1 | // ================================================================ // |
---|
2 | // // |
---|
3 | // File : TreeNode.h // |
---|
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 | #ifndef TREENODE_H |
---|
13 | #define TREENODE_H |
---|
14 | |
---|
15 | #ifndef ARBDBT_H |
---|
16 | #include "arbdbt.h" |
---|
17 | #endif |
---|
18 | #ifndef _GLIBCXX_ALGORITHM |
---|
19 | #include <algorithm> |
---|
20 | #endif |
---|
21 | |
---|
22 | #define rt_assert(cond) arb_assert(cond) |
---|
23 | |
---|
24 | #if defined(DEBUG) || defined(UNIT_TESTS) // UT_DIFF |
---|
25 | # define PROVIDE_TREE_STRUCTURE_TESTS |
---|
26 | #endif |
---|
27 | #if defined(DEVEL_RALF) && defined(PROVIDE_TREE_STRUCTURE_TESTS) |
---|
28 | # define AUTO_CHECK_TREE_STRUCTURE // Note: dramatically slows down most tree operations |
---|
29 | #endif |
---|
30 | |
---|
31 | class TreeRoot; |
---|
32 | class TreeNode; |
---|
33 | class ARB_edge; |
---|
34 | |
---|
35 | enum TreeOrder { // contains bit values! |
---|
36 | ORDER_BIG_DOWN = 1, // bit 0 set -> big branches down |
---|
37 | ORDER_BIG_TO_EDGE = 2, // bit 1 set -> big branches to edge |
---|
38 | ORDER_BIG_TO_CENTER = 4, // bit 2 set -> big branches to center |
---|
39 | ORDER_ALTERNATING = 8, // bit 3 set -> alternate bit 0 |
---|
40 | |
---|
41 | // user visible orders: |
---|
42 | BIG_BRANCHES_TO_TOP = 0, |
---|
43 | BIG_BRANCHES_TO_BOTTOM = ORDER_BIG_DOWN, |
---|
44 | BIG_BRANCHES_TO_EDGE = ORDER_BIG_TO_EDGE, |
---|
45 | BIG_BRANCHES_TO_CENTER = ORDER_BIG_TO_CENTER, |
---|
46 | BIG_BRANCHES_ALTERNATING = ORDER_BIG_TO_CENTER|ORDER_ALTERNATING, |
---|
47 | }; |
---|
48 | |
---|
49 | #define DEFINE_READ_ACCESSORS(TYPE, ACCESS, MEMBER) \ |
---|
50 | TYPE ACCESS() { return MEMBER; } \ |
---|
51 | const TYPE ACCESS() const { return MEMBER; } |
---|
52 | |
---|
53 | class TreeRoot : virtual Noncopyable { |
---|
54 | TreeNode *rootNode; // root node of the tree |
---|
55 | bool deleteWithNodes; |
---|
56 | |
---|
57 | protected: |
---|
58 | void predelete() { |
---|
59 | // should be called from dtor of derived class defining makeNode/destroyNode |
---|
60 | if (rootNode) { |
---|
61 | destroyNode(rootNode); |
---|
62 | rt_assert(!rootNode); |
---|
63 | } |
---|
64 | } |
---|
65 | public: |
---|
66 | explicit TreeRoot(bool deleteWithNodes_) |
---|
67 | : rootNode(NULL), |
---|
68 | deleteWithNodes(deleteWithNodes_) |
---|
69 | { |
---|
70 | /*! Create a TreeRoot for a TreeNode. |
---|
71 | * Purpose: |
---|
72 | * - act as TreeNode factory |
---|
73 | * - place to store the current rootNode |
---|
74 | * - place to store other tree related information by deriving from TreeRoot |
---|
75 | * |
---|
76 | * @param nodeMaker_ heap-copy of a RootedTreeNodeFactory, will be deleted when this is destructed |
---|
77 | * @param deleteWithNodes_ true -> delete TreeRoot when the rootNode gets destroyed (TreeRoot needs to be a heap-copy in that case) |
---|
78 | * |
---|
79 | * Ressource handling of the tree structure is quite difficult (and error-prone). |
---|
80 | * There are two common use-cases: |
---|
81 | * 1. TreeRoot is owned by some other object/scope |
---|
82 | * - pass false for deleteWithNodes_ |
---|
83 | * - you may or may not destroy (parts of) the TreeNode manually |
---|
84 | * 2. TreeRoot is owned by the TreeNode |
---|
85 | * - pass true for deleteWithNodes_ |
---|
86 | * - when the rootNode gets destroyed, the TreeRoot will be destroyed as well |
---|
87 | */ |
---|
88 | } |
---|
89 | virtual ~TreeRoot(); |
---|
90 | virtual void change_root(TreeNode *old, TreeNode *newroot); |
---|
91 | |
---|
92 | void delete_by_node() { |
---|
93 | if (deleteWithNodes) { |
---|
94 | rt_assert(!rootNode); |
---|
95 | delete this; |
---|
96 | } |
---|
97 | } |
---|
98 | |
---|
99 | virtual TreeNode *makeNode() const = 0; |
---|
