1 | #include <cmath> |
---|
2 | #include <cstdio> |
---|
3 | #include <cstdlib> |
---|
4 | #include <cstring> |
---|
5 | #include <iostream> |
---|
6 | |
---|
7 | #include <sys/times.h> |
---|
8 | |
---|
9 | #include "ps_tools.hxx" |
---|
10 | #include "ps_database.hxx" |
---|
11 | #include "ps_bitmap.hxx" |
---|
12 | #include "ps_candidate.hxx" |
---|
13 | |
---|
14 | using namespace std; |
---|
15 | |
---|
16 | template<class T> |
---|
17 | void PS_print_set_ranges( const char *_set_name, const set<T> &_set, const bool _cr_at_end = true ) { |
---|
18 | fflush( stdout ); |
---|
19 | printf( "%s size (%3zu) : ", _set_name, _set.size() ); |
---|
20 | if (_set.size() == 0) { |
---|
21 | printf( "(empty)" ); |
---|
22 | } else { |
---|
23 | typename set<T>::const_iterator range_begin = _set.begin(); |
---|
24 | typename set<T>::const_iterator range_end = range_begin; |
---|
25 | typename set<T>::const_iterator it = _set.begin(); |
---|
26 | for ( ++it; |
---|
27 | it != _set.end(); |
---|
28 | ++it ) { |
---|
29 | if (*it == (*range_end)+1) { |
---|
30 | range_end = it; |
---|
31 | } else { |
---|
32 | if (range_end == range_begin) { |
---|
33 | cout << *range_begin << " "; |
---|
34 | } else { |
---|
35 | cout << *range_begin << "-" << *range_end << " "; |
---|
36 | } |
---|
37 | range_begin = it; |
---|
38 | range_end = it; |
---|
39 | } |
---|
40 | } |
---|
41 | cout << *range_begin; |
---|
42 | if (range_end != range_begin) cout << "-" << *range_end; |
---|
43 | } |
---|
44 | if (_cr_at_end) cout << "\n"; |
---|
45 | fflush( stdout ); |
---|
46 | } |
---|
47 | |
---|
48 | |
---|
49 | template<class T1,class T2> |
---|
50 | void PS_print_map_ranges( const char *_map_name, const map<T1,T2> &_map, const bool _compare_keys = true, const bool _cr_at_end = true ) { |
---|
51 | fflush( stdout ); |
---|
52 | if (_map.size() == 0) { |
---|
53 | printf( "%s size ( 0) : (empty)", _map_name ); |
---|
54 | } else { |
---|
55 | if (_compare_keys) { |
---|
56 | printf( "%s size (%3i) : ", _map_name, _map.size() ); |
---|
57 | typename map<T1,T2>::const_iterator range_begin = _map.begin(); |
---|
58 | typename map<T1,T2>::const_iterator range_end = range_begin; |
---|
59 | typename map<T1,T2>::const_iterator it = _map.begin(); |
---|
60 | for ( ++it; |
---|
61 | it != _map.end(); |
---|
62 | ++it ) { |
---|
63 | if (it->first == range_end->first+1) { |
---|
64 | range_end = it; |
---|
65 | } else { |
---|
66 | if (range_end == range_begin) { |
---|
67 | cout << "(" << range_begin->first << "," << range_begin->second << ") "; |
---|
68 | } else { |
---|
69 | cout << "(" << range_begin->first << "-" << range_end->first << "," << range_begin->second << ") "; |
---|
70 | } |
---|
71 | range_begin = it; |
---|
72 | range_end = it; |
---|
73 | } |
---|
74 | } |
---|
75 | if (range_end == range_begin) { |
---|
76 | cout << "(" << range_begin->first << "," << range_begin->second << ") "; |
---|
77 | } else { |
---|
78 | cout << "(" << range_begin->first << "-" << range_end->first << "," << range_begin->second << ") "; |
---|
79 | } |
---|
80 | } else { |
---|
81 | map<T2,set<pair<T1,T1> > > value2indices; |
---|
82 | map<T2,unsigned long int> value2count; |
---|
83 | pair<T1,T1> range; |
---|
84 | range.first = _map.begin()->first; |
---|
85 | range.second = range.first; |
---|
86 | T2 cur_value = _map.begin()->second; |
---|
87 | typename map<T1,T2>::const_iterator it = _map.begin(); |
---|
88 | for ( ++it; |
---|
89 | it != _map.end(); |
---|
90 | ++it ) { |
---|
91 | if (it->second == cur_value) { |
---|
92 | if (it->first == range.second+1) { |
---|
93 | range.second = it->first; |
---|
94 | } else { |
---|
95 | value2indices[ cur_value ].insert( range ); |
---|
96 | value2count[ cur_value ] += range.second - range.first +1; |
---|
97 | range.first = it->first; |
---|
98 | range.second = it->first; |
---|
99 | } |
---|
100 | } else { |
---|
101 | value2indices[ cur_value ].insert( range ); |
---|
102 | value2count[ cur_value ] += range.second - range.first +1; |
---|
103 | range.first = it->first; |
---|
104 | range.second = it->first; |
---|
105 | cur_value = it->second; |
---|
106 | } |
---|
107 | } |
---|
108 | value2indices[ cur_value ].insert( range ); |
---|
109 | value2count[ cur_value ] += range.second - range.first +1; |
---|
110 | for ( typename map<T2,set<pair<T1,T1> > >::const_iterator value = value2indices.begin(); |
---|
111 | value != value2indices.end(); |
---|
112 | ++value ) { |
---|
113 | if (value != value2indices.begin()) cout << "\n"; |
---|
114 | printf( "%s size (%3i) : value (", _map_name, _map.size() ); |
---|
115 | cout << value->first << ") count (" << value2count[ value->first ] << ") ["; |
---|
116 | for ( typename set<pair<T1,T1> >::const_iterator indices = value->second.begin(); |
---|
117 | indices != value->second.end(); |
---|
118 | ++indices ) { |
---|
119 | if (indices != value->second.begin()) cout << " "; |
---|
120 | cout << indices->first; |
---|
121 | if (indices->first != indices->second) cout << "-" << indices->second; |
---|
122 | } |
---|
123 | cout << "]," << value->first << ")"; |
---|
124 | } |
---|
125 | } |
---|
126 | } |
---|
127 | if (_cr_at_end) cout << "\n"; |
---|
128 | fflush( stdout ); |
---|
129 | } |
---|
130 | |
---|
131 | // |
---|
132 | // common globals |
---|
133 | // |
---|
134 | |
---|
135 | bool __VERBOSE = false; |
---|
136 | SpeciesID __MAX_ID; |
---|
137 | SpeciesID __MIN_ID; |
---|
138 | SpeciesID __SPECIES_COUNT; |
---|
139 | unsigned long __BITS_IN_MAP; |
---|
140 | PS_BitMap_Counted *__MAP; |
---|
141 | PS_BitMap_Counted *__PRESET_MAP; |
---|
142 | IDSet __SOURCE_ID_SET; |
---|
143 | PS_BitSet::IndexSet __TARGET_ID_SET; |
---|
144 | |
---|
145 | // |
---|
146 | // globals for PS_calc_next_speciesid_sets, |
---|
147 | // PS_calc_next_speciesid_sets_for_candidate |
---|
148 | // |
---|
149 | |
---|
150 | // count of trues for a source_id may be max 5% |
---|
151 | // (of the difference between __SPECIES_COUNT and the lowest |
---|
152 | // count of trues per species) higher than the lowest count |
---|
153 | // of trues for the species in __SOURCE_ID_SET |
---|
154 | #define __TRESHOLD_PERCENTAGE_NEXT_SOURCE_ID_SET 5 |
---|
155 | // target_id must be at least in 95% of total target_id_sets |
---|
156 | // to be in __TARGET_ID_SET |
---|
157 | #define __TRESHOLD_PERCENTAGE_NEXT_TARGET_ID_SET 95 |
---|
158 | |
---|
159 | SpeciesID __MIN_SETS_ID; |
---|
160 | SpeciesID __MAX_SETS_ID; |
---|
161 | |
---|
162 | // |
---|
163 | // globals for PS_find_probes |
---|
164 | // |
---|
165 | |
---|
166 | // initially a probe must match 40-60% of species |
---|
167 | // in the ID-sets to be a candidate |
---|
168 | // if PS_find_probes fails to find candidates within this range |
---|
169 | // it is repeated with a broadened range (by 5% each border) |
---|
170 | #define __MIN_PERCENTAGE_SET_MATCH 40 |
---|
171 | #define __MAX_PERCENTAGE_SET_MATCH 60 |
---|
172 | |
---|
173 | float __SOURCE_MIN_MATCH_COUNT; |
---|
174 | float __SOURCE_MAX_MATCH_COUNT; |
---|
175 | float __TARGET_MIN_MATCH_COUNT; |
---|
176 | float __TARGET_MAX_MATCH_COUNT; |
---|
177 | float __SOURCE_PERFECT_MATCH_COUNT; |
---|
178 | float __TARGET_PERFECT_MATCH_COUNT; |
---|
179 | unsigned long __PROBES_COUNTER; |
---|
180 | unsigned long __PROBES_REMOVED; |
---|
181 | PS_CandidatePtr __CANDIDATES_ROOT; |
---|
182 | unsigned long __CANDIDATES_COUNTER; |
---|
183 | unsigned long __CANDIDATES_TODO; |
---|
184 | unsigned long __CANDIDATES_FINISHED; |
---|
185 | unsigned long __MAX_DEPTH; |
---|
186 | |
---|
187 | // |
---|
