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/////////////////////////////////////////////////////////////////////////////
// File: gnContigSpec.cpp
// Purpose: Abstract Contig Spec class
// Description: Defines an interface for contig specs
// Changes:
// Version: libGenome 0.5.1
// Author: Aaron Darling
// Modified by:
// Copyright: (c) Aaron Darling
// Licenses: See COPYING file for details
/////////////////////////////////////////////////////////////////////////////
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#include "libGenome/gnContigSpec.h"
#include "libGenome/gnFilter.h"
using namespace std;
namespace genome {
void gnContigSpec::CropStart( gnSeqI cropLen ){
m_start = m_reverseComplement ? (GetSourceLength() + m_start - cropLen) % GetSourceLength() : (m_start + cropLen) % GetSourceLength();
m_length -= cropLen;
return;
}
void gnContigSpec::CropEnd( gnSeqI cropLen ){
m_length -= cropLen;
}
void gnContigSpec::SetReverseComplement( const boolean value )
{
//translate coordinates if revComp has changed.
if((m_reverseComplement != value) && (m_length > 0))
m_start = (m_start + m_length) % GetSourceLength();
m_reverseComplement = value;
}
boolean gnContigSpec::SeqRead(const gnSeqI start, gnSeqC* buf, gnSeqI& bufLen, const uint32 contigI ) const{
boolean success;
bufLen = bufLen < m_length - start? bufLen : m_length - start; //trim the read down to size.
gnSeqI readable = bufLen;
gnSeqI read_start = start; // coordinate translation
if(contigI == ALL_CONTIGS)
read_start = m_reverseComplement ? (m_start - start - readable + GetSourceLength()) % GetSourceLength() : start + m_start;
success = Read(read_start, buf, readable);
if(m_circular){
gnSeqI beginread = bufLen - readable; //read whatever couldn't be read before
read_start = m_reverseComplement ? (m_start - readable + GetSourceLength()) % GetSourceLength() : m_start;
success = Read(read_start , buf + readable, beginread);
readable += beginread;
}
bufLen = readable;
if(m_reverseComplement)
gnFilter::DNAComplementFilter()->ReverseFilter(&buf, bufLen);
return success;
}
void gnContigSpec::Clear(){
gnBaseSpec::Clear();
m_start = 0;
m_length = 0;
m_SourceContigIndex = ALL_CONTIGS;
}
} // end namespace genome
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