---|
473 | } |
---|
474 | |
---|
475 | void ARB_edge::virtually_distribute_length(GBT_LEN len, RootedTree::LengthCollector& collect) const { |
---|
476 | /*! distribute length to all adjacent edges. |
---|
477 | * Longer edges receive more than shorter ones. |
---|
478 | * |
---|
479 | * Edges with length zero will not be changed, instead both edges "beyond" |
---|
480 | * the edge will be affected (they will be affected equally to direct edges, |
---|
481 | * because edges at multifurcations are considered to BE direct edges). |
---|
482 | * |
---|
483 | * Note: length will not be distributed to tree-struction itself (yet), but collected in 'collect' |
---|
484 | */ |
---|
485 | |
---|
486 | ARB_edge backEdge = inverse(); |
---|
487 | GBT_LEN len_fwd, len_bwd; |
---|
488 | { |
---|
489 | GBT_LEN dist_fwd = adjacent_distance(); |
---|
490 | GBT_LEN dist_bwd = backEdge.adjacent_distance(); |
---|
491 | GBT_LEN lenW = len/(dist_fwd+dist_bwd); |
---|
492 | len_fwd = lenW*dist_fwd; |
---|
493 | len_bwd = lenW*dist_bwd; |
---|
494 | |
---|
495 | } |
---|
496 | |
---|
497 | if (is_normal(len_fwd)) virtually_distribute_length_forward(len_fwd, collect); |
---|
498 | if (is_normal(len_bwd)) backEdge.virtually_distribute_length_forward(len_bwd, collect); |
---|
499 | } |
---|
500 | |
---|
501 | void RootedTree::eliminate_and_collect(const multifurc_limits& below, LengthCollector& collect) { |
---|
502 | /*! eliminate edges specified by 'below' and |
---|
503 | * store their length in 'collect' for later distribution. |
---|
504 | */ |
---|
505 | rt_assert(!is_root_node()); |
---|
506 | if (!is_leaf || below.applyAtLeafs) { |
---|
507 | double value; |
---|
508 | switch (parse_bootstrap(value)) { |
---|
509 | case REMARK_NONE: |
---|
510 | value = 100.0; |
---|
511 | // fall-through |
---|
512 | case REMARK_BOOTSTRAP: |
---|
513 | if (value<below.bootstrap && get_branchlength_unrooted()<below.branchlength) { |
---|
514 | collect.eliminate_parent_edge(this); |
---|
515 | } |
---|
516 | break; |
---|
517 | |
---|
518 | case REMARK_OTHER: break; |
---|
519 | } |
---|
520 | } |
---|
521 | |
---|
522 | if (!is_leaf) { |
---|
523 | get_leftson() ->eliminate_and_collect(below, collect); |
---|
524 | get_rightson()->eliminate_and_collect(below, collect); |
---|
525 | } |
---|
526 | } |
---|
527 | |
---|
528 | void ARB_edge::multifurcate() { |
---|
529 | /*! eliminate edge and distribute length to adjacent edges |
---|
530 | * - sets its length to zero |
---|
531 | * - removes remark (bootstrap) |
---|
532 | * - distributes length to neighbour-branches |
---|
533 | */ |
---|
534 | RootedTree::LengthCollector collector; |
---|
535 | collector.eliminate_parent_edge(son()); |
---|
536 | collector.independent_distribution(); |
---|
537 | } |
---|
538 | void RootedTree::multifurcate() { |
---|
539 | /*! eliminate branch from 'this' to 'father' (or brother @ root) |
---|
540 | * @see ARB_edge::multifurcate() |
---|
541 | */ |
---|
542 | rt_assert(father); // cannot multifurcate at root; call with son of root to multifurcate root-edge |
---|
543 | if (father) parentEdge(this).multifurcate(); |
---|
544 | } |
---|
545 | |
---|
546 | void RootedTree::set_branchlength_preserving(GBT_LEN new_len) { |
---|
547 | /*! set branchlength to 'new_len' while preserving overall distance in tree. |
---|
548 | * |
---|
549 | * Always works on unrooted tree (i.e. lengths @ root are treated correctly). |
---|
550 | * Length is preserved as in multifurcate() |
---|
551 | */ |
---|
552 | |
---|
553 | GBT_LEN old_len = get_branchlength_unrooted(); |
---|
554 | GBT_LEN change = new_len-old_len; |
---|
555 | |
---|
556 | char *old_remark = nulldup(get_remark()); |
---|
557 | |
---|
558 | // distribute the negative 'change' to neighbours: |
---|
559 | set_branchlength_unrooted(-change); |
---|
560 | multifurcate(); |
---|
561 | |
---|
562 | set_branchlength_unrooted(new_len); |
---|
563 | use_as_remark(old_remark); // restore remark (was removed by multifurcate()) |
---|
564 | } |
---|
565 | |
---|
566 | void RootedTree::multifurcate_whole_tree(const multifurc_limits& below) { |
---|
567 | /*! multifurcate all branches specified by 'below' |
---|
568 | * - step 1: eliminate all branches, store eliminated lengths |
---|
569 | * - step 2: calculate length distribution for all adjacent branches (proportionally to original length of each branch) |
---|
570 | * - step 3: apply distributed length |
---|
571 | */ |
---|
572 | RootedTree *root = get_root_node(); |
---|
573 | LengthCollector collector; |
---|
574 | |
---|
575 | // step 1: |
---|
576 | root->get_leftson()->eliminate_and_collect(below, collector); |
---|
577 | root->get_rightson()->eliminate_and_collect(below, collector); |
---|
578 | // root-edge is handled twice by the above calls. |
---|
579 | // Unproblematic: first call will eliminate root-edge, so second call will do nothing. |
---|
580 | |
---|
581 | // step 2 and 3: |
---|
582 | collector.independent_distribution(); |
---|
583 | } |
---|
584 | |
---|