100 | virtual void destroyNode(TreeNode *node) const = 0; |
---|
101 | |
---|
102 | DEFINE_READ_ACCESSORS(TreeNode*, get_root_node, rootNode); |
---|
103 | |
---|
104 | ARB_edge find_innermost_edge(); |
---|
105 | }; |
---|
106 | MARK_NONFINAL_METHOD(TreeRoot,void,change_root,(TreeNode*,TreeNode*)); |
---|
107 | |
---|
108 | struct TreeNode : virtual Noncopyable { |
---|
109 | bool is_leaf; |
---|
110 | TreeNode *father, *leftson, *rightson; |
---|
111 | GBT_LEN leftlen, rightlen; |
---|
112 | GBDATA *gb_node; |
---|
113 | char *name; |
---|
114 | |
---|
115 | private: |
---|
116 | char *remark_branch; // remark_branch normally contains some bootstrap value in format 'xx%' |
---|
117 | // if you store other info there, please make sure that this info does not start with digits!! |
---|
118 | // Otherwise the tree export routines will not work correctly! |
---|
119 | |
---|
120 | GBT_LEN& length_ref() { return is_leftson() ? father->leftlen : father->rightlen; } |
---|
121 | const GBT_LEN& length_ref() const { return const_cast<TreeNode*>(this)->length_ref(); } |
---|
122 | |
---|
123 | protected: |
---|
124 | TreeNode*& self_ref() { |
---|
125 | return is_leftson() ? father->leftson : father->rightson; |
---|
126 | } |
---|
127 | void unlink_from_father() { |
---|
128 | if (father) { |
---|
129 | self_ref() = NULL; |
---|
130 | father = NULL; |
---|
131 | } |
---|
132 | } |
---|
133 | |
---|
134 | char *swap_remark(char *new_remark) { |
---|
135 | char *result = remark_branch; |
---|
136 | remark_branch = new_remark; |
---|
137 | return result; |
---|
138 | } |
---|
139 | |
---|
140 | public: |
---|
141 | |
---|
142 | DEFINE_READ_ACCESSORS(TreeNode*, get_father, father); |
---|
143 | DEFINE_READ_ACCESSORS(TreeNode*, get_leftson, leftson); |
---|
144 | DEFINE_READ_ACCESSORS(TreeNode*, get_rightson, rightson); |
---|
145 | |
---|
146 | bool is_son_of(const TreeNode *Father) const { |
---|
147 | return father == Father && |
---|
148 | (father->leftson == this || father->rightson == this); |
---|
149 | } |
---|
150 | bool is_leftson() const { |
---|
151 | gb_assert(is_son_of(get_father())); // do only call with sons! |
---|
152 | return father->leftson == this; |
---|
153 | } |
---|
154 | bool is_rightson() const { |
---|
155 | gb_assert(is_son_of(get_father())); // do only call with sons! |
---|
156 | return father->rightson == this; |
---|
157 | } |
---|
158 | |
---|
159 | bool is_inside(const TreeNode *subtree) const { |
---|
160 | return this == subtree || (father && get_father()->is_inside(subtree)); |
---|
161 | } |
---|
162 | bool is_anchestor_of(const TreeNode *descendant) const { |
---|
163 | return !is_leaf && descendant != this && descendant->is_inside(this); |
---|
164 | } |
---|
165 | const TreeNode *ancestor_common_with(const TreeNode *other) const; |
---|
166 | TreeNode *ancestor_common_with(TreeNode *other) { return const_cast<TreeNode*>(ancestor_common_with(const_cast<const TreeNode*>(other))); } |
---|
167 | |
---|
168 | GBT_LEN get_branchlength() const { return length_ref(); } |
---|
169 | void set_branchlength(GBT_LEN newlen) { |
---|
170 | gb_assert(!is_nan_or_inf(newlen)); |
---|
171 | length_ref() = newlen; |
---|
172 | } |
---|
173 | |
---|
174 | GBT_LEN get_branchlength_unrooted() const { |
---|
175 | //! like get_branchlength, but root-edge is treated correctly |
---|
176 | if (father->is_root_node()) { |
---|
177 | return father->leftlen+father->rightlen; |
---|
178 | } |
---|
179 | return get_branchlength(); |
---|
180 | } |
---|
181 | void set_branchlength_unrooted(GBT_LEN newlen) { |
---|
182 | //! like set_branchlength, but root-edge is treated correctly |
---|
183 | if (father->is_root_node()) { |
---|
184 | father->leftlen = newlen/2; |
---|
185 | father->rightlen = newlen-father->leftlen; // make sure sum equals newlen |
---|
186 | } |
---|
