viewvc.cgi/PrimerMatch/filter_bitvec.cc

/**************************************************************************
 * This code is part of the supporting infrastructure for ATA Mapper. 
 * Copyright (C) 2002,2003,2004 Applera Corporation. All rights reserved.
 * Author: Nathan Edwards
 * 
 * This program is free software; you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation; either version 2 of the License, or
 * (at your option) any later version.
 * 
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 * 
 * You should have received (LICENSE.txt) a copy of the GNU General Public 
 * License along with this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
 *************************************************************************/


#include "filter_bitvec.h"
#include "primer_alignment.h"
// #include "sortedvector.t"

filter_bitvec::filter_bitvec(unsigned int k, char eos, 
                             bool wc, bool tn, bool id, bool dm) :
  num_patterns_(0)
{
  pm_ = new shift_and_inexact(k,eos,wc,tn,id,dm);
}

filter_bitvec::~filter_bitvec() {
  delete pm_;
}

unsigned int filter_bitvec::mismatches() const {
  return pm_->mismatches();
}

void filter_bitvec::mismatches(unsigned int k) {
  pm_->mismatches(k);
}

bool filter_bitvec::wildcards() const {
  return pm_->wildcards();
}

void filter_bitvec::wildcards(bool wc) {
  pm_->wildcards(wc);
}

bool filter_bitvec::wildcard_text_N() const {
  return pm_->wildcard_text_N();
}

void filter_bitvec::wildcard_text_N(bool tn) {
  pm_->wildcard_text_N(tn);
}

bool filter_bitvec::indels() const {
  return pm_->indels();
}

void filter_bitvec::indels(bool id) {
  pm_->indels(id);
}

bool filter_bitvec::dna_mut() const {
  return pm_->dna_mut();
}

void filter_bitvec::dna_mut(bool dm) {
  pm_->dna_mut(dm);
}

char filter_bitvec::eos_char() const {
  return pm_->eos_char();
}

void filter_bitvec::eos_char(char c) {
  pm_->eos_char(c);
}

long unsigned int 
filter_bitvec::add_pattern(std::string const & pat, unsigned long id,
                          int esb, int eeb) {
  add_pattern_(pat,id,esb,eeb);
  num_patterns_++;
  return id;
}

bool 
filter_bitvec::find_patterns(CharacterProducer & cp, 
                             pattern_hit_vector & phs,
                             long unsigned minka) {
  // checkpoint;

  // the eos_char we store in the shift_and_inexact is normalized, so
  // we much unnormalize it before passing it on to the
  // editdist_alignment class.
  editdist_alignment pa(0,0,mismatches(),cp.ch(eos_char()),
                        wildcards(),wildcard_text_N(),
                        indels(),dna_mut(),0,0,true);
  pattern_hit_vector::iterator it,it1,it2;
  l.reserve(minka*2);
  bool more;
  while ((more=pm_->find_patterns(cp,l,minka))||!l.empty()) {
    // checkpoint;
    FILE_POSITION_TYPE oldcharspos;
    oldcharspos = cp.pos();
    l.normalize();
    // checkpoint;
    it = l.begin();
    while (it != l.end()) {
      // checkpoint;
      FILE_POSITION_TYPE firstpos = it->key();
      if (firstpos > 0) {
        long unsigned int pid = it->value()->id();
        FILE_POSITION_TYPE pos = firstpos;
        // checkpoint;
        // cerr << pid << " " << firstpos << endl;
        tinylist<pattern_hit_vector::iterator> adj;
        adj.push_front(it);
        it1 = it+1;
        while (it1 != l.end() && it1->key() <= pos+2*mismatches()+1) {
          // checkpoint;
          if (it1->value()->id() == pid) {
            // checkpoint;
            // cerr << it1->value()->id() << " " << it1->key() << endl;
            pos = it1->key();
            adj.push_front(it1);
          }
          ++it1;
          // checkpoint;
        }
        // checkpoint;
        if (oldcharspos < pos+2*mismatches()+1 && more) {
          // end of returned hit condition...
          // checkpoint;
          break;
        } else {
          // checkpoint;
          // cerr << pid << " " << firstpos << " " << pos << endl;
          pattern_list::const_iterator plit = plit_[pid];
          pa.reset();
          pa.poslb(firstpos);
          pa.posub(pos);
          pa.exact_start_bases(plit->exact_start_bases());
          pa.exact_end_bases(plit->exact_end_bases());
          // cerr << plit->pattern() << endl;
          // checkpoint;
          if (pa.align(cp,plit->pattern())) {
            // checkpoint;
            phs.push_back(pa.end(),plit);
          }
          tinylist<pattern_hit_vector::iterator>::iterator adjit;
          adjit = adj.begin();
          while (adjit != adj.end()) {
            (*adjit)->key() = 0;
            ++adjit;
          }
        }
      }
      ++it;
    }
    // Move everything with valid key to beginning...
    // int i,i1;
    it=l.begin();
    it1=l.begin();
    // i=0;
    // i1=0;
    long unsigned int newsize=0;
    while (it!=l.end()) {
      // cerr << i << " " << i1 << endl;
      // cerr << l.key(it) << " " << l.value(it)->id() << endl;
      if (it->key() != 0) {
        if (it != it1) {
          it1->key() = it->key();
          it1->value() = it->value();
        }
        ++newsize;
        ++it1;
        // i1++;
      }
      ++it;
      // i++;
    }
    // cerr << newsize << endl;
    l.resize(newsize);
    // checkpoint;
    // it=l.begin();
    // while (it!=l.end()) {
    // cerr << it->key() << " " << it->value()->id() << endl;
    // ++it;
    // }
    cp.pos(oldcharspos);
    report_progress(cp);
    if (phs.size() >= minka || 
        (more==false && phs.size() > 0)) return true;
  }
  return false;
}

