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/* $Id: stsfilter.cpp,v 1.4 2004/06/03 23:37:22 rotmistr Exp $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* =========================================================================
*
* Author: Kirill Rotmistrovsky
*
* ========================================================================= */
#include <epcr/hashset.hpp>
#include <epcr/stsmatch_i.hpp>
#include <stdexcept>
USING_NCBI_SCOPE;
USING_SCOPE(EPCR_SCOPE);
#define DBG fprintf(stdout,__FILE__"[%d]\n",__LINE__);
#define SHOWI(a) fprintf(stdout,__FILE__"[%d] "#a"=%d\n",__LINE__,a);
#define SHOWS(a) \
fprintf(stdout,__FILE__"[%d] "#a"=%.*s\n",__LINE__,a.length(),a.data());
bool CPcrMachinePostprocess::OrderByPos2Pos1(const SOutput& o1,
const SOutput& o2)
{
return (o1.pos2<o2.pos2 || o1.pos2==o2.pos2 && o1.pos1<o2.pos1);
}
int CPcrMachinePostprocess::Compare(const SOutput& a, const SOutput& b,
int min_len, int max_len)
{
if(a.gaps()>b.gaps()) return -1;
if(a.gaps()<b.gaps()) return +1;
if(a.mism()>b.mism()) return -1;
if(a.mism()<b.mism()) return +1;
int lb=(b.pos2-b.pos1);
int la=(a.pos2-a.pos1);
if(la >= min_len && la <= max_len) {
if(lb >= min_len && lb <= max_len) {
return lb-la;
} else return 1;
} else {
if(lb >= min_len && lb <= max_len) {
return -1;
} else {
int da=(la < min_len)?min_len-la:la-max_len;
int db=(lb < min_len)?min_len-lb:lb-max_len;
return db-da;
}
}
}
bool CPcrMachinePostprocess::Overlap(int l1, int l2,
const SOutput& a, const SOutput& b)
{
return (abs(a.pos2-b.pos2)<l2 && abs(a.pos1-b.pos1)<l1);
}
void CPcrMachinePostprocess::Flush()
{
for(TAllHits_I i=m_OutQueues.begin(); i!=m_OutQueues.end(); ++i) {
// 1st: cluster
// 2nd: select best per cluster
if(i->second.size()==0) continue;
int l1=i->first->GetPrimerLength(0);
int l2=i->first->GetPrimerLength(1);
int lo=i->first->GetSizeLo();
int hi=i->first->GetSizeHi();
TStsHits& hits=i->second;
while(hits.size()) {
TStsHits todo;
TStsHits cluster;
cluster.push_back(hits.back());
SOutput best=cluster.front();
hits.pop_back();
for(TStsHits_CI j=hits.begin(); j!=hits.end(); ++j) {
bool overlaps=false;
for(TStsHits_CI h=cluster.begin(); h!=cluster.end(); ++h)
if(Overlap(l1,l2,*j,*h)) { overlaps=true; break; }
if(overlaps) {
if(Compare(*j,best,lo,hi)>=0) best=*j;
cluster.push_back(*j);
} else {
todo.push_back(*j);
}
}
SScore sc(best.length(),best.mism_l, best.mism_r,
best.gaps_l, best.gaps_r);
m_Callback->CbkMatch(i->first, best.pos1, best.pos2, &sc);
hits=todo;
}
}
m_OutQueues.clear();
}
void CPcrMachinePostprocess::CbkMatch(const ISts * sts,
unsigned pos1, unsigned pos2,
const SScore* score)
{
SOutput o(pos1,pos2,
score->mism_l,score->mism_r,
score->gaps_l,score->gaps_r);
TStsHits& hits=m_OutQueues[sts];
if(hits.size() && hits.back()==o) return;
hits.push_back(o);
}
/*
* $Log: stsfilter.cpp,v $
* Revision 1.4 2004/06/03 23:37:22 rotmistr
* New aligner added.
*
* Revision 1.3 2004/03/25 19:36:52 rotmistr
* API: separate left and right primers mism/gaps in forward API
*
* Revision 1.2 2004/02/04 21:23:22 rotmistr
* - gcc-3.3.2 compatible
* - better postfiltering for reverse-e-PCR for discontiguos words
* - cgi added, that supports:
* -- contig to chromosome mapping
* -- simple mapviewer links
* -- unists links
* -- discontiguos words
*
* Revision 1.1 2004/01/28 23:27:02 rotmistr
* "Best of overlapping" hit selection postprocessor added.
*
*/
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