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gnContigSpec.cpp

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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
/////////////////////////////////////////////////////////////////////////////

#include "gn/gnContigSpec.h"
#include "gn/gnFilter.h"

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, uint32& 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;
}

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