void 
filter_bitvec::init(CharacterProducer & cp) {
  assert(pm_!=((void*)0));
  plit_.resize(num_patterns_+1);
  long unsigned int id;
  tinylist<pattern_list_element>::const_iterator it;
  for (it=patterns().begin();it!=patterns().end();++it) {
    id = pm_->add_pattern(it->pattern());
    plit_[id] = it;
  }
  pm_->init(cp);
}

void filter_bitvec::reset() {
  pm_->reset();
}


/*


      // checkpoint;
      std::list<pattern_hit*>::iterator it,it1,nextit;
      unsigned long int mindist=MAXINT;
      bool assigned_nextit=false;
      std::list<std::list<pattern_hit*>::iterator> adj;
      std::list<std::list<pattern_hit*>::iterator>::iterator it2;
      it = pas.begin();
      // cerr << "it: " << (*it)->pattern_id() << " " << (*it)->pos() << " " << ((pattern_hit_w_dist*)(*it))->editdist() << endl;
      long unsigned int pos;
      while (it!=pas.end()) {
        // checkpoint;
        it1=it;
        mindist=((pattern_hit_w_dist*)(*it1))->editdist();
        // cerr << "it1: " << (*it1)->pattern_id() << " " << (*it1)->pos() << " " << ((pattern_hit_w_dist*)(*it1))->editdist() << endl;
        // cerr << "mindist: " << mindist << endl;
        pos=(*it)->pos();
        // checkpoint;
        adj.clear();
        // checkpoint;
        assigned_nextit=false;
        while (it1 != pas.end() && 
               (*it1)->pos() <= pos+2*k_+1) {
          // checkpoint;
          if ((*it)->pattern_id() == (*it1)->pattern_id()) {
            if (mindist > ((pattern_hit_w_dist*)(*it1))->editdist()) {
              // cerr << "mindist: " << mindist << endl;
              mindist = ((pattern_hit_w_dist*)(*it1))->editdist();
            }
            adj.push_back(it1);
          } else {
            if (!assigned_nextit) {
              nextit=it1;
              assigned_nextit=true;
            }
          }
          // checkpoint;
          pos = (*it1)->pos();
          it1++;
          // if (it1 != pas.end()) {
          // cerr << "it1: " << (*it1)->pattern_id() << " " << (*it1)->pos() << " " << ((pattern_hit_w_dist*)(*it1))->editdist() << endl;
          // }
        }
        // checkpoint;
        // cerr << adj.size() << " " << mindist << endl;
        if (adj.size() > 1) {
          // checkpoint;
          it2  = adj.begin();
          bool assigned_keptit=false;
          std::list<pattern_hit*>::iterator keptit;
          while (it2 != adj.end()) {
            if (((pattern_hit_w_dist*)(**it2))->editdist() > mindist || 
                assigned_keptit) {
              // cerr << "erase *it2: " << (**it2)->pattern_id() << " " << (**it2)->pos() << " " << ((pattern_hit_w_dist*)(**it2))->editdist() << endl;
              delete **it2;
              pas.erase(*it2);
            } else {
              // cerr << "keep  *it2: " << (**it2)->pattern_id() << " " << (**it2)->pos() << " " << ((pattern_hit_w_dist*)(**it2))->editdist() << endl;       
              if (!assigned_keptit) {
                keptit=*it2;
                assigned_keptit=true;
              }
            }
            it2++;
          }
          if (assigned_nextit) {
            it = nextit;
          } else {
            it = keptit;
            it++;
          }
        } else {
          it++;
        }
        // if (it != pas.end()) {
        // cerr << "it: " << (*it)->pattern_id() << " " << (*it)->pos() << " " << ((pattern_hit_w_dist*)(*it))->editdist() << endl;
        // }
      }
      // checkpoint;


