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gnStringSpec.cpp

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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
/////////////////////////////////////////////////////////////////////////////

#include "gn/gnStringSpec.h"
#include <string>

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;
}

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