188 | // globals for PS_find_probe_for_sets |
---|
189 | // PS_test_candidate_on_bitmap |
---|
190 | // |
---|
191 | |
---|
192 | IDSet __PATH; |
---|
193 | |
---|
194 | // |
---|
195 | // globals for PS_descend |
---|
196 | // |
---|
197 | char *__PATH_IN_CANDIDATES; |
---|
198 | |
---|
199 | |
---|
200 | unsigned long int PS_test_candidate_on_bitmap( float *_filling_level = 0, |
---|
201 | PS_BitMap_Counted *_map = 0 ) { |
---|
202 | // returns number of locations in __MAP that would be switched |
---|
203 | // from false to true by __PATH |
---|
204 | |
---|
205 | // iterate over all IDs except path |
---|
206 | IDSetCIter path_iter = __PATH.begin(); |
---|
207 | SpeciesID next_path_ID = *path_iter; |
---|
208 | unsigned long int gain = 0; |
---|
209 | if (_map) { |
---|
210 | for ( SpeciesID not_in_path_ID = __MIN_ID; |
---|
211 | not_in_path_ID <= __MAX_ID; |
---|
212 | ++not_in_path_ID) { |
---|
213 | if (not_in_path_ID == next_path_ID) { // if i run into a ID in path |
---|
214 | ++path_iter; // advance to next path ID |
---|
215 | next_path_ID = (path_iter == __PATH.end()) ? -1 : *path_iter; |
---|
216 | continue; // skip this ID |
---|
217 | } |
---|
218 | // iterate over path IDs |
---|
219 | for ( IDSetCIter path_ID = __PATH.begin(); |
---|
220 | path_ID != __PATH.end(); |
---|
221 | ++path_ID) { |
---|
222 | if (not_in_path_ID == *path_ID) |
---|
223 | continue; // obviously a probe cant differ a species from itself |
---|
224 | if (not_in_path_ID > *path_ID) { |
---|
225 | gain += (_map->get( not_in_path_ID, *path_ID ) == false); |
---|
226 | } else { |
---|
227 | gain += (_map->get( *path_ID, not_in_path_ID ) == false); |
---|
228 | } |
---|
229 | } |
---|
230 | } |
---|
231 | } else { |
---|
232 | for ( SpeciesID not_in_path_ID = __MIN_ID; |
---|
233 | not_in_path_ID <= __MAX_ID; |
---|
234 | ++not_in_path_ID) { |
---|
235 | if (not_in_path_ID == next_path_ID) { // if i run into a ID in path |
---|
236 | ++path_iter; // advance to next path ID |
---|
237 | next_path_ID = (path_iter == __PATH.end()) ? -1 : *path_iter; |
---|
238 | continue; // skip this ID |
---|
239 | } |
---|
240 | // iterate over path IDs |
---|
241 | for ( IDSetCIter path_ID = __PATH.begin(); |
---|
242 | path_ID != __PATH.end(); |
---|
243 | ++path_ID) { |
---|
244 | if (not_in_path_ID == *path_ID) |
---|
245 | continue; // obviously a probe cant differ a species from itself |
---|
246 | if (not_in_path_ID > *path_ID) { |
---|
247 | gain += (__MAP->get( not_in_path_ID, *path_ID ) == false); |
---|
248 | } else { |
---|
249 | gain += (__MAP->get( *path_ID, not_in_path_ID ) == false); |
---|
250 | } |
---|
251 | } |
---|
252 | } |
---|
253 | } |
---|
254 | if (_filling_level) { |
---|
255 | unsigned long int trues = (_map) ? _map->getCountOfTrues() + gain : __MAP->getCountOfTrues() + gain; |
---|
256 | *_filling_level = ((float)trues / __BITS_IN_MAP)*100.0; |
---|
257 | } |
---|
258 | return gain; |
---|
259 | } |
---|
260 | |
---|
261 | |
---|
262 | bool PS_test_sets_on_path( float &_distance ) { |
---|
263 | long count_matched_source = 0; |
---|
264 | long count_matched_target = 0; |
---|
265 | SpeciesID path_id; |
---|
266 | IDSetCIter path_end = __PATH.end(); |
---|
267 | IDSetCIter path = __PATH.begin(); |
---|
268 | IDSetCIter source_end = __SOURCE_ID_SET.end(); |
---|
269 | IDSetCIter source = __SOURCE_ID_SET.begin(); |
---|
270 | PS_BitSet::IndexSet::const_iterator target_end = __TARGET_ID_SET.end(); |
---|
271 | PS_BitSet::IndexSet::const_iterator target = __TARGET_ID_SET.begin(); |
---|
272 | |
---|
273 | while (path != path_end) { |
---|
274 | path_id = *path; |
---|
275 | while ((*target < path_id) && (target != target_end)) { |
---|
276 | ++target; |
---|
277 | } |
---|
278 | if ((target != target_end) && (*target == path_id)) |
---|
279 | ++count_matched_target; |
---|
280 | while ((*source < path_id) && (source != source_end)) { |
---|
281 | ++source; |
---|
282 | } |
---|
283 | if ((source != source_end) && (*source == path_id)) |
---|
284 | ++count_matched_source; |
---|
285 | ++path; |
---|
286 | } |
---|
287 | |
---|
288 | if ((count_matched_source > __SOURCE_MIN_MATCH_COUNT) && |
---|
289 | (count_matched_source < __SOURCE_MAX_MATCH_COUNT) && |
---|
290 | (count_matched_target > __TARGET_MIN_MATCH_COUNT) && |
---|
291 | (count_matched_target < __TARGET_MAX_MATCH_COUNT)) { |
---|
292 | _distance = fabs( __SOURCE_PERFECT_MATCH_COUNT - count_matched_source ) + fabs( __TARGET_PERFECT_MATCH_COUNT - count_matched_target ); |
---|
293 | return true; |
---|
294 | } |
---|
295 | return false; |
---|
296 | } |
---|
297 | |
---|
298 | void PS_find_probe_for_sets( const PS_NodePtr _ps_node, PS_CandidatePtr _candidate_parent ) { |
---|
299 | // scan subtree starting with _ps_node for candidates |
---|
300 | |
---|
301 | SpeciesID id = _ps_node->getNum(); |
---|
302 | bool has_probes = _ps_node->hasProbes(); |
---|
303 | |
---|
304 | // |
---|
305 | // append ID to path |
---|
306 | // |
---|
307 | __PATH.insert( id ); |
---|
308 | |
---|
309 | // |
---|
310 | // dont look at path until ID is greater than lowest ID in the sets of IDs |
---|
311 | // also dont use a node if its already used as candidate |
---|
312 | // |
---|
313 | if ((id >= __MIN_SETS_ID) && has_probes && !_candidate_parent->alreadyUsedNode(_ps_node)) { |
---|
314 | ++__PROBES_COUNTER; |
---|
315 | if (__VERBOSE && (__PROBES_COUNTER % 100 == 0)) printf( "%8lup %8luc\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b", __PROBES_COUNTER, __CANDIDATES_COUNTER ); fflush( stdout ); |
---|
316 | // make intersections of __PATH with __SOURCE_ID_SET and __TARGET_ID_SET |
---|
317 | float distance_to_perfect_match; |
---|
318 | if (PS_test_sets_on_path( distance_to_perfect_match )) { |
---|
319 | unsigned long gain = PS_test_candidate_on_bitmap(); // no -> calc gain and make new candidate node |
---|
320 | int status = (gain < (unsigned)__SPECIES_COUNT / 100) |
---|
321 | ? 0 |
---|
322 | : _candidate_parent->addChild( static_cast<unsigned long>(distance_to_perfect_match), gain, _ps_node, __PATH ); |
---|
323 | if (status > 0) { |
---|
324 | if (status == 2) { |
---|
325 | // printf( " PS_find_probe_for_sets() : new candidate: count_matched_source (%li/%.0f) count_matched_target (%li/%.0f) distance (%4.0f) path (%i) gain (%li) node (%p)\n", |
---|
326 | // count_matched_source, __SOURCE_PERFECT_MATCH_COUNT, |
---|
327 | // count_matched_target, __TARGET_PERFECT_MATCH_COUNT, |
---|
328 | // distance_to_perfect_match, |
---|
329 | // __PATH.size(), gain, &(*_ps_node) ); |
---|
330 | ++__CANDIDATES_COUNTER; |
---|
331 | if (__VERBOSE) printf( "%8lup %8luc\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b", __PROBES_COUNTER, __CANDIDATES_COUNTER ); fflush( stdout ); |
---|
332 | // } else { |
---|
333 | // printf( " PS_find_probe_for_sets() : upd candidate: count_matched_source (%li/%.0f) count_matched_target (%li/%.0f) distance (%4.0f) path (%i) gain (%li) node (%p)\n", |
---|
334 | // count_matched_source, __SOURCE_PERFECT_MATCH_COUNT, |
---|
335 | // count_matched_target, __TARGET_PERFECT_MATCH_COUNT, |
---|
336 | // distance_to_perfect_match, |
---|
337 | // __PATH.size(), gain, &(*_ps_node) ); |
---|
338 | } |
---|
339 | fflush( stdout ); |
---|
340 | } // if status (of addChild) |
---|
341 | } |
---|
342 | } |
---|
343 | |
---|
344 | // |
---|
345 | // step down the children if either ID is lower than highest |
---|
346 | // ID in the set of ID-pairs or the node has no probes |
---|
347 | // |
---|
348 | if ((id < __MAX_SETS_ID) || (! has_probes)) { |
---|
349 | for ( PS_NodeMapConstIterator i = _ps_node->getChildrenBegin(); |