187 | else { |
---|
188 | set_branchlength(newlen); |
---|
189 | } |
---|
190 | } |
---|
191 | |
---|
192 | GBT_LEN sum_child_lengths() const; |
---|
193 | GBT_LEN root_distance() const { |
---|
194 | //! returns distance from node to root (including nodes own length) |
---|
195 | return father ? get_branchlength()+father->root_distance() : 0.0; |
---|
196 | } |
---|
197 | GBT_LEN intree_distance_to(const TreeNode *other) const { |
---|
198 | const TreeNode *ancestor = ancestor_common_with(other); |
---|
199 | return root_distance() + other->root_distance() - 2*ancestor->root_distance(); |
---|
200 | } |
---|
201 | |
---|
202 | enum bs100_mode { BS_UNDECIDED, BS_REMOVE, BS_INSERT }; |
---|
203 | bs100_mode toggle_bootstrap100(bs100_mode mode = BS_UNDECIDED); // toggle bootstrap '100%' <-> '' |
---|
204 | void remove_bootstrap(); // remove bootstrap values from subtree |
---|
205 | |
---|
206 | void reset_branchlengths(); // reset branchlengths of subtree to tree_defaults::LENGTH |
---|
207 | void scale_branchlengths(double factor); |
---|
208 | |
---|
209 | void bootstrap2branchlen(); // copy bootstraps to branchlengths |
---|
210 | void branchlen2bootstrap(); // copy branchlengths to bootstraps |
---|
211 | |
---|
212 | GBT_RemarkType parse_bootstrap(double& bootstrap) const { |
---|
213 | /*! analyse 'remark_branch' and return GBT_RemarkType. |
---|
214 | * If result is REMARK_BOOTSTRAP, 'bootstrap' contains the bootstrap value |
---|
215 | */ |
---|
216 | if (!remark_branch) return REMARK_NONE; |
---|
217 | |
---|
218 | const char *end = 0; |
---|
219 | bootstrap = strtod(remark_branch, (char**)&end); |
---|
220 | |
---|
221 | bool is_bootstrap = end[0] == '%' && end[1] == 0; |
---|
222 | return is_bootstrap ? REMARK_BOOTSTRAP : REMARK_OTHER; |
---|
223 | } |
---|
224 | const char *get_remark() const { return remark_branch; } |
---|
225 | void use_as_remark(char *newRemark) { freeset(remark_branch, newRemark); } |
---|
226 | void set_remark(const char *newRemark) { freedup(remark_branch, newRemark); } |
---|
227 | void set_bootstrap(double bootstrap) { use_as_remark(GBS_global_string_copy("%i%%", int(bootstrap+0.5))); } // @@@ protect against "100%"? |
---|
228 | void remove_remark() { use_as_remark(NULL); } |
---|
229 | |
---|
230 | private: |
---|
231 | |
---|
232 | friend void TreeRoot::change_root(TreeNode *old, TreeNode *newroot); |
---|
233 | |
---|
234 | TreeRoot *tree_root; |
---|
235 | |
---|
236 | // ------------------ |
---|
237 | // functions |
---|
238 | |
---|
239 | void reorder_subtree(TreeOrder mode); |
---|
240 | |
---|
241 | protected: |
---|
242 | void set_tree_root(TreeRoot *new_root); |
---|
243 | |
---|
244 | bool at_root() const { |
---|
245 | //! return true for root-node and its sons |
---|
246 | return !father || !father->father; |
---|
247 | } |
---|
248 | virtual ~TreeNode() { |
---|
249 | if (tree_root) { |
---|
250 | rt_assert(tree_root->get_root_node() == this); // you may only free the root-node or unlinked nodes (i.e. such with tree_root==NULL) |
---|
251 | |
---|
252 | TreeRoot *root = tree_root; |
---|
253 | root->TreeRoot::change_root(this, NULL); |
---|
254 | root->delete_by_node(); |
---|
255 | } |
---|
256 | delete leftson; gb_assert(!leftson); // cannot use destroy here |
---|
257 | delete rightson; gb_assert(!rightson); |
---|
258 | |
---|
259 | unlink_from_father(); |
---|
260 | |
---|
261 | free(name); |
---|
262 | free(remark_branch); |
---|
263 | } |
---|
264 | void destroy() { |
---|
265 | rt_assert(knownNonNull(this)); |
---|
266 | TreeRoot *myRoot = get_tree_root(); |
---|
267 | rt_assert(myRoot); // if this fails, you need to use destroy(TreeRoot*), i.e. destroy(TreeNode*, TreeRoot*) |
---|
268 | myRoot->destroyNode(this); |
---|
269 | } |
---|
270 | void destroy(TreeRoot *viaRoot) { |
---|
