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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
/////////////////////////////////////////////////////////////////////////////
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#include "libGenome/gnSourceSpec.h"
using namespace std;
namespace genome {
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;
}
} // end namespace genome
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