---|
350 | i != _ps_node->getChildrenEnd(); |
---|
351 | ++i) { |
---|
352 | PS_find_probe_for_sets( i->second, _candidate_parent ); |
---|
353 | } |
---|
354 | } |
---|
355 | |
---|
356 | // |
---|
357 | // remove ID from path |
---|
358 | // |
---|
359 | __PATH.erase( id ); |
---|
360 | } |
---|
361 | |
---|
362 | void PS_find_probes( const PS_NodePtr _root_node, const int _round, PS_CandidatePtr _candidate_parent, const float _filling_level ) { |
---|
363 | // scan PS_Node-tree for candidates to raise filling level of __MAP |
---|
364 | |
---|
365 | __PROBES_COUNTER = 0; |
---|
366 | __CANDIDATES_COUNTER = 0; |
---|
367 | __SOURCE_MIN_MATCH_COUNT = (__SOURCE_ID_SET.size() * (__MIN_PERCENTAGE_SET_MATCH - (_round * 5))) / 100.0; |
---|
368 | __SOURCE_MAX_MATCH_COUNT = (__SOURCE_ID_SET.size() * (__MAX_PERCENTAGE_SET_MATCH + (_round * 5))) / 100.0; |
---|
369 | __TARGET_MIN_MATCH_COUNT = (__TARGET_ID_SET.size() * (__MIN_PERCENTAGE_SET_MATCH - (_round * 5))) / 100.0; |
---|
370 | __TARGET_MAX_MATCH_COUNT = (__TARGET_ID_SET.size() * (__MAX_PERCENTAGE_SET_MATCH + (_round * 5))) / 100.0; |
---|
371 | __SOURCE_PERFECT_MATCH_COUNT = __SOURCE_ID_SET.size() / 2.0; |
---|
372 | __TARGET_PERFECT_MATCH_COUNT = __TARGET_ID_SET.size() / 2.0; |
---|
373 | __MIN_SETS_ID = (*__SOURCE_ID_SET.begin() < *__TARGET_ID_SET.begin()) ? *__SOURCE_ID_SET.begin() : *__TARGET_ID_SET.begin(); |
---|
374 | __MAX_SETS_ID = (*__SOURCE_ID_SET.rbegin() < *__TARGET_ID_SET.rbegin()) ? *__SOURCE_ID_SET.rbegin() : *__TARGET_ID_SET.rbegin(); |
---|
375 | printf( "PS_find_probes(%i) : source match %10.3f .. %10.3f target match %10.3f .. %10.3f\n", _round, __SOURCE_MIN_MATCH_COUNT, __SOURCE_MAX_MATCH_COUNT, __TARGET_MIN_MATCH_COUNT, __TARGET_MAX_MATCH_COUNT ); fflush( stdout ); |
---|
376 | // int c = 0; |
---|
377 | struct tms before; |
---|
378 | times( &before ); |
---|
379 | for ( PS_NodeMapConstIterator i = _root_node->getChildrenBegin(); |
---|
380 | (i != _root_node->getChildrenEnd()) && (i->first < __MAX_SETS_ID); |
---|
381 | ++i/*,++c*/ ) { |
---|
382 | //if (c % 100 == 0) printf( "PS_find_probe_for_sets( %i ) : %i/%i 1st level nodes -> %li/%li candidates of %li probes looked at\n", i->first, c+1, _root_node->countChildren(), __CANDIDATES_COUNTER, __CANDIDATES_TOTAL_COUNTER, __PROBES_TOTAL_COUNTER ); |
---|
383 | __PATH.clear(); |
---|
384 | PS_find_probe_for_sets( i->second, _candidate_parent ); |
---|
385 | } |
---|
386 | printf( "PS_find_probes(%i) : %li candidates of %li probes visited ", _round, __CANDIDATES_COUNTER, __PROBES_COUNTER ); |
---|
387 | PS_print_time_diff( &before ); |
---|
388 | // reduce candidates to best,worst and middle gain |
---|
389 | _candidate_parent->reduceChildren( _filling_level ); |
---|
390 | for ( PS_CandidateByGainMapCIter c = _candidate_parent->children.begin(); |
---|
391 | c != _candidate_parent->children.end(); |
---|
392 | ++c ) { |
---|
393 | printf( "PS_find_probes(%i) : ", _round ); |
---|
394 | c->second->print(); |
---|
395 | ++__CANDIDATES_TODO; |
---|
396 | } |
---|
397 | fflush( stdout ); |
---|
398 | } |
---|
399 | |
---|
400 | void PS_calc_next_speciesid_sets() { |
---|
401 | // scan __MAP to find sets of IDs that need differentiation most |
---|
402 | |
---|
403 | // |
---|
404 | // 1. __SOURCE_ID_SET |
---|
405 | // scan bitmap for species that need more matches |
---|
406 | // |
---|
407 | SpeciesID highest_count; |
---|
408 | SpeciesID lowest_count; |
---|
409 | float treshold; |
---|
410 | SpeciesID count; |
---|
411 | |
---|
412 | // first pass -- get lowest count of trues and calc treshold |
---|
413 | lowest_count = __SPECIES_COUNT; |
---|
414 | highest_count = 0; |
---|
415 | for ( SpeciesID id = __MIN_ID; |
---|
416 | id <= __MAX_ID; |
---|
417 | ++id) { |
---|
418 | count = __MAP->getCountFor( id ); |
---|
419 | if (count == __SPECIES_COUNT-__MIN_ID-1) continue; // i cannot improve species that can be differed from all others |
---|
420 | if (count > highest_count) highest_count = count; |
---|
421 | if (count < lowest_count) lowest_count = count; |
---|
422 | } |
---|
423 | treshold = ( ((__SPECIES_COUNT-lowest_count) * __TRESHOLD_PERCENTAGE_NEXT_SOURCE_ID_SET) / 100.0 ) + lowest_count; |
---|
424 | printf( "PS_calc_next_speciesid_sets() : SOURCE count 1's [%i..%i] treshold (%.3f)", lowest_count, highest_count, treshold ); |
---|
425 | |
---|
426 | // second pass -- get IDs where count is below or equal treshold |
---|
427 | __SOURCE_ID_SET.clear(); |
---|
428 | for ( SpeciesID id = __MIN_ID; |
---|
429 | id <= __MAX_ID; |
---|
430 | ++id) { |
---|
431 | if (__MAP->getCountFor( id ) <= treshold) __SOURCE_ID_SET.insert( id ); |
---|
432 | } |
---|
433 | PS_print_set_ranges( " __SOURCE_ID_SET", __SOURCE_ID_SET ); |
---|
434 | |
---|
435 | // |
---|
436 | // 2. __TARGET_ID_SET |
---|
437 | // scan bitmap for species IDs that need to be distinguished from MOST species in __SOURCE_ID_SET |
---|
438 | // |
---|
439 | ID2IDMap count_falses_per_id; |
---|
440 | |
---|
441 | // first -- get the IDs that need differentiation from __SOURCE_ID_SET |
---|
442 | unsigned long count_iterations = 0; |
---|
443 | for ( IDSetCIter source_id = __SOURCE_ID_SET.begin(); |
---|
444 | source_id != __SOURCE_ID_SET.end(); |
---|
445 | ++source_id,++count_iterations ) { |
---|
446 | //if (count_iterations % 100 == 0) printf( "PS_calc_next_speciesid_sets() : set #%li of %i\n", count_iterations+1, __SOURCE_ID_SET.size() ); |
---|
447 | // get 'next_target_set' |
---|
448 | __MAP->getFalseIndicesFor( *source_id, __TARGET_ID_SET ); |
---|
449 | // count falses per SpeciesID |
---|
450 | for ( PS_BitSet::IndexSet::iterator target_id = __TARGET_ID_SET.begin(); |
---|
451 | target_id != __TARGET_ID_SET.end(); |
---|
452 | ++target_id) { |
---|
453 | if ((*target_id < __MIN_ID) || (*target_id > __MAX_ID)) continue; // skip ID's that are outside DB-IDs-range (like zero if __MIN_ID is one) |
---|
454 | if (*target_id != *source_id) ++count_falses_per_id[ *target_id ]; |
---|
455 | } |
---|
456 | } |
---|
457 | //PS_print_map_ranges( "PS_calc_next_speciesid_sets() : count_falses_per_id", count_falses_per_id, false ); |
---|
458 | |
---|
459 | // second -- get highest count of falses and calc treshold |
---|
460 | lowest_count = __SPECIES_COUNT; |
---|
461 | highest_count = 0; |
---|
462 | for ( ID2IDMapCIter count_per_id = count_falses_per_id.begin(); |
---|
463 | count_per_id != count_falses_per_id.end(); |
---|
464 | ++count_per_id ) { |
---|
465 | if (count_per_id->second > highest_count) highest_count = count_per_id->second; |
---|
466 | if (count_per_id->second < lowest_count) lowest_count = count_per_id->second; |
---|
467 | } |
---|
468 | printf( "PS_calc_next_speciesid_sets() : TARGET count 0's [%i..%i]", lowest_count, highest_count ); |
---|
469 | |
---|
470 | // third -- put all IDs in __TARGET_ID_SET that are needed most by species from __SOURCE_ID_SET |
---|
471 | __TARGET_ID_SET.clear(); |
---|
472 | for ( ID2IDMapCIter count_per_id = count_falses_per_id.begin(); |
---|
473 | count_per_id != count_falses_per_id.end(); |
---|
474 | ++count_per_id ) { |
---|
475 | if (count_per_id->second == highest_count) __TARGET_ID_SET.insert( count_per_id->first ); |
---|
476 | } |
---|
477 | PS_print_set_ranges( " __TARGET_ID_SET", __TARGET_ID_SET ); |
---|
478 | } |
---|
479 | |
---|
480 | void PS_apply_path_to_bitmap( IDSet &_path, const bool _silent = false, PS_BitMap_Counted *_map = 0 ) { |
---|
481 | // set true in __MAP for all combinations of IDs (in _path , not in _path) |
---|
482 | |
---|
483 | // iterate over all IDs except path |
