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gnABISource.cpp

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/////////////////////////////////////////////////////////////////////////////
// File:            gnABISource.h
// Purpose:         Implements gnBaseSource for .ABI files
// Description:     
// Changes:        
// Version:         libGenome 0.5.1 
// Author:          Aaron Darling 
// Modified by:     
// Copyright:       (c) Aaron Darling 
// Licenses:        See COPYING file for details
/////////////////////////////////////////////////////////////////////////////
#include "gn/gnABISource.h"

gnABISource::gnABISource()
{
        m_openString = "";
        m_pFilter = gnFilter::fullDNASeqFilter();
}
gnABISource::gnABISource( const gnABISource& s ) : gnFileSource(s)
{
        vector< gnFileContig* >::const_iterator iter = s.m_contigList.begin();
        for( ; iter != s.m_contigList.end(); ++iter )
        {
                m_contigList.push_back( *iter );
        }
}
gnABISource::~gnABISource()
{
        m_ifstream.close();
        vector< gnFileContig* >::iterator iter = m_contigList.begin();
        for( ; iter != m_contigList.end(); ++iter )
        {
                gnFileContig* fg = *iter;
                *iter = 0;
                delete fg;
        }
}

// Contig Access methods        
boolean gnABISource::HasContig( const string& name ) const
{
        vector< gnFileContig* const>::iterator iter = m_contigList.begin();
        for( ; iter != m_contigList.end(); ++iter )
        {
                if( name == (*iter)->GetName() )
                        return true;
        }
        return false;
}
uint32 gnABISource::GetContigID( const string& name ) const
{
        vector< gnFileContig* const>::iterator iter = m_contigList.begin();
        for( ; iter != m_contigList.end(); ++iter )
        {
                if( name == (*iter)->GetName() )
                        return iter - m_contigList.begin();
        }
        return ALL_CONTIGS;
}

string gnABISource::GetContigName( uint32 i ) const{
        if( i < m_contigList.size() ){
                return m_contigList[i]->GetName();
        }
        return "";
}

gnSeqI gnABISource::GetContigSeqLength( uint32 i ) const{
        if( i < m_contigList.size() )
        {
                return m_contigList[i]->GetSeqLength();
        }else if( i == ALL_CONTIGS){
                gnSeqI seqlen = 0;
                for(int j=0; j < m_contigList.size(); j++)
                        seqlen += m_contigList[j]->GetSeqLength();
                return seqlen;
        }
        return GNSEQI_ERROR;
}

boolean gnABISource::SeqRead( const gnSeqI start, char* buf, gnSeqI& bufLen, const uint32 contigI )
{
        return false;
}

boolean gnABISource::SeqSeek( const gnSeqI start, const uint32& contigI, uint64& startPos, uint64& readableBytes ){
        return SeqStartPos( start, *(m_contigList[contigI]), startPos, readableBytes );
}

boolean gnABISource::SeqStartPos( const gnSeqI start, gnFileContig& contig, uint64& startPos, uint64& readableBytes )
{
        return false;
}

gnFileContig* gnABISource::GetFileContig( const uint32 contigI ) const{
        if(m_contigList.size() > contigI)
                return m_contigList[contigI];
        return NULL;
}
 
boolean gnABISource::ParseStream( istream& fin )
{
        return false;
}

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