271 | rt_assert(knownNonNull(this)); |
---|
272 | #if defined(ASSERTION_USED) |
---|
273 | TreeRoot *myRoot = get_tree_root(); |
---|
274 | rt_assert(!myRoot || myRoot == viaRoot); |
---|
275 | #endif |
---|
276 | viaRoot->destroyNode(this); |
---|
277 | } |
---|
278 | |
---|
279 | public: |
---|
280 | TreeNode(TreeRoot *root) |
---|
281 | : is_leaf(false), |
---|
282 | father(NULL), leftson(NULL), rightson(NULL), |
---|
283 | leftlen(0.0), rightlen(0.0), |
---|
284 | gb_node(NULL), |
---|
285 | name(NULL), |
---|
286 | remark_branch(NULL), |
---|
287 | tree_root(root) |
---|
288 | {} |
---|
289 | static void destroy(TreeNode *that) { // replacement for destructor |
---|
290 | if (that) that->destroy(); |
---|
291 | } |
---|
292 | static void destroy(TreeNode *that, TreeRoot *root) { |
---|
293 | if (that) that->destroy(root); |
---|
294 | } |
---|
295 | |
---|
296 | TreeNode *fixDeletedSon(); // @@@ review (design) |
---|
297 | |
---|
298 | void unlink_from_DB(); |
---|
299 | |
---|
300 | void announce_tree_constructed() { // @@@ use this function or just call change_root instead? |
---|
301 | // (has to be) called after tree has been constructed |
---|
302 | gb_assert(!father); // has to be called with root-node! |
---|
303 | get_tree_root()->change_root(NULL, this); |
---|
304 | } |
---|
305 | |
---|
306 | virtual unsigned get_leaf_count() const = 0; |
---|
307 | virtual void compute_tree() = 0; |
---|
308 | |
---|
309 | void forget_origin() { set_tree_root(NULL); } |
---|
310 | void forget_relatives() { |
---|
311 | leftson = NULL; |
---|
312 | rightson = NULL; |
---|
313 | father = NULL; |
---|
314 | } |
---|
315 | |
---|
316 | TreeRoot *get_tree_root() const { return tree_root; } |
---|
317 | |
---|
318 | const TreeNode *get_root_node() const { |
---|
319 | if (!tree_root) return NULL; // nodes removed from tree have no root-node |
---|
320 | |
---|
321 | const TreeNode *root = tree_root->get_root_node(); |
---|
322 | rt_assert(is_inside(root)); // this is not in tree - behavior of get_root_node() changed! |
---|
323 | return root; |
---|
324 | } |
---|
325 | TreeNode *get_root_node() { return const_cast<TreeNode*>(const_cast<const TreeNode*>(this)->get_root_node()); } |
---|
326 | |
---|
327 | bool is_root_node() const { return get_root_node() == this; } |
---|
328 | virtual void set_root(); |
---|
329 | |
---|
330 | TreeNode *get_brother() { |
---|
331 | rt_assert(!is_root_node()); // root node has no brother |
---|
332 | rt_assert(father); // this is a removed node (not root, but no father) |
---|
333 | return is_leftson() ? get_father()->get_rightson() : get_father()->get_leftson(); |
---|
334 | } |
---|
335 | const TreeNode *get_brother() const { |
---|
336 | return const_cast<const TreeNode*>(const_cast<TreeNode*>(this)->get_brother()); |
---|
337 | } |
---|
338 | |
---|
339 | bool is_named_group() const { |
---|
340 | rt_assert(!is_leaf); // checking whether a leaf is a group |
---|
341 | return gb_node && name; |
---|
342 | } |
---|
343 | const char *get_group_name() const { |
---|
344 | return is_named_group() ? name : NULL; |
---|
345 | } |
---|
346 | TreeNode *find_parent_group() { |
---|
347 | TreeNode *parent = get_father(); |
---|
348 | while (parent && !parent->is_named_group()) { |
---|
349 | parent = parent->get_father(); |
---|
350 | } |
---|
351 | return parent; |
---|
352 | } |
---|
353 | const TreeNode *find_parent_group() const { |
---|
354 | return const_cast<const TreeNode*>(const_cast<TreeNode*>(this)->find_parent_group()); |
---|
355 | } |
---|
356 | int calculate_tax_level() const { |
---|
357 | int taxLev = is_named_group(); |
---|
358 | const TreeNode *parent = find_parent_group(); |
---|
359 | if (parent) taxLev += parent->calculate_tax_level(); |
---|
360 | return taxLev; |
---|
361 | } |
---|
362 | |
---|
363 | virtual void swap_sons() { |