---|
484 | IDSetCIter path_iter = _path.begin(); |
---|
485 | SpeciesID next_path_ID = *path_iter; |
---|
486 | unsigned long int gain = 0; |
---|
487 | if (_map) { // called for a 'private' map ? |
---|
488 | for ( SpeciesID not_in_path_ID = __MIN_ID; |
---|
489 | not_in_path_ID <= __MAX_ID; |
---|
490 | ++not_in_path_ID) { |
---|
491 | if (not_in_path_ID == next_path_ID) { // if i run into a ID in path |
---|
492 | ++path_iter; // advance to next path ID |
---|
493 | next_path_ID = (path_iter == _path.end()) ? -1 : *path_iter; |
---|
494 | continue; // skip this ID |
---|
495 | } |
---|
496 | // iterate over path IDs |
---|
497 | for ( IDSetCIter path_ID = _path.begin(); |
---|
498 | path_ID != _path.end(); |
---|
499 | ++path_ID) { |
---|
500 | if (not_in_path_ID == *path_ID) continue; // obviously a probe cant differ a species from itself |
---|
501 | if (not_in_path_ID > *path_ID) { |
---|
502 | gain += (_map->set( not_in_path_ID, *path_ID, true ) == false); |
---|
503 | } else { |
---|
504 | gain += (_map->set( *path_ID, not_in_path_ID, true ) == false); |
---|
505 | } |
---|
506 | } |
---|
507 | } |
---|
508 | } else { // called for __MAP |
---|
509 | for ( SpeciesID not_in_path_ID = __MIN_ID; |
---|
510 | not_in_path_ID <= __MAX_ID; |
---|
511 | ++not_in_path_ID) { |
---|
512 | if (not_in_path_ID == next_path_ID) { // if i run into a ID in path |
---|
513 | ++path_iter; // advance to next path ID |
---|
514 | next_path_ID = (path_iter == _path.end()) ? -1 : *path_iter; |
---|
515 | continue; // skip this ID |
---|
516 | } |
---|
517 | // iterate over path IDs |
---|
518 | for ( IDSetCIter path_ID = _path.begin(); |
---|
519 | path_ID != _path.end(); |
---|
520 | ++path_ID) { |
---|
521 | if (not_in_path_ID == *path_ID) continue; // obviously a probe cant differ a species from itself |
---|
522 | if (not_in_path_ID > *path_ID) { |
---|
523 | gain += (__MAP->set( not_in_path_ID, *path_ID, true ) == false); |
---|
524 | } else { |
---|
525 | gain += (__MAP->set( *path_ID, not_in_path_ID, true ) == false); |
---|
526 | } |
---|
527 | } |
---|
528 | } |
---|
529 | } |
---|
530 | unsigned long int sets = (__SPECIES_COUNT-_path.size())*_path.size(); |
---|
531 | if (!_silent) printf( "PS_apply_path_to_bitmap() : gain %lu of %lu -- %.2f%% -> wasted %lu\n", gain, sets, ((float)gain/sets)*100.0, sets-gain ); |
---|
532 | //__MAP->recalcCounters(); |
---|
533 | } |
---|
534 | |
---|
535 | float PS_filling_level( PS_CandidatePtr _candidate = 0 ) { |
---|
536 | // returns filling level of __MAP |
---|
537 | |
---|
538 | unsigned long trues = __MAP->getCountOfTrues(); |
---|
539 | float percentage = ((float)trues / __BITS_IN_MAP)*100.0; |
---|
540 | if (_candidate) { |
---|
541 | _candidate->filling_level = percentage; |
---|
542 | _candidate->false_IDs = __BITS_IN_MAP - trues; |
---|
543 | } else { |
---|
544 | printf( "PS_filling_level() : bitmap (%lu) now has %lu trues and %lu falses -- %.5f%% filled\n", __BITS_IN_MAP, trues, __BITS_IN_MAP-trues, percentage ); |
---|
545 | } |
---|
546 | return percentage; |
---|
547 | } |
---|
548 | |
---|
549 | void PS_GNUPlot( const char *_out_prefix, const long _iteration, const IDSet &_path, const ID2IDSet &_noMatches ) { |
---|
550 | // generate data- and commandfiles for GNUPlot to display __MAP and its count_trues_per_id |
---|
551 | |
---|
552 | char *buffer = (char *)malloc( 4096 ); |
---|
553 | // open data file |
---|
554 | sprintf( buffer, "%s.%06li", _out_prefix, _iteration ); |
---|
555 | char *data_name = strdup( buffer ); |
---|
556 | PS_FileBuffer *file = new PS_FileBuffer( data_name, PS_FileBuffer::WRITEONLY ); |
---|
557 | // output data |
---|
558 | long size = sprintf( buffer, "# CANDIDATE #%li path (%zu)\n", _iteration, _path.size() ); |
---|
559 | file->put( buffer, size ); |
---|
560 | for ( IDSetCIter i = _path.begin(); |
---|
561 | i != _path.end(); |
---|
562 | ++i ) { |
---|
563 | size = sprintf( buffer, "# %i\n", *i ); |
---|
564 | file->put( buffer, size ); |
---|
565 | } |
---|
566 | size = sprintf( buffer, "#noMatches (%zu)\n", _noMatches.size() ); |
---|
567 | file->put( buffer, size ); |
---|
568 | for ( ID2IDSetCIter p = _noMatches.begin(); |
---|
569 | p != _noMatches.end(); |
---|
570 | ++p ) { |
---|
571 | size = sprintf( buffer, "%i %i\n", p->first, p->second ); |
---|
572 | file->put( buffer, size ); |
---|
573 | } |
---|
574 | size = sprintf( buffer, "\n\n" ); |
---|
575 | file->put( buffer, size ); |
---|
576 | sprintf( buffer, "Bitmap after %li. candidate", _iteration ); |
---|
577 | char *title = strdup( buffer ); |
---|
578 | __MAP->printGNUplot( title, buffer, file ); |
---|
579 | // open gnuplot command file |
---|
580 | sprintf( buffer, "%s.%06li.gnuplot", _out_prefix, _iteration ); |
---|
581 | file->reinit( buffer, PS_FileBuffer::WRITEONLY ); |
---|
582 | // output gnuplot commands |
---|
583 | size = sprintf( buffer, "set terminal png color\nset output '%06li.bitmap.png\n", _iteration ); |
---|
584 | file->put( buffer, size ); |
---|
585 | size = sprintf( buffer, "set yrange [%i:%i] reverse\nset xrange [%i:%i]\n", __MIN_ID,__MAX_ID,__MIN_ID,__MAX_ID ); |
---|
586 | file->put( buffer, size ); |
---|
587 | size = sprintf( buffer, "set size square\nset title '%li. iteration'\nset pointsize 0.5\n", _iteration ); |
---|
588 | file->put( buffer, size ); |
---|
589 | size = sprintf( buffer, "plot '%s' index 1 title 'match ()' with dots 2,'%s' index 0 title 'no match (30)' with points 1\n", data_name, data_name ); |
---|
590 | file->put( buffer, size ); |
---|
591 | size = sprintf( buffer, "set terminal png color\nset output '%06li.counters.png\n", _iteration ); |
---|
592 | file->put( buffer, size ); |
---|
593 | size = sprintf( buffer, "set yrange [] noreverse\nset size nosquare\n" ); |
---|
594 | file->put( buffer, size ); |
---|
595 | size = sprintf( buffer, "plot '%s' index 2 title 'count/species' with impulses 2,'%s' index 3 title 'species/count' with points 1", data_name, data_name ); |
---|
596 | file->put( buffer, size ); |
---|
597 | |
---|
598 | delete file; |
---|
599 | free( title ); |
---|
600 | free( data_name ); |
---|
601 | free( buffer ); |
---|
602 | } |
---|
603 | |
---|
604 | PS_CandidatePtr PS_ascend( PS_CandidatePtr _last_candidate ) { |
---|
605 | // 'remove' _last_candidate from __MAP by applying its parent's |
---|
606 | // paths to a fresh __MAP |
---|
607 | |
---|
608 | // |
---|
609 | // make fresh __MAP |
---|
610 | // |
---|
611 | __MAP->copy( __PRESET_MAP ); |
---|
612 | // |
---|
613 | // apply paths of parent-candidates to __MAP |
---|
614 | // |
---|
615 | PS_CandidatePtr parent = _last_candidate->parent; |
---|
616 | while ((parent != 0) && (parent->path.size() > 0)) { |
---|
617 | PS_apply_path_to_bitmap( parent->path, true ); |
---|
618 | parent = parent->parent; |
---|
619 | } |
---|
620 | printf( "ASCEND " ); |
---|
621 | PS_filling_level(); |
---|
622 | // |
---|
623 | // return the parent of the given candidate |
---|
624 | // |
---|
625 | return _last_candidate->parent; |
---|
626 | } |
---|
627 | |
---|
628 | |
---|
629 | void PS_descend( PS_CandidatePtr _candidate_parent, const PS_NodePtr _root_node, unsigned long _depth, const float _filling_level ) { |
---|
630 | struct tms before; |
---|
631 | times( &before ); |
---|
632 | |
---|
633 | printf( "\nDESCEND ==================== depth (%lu / %lu) candidates (%lu / %lu -> %lu left) ====================\n", |
---|
634 | _depth, |
---|
635 | __MAX_DEPTH, |
---|
636 | __CANDIDATES_FINISHED, |
---|
637 | __CANDIDATES_TODO, |
---|
638 | __CANDIDATES_TODO-__CANDIDATES_FINISHED ); fflush( stdout ); |