*/
Revision:	1.2
Committed:	Wed May 4 18:03:44 2005 UTC (12 years, 1 month ago) by nje01
Branch:	MAIN
CVS Tags:	HEAD
Changes since 1.1:	+11 -3 lines
Log Message:	Small bug fixes, plus codon based edit distance for peptide searching.
Line	File contents
1	/**************************************************************************
2	* This code is part of the supporting infrastructure for ATA Mapper.
3	* Copyright (C) 2002,2003,2004 Applera Corporation. All rights reserved.
4	* Author: Nathan Edwards
5	*
6	* This program is free software; you can redistribute it and/or modify
7	* it under the terms of the GNU General Public License as published by
8	* the Free Software Foundation; either version 2 of the License, or
9	* (at your option) any later version.
10	*
11	* This program is distributed in the hope that it will be useful,
12	* but WITHOUT ANY WARRANTY; without even the implied warranty of
13	* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
14	* GNU General Public License for more details.
15	*
16	* You should have received (LICENSE.txt) a copy of the GNU General Public
17	* License along with this program; if not, write to the Free Software
18	* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
19	*************************************************************************/
20
21
22	#include "filter_bitvec.h"
23	#include "primer_alignment.h"
24	// #include "sortedvector.t"
25
26	filter_bitvec::filter_bitvec(unsigned int k, char eos,
27	bool wc, bool tn, bool id, bool dm) :
28	num_patterns_(0)
29	{
30	pm_ = new shift_and_inexact(k,eos,wc,tn,id,dm);
31	}
32
33	filter_bitvec::~filter_bitvec() {
34	delete pm_;
35	}
36
37	unsigned int filter_bitvec::mismatches() const {
38	return pm_->mismatches();
39	}
40
41	void filter_bitvec::mismatches(unsigned int k) {
42	pm_->mismatches(k);
43	}
44
45	bool filter_bitvec::wildcards() const {
46	return pm_->wildcards();
47	}
48
49	void filter_bitvec::wildcards(bool wc) {
50	pm_->wildcards(wc);
51	}
52
53	bool filter_bitvec::wildcard_text_N() const {
54	return pm_->wildcard_text_N();
55	}
56
57	void filter_bitvec::wildcard_text_N(bool tn) {
58	pm_->wildcard_text_N(tn);
59	}
60
61	bool filter_bitvec::indels() const {
62	return pm_->indels();
63	}
64
65	void filter_bitvec::indels(bool id) {
66	pm_->indels(id);
67	}
68
69	bool filter_bitvec::dna_mut() const {
70	return pm_->dna_mut();
71	}
72
73	void filter_bitvec::dna_mut(bool dm) {
74	pm_->dna_mut(dm);
75	}
76
77	char filter_bitvec::eos_char() const {
78	return pm_->eos_char();
79	}
80
81	void filter_bitvec::eos_char(char c) {
82	pm_->eos_char(c);
83	}
84
85	long unsigned int
86	filter_bitvec::add_pattern(std::string const & pat, unsigned long id,
87	int esb, int eeb) {
88	add_pattern_(pat,id,esb,eeb);
89	num_patterns_++;
90	return id;
91	}
92
93	bool
94	filter_bitvec::find_patterns(CharacterProducer & cp,
95	pattern_hit_vector & phs,
96	long unsigned minka) {
97	// checkpoint;
98