---|
364 | rt_assert(!is_leaf); // @@@ if never fails -> remove condition below |
---|
365 | if (!is_leaf) { |
---|
366 | std::swap(leftson, rightson); |
---|
367 | std::swap(leftlen, rightlen); |
---|
368 | } |
---|
369 | } |
---|
370 | void rotate_subtree(); // flip whole subtree ( = recursive swap_sons()) |
---|
371 | void reorder_tree(TreeOrder mode); |
---|
372 | |
---|
373 | TreeNode *findLeafNamed(const char *wantedName); |
---|
374 | |
---|
375 | GBT_LEN reset_length_and_bootstrap() { |
---|
376 | //! remove remark + zero but return branchlen |
---|
377 | remove_remark(); |
---|
378 | GBT_LEN len = get_branchlength_unrooted(); |
---|
379 | set_branchlength_unrooted(0.0); |
---|
380 | return len; |
---|
381 | } |
---|
382 | |
---|
383 | struct multifurc_limits { |
---|
384 | double bootstrap; |
---|
385 | double branchlength; |
---|
386 | bool applyAtLeafs; |
---|
387 | multifurc_limits(double bootstrap_, double branchlength_, bool applyAtLeafs_) |
---|
388 | : bootstrap(bootstrap_), |
---|
389 | branchlength(branchlength_), |
---|
390 | applyAtLeafs(applyAtLeafs_) |
---|
391 | {} |
---|
392 | }; |
---|
393 | class LengthCollector; |
---|
394 | |
---|
395 | void multifurcate(); |
---|
396 | void set_branchlength_preserving(GBT_LEN new_len); |
---|
397 | |
---|
398 | void multifurcate_whole_tree(const multifurc_limits& below); |
---|
399 | private: |
---|
400 | void eliminate_and_collect(const multifurc_limits& below, LengthCollector& collect); |
---|
401 | public: |
---|
402 | |
---|
403 | #if defined(PROVIDE_TREE_STRUCTURE_TESTS) |
---|
404 | Validity is_valid() const; |
---|
405 | #endif // PROVIDE_TREE_STRUCTURE_TESTS |
---|
406 | }; |
---|
407 | MARK_NONFINAL_METHOD(TreeNode,void,swap_sons,()); |
---|
408 | MARK_NONFINAL_METHOD(TreeNode,void,set_root,()); |
---|
409 | |
---|
410 | inline void destroy(TreeNode *that) { |
---|
411 | TreeNode::destroy(that); |
---|
412 | } |
---|
413 | inline void destroy(TreeNode *that, TreeRoot *root) { |
---|
414 | TreeNode::destroy(that, root); |
---|
415 | } |
---|
416 | |
---|
417 | // --------------------------------------------------------------------------------------- |
---|
418 | // macros to overwrite accessors in classes derived from TreeRoot or TreeNode: |
---|
419 | |
---|
420 | #define DEFINE_TREE_ROOT_ACCESSORS(RootType, TreeType) \ |
---|
421 | DEFINE_DOWNCAST_ACCESSORS(TreeType, get_root_node, TreeRoot::get_root_node()) |
---|
422 | |
---|
423 | #define DEFINE_TREE_RELATIVES_ACCESSORS(TreeType) \ |
---|
424 | DEFINE_DOWNCAST_ACCESSORS(TreeType, get_father, father); \ |
---|
425 | DEFINE_DOWNCAST_ACCESSORS(TreeType, get_leftson, leftson); \ |
---|
426 | DEFINE_DOWNCAST_ACCESSORS(TreeType, get_rightson, rightson); \ |
---|
427 | DEFINE_DOWNCAST_ACCESSORS(TreeType, get_brother, TreeNode::get_brother()); \ |
---|
428 | DEFINE_DOWNCAST_ACCESSORS(TreeType, get_root_node, TreeNode::get_root_node()); \ |
---|
429 | TreeType *findLeafNamed(const char *wantedName) { return DOWNCAST(TreeType*, TreeNode::findLeafNamed(wantedName)); } |
---|
430 | |
---|
431 | #define DEFINE_TREE_ACCESSORS(RootType, TreeType) \ |
---|
432 | DEFINE_DOWNCAST_ACCESSORS(RootType, get_tree_root, TreeNode::get_tree_root()); \ |
---|
433 | DEFINE_TREE_RELATIVES_ACCESSORS(TreeType) |
---|
434 | |
---|
435 | |
---|
436 | // ------------------------- |
---|
437 | // structure tests |
---|
438 | |
---|
439 | #if defined(PROVIDE_TREE_STRUCTURE_TESTS) |
---|
440 | template <typename TREE> |
---|
441 | inline Validity tree_is_valid(const TREE *tree, bool acceptNULL) { |
---|
442 | if (tree) return tree->is_valid(); |
---|
443 | return Validity(acceptNULL, "NULL tree"); |
---|
444 | } |
---|
445 | #endif |
---|
446 | |
---|
447 | #if defined(AUTO_CHECK_TREE_STRUCTURE) |
---|
448 | #define ASSERT_VALID_TREE(tree) rt_assert(tree_is_valid(tree, false)) |