---|
639 | printf( "DESCEND PATH : (%s)\n\n", __PATH_IN_CANDIDATES ); |
---|
640 | |
---|
641 | // |
---|
642 | // calc source- and target-set of IDs |
---|
643 | // |
---|
644 | PS_calc_next_speciesid_sets(); |
---|
645 | printf( "\nDESCEND ---------- calculated next speciesid-sets ----------\n\n" ); fflush( stdout ); |
---|
646 | |
---|
647 | // |
---|
648 | // search for candidates to improve filling level of __MAP using the source- and target-set of IDs |
---|
649 | // max. 3 rounds |
---|
650 | // |
---|
651 | int round = 0; |
---|
652 | for (; (round < 3) && (_candidate_parent->children.size() == 0); ++round) { |
---|
653 | PS_find_probes( _root_node, round, _candidate_parent, _filling_level ); |
---|
654 | } |
---|
655 | printf( "\nDESCEND ---------- searched probe for speciesid-sets [rounds : %i] candidates (%lu / %lu -> %lu left) ----------\n\n", |
---|
656 | round, |
---|
657 | __CANDIDATES_FINISHED, |
---|
658 | __CANDIDATES_TODO, |
---|
659 | __CANDIDATES_TODO-__CANDIDATES_FINISHED ); fflush( stdout ); |
---|
660 | |
---|
661 | // |
---|
662 | // descend down each (of the max 3) candidate(s) |
---|
663 | // |
---|
664 | char count = '0'+_candidate_parent->children.size(); |
---|
665 | for ( PS_CandidateByGainMapRIter next_candidate_it = _candidate_parent->children.rbegin(); |
---|
666 | next_candidate_it != _candidate_parent->children.rend(); |
---|
667 | ++next_candidate_it, --count ) { |
---|
668 | PS_CandidatePtr next_candidate = &(*next_candidate_it->second); |
---|
669 | ++__CANDIDATES_FINISHED; |
---|
670 | // |
---|
671 | // apply candidate to __MAP |
---|
672 | // |
---|
673 | printf( "[%p] ", next_candidate ); |
---|
674 | PS_apply_path_to_bitmap( next_candidate->path ); |
---|
675 | printf( "[%p] ", next_candidate ); |
---|
676 | PS_filling_level( next_candidate ); |
---|
677 | next_candidate->depth = _depth+1; |
---|
678 | next_candidate->print( 0,false,false ); |
---|
679 | // |
---|
680 | // step down |
---|
681 | // |
---|
682 | if ((next_candidate->filling_level < 75.0) && (_depth+1 < __MAX_DEPTH)) { |
---|
683 | __PATH_IN_CANDIDATES[ _depth ] = count; |
---|
684 | __PATH_IN_CANDIDATES[ _depth+1 ] = '\x00'; |
---|
685 | PS_descend( next_candidate, _root_node, _depth+1, next_candidate->filling_level ); |
---|
686 | } |
---|
687 | // |
---|
688 | // remove candidate from __MAP |
---|
689 | // |
---|
690 | PS_ascend( next_candidate ); |
---|
691 | } |
---|
692 | |
---|
693 | printf( "\nDESCEND ~~~~~~~~~~~~~~~~~~~~ depth (%li) max depth (%li) candidates (%lu / %lu -> %lu left) ~~~~~~~~~~~~~~~~~~~~ ", |
---|
694 | _depth, |
---|
695 | __MAX_DEPTH, |
---|
696 | __CANDIDATES_FINISHED, |
---|
697 | __CANDIDATES_TODO, |
---|
698 | __CANDIDATES_TODO-__CANDIDATES_FINISHED ); |
---|
699 | PS_print_time_diff( &before ); |
---|
700 | printf( "\n" ); fflush( stdout ); |
---|
701 | } |
---|
702 | |
---|
703 | void PS_make_map_for_candidate( PS_CandidatePtr _candidate ) { |
---|
704 | // make __MAP for _candidate |
---|
705 | |
---|
706 | if (_candidate->map) return; // if candidate already has its map return |
---|
707 | _candidate->map = new PS_BitMap_Counted( false, __MAX_ID+1 ); |
---|
708 | _candidate->map->copy( __PRESET_MAP ); |
---|
709 | PS_apply_path_to_bitmap( _candidate->path, true, _candidate->map ); // apply _candidate's path |
---|
710 | PS_CandidatePtr parent = _candidate->parent; |
---|
711 | while ((parent != 0) && (parent->path.size() > 0)) { // apply parent's paths |
---|
712 | PS_apply_path_to_bitmap( parent->path, true, _candidate->map ); |
---|
713 | parent = parent->parent; |
---|
714 | } |
---|
715 | } |
---|
716 | |
---|
717 | // void PS_calc_next_speciesid_sets_for_candidate( PS_CandidatePtr _candidate ) { |
---|
718 | // make __MAP for _candidate and search for best source/target-sets |
---|
719 | // // |
---|
720 | // // 1. __MAP for _candidate |
---|
721 | // // |
---|
722 | // PS_make_map_for_candidate( _candidate ); |
---|
723 | // // |
---|
724 | // // 2. __SOURCE_ID_SET |
---|
725 | // // scan bitmap for species that need more matches |
---|
726 | // // |
---|
727 | // SpeciesID highest_count; |
---|
728 | // SpeciesID lowest_count; |
---|
729 | // SpeciesID count; |
---|
730 | |
---|
731 | // // first pass -- get lowest/highest count of trues |
---|
732 | // lowest_count = __SPECIES_COUNT; |
---|
733 | // highest_count = 0; |
---|
734 | // for ( SpeciesID id = __MIN_ID; |
---|
735 | // id <= __MAX_ID; |
---|
736 | // ++id) { |
---|
737 | // count = _candidate->map->getCountFor( id ); |
---|
738 | // if (count == __SPECIES_COUNT-__MIN_ID-1) continue; // i cannot improve species that can be differed from all others |
---|
739 | // if (count < lowest_count) lowest_count = count; |
---|
740 | // if (count > highest_count) highest_count = count; |
---|
741 | // } |
---|
742 | // //printf( "PS_calc_next_speciesid_sets_for_candidate() : SOURCE count 1's [%i..%i]\n", lowest_count, highest_count ); |
---|
743 | |
---|
744 | // // second pass -- get IDs where count is equal to lowest_count or highest_count |
---|
745 | // IDSet highest_count_src_ids; |
---|
746 | // IDSet lowest_count_src_ids; |
---|
747 | // for ( SpeciesID id = __MIN_ID; |
---|
748 | // id <= __MAX_ID; |
---|
749 | // ++id) { |
---|
750 | // count = _candidate->map->getCountFor( id ); |
---|
751 | // if (count == lowest_count) lowest_count_src_ids.insert( id ); |
---|
752 | // if (count == highest_count) highest_count_src_ids.insert( id ); |
---|
753 | // } |
---|
754 | // if (_candidate->source_set) { |
---|
755 | // _candidate->source_set->clear(); |
---|
756 | // _candidate->source_set->insert( lowest_count_src_ids.begin(), lowest_count_src_ids.end() ); |
---|
757 | // } else { |
---|
758 | // _candidate->source_set = new IDSet( lowest_count_src_ids ); |
---|
759 | // } |
---|
760 | // _candidate->source_set->insert( highest_count_src_ids.begin(), highest_count_src_ids.end() ); |
---|
761 | // //PS_print_set_ranges( " lowest_count_src_ids", lowest_count_src_ids ); |
---|
762 | // //PS_print_set_ranges( " highest_count_src_ids", highest_count_src_ids ); |
---|
763 | // if (*(_candidate->source_set->begin()) < __MIN_SETS_ID) __MIN_SETS_ID = *(_candidate->source_set->begin()); |
---|
764 | // if (*(_candidate->source_set->rbegin()) > __MAX_SETS_ID) __MAX_SETS_ID = *(_candidate->source_set->rbegin()); |
---|
765 | |
---|
766 | // // |
---|
767 | // // 3. __TARGET_ID_SET |
---|
768 | // // scan bitmap for species IDs that need to be distinguished from MOST species in lowest_count_src_ids |
---|
769 | // // |
---|
770 | // ID2IDMap count_falses_per_id; |
---|
771 | |
---|
772 | // // first -- get the IDs that need differentiation from __SOURCE_ID_SET |
---|
773 | // for ( IDSetCIter source_id = lowest_count_src_ids.begin(); |
---|
774 | // source_id != lowest_count_src_ids.end(); |
---|
775 | // ++source_id ) { |
---|
776 | // // get 'next_target_set' |
---|
777 | // _candidate->map->getFalseIndicesFor( *source_id, __TARGET_ID_SET ); |
---|
778 | // // count falses per SpeciesID |
---|
779 | // for ( PS_BitSet::IndexSet::iterator target_id = __TARGET_ID_SET.begin(); |
---|
780 | // target_id != __TARGET_ID_SET.end(); |
---|
781 | // ++target_id) { |
---|
782 | // if ((*target_id < __MIN_ID) || (*target_id > __MAX_ID)) continue; // skip ID's that are outside DB-IDs-range (like zero if __MIN_ID is one) |
---|
783 | // if (*target_id != *source_id) ++count_falses_per_id[ *target_id ]; |
---|
784 | // } |
---|
785 | // } |
---|
786 | // //printf( "\n" ); |
---|
787 | // //PS_print_map_ranges( "PS_calc_next_speciesid_sets_for_candidate() : count_falses_per_id", count_falses_per_id, false ); |