99	// the eos_char we store in the shift_and_inexact is normalized, so
100	// we much unnormalize it before passing it on to the
101	// editdist_alignment class.
102	editdist_alignment pa(0,0,mismatches(),cp.ch(eos_char()),
103	wildcards(),wildcard_text_N(),
104	indels(),dna_mut(),0,0,true);
105	pattern_hit_vector::iterator it,it1,it2;
106	l.reserve(minka*2);
107	bool more;
108	while ((more=pm_->find_patterns(cp,l,minka))\|\|!l.empty()) {
109	// checkpoint;
110	FILE_POSITION_TYPE oldcharspos;
111	oldcharspos = cp.pos();
112	l.normalize();
113	// checkpoint;
114	it = l.begin();
115	while (it != l.end()) {
116	// checkpoint;
117	FILE_POSITION_TYPE firstpos = it->key();
118	if (firstpos > 0) {
119	long unsigned int pid = it->value()->id();
120	FILE_POSITION_TYPE pos = firstpos;
121	// checkpoint;
122	// cerr << pid << " " << firstpos << endl;
123	tinylist<pattern_hit_vector::iterator> adj;
124	adj.push_front(it);
125	it1 = it+1;
126	while (it1 != l.end() && it1->key() <= pos+2*mismatches()+1) {
127	// checkpoint;
128	if (it1->value()->id() == pid) {
129	// checkpoint;
130	// cerr << it1->value()->id() << " " << it1->key() << endl;
131	pos = it1->key();
132	adj.push_front(it1);
133	}
134	++it1;
135	// checkpoint;
136	}
137	// checkpoint;
138	if (oldcharspos < pos+2*mismatches()+1 && more) {
139	// end of returned hit condition...
140	// checkpoint;
141	break;
142	} else {
143	// checkpoint;
144	// cerr << pid << " " << firstpos << " " << pos << endl;
145	pattern_list::const_iterator plit = plit_[pid];
146	pa.reset();
147	pa.poslb(firstpos);
148	pa.posub(pos);
149	pa.exact_start_bases(plit->exact_start_bases());
150	pa.exact_end_bases(plit->exact_end_bases());
151	// cerr << plit->pattern() << endl;
152	// checkpoint;
153	if (pa.align(cp,plit->pattern())) {
154	// checkpoint;
155	phs.push_back(pa.end(),plit);
156	}
157	tinylist<pattern_hit_vector::iterator>::iterator adjit;
158	adjit = adj.begin();
159	while (adjit != adj.end()) {
160	(*adjit)->key() = 0;
161	++adjit;
162	}
163	}
164	}
165	++it;
166	}
167	// Move everything with valid key to beginning...
168	// int i,i1;
169	it=l.begin();
170	it1=l.begin();
171	// i=0;
172	// i1=0;
173	long unsigned int newsize=0;
174	while (it!=l.end()) {
175	// cerr << i << " " << i1 << endl;
176	// cerr << l.key(it) << " " << l.value(it)->id() << endl;
177	if (it->key() != 0) {
178	if (it != it1) {
179	it1->key() = it->key();
180	it1->value() = it->value();
181	}
182	++newsize;
183	++it1;
184	// i1++;
185	}
186	++it;
187	// i++;
188	}
189	// cerr << newsize << endl;
190	l.resize(newsize);
191	// checkpoint;
192	// it=l.begin();
193	// while (it!=l.end()) {
194	// cerr << it->key() << " " << it->value()->id() << endl;
195	// ++it;
196	// }
197	cp.pos(oldcharspos);
198	report_progress(cp);
199	if (phs.size() >= minka \|\|
200	(more==false && phs.size() > 0)) return true;
201	}
202	return false;
203	}
204
205	void
206	filter_bitvec::init(CharacterProducer & cp) {
207	assert(pm_!=((void*)0));
