---

gnFileContig.cpp

Go to the documentation of this file.

/////////////////////////////////////////////////////////////////////////////
// File:            gnFileContig.h
// Purpose:         File Position holder.
// Description:     
// Changes:        
// Version:         libGenome 0.5.1 
// Author:          Aaron Darling 
// Modified by:     
// Copyright:       (c) Aaron Darling 
// Licenses:        See COPYING file for details
/////////////////////////////////////////////////////////////////////////////
#include "gn/gnFileContig.h"
#include <iostream>

gnFileContig::gnFileContig()
{
        Clear();
}
gnFileContig::gnFileContig( string nameStr, const uint64 s, const uint64 e )
{
        Clear();
        m_name = nameStr;
        m_fileStartEnd.first = s;
        m_fileStartEnd.second = e;
}
gnFileContig::gnFileContig( const gnFileContig& fc )
{
        m_name = fc.m_name;
        m_seqLength = fc.m_seqLength;
        m_fileStartEnd = fc.m_fileStartEnd;
        for( uint32 i=0; i < CONTIG_SECTION_SIZE; ++i )
                m_startEndArray[i] = fc.m_startEndArray[i];
        m_repeatSeqGap = fc.m_repeatSeqGap;
        m_repeatSeqGapSize = fc.m_repeatSeqGapSize;
}
gnFileContig::~gnFileContig()
{
}
void gnFileContig::Clear()
{
        m_name = "";
        m_seqLength = 0;
        m_fileStartEnd = pair<uint64,uint64>(0,0);
        for( uint32 i=0; i < CONTIG_SECTION_SIZE; ++i )
                m_startEndArray[i] = pair<uint64,uint64>(0,0);
        m_repeatSeqGap = false;
        m_repeatSeqGapSize = pair<uint64,uint64>(0,0);
}

boolean gnFileContig::SetRepeatSeqSize( const uint64 seqSize )
{
        if( !m_repeatSeqGap )
                return false;
        if( m_repeatSeqGapSize.first == seqSize )
                return true;
        if( m_repeatSeqGapSize.first == 0 )
        {
                m_repeatSeqGapSize.first = seqSize;
                return true;
        }
        m_repeatSeqGap = false;
        return false;
}
boolean gnFileContig::SetRepeatGapSize( const uint64 gapSize )
{
        if( !m_repeatSeqGap )
                return false;
        if( m_repeatSeqGapSize.second == gapSize )
                return true;
        if( m_repeatSeqGapSize.second == 0 )
        {
                m_repeatSeqGapSize.second = gapSize;
                return true;
        }
        m_repeatSeqGap = false;
        return false;
}

---