---|
788 | |
---|
789 | // // second -- get highest count of falses and calc treshold |
---|
790 | // lowest_count = __SPECIES_COUNT; |
---|
791 | // highest_count = 0; |
---|
792 | // for ( ID2IDMapCIter count_per_id = count_falses_per_id.begin(); |
---|
793 | // count_per_id != count_falses_per_id.end(); |
---|
794 | // ++count_per_id ) { |
---|
795 | // if (count_per_id->second > highest_count) highest_count = count_per_id->second; |
---|
796 | // if (count_per_id->second < lowest_count) lowest_count = count_per_id->second; |
---|
797 | // } |
---|
798 | // //printf( "PS_calc_next_speciesid_sets_for_candidate() : TARGET count 0's [%i..%i]\n", lowest_count, highest_count ); |
---|
799 | |
---|
800 | // // third -- put all IDs in __TARGET_ID_SET that are needed most by species from lowest_count_src_ids |
---|
801 | // if (_candidate->target_set) { |
---|
802 | // _candidate->target_set->clear(); |
---|
803 | // } else { |
---|
804 | // _candidate->target_set = new IDSet(); |
---|
805 | // } |
---|
806 | // __TARGET_ID_SET.clear(); |
---|
807 | // for ( ID2IDMapCIter count_per_id = count_falses_per_id.begin(); |
---|
808 | // count_per_id != count_falses_per_id.end(); |
---|
809 | // ++count_per_id ) { |
---|
810 | // if (count_per_id->second == highest_count) __TARGET_ID_SET.insert( count_per_id->first ); |
---|
811 | // } |
---|
812 | // //PS_print_set_ranges( " target_set (by lowest count of trues) ", __TARGET_ID_SET ); |
---|
813 | // _candidate->target_set->insert( __TARGET_ID_SET.begin(), __TARGET_ID_SET.end() ); |
---|
814 | |
---|
815 | // // fourth -- put all IDs in __TARGET_ID_SET that are needed by species from highest_count_src_ids |
---|
816 | // PS_BitSet::IndexSet next_target_ids; |
---|
817 | // __TARGET_ID_SET.clear(); |
---|
818 | // for ( IDSetCIter source_id = highest_count_src_ids.begin(); |
---|
819 | // source_id != highest_count_src_ids.end(); |
---|
820 | // ++source_id ) { |
---|
821 | // // get next target-IDs |
---|
822 | // _candidate->map->getFalseIndicesFor( *source_id, next_target_ids ); |
---|
823 | // // 'append' target-IDs |
---|
824 | // for ( PS_BitSet::IndexSet::iterator target_id = next_target_ids.begin(); |
---|
825 | // target_id != next_target_ids.end(); |
---|
826 | // ++target_id) { |
---|
827 | // if ((*target_id < __MIN_ID) || (*target_id > __MAX_ID)) continue; // skip ID's that are outside DB-IDs-range (like zero if __MIN_ID is one) |
---|
828 | // if (*target_id != *source_id) __TARGET_ID_SET.insert( *target_id ); |
---|
829 | // } |
---|
830 | // } |
---|
831 | // //PS_print_set_ranges( " target_set (by highest count of trues)", __TARGET_ID_SET ); |
---|
832 | // _candidate->target_set->insert( __TARGET_ID_SET.begin(), __TARGET_ID_SET.end() ); |
---|
833 | |
---|
834 | // if (*(__TARGET_ID_SET.begin()) < __MIN_SETS_ID) __MIN_SETS_ID = *(__TARGET_ID_SET.begin()); |
---|
835 | // if (*(__TARGET_ID_SET.rbegin()) > __MAX_SETS_ID) __MAX_SETS_ID = *(__TARGET_ID_SET.rbegin()); |
---|
836 | // //printf( "\n" ); fflush( stdout ); |
---|
837 | // } |
---|
838 | |
---|
839 | |
---|
840 | void PS_get_leaf_candidates( PS_CandidatePtr _candidate_parent, |
---|
841 | PS_CandidateSet &_leaf_candidates, |
---|
842 | const bool _ignore_passes_left = false ) { |
---|
843 | |
---|
844 | for ( PS_CandidateByGainMapIter next_candidate = _candidate_parent->children.begin(); |
---|
845 | next_candidate != _candidate_parent->children.end(); |
---|
846 | ++next_candidate ) { |
---|
847 | |
---|
848 | if ((next_candidate->second->children.size() == 0) && |
---|
849 | ((next_candidate->second->passes_left > 0) || _ignore_passes_left)){ |
---|
850 | _leaf_candidates.insert( next_candidate->second ); |
---|
851 | } |
---|
852 | PS_get_leaf_candidates( &(*next_candidate->second), _leaf_candidates, _ignore_passes_left ); |
---|
853 | } |
---|
854 | } |
---|
855 | |
---|
856 | |
---|
857 | // bool PS_test_candidate_sets_on_path( PS_CandidatePtr _candidate ) { |
---|
858 | // int round = PS_Candidate::MAX_PASSES - _candidate->passes_left; |
---|
859 | // __SOURCE_MIN_MATCH_COUNT = (_candidate->source_set->size() * (__MIN_PERCENTAGE_SET_MATCH - (round * 5))) / 100.0; |
---|
860 | // __SOURCE_MAX_MATCH_COUNT = (_candidate->source_set->size() * (__MAX_PERCENTAGE_SET_MATCH + (round * 5))) / 100.0; |
---|
861 | // __TARGET_MIN_MATCH_COUNT = (_candidate->target_set->size() * (__MIN_PERCENTAGE_SET_MATCH - (round * 5))) / 100.0; |
---|
862 | // __TARGET_MAX_MATCH_COUNT = (_candidate->target_set->size() * (__MAX_PERCENTAGE_SET_MATCH + (round * 5))) / 100.0; |
---|
863 | // long count_matched_source = 0; |
---|
864 | // long count_matched_target = 0; |
---|
865 | // SpeciesID path_id; |
---|
866 | // IDSetCIter path_end = __PATH.end(); |
---|
867 | // IDSetCIter path = __PATH.begin(); |
---|
868 | // IDSetCIter source_end = _candidate->source_set->end(); |
---|
869 | // IDSetCIter source = _candidate->source_set->begin(); |
---|
870 | // IDSetCIter target_end = _candidate->target_set->end(); |
---|
871 | // IDSetCIter target = _candidate->target_set->begin(); |
---|
872 | |
---|
873 | // while (path != path_end) { |
---|
874 | // path_id = *path; |
---|
875 | // while ((*target < path_id) && (target != target_end)) { |
---|
876 | // ++target; |
---|
877 | // } |
---|
878 | // if ((target != target_end) && (*target == path_id)) |
---|
879 | // ++count_matched_target; |
---|
880 | // while ((*source < path_id) && (source != source_end)) { |
---|
881 | // ++source; |
---|
882 | // } |
---|
883 | // if ((source != source_end) && (*source == path_id)) |
---|
884 | // ++count_matched_source; |
---|
885 | // ++path; |
---|
886 | // } |
---|
887 | |
---|
888 | // if ((count_matched_source > __SOURCE_MIN_MATCH_COUNT) && |
---|
889 | // (count_matched_source < __SOURCE_MAX_MATCH_COUNT) && |
---|
890 | // (count_matched_target > __TARGET_MIN_MATCH_COUNT) && |
---|
891 | // (count_matched_target < __TARGET_MAX_MATCH_COUNT)) { |
---|
892 | // return true; |
---|
893 | // } |
---|
894 | // return false; |
---|
895 | // } |
---|
896 | |
---|
897 | void PS_get_next_candidates_descend( PS_NodePtr _ps_node, PS_CandidateSet &_leaf_candidates ) { |
---|
898 | // scan PS_node-tree for next candidates for each of _leaf_candidates |
---|
899 | |
---|
900 | SpeciesID id = _ps_node->getNum(); |
---|
901 | bool has_probes = _ps_node->hasProbes(); |
---|
902 | |
---|
903 | // |
---|
904 | // append ID to path |
---|
905 | // |
---|
906 | __PATH.insert( id ); |
---|
907 | |
---|
908 | // |
---|
909 | // dont look at path until ID is greater than lowest ID in the sets of IDs |
---|
910 | // also dont use a node if its already used as candidate |
---|
911 | // |
---|
912 | if ((id >= __MIN_SETS_ID) && has_probes) { |
---|
913 | unsigned long total_gain_of_node = 0; |
---|
914 | unsigned long total_tests_per_node = 0; |
---|
915 | ++__PROBES_COUNTER; |
---|
916 | // iterate over _leaf_candidates |
---|
917 | for ( PS_CandidateSetIter candidate_iter = _leaf_candidates.begin(); |
---|
918 | candidate_iter != _leaf_candidates.end(); |
---|
919 | ++candidate_iter ) { |
---|
920 | PS_CandidateSPtr candidate = *candidate_iter; |
---|
921 | |
---|
922 | // next leaf-candidate if the probe was already used for current candidate |
---|
923 | if (candidate->alreadyUsedNode( _ps_node )) continue; |
---|
924 | |
---|
925 | ++__CANDIDATES_COUNTER; // possible candidates |
---|
926 | if (__VERBOSE) printf( "%8lup %8lur %8luc %8lug %8luu\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b", |
---|
927 | __PROBES_COUNTER, |
---|
