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/////////////////////////////////////////////////////////////////////////////
// File: gnStringSpec.cpp
// Purpose: implements gnContigSpec for strings
// Description: stores sequence in memory
// 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/gnStringSpec.h"
#include <string>
#include <cstring>
using namespace std;
namespace genome {
gnStringSpec::gnStringSpec()
{
gnContigSpec::Clear();
}
gnStringSpec::gnStringSpec( const string& m_string, gnSeqI start, gnSeqI endI, boolean revComp)
{
m_seqString = m_string;
m_start = start;
gnSeqI actual_len = m_seqString.length();
//reverse comp has the end b.p. first, then start. switch them.
m_start = revComp ? endI : start;
gnSeqI actual_end = revComp ? start : endI;
//trim start and end down if they are too big.
actual_end = actual_end < actual_len ? actual_end : actual_len -1;
m_start = m_start < actual_len ? m_start : actual_len - 1;
if(actual_len == 0)
m_start = 0;
//if start is after end, we're using a circular sequence.
m_circular = m_start > actual_end ? true : false;
//if circular, the length will be different.
m_length = m_circular ? (actual_len - m_start) + actual_end : actual_end - m_start + 1;
m_reverseComplement = revComp;
m_SourceContigIndex = ALL_CONTIGS;
}
gnStringSpec::gnStringSpec( const gnStringSpec& s )
{
m_seqString = s.m_seqString;
m_sourceName = s.m_sourceName;
m_name = s.m_name;
m_start = s.m_start;
m_length = s.m_length;
m_reverseComplement = s.m_reverseComplement;
m_circular = s.m_circular;
m_SourceContigIndex = s.m_SourceContigIndex;
}
gnStringSpec::~gnStringSpec()
{
Clear();
}
void gnStringSpec::Clear()
{
gnContigSpec::Clear();
m_seqString = "";
}
gnStringSpec* gnStringSpec::CloneRange( const gnSeqI startI, const gnSeqI len ) const{
gnStringSpec* destSpec = new gnStringSpec();
destSpec->m_seqString = m_seqString.substr(m_start + startI, len);
destSpec->m_sourceName = m_sourceName;
destSpec->m_name = m_name;
destSpec->m_start = 0;
destSpec->m_length = destSpec->m_seqString.length();
destSpec->m_reverseComplement = m_reverseComplement;
destSpec->m_circular = m_circular;
destSpec->m_SourceContigIndex = m_SourceContigIndex;
return destSpec;
}
} // end namespace genome
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