---|
449 | #define ASSERT_VALID_TREE_OR_NULL(tree) rt_assert(tree_is_valid(tree, true)) |
---|
450 | #else |
---|
451 | #define ASSERT_VALID_TREE(tree) |
---|
452 | #define ASSERT_VALID_TREE_OR_NULL(tree) |
---|
453 | #endif // AUTO_CHECK_TREE_STRUCTURE |
---|
454 | |
---|
455 | #if defined(PROVIDE_TREE_STRUCTURE_TESTS) && defined(UNIT_TESTS) |
---|
456 | |
---|
457 | #define TEST_EXPECT_VALID_TREE(tree) TEST_VALIDITY(tree_is_valid(tree, false)) |
---|
458 | #define TEST_EXPECT_VALID_TREE_OR_NULL(tree) TEST_VALIDITY(tree_is_valid(tree, true)) |
---|
459 | #define TEST_EXPECT_VALID_TREE__BROKEN(tree,why) TEST_VALIDITY__BROKEN(tree_is_valid(tree, false), why) |
---|
460 | #define TEST_EXPECT_VALID_TREE_OR_NULL__BROKEN(tree,why) TEST_VALIDITY__BROKEN(tree_is_valid(tree, true), why) |
---|
461 | |
---|
462 | #else |
---|
463 | |
---|
464 | #define TEST_EXPECT_VALID_TREE(tree) |
---|
465 | #define TEST_EXPECT_VALID_TREE_OR_NULL(tree) |
---|
466 | #define TEST_EXPECT_VALID_TREE__BROKEN(tree) |
---|
467 | #define TEST_EXPECT_VALID_TREE_OR_NULL__BROKEN(tree) |
---|
468 | |
---|
469 | #endif |
---|
470 | |
---|
471 | // -------------------- |
---|
472 | // SimpleTree |
---|
473 | |
---|
474 | struct SimpleRoot : public TreeRoot { |
---|
475 | inline SimpleRoot(); |
---|
476 | inline TreeNode *makeNode() const OVERRIDE; |
---|
477 | inline void destroyNode(TreeNode *node) const OVERRIDE; |
---|
478 | }; |
---|
479 | |
---|
480 | class SimpleTree FINAL_TYPE : public TreeNode { |
---|
481 | protected: |
---|
482 | ~SimpleTree() OVERRIDE {} |
---|
483 | friend class SimpleRoot; |
---|
484 | public: |
---|
485 | SimpleTree(SimpleRoot *sroot) : TreeNode(sroot) {} |
---|
486 | |
---|
487 | // TreeNode interface |
---|
488 | unsigned get_leaf_count() const OVERRIDE { |
---|
489 | rt_assert(0); // @@@ impl? |
---|
490 | return 0; |
---|
491 | } |
---|
492 | void compute_tree() OVERRIDE {} |
---|
493 | }; |
---|
494 | |
---|
495 | SimpleRoot::SimpleRoot() : TreeRoot(true) {} |
---|
496 | inline TreeNode *SimpleRoot::makeNode() const { return new SimpleTree(const_cast<SimpleRoot*>(this)); } |
---|
497 | inline void SimpleRoot::destroyNode(TreeNode *node) const { delete DOWNCAST(SimpleTree*,node); } |
---|
498 | |
---|
499 | // ---------------------- |
---|
500 | // ARB_edge_type |
---|
501 | |
---|
502 | enum ARB_edge_type { |
---|
503 | EDGE_TO_ROOT, // edge points towards the root node |
---|
504 | EDGE_TO_LEAF, // edge points away from the root node |
---|
505 | ROOT_EDGE, // edge between sons of root node |
---|
506 | }; |
---|
507 | |
---|
508 | class ARB_edge { |
---|
509 | // ARB_edge is a directional edge between two non-root-nodes of the same tree |
---|
510 | // (can act as iterator for TreeNode) |
---|
511 | |
---|
512 | TreeNode *from, *to; |
---|
513 | ARB_edge_type type; |
---|
514 | |
---|
515 | ARB_edge_type detectType() const { |
---|
516 | rt_assert(to != from); |
---|
517 | rt_assert(!from->is_root_node()); // edges cannot be at root - use edge between sons of root! |
---|
518 | rt_assert(!to->is_root_node()); |
---|
519 | |
---|
520 | if (from->father == to) return EDGE_TO_ROOT; |
---|
521 | if (to->father == from) return EDGE_TO_LEAF; |
---|
522 | |
---|
523 | rt_assert(from->get_brother() == to); // no edge exists between 'from' and 'to' |
---|
524 | rt_assert(to->get_father()->is_root_node()); |
---|
525 | return ROOT_EDGE; |
---|
526 | } |
---|
527 | |
---|
528 | GBT_LEN adjacent_distance() const; |
---|
529 | GBT_LEN length_or_adjacent_distance() const { |
---|
530 | { |
---|
531 | GBT_LEN len = length(); |
---|
532 | if (len>0.0) return len; |
---|
533 | } |
---|
534 | return adjacent_distance(); |
---|
535 | } |
---|
536 | |
---|
537 | void virtually_add_or_distribute_length_forward(GBT_LEN len, TreeNode::LengthCollector& collect) const; |