928 | __PROBES_REMOVED, |
---|
929 | __CANDIDATES_COUNTER, |
---|
930 | __CANDIDATES_TODO, |
---|
931 | __CANDIDATES_FINISHED ); fflush( stdout ); |
---|
932 | |
---|
933 | // next leaf-candidate if __PATH doesnt fulfill matching criteria |
---|
934 | unsigned long matches = candidate->matchPathOnOneFalseIDs( __PATH ); |
---|
935 | if (matches < candidate->one_false_IDs_matches) continue; |
---|
936 | |
---|
937 | ++__CANDIDATES_TODO; // good candidates |
---|
938 | if (__VERBOSE) printf( "%8lup %8lur %8luc %8lug %8luu\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b", |
---|
939 | __PROBES_COUNTER, |
---|
940 | __PROBES_REMOVED, |
---|
941 | __CANDIDATES_COUNTER, |
---|
942 | __CANDIDATES_TODO, |
---|
943 | __CANDIDATES_FINISHED ); fflush( stdout ); |
---|
944 | |
---|
945 | // test node on candidate's bitmap |
---|
946 | float filling_level; |
---|
947 | ++total_tests_per_node; |
---|
948 | unsigned long gain = PS_test_candidate_on_bitmap( &filling_level, candidate->map ); |
---|
949 | total_gain_of_node += gain; |
---|
950 | if (candidate->updateBestChild( gain, matches, filling_level, _ps_node, __PATH )) { |
---|
951 | ++__CANDIDATES_FINISHED; // used candiates |
---|
952 | if (__VERBOSE) printf( "%8lup %8lur %8luc %8lug %8luu\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b", |
---|
953 | __PROBES_COUNTER, |
---|
954 | __PROBES_REMOVED, |
---|
955 | __CANDIDATES_COUNTER, |
---|
956 | __CANDIDATES_TODO, |
---|
957 | __CANDIDATES_FINISHED ); fflush( stdout ); |
---|
958 | } |
---|
959 | } |
---|
960 | if ((total_tests_per_node == _leaf_candidates.size()) && |
---|
961 | (total_gain_of_node == 0)) { |
---|
962 | ++__PROBES_REMOVED; |
---|
963 | if (__VERBOSE) printf( "%8lup %8lur %8luc %8lug %8luu\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b", |
---|
964 | __PROBES_COUNTER, |
---|
965 | __PROBES_REMOVED, |
---|
966 | __CANDIDATES_COUNTER, |
---|
967 | __CANDIDATES_TODO, |
---|
968 | __CANDIDATES_FINISHED ); fflush( stdout ); |
---|
969 | _ps_node->removeProbes(); |
---|
970 | } |
---|
971 | } |
---|
972 | |
---|
973 | // |
---|
974 | // step down the children if either ID is lower than highest |
---|
975 | // ID in the set of ID-pairs or the node has no probes |
---|
976 | // |
---|
977 | if ((id < __MAX_SETS_ID) || (! has_probes)) { |
---|
978 | for ( PS_NodeMapConstIterator i = _ps_node->getChildrenBegin(); |
---|
979 | i != _ps_node->getChildrenEnd(); |
---|
980 | ++i) { |
---|
981 | PS_get_next_candidates_descend( i->second, _leaf_candidates ); |
---|
982 | } |
---|
983 | } |
---|
984 | |
---|
985 | // |
---|
986 | // remove ID from path |
---|
987 | // |
---|
988 | __PATH.erase( id ); |
---|
989 | } |
---|
990 | |
---|
991 | |
---|
992 | void PS_get_next_candidates( const PS_NodePtr _root_node, |
---|
993 | PS_CandidateSet &_leaf_candidates ) { |
---|
994 | struct tms before; |
---|
995 | times( &before ); |
---|
996 | // first calc source/target/false_IDs sets |
---|
997 | printf( "PS_get_next_candidates() : initializing %zu candidates..\n", _leaf_candidates.size() ); fflush( stdout ); |
---|
998 | __PROBES_COUNTER = 0; |
---|
999 | __PROBES_REMOVED = 0; |
---|
1000 | __CANDIDATES_COUNTER = 0; |
---|
1001 | __CANDIDATES_TODO = 0; |
---|
1002 | __CANDIDATES_FINISHED = 0; |
---|
1003 | __MIN_SETS_ID = __MAX_ID; |
---|
1004 | __MAX_SETS_ID = __MIN_ID; |
---|
1005 | for ( PS_CandidateSetIter iter = _leaf_candidates.begin(); |
---|
1006 | iter != _leaf_candidates.end(); |
---|
1007 | ++iter ) { |
---|
1008 | PS_CandidateSPtr candidate = *iter; |
---|
1009 | if (!candidate->map) { // if candidate has no map yet |
---|
1010 | candidate->getParentMap(); // try to get its parent's map |
---|
1011 | if (candidate->map) { // if parent had a map (if not a new map is created in PS_calc_next_speciesid_sets_for_candidate |
---|
1012 | PS_apply_path_to_bitmap( candidate->path, true, candidate->map ); // apply candidate's path |
---|
1013 | } |
---|
1014 | } |
---|
1015 | PS_make_map_for_candidate( &(*candidate) ); |
---|
1016 | candidate->initFalseIDs( __MIN_ID, __MAX_ID, __MIN_SETS_ID, __MAX_SETS_ID ); |
---|
1017 | //candidate->print(); |
---|
1018 | } |
---|
1019 | // scan tree |
---|
1020 | printf( "PS_get_next_candidates() : " ); fflush( stdout ); |
---|
1021 | for ( PS_NodeMapConstIterator node_iter = _root_node->getChildrenBegin(); |
---|
1022 | (node_iter != _root_node->getChildrenEnd()) && (node_iter->first < __MAX_SETS_ID); |
---|
1023 | ++node_iter ) { |
---|
1024 | __PATH.clear(); |
---|
1025 | PS_get_next_candidates_descend( node_iter->second, _leaf_candidates ); |
---|
1026 | } |
---|
1027 | printf( "looked at probes (%lu) -> removed probes (%lu) possible candidates (%lu) -> good candidates (%lu) -> used candidates (%lu)\nPS_get_next_candidates() : ", |
---|
1028 | __PROBES_COUNTER, |
---|
1029 | __PROBES_REMOVED, |
---|
1030 | __CANDIDATES_COUNTER, |
---|
1031 | __CANDIDATES_TODO, |
---|
1032 | __CANDIDATES_FINISHED ); fflush( stdout ); |
---|
1033 | PS_print_time_diff( &before ); |
---|
1034 | |
---|
1035 | // 'descend' candidates |
---|
1036 | for ( PS_CandidateSetIter iter = _leaf_candidates.begin(); |
---|
1037 | iter != _leaf_candidates.end(); |
---|
1038 | ++iter ) { |
---|
1039 | PS_CandidateSPtr candidate = *iter; |
---|
1040 | candidate->print(); |
---|
1041 | candidate->decreasePasses(); |
---|
1042 | } |
---|
1043 | |
---|
1044 | _leaf_candidates.clear(); |
---|
1045 | PS_get_leaf_candidates( __CANDIDATES_ROOT, _leaf_candidates ); |
---|
1046 | } |
---|
1047 | |
---|
1048 | // ==================================================== |
---|
1049 | // ==================================================== |
---|
1050 | int main( int argc, |
---|
1051 | char *argv[] ) { |
---|
1052 | // |
---|
1053 | // check arguments |
---|
1054 | // |
---|
1055 | if (argc < 5) { |
---|
1056 | printf( "Missing argument\n Usage %s <database name> <result filename> <[-]candidates filename> <final candidates filename> [--verbose] [result filename prefix for output files]\n", argv[0] ); |
---|
1057 | exit( 1 ); |
---|
1058 | } |
---|
1059 | |
---|
1060 | const char *input_DB_name = argv[1]; |
---|
1061 | const char *result_in_filename = argv[2]; |
---|
1062 | const char *candidates_filename = argv[3]; |
---|
1063 | const char *final_candidates_filename = argv[4]; |
---|
1064 | const char *result_out_prefix = (argc > 5) ? argv[5] : 0; |
---|
1065 | if (argc > 5) { |
---|
1066 | if (strcmp(result_out_prefix,"--verbose") == 0) { |
---|
1067 | __VERBOSE = true; |
---|
1068 | result_out_prefix = (argc > 6) ? argv[6] : 0; |
---|
1069 | } |
---|
1070 | } |
---|
1071 | // |
---|
1072 | // open probe-set-database |
---|
1073 | // |
---|
1074 | printf( "Opening probe-set-database '%s'..\n", input_DB_name ); |
---|
1075 | PS_Database *db = new PS_Database( input_DB_name, PS_Database::READONLY ); |
---|
1076 | db->load(); |
---|
1077 | __MAX_ID = db->getMaxID(); |
---|
1078 | __MIN_ID = db->getMinID(); |
---|
1079 | __SPECIES_COUNT = db->getSpeciesCount(); |
---|
1080 | printf( "min ID (%i) max ID (%i) count of species (%i)\n", __MIN_ID, __MAX_ID, __SPECIES_COUNT ); |
---|
1081 | printf( "..loaded database (enter to continue)\n" ); fflush( stdout ); |
---|
1082 | |
---|
1083 | // |
---|
1084 | // open result file for preset bitmap |
---|
1085 | // |
---|
1086 | printf( "Opening result file %s..\n", result_in_filename ); |
---|
1087 | PS_FileBuffer *result_file = new PS_FileBuffer( result_in_filename, PS_FileBuffer::READONLY ); |
---|
1088 | long size; |
---|
1089 | ID2IDSet noMatches; |
---|
1090 | SpeciesID id1,id2; |
---|
1091 | printf( "reading no matches : " ); |