208	plit_.resize(num_patterns_+1);
209	long unsigned int id;
210	tinylist<pattern_list_element>::const_iterator it;
211	for (it=patterns().begin();it!=patterns().end();++it) {
212	id = pm_->add_pattern(it->pattern());
213	plit_[id] = it;
214	}
215	pm_->init(cp);
216	}
217
218	void filter_bitvec::reset() {
219	pm_->reset();
220	}
221
222
223
224	/*
225
226
227	// checkpoint;
228	std::list<pattern_hit*>::iterator it,it1,nextit;
229	unsigned long int mindist=MAXINT;
230	bool assigned_nextit=false;
231	std::list<std::list<pattern_hit*>::iterator> adj;
232	std::list<std::list<pattern_hit*>::iterator>::iterator it2;
233	it = pas.begin();
234	// cerr << "it: " << (it)->pattern_id() << " " << (it)->pos() << " " << ((pattern_hit_w_dist)(it))->editdist() << endl;
235	long unsigned int pos;
236	while (it!=pas.end()) {
237	// checkpoint;
238	it1=it;
239	mindist=((pattern_hit_w_dist)(it1))->editdist();
240	// cerr << "it1: " << (it1)->pattern_id() << " " << (it1)->pos() << " " << ((pattern_hit_w_dist)(it1))->editdist() << endl;
241	// cerr << "mindist: " << mindist << endl;
242	pos=(*it)->pos();
243	// checkpoint;
244	adj.clear();
245	// checkpoint;
246	assigned_nextit=false;
247	while (it1 != pas.end() &&
248	(it1)->pos() <= pos+2k_+1) {
249	// checkpoint;
250	if ((it)->pattern_id() == (it1)->pattern_id()) {
251	if (mindist > ((pattern_hit_w_dist)(it1))->editdist()) {
252	// cerr << "mindist: " << mindist << endl;
253	mindist = ((pattern_hit_w_dist)(it1))->editdist();
254	}
255	adj.push_back(it1);
256	} else {
257	if (!assigned_nextit) {
258	nextit=it1;
259	assigned_nextit=true;
260	}
261	}
262	// checkpoint;
263	pos = (*it1)->pos();
264	it1++;
265	// if (it1 != pas.end()) {
266	// cerr << "it1: " << (it1)->pattern_id() << " " << (it1)->pos() << " " << ((pattern_hit_w_dist)(it1))->editdist() << endl;
267	// }
268	}
269	// checkpoint;
270	// cerr << adj.size() << " " << mindist << endl;
271	if (adj.size() > 1) {
272	// checkpoint;
273	it2 = adj.begin();
274	bool assigned_keptit=false;
275	std::list<pattern_hit*>::iterator keptit;
276	while (it2 != adj.end()) {
277	if (((pattern_hit_w_dist)(*it2))->editdist() > mindist \|\|
278	assigned_keptit) {
279	// cerr << "erase it2: " << (it2)->pattern_id() << " " << (it2)->pos() << " " << ((pattern_hit_w_dist)(**it2))->editdist() << endl;
280	delete **it2;
281	pas.erase(*it2);
282	} else {
283	// cerr << "keep it2: " << (it2)->pattern_id() << " " << (it2)->pos() << " " << ((pattern_hit_w_dist)(**it2))->editdist() << endl;
284	if (!assigned_keptit) {
285	keptit=*it2;
286	assigned_keptit=true;
287	}
288	}
289	it2++;
290	}
291	if (assigned_nextit) {
292	it = nextit;
293	} else {
294	it = keptit;
295	it++;
296	}
297	} else {
298	it++;
299	}
300	// if (it != pas.end()) {
301	// cerr << "it: " << (it)->pattern_id() << " " << (it)->pos() << " " << ((pattern_hit_w_dist)(it))->editdist() << endl;
302	// }
303	}
304	// checkpoint;
305
306
307
308
309
310
311	*/