---|
538 | void virtually_distribute_length_forward(GBT_LEN len, TreeNode::LengthCollector& collect) const; |
---|
539 | public: |
---|
540 | void virtually_distribute_length(GBT_LEN len, TreeNode::LengthCollector& collect) const; // @@@ hm public :( |
---|
541 | private: |
---|
542 | |
---|
543 | #if defined(UNIT_TESTS) // UT_DIFF |
---|
544 | friend void TEST_edges(); |
---|
545 | #endif |
---|
546 | |
---|
547 | public: |
---|
548 | ARB_edge(TreeNode *From, TreeNode *To) : |
---|
549 | from(From), |
---|
550 | to(To), |
---|
551 | type(detectType()) |
---|
552 | {} |
---|
553 | ARB_edge(TreeNode *From, TreeNode *To, ARB_edge_type Type) : |
---|
554 | from(From), |
---|
555 | to(To), |
---|
556 | type(Type) |
---|
557 | { |
---|
558 | rt_assert(type == detectType()); |
---|
559 | } |
---|
560 | ARB_edge(const ARB_edge& otherEdge) : |
---|
561 | from(otherEdge.from), |
---|
562 | to(otherEdge.to), |
---|
563 | type(otherEdge.type) |
---|
564 | { |
---|
565 | rt_assert(type == detectType()); |
---|
566 | } |
---|
567 | |
---|
568 | ARB_edge_type get_type() const { return type; } |
---|
569 | TreeNode *source() const { return from; } |
---|
570 | TreeNode *dest() const { return to; } |
---|
571 | |
---|
572 | TreeNode *son() const { return type == EDGE_TO_ROOT ? from : to; } |
---|
573 | TreeNode *other() const { return type == EDGE_TO_ROOT ? to : from; } |
---|
574 | |
---|
575 | GBT_LEN length() const { |
---|
576 | if (type == ROOT_EDGE) return from->get_branchlength() + to->get_branchlength(); |
---|
577 | return son()->get_branchlength(); |
---|
578 | } |
---|
579 | void set_length(GBT_LEN len) { |
---|
580 | if (type == ROOT_EDGE) { |
---|
581 | from->set_branchlength(len/2); |
---|
582 | to->set_branchlength(len/2); |
---|
583 | } |
---|
584 | else { |
---|
585 | son()->set_branchlength(len); |
---|
586 | } |
---|
587 | } |
---|
588 | GBT_LEN eliminate() { |
---|
589 | //! eliminates edge (zeroes length and bootstrap). returns eliminated length. |
---|
590 | if (type == ROOT_EDGE) { |
---|
591 | return source()->reset_length_and_bootstrap() + dest()->reset_length_and_bootstrap(); |
---|
592 | } |
---|
593 | return son()->reset_length_and_bootstrap(); |
---|
594 | } |
---|
595 | |
---|
596 | ARB_edge inverse() const { |
---|
597 | return ARB_edge(to, from, ARB_edge_type(type == ROOT_EDGE ? ROOT_EDGE : (EDGE_TO_LEAF+EDGE_TO_ROOT)-type)); |
---|
598 | } |
---|
599 | |
---|
600 | // iterator functions: endlessly iterate over all edges of tree |
---|
601 | // - next: forward (=towards dest()) |
---|
602 | // - previous: backward (=back before source()) |
---|
603 | // - counter: forward descends left (=upper) son first |
---|
604 | // - non-counter: forward descends right (=lower) son first |
---|
605 | |
---|
606 | ARB_edge next() const { // descends rightson first (traverses leaf-edges from bottom to top) |
---|
607 | if (type == EDGE_TO_ROOT) { |
---|
608 | rt_assert(from->is_son_of(to)); |
---|
609 | if (from->is_rightson()) return ARB_edge(to, to->get_leftson(), EDGE_TO_LEAF); |
---|
610 | TreeNode *father = to->get_father(); |
---|
611 | if (father->is_root_node()) return ARB_edge(to, to->get_brother(), ROOT_EDGE); |
---|
612 | return ARB_edge(to, father, EDGE_TO_ROOT); |
---|
613 | } |
---|
614 | if (is_edge_to_leaf()) return inverse(); |
---|
615 | return ARB_edge(to, to->get_rightson(), EDGE_TO_LEAF); |
---|
616 | } |
---|
617 | ARB_edge previous() const { // inverse of next(). (traverses leaf-edges from top to bottom) |
---|
618 | if (type == EDGE_TO_LEAF) { |
---|
619 | rt_assert(to->is_son_of(from)); |
---|
620 | if (to->is_leftson()) return ARB_edge(from->get_rightson(), from, EDGE_TO_ROOT); |
---|
621 | TreeNode *father = from->get_father(); |
---|
622 | if (father->is_root_node()) return ARB_edge(from->get_brother(), from, ROOT_EDGE); |