---|
1092 | result_file->get_long( size ); |
---|
1093 | printf( "(%li)\n", size ); fflush( stdout ); |
---|
1094 | for ( long i=0; |
---|
1095 | i < size; |
---|
1096 | ++i ) { |
---|
1097 | result_file->get_int( id1 ); |
---|
1098 | result_file->get_int( id2 ); |
---|
1099 | printf( " %i,%i", id1, id2 ); |
---|
1100 | if (id1 < id2) { |
---|
1101 | noMatches.insert( ID2IDPair(id1,id2) ); |
---|
1102 | } else { |
---|
1103 | noMatches.insert( ID2IDPair(id2,id1) ); |
---|
1104 | } |
---|
1105 | } |
---|
1106 | printf( "\nreading one matches : " ); |
---|
1107 | result_file->get_long( size ); |
---|
1108 | printf( "(%li)\n", size ); fflush( stdout ); |
---|
1109 | long path_length; |
---|
1110 | SpeciesID path_id; |
---|
1111 | IDSet path; |
---|
1112 | IDID2IDSetMap oneMatchesMap; |
---|
1113 | for ( long i=0; |
---|
1114 | i < size; |
---|
1115 | ++i) { |
---|
1116 | path.clear(); |
---|
1117 | result_file->get_int( id1 ); |
---|
1118 | result_file->get_int( id2 ); |
---|
1119 | result_file->get_long( path_length ); |
---|
1120 | printf( "%i,%i path(%li)", id1, id2, path_length ); |
---|
1121 | while (path_length-- > 0) { |
---|
1122 | result_file->get_int( path_id ); |
---|
1123 | printf( " %i", path_id ); |
---|
1124 | path.insert( path_id ); |
---|
1125 | } |
---|
1126 | printf( "\n" ); |
---|
1127 | oneMatchesMap[ ID2IDPair(id1,id2) ] = path; |
---|
1128 | } |
---|
1129 | printf( "loading preset bitmap..\n" ); fflush( stdout ); |
---|
1130 | __BITS_IN_MAP = ((__MAX_ID+1)*__MAX_ID)/2 + __MAX_ID+1; |
---|
1131 | __MAP = new PS_BitMap_Counted( result_file ); |
---|
1132 | __PRESET_MAP = new PS_BitMap_Counted( false, __MAX_ID+1 ); |
---|
1133 | for (id1 = 0; id1 < __MIN_ID; ++id1 ) { |
---|
1134 | for (id2 = 0; id2 <= __MAX_ID; ++id2 ) { |
---|
1135 | if (id1 > id2) { |
---|
1136 | __MAP->setTrue( id1,id2 ); |
---|
1137 | } else { |
---|
1138 | __MAP->setTrue( id2,id1 ); |
---|
1139 | } |
---|
1140 | } |
---|
1141 | } |
---|
1142 | for ( SpeciesID id = 0; id <= __MAX_ID; ++id ) { |
---|
1143 | __MAP->setTrue( id,id ); |
---|
1144 | } |
---|
1145 | __MAP->recalcCounters(); |
---|
1146 | __PRESET_MAP->copy( __MAP ); |
---|
1147 | printf( "..loaded result file (enter to continue)\n" ); |
---|
1148 | printf( "cleaning up... result file\n" ); fflush( stdout ); |
---|
1149 | delete result_file; |
---|
1150 | |
---|
1151 | // |
---|
1152 | // create or read candidates |
---|
1153 | // |
---|
1154 | __CANDIDATES_ROOT = new PS_Candidate( 0.0 ); |
---|
1155 | PS_FileBuffer *candidates_file; |
---|
1156 | struct tms before; |
---|
1157 | if (candidates_filename[0] != '-') { |
---|
1158 | printf( "searching candidates..\n" ); |
---|
1159 | // |
---|
1160 | // recursively build a tree of candidates |
---|
1161 | // |
---|
1162 | __MAX_DEPTH = 0; |
---|
1163 | for ( long species_count = __SPECIES_COUNT; species_count > 0; species_count >>= 1 ) { |
---|
1164 | ++__MAX_DEPTH; |
---|
1165 | } |
---|
1166 | __MAX_DEPTH = (__MAX_DEPTH * 3) >> 1; |
---|
1167 | __PATH_IN_CANDIDATES = (char *)calloc( __MAX_DEPTH+1, sizeof(char) ); |
---|
1168 | __CANDIDATES_TODO = 0; |
---|
1169 | __CANDIDATES_FINISHED = 0; |
---|
1170 | times( &before ); |
---|
1171 | PS_descend( __CANDIDATES_ROOT, db->getConstRootNode(), 0, 0.0 ); |
---|
1172 | printf( "PS_descend : total " ); |
---|
1173 | PS_print_time_diff( &before ); |
---|
1174 | |
---|
1175 | // |
---|
1176 | // save candidates |
---|
1177 | // |
---|
1178 | printf( "saving candidates to %s..\n", candidates_filename ); |
---|
1179 | candidates_file = new PS_FileBuffer( candidates_filename, PS_FileBuffer::WRITEONLY ); |
---|
1180 | __CANDIDATES_ROOT->false_IDs = __BITS_IN_MAP; |
---|
1181 | __CANDIDATES_ROOT->save( candidates_file, __BITS_IN_MAP ); |
---|
1182 | } else { |
---|
1183 | printf( "loading candidates..\n" ); |
---|
1184 | candidates_file = new PS_FileBuffer( candidates_filename+1, PS_FileBuffer::READONLY ); |
---|
1185 | __CANDIDATES_ROOT->load( candidates_file, __BITS_IN_MAP, db->getConstRootNode() ); |
---|
1186 | printf( "..loaded candidates file (enter to continue)\n" ); |
---|
1187 | } |
---|
1188 | printf( "cleaning up... candidates file\n" ); fflush( stdout ); |
---|
1189 | delete candidates_file; |
---|
1190 | |
---|
1191 | // |
---|
1192 | // scan candidates-tree for leaf candidates |
---|
1193 | // |
---|
1194 | printf( "CANDIDATES :\n" ); |
---|
1195 | __CANDIDATES_ROOT->print(); |
---|
1196 | printf( "\nsearching leaf candidates.. " ); |
---|
1197 | PS_CandidateSet leaf_candidates; |
---|
1198 | PS_get_leaf_candidates( __CANDIDATES_ROOT, leaf_candidates ); |
---|
1199 | printf( "%zu\n", leaf_candidates.size() ); |
---|
1200 | |
---|
1201 | // |
---|
1202 | // scan tree for next candidates (below the ones in leaf_candidates) |
---|
1203 | // |
---|
1204 | times( &before ); |
---|
1205 | long round = 0; |
---|
1206 | while ((leaf_candidates.size() > 0) && |
---|
1207 | (round < 200)) { |
---|
1208 | printf( "\nsearching next candidates [round #%li]..\n", ++round ); |
---|
1209 | PS_get_next_candidates( db->getConstRootNode(), leaf_candidates ); |
---|
1210 | |
---|
1211 | // printf( "\nCANDIDATES :\n" ); |
---|
1212 | // __CANDIDATES_ROOT->print(); |
---|
1213 | printf( "rounds %li total ", round ); |
---|
1214 | PS_print_time_diff( &before ); |
---|
1215 | // getchar(); |
---|
1216 | } |
---|
1217 | |
---|
1218 | printf( "\nFINAL CANDIDATES:\n" ); |
---|
1219 | __CANDIDATES_ROOT->print( 0,true ); |
---|
1220 | printf( "\nfinal leaf candidates.. (%zu)\n", leaf_candidates.size() ); |
---|
1221 | PS_get_leaf_candidates( __CANDIDATES_ROOT, leaf_candidates, true ); |
---|
1222 | for ( PS_CandidateSetIter c = leaf_candidates.begin(); |
---|
1223 | c != leaf_candidates.end(); |
---|
1224 | ++c ) { |
---|
1225 | (*(*c)).print(); |
---|
1226 | } |
---|
1227 | |
---|
1228 | // |
---|
1229 | // save final candidates |
---|
1230 | // |
---|
1231 | printf( "saving final candidates to %s..\n", final_candidates_filename ); |
---|
1232 | candidates_file = new PS_FileBuffer( final_candidates_filename, PS_FileBuffer::WRITEONLY ); |
---|
1233 | __CANDIDATES_ROOT->save( candidates_file, __BITS_IN_MAP ); |
---|
1234 | printf( "cleaning up... candidates file\n" ); fflush( stdout ); |
---|
1235 | delete candidates_file; |
---|
1236 | |
---|
1237 | // |
---|
1238 | // starting with the best candidate print the __MAP for each |
---|
1239 | // depth walking up to root of candidates-tree |
---|
1240 | // |
---|
1241 | if (result_out_prefix) { |
---|
1242 | // put __MAP in the state 'after applying best_candidate and its parents' |
---|
1243 | PS_CandidateSPtr best_candidate_smart = *leaf_candidates.begin(); |
---|
1244 | PS_CandidatePtr best_candidate = &(*best_candidate_smart); |
---|
1245 | PS_ascend( best_candidate ); |
---|
1246 | PS_apply_path_to_bitmap( best_candidate->path ); |
---|
1247 | while (best_candidate) { |
---|
1248 | PS_GNUPlot( result_out_prefix, __MAX_DEPTH--, best_candidate->path, noMatches ); |
---|
1249 | best_candidate = PS_ascend( best_candidate ); |
---|
1250 | } |
---|
1251 | } |
---|
1252 | |
---|
1253 | // |
---|
1254 | // clean up |
---|
1255 | // |
---|
1256 | printf( "cleaning up... candidates\n" ); fflush( stdout ); |
---|
1257 | delete __CANDIDATES_ROOT; |
---|
1258 | free( __PATH_IN_CANDIDATES ); |
---|
1259 | printf( "cleaning up... database\n" ); fflush( stdout ); |
---|
1260 | delete db; |
---|
1261 | printf( "cleaning up... bitmaps\n" ); fflush( stdout ); |
---|
1262 | delete __PRESET_MAP; |
---|
1263 | delete __MAP; |
---|
1264 | |
---|
1265 | return 0; |
---|
1266 | } |
---|