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gnSourceSpec.cpp

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/////////////////////////////////////////////////////////////////////////////
// File:            gnSourceSpec.cpp
// Purpose:         implements gnContigSpec for source specs
// Description:     
// Changes:        
// Version:         libGenome 0.5.1 
// Author:          Aaron Darling 
// Modified by:     
// Copyright:       (c) Aaron Darling 
// Licenses:        See COPYING file for details
/////////////////////////////////////////////////////////////////////////////

#include "gn/gnSourceSpec.h"

gnSourceSpec::gnSourceSpec()
{
        Clear();
}

gnSourceSpec::gnSourceSpec( const gnSourceSpec& s )
{
        m_pSource = s.m_pSource;
        m_sourceName = string(s.m_sourceName);
        m_name = string(s.m_name);
        m_SourceContigIndex = s.m_SourceContigIndex;
        m_start = s.m_start;
        m_length = s.m_length;
        m_reverseComplement = s.m_reverseComplement;
        m_circular = s.m_circular;
}

gnSourceSpec::gnSourceSpec( gnBaseSource* source, const uint32 m_ContigIndex, const gnSeqI start, const gnSeqI endI, const boolean revComp)
{
        m_pSource = source;
        m_SourceContigIndex = m_ContigIndex;
        m_name = "";
        m_reverseComplement = revComp;
        m_circular = false;
        m_start = start;
        
        gnSeqI actual_len = source->GetContigSeqLength(m_ContigIndex);
        gnSeqI actual_end = endI;
        if(actual_len == 0)     
                return; //this is a bogus gnSourceSpec

        //trim start and end down if they are too big.
        m_start = m_start < actual_len ? m_start : actual_len - 1;
        actual_end = actual_end < actual_len ? actual_end : actual_len - 1;
        //set the circularity and length
        if(revComp){
                m_circular = m_start < actual_end ? true : false;
                m_length = ((m_start - actual_end + actual_len) % actual_len);
        }else{
                m_circular = m_start > actual_end ? true : false;
                m_length = ((actual_end - m_start + actual_len) % actual_len);
        }
        if(actual_len != 0)
                m_length++;

}

gnSourceSpec::~gnSourceSpec()
{
}

void gnSourceSpec::Clear()
{
        gnContigSpec::Clear();
        m_SourceContigIndex = 0;
        m_pSource = NULL;
}

gnSourceSpec* gnSourceSpec::CloneRange( const gnSeqI startI, const gnSeqI len ) const{
        gnSourceSpec* destSpec = new gnSourceSpec();
        destSpec->m_pSource = m_pSource;
        destSpec->m_sourceName = m_sourceName;
        destSpec->m_name = m_name;
        destSpec->m_SourceContigIndex = m_SourceContigIndex;
        destSpec->m_start = m_start + startI;
        destSpec->m_length = len < m_length - startI ? len : m_length - startI;
        destSpec->m_reverseComplement = m_reverseComplement;
        destSpec->m_circular = m_circular;
        return destSpec;
}

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