---|
623 | return ARB_edge(father, from, EDGE_TO_LEAF); |
---|
624 | } |
---|
625 | if (is_edge_from_leaf()) return inverse(); |
---|
626 | return ARB_edge(from->get_leftson(), from, EDGE_TO_ROOT); |
---|
627 | } |
---|
628 | |
---|
629 | ARB_edge counter_next() const { // descends leftson first (traverses leaf-edges from top to bottom) |
---|
630 | if (type == EDGE_TO_ROOT) { |
---|
631 | rt_assert(from->is_son_of(to)); |
---|
632 | if (from->is_leftson()) return ARB_edge(to, to->get_rightson(), EDGE_TO_LEAF); |
---|
633 | TreeNode *father = to->get_father(); |
---|
634 | if (father->is_root_node()) return ARB_edge(to, to->get_brother(), ROOT_EDGE); |
---|
635 | return ARB_edge(to, father, EDGE_TO_ROOT); |
---|
636 | } |
---|
637 | if (is_edge_to_leaf()) return inverse(); |
---|
638 | return ARB_edge(to, to->get_leftson(), EDGE_TO_LEAF); |
---|
639 | } |
---|
640 | ARB_edge counter_previous() const { // inverse of counter_next(). (traverses leaf-edges from bottom to top) |
---|
641 | if (type == EDGE_TO_LEAF) { |
---|
642 | rt_assert(to->is_son_of(from)); |
---|
643 | if (to->is_rightson()) return ARB_edge(from->get_leftson(), from, EDGE_TO_ROOT); |
---|
644 | TreeNode *father = from->get_father(); |
---|
645 | if (father->is_root_node()) return ARB_edge(from->get_brother(), from, ROOT_EDGE); |
---|
646 | return ARB_edge(father, from, EDGE_TO_LEAF); |
---|
647 | } |
---|
648 | if (is_edge_from_leaf()) return inverse(); |
---|
649 | return ARB_edge(from->get_rightson(), from, EDGE_TO_ROOT); |
---|
650 | } |
---|
651 | |
---|
652 | static int iteration_count(int leafs_in_tree) { |
---|
653 | /*! returns number of different edges produced by next() / previous(): |
---|
654 | * - each edge is visited twice (once in each direction) |
---|
655 | */ |
---|
656 | return leafs_2_edges(leafs_in_tree, UNROOTED) * 2; |
---|
657 | } |
---|
658 | |
---|
659 | bool operator == (const ARB_edge& otherEdge) const { |
---|
660 | return from == otherEdge.from && to == otherEdge.to; |
---|
661 | } |
---|
662 | bool operator != (const ARB_edge& otherEdge) const { |
---|
663 | return !operator == (otherEdge); |
---|
664 | } |
---|
665 | |
---|
666 | bool is_edge_to_leaf() const { |
---|
667 | //! true if edge is leaf edge AND points towards the leaf |
---|
668 | return dest()->is_leaf; |
---|
669 | } |
---|
670 | bool is_edge_from_leaf() const { |
---|
671 | //! true if edge is leaf edge AND points away from the leaf |
---|
672 | return source()->is_leaf; |
---|
673 | } |
---|
674 | bool is_inner_edge() const { |
---|
675 | //! true for inner edges |
---|
676 | return !is_edge_to_leaf() && !is_edge_from_leaf(); |
---|
677 | } |
---|
678 | |
---|
679 | void set_root() { son()->set_root(); } |
---|
680 | |
---|
681 | void multifurcate(); |
---|
682 | |
---|
683 | }; |
---|
684 | |
---|
685 | inline ARB_edge parentEdge(TreeNode *son) { |
---|
686 | /*! returns edge to father (or to brother for sons of root). |
---|
687 | * Cannot be called with root-node (but can be called with each end of any ARB_edge) |
---|
688 | */ |
---|
689 | TreeNode *father = son->get_father(); |
---|
690 | rt_assert(father); |
---|
691 | |
---|
692 | if (father->is_root_node()) return ARB_edge(son, son->get_brother(), ROOT_EDGE); |
---|
693 | return ARB_edge(son, father, EDGE_TO_ROOT); |
---|
694 | } |
---|
695 | inline ARB_edge leafEdge(TreeNode *leaf) { |
---|
696 | rt_assert(leaf->is_leaf); |
---|
697 | return parentEdge(leaf).inverse(); |
---|
698 | } |
---|
699 | |
---|
700 | inline ARB_edge rootEdge(TreeRoot *root) { |
---|
701 | TreeNode *root_node = root->get_root_node(); |
---|
702 | return ARB_edge(root_node->get_leftson(), root_node->get_rightson(), ROOT_EDGE); |
---|
703 | } |
---|
704 | |
---|
705 | #else |
---|
706 | #error TreeNode.h included twice |
---|
707 | #endif // TREENODE_H |
---|