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/////////////////////////////////////////////////////////////////////////////
// File: gnStringSpec.h
// Purpose: implements gnContigSpec for strings
// 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
#ifndef _gnStringSpec_h_
#define _gnStringSpec_h_
#include "libGenome/gnDefs.h"
#include <cstdlib>
#include <cstring>
#include <string>
#include "libGenome/gnContigSpec.h"
#include "libGenome/gnBaseSource.h"
namespace genome {
/**
* gnStringSpec stores a sequence and annotation data in memory.
* For a more complete description see the gnBaseSpec documentation.
*/
class GNDLLEXPORT gnStringSpec : public gnContigSpec
{
public:
/**
* Empty constructor.
*/
gnStringSpec();
/**
* Constructor, creates a gnStringSpec using sequence data in the given std::string.
* A circular spec will be created if the end index is greater than the start.
* @param m_string The std::string to read base pairs from.
* @param startI The index to start reading base pairs from the std::string.
* @param endI The index to stop reading base pairs from the std::string.
* @param revComp True if the sequence is read reverse complement.
*/
gnStringSpec( const std::string& m_string, const gnSeqI startI=0, const gnSeqI endI=GNSEQI_END, const boolean revComp = false);
/**
* Copy constructor.
* @param s the gnStringSpec to copy.
*/
gnStringSpec( const gnStringSpec& s );
~gnStringSpec();
// Clone
gnStringSpec* Clone() const;
virtual void Clear();
// Value Access methods
virtual gnSeqI GetSourceLength() const;
// Source Spec Specific functions
virtual gnBaseSource *GetSource() const;
/**
* Copies a specified range of bases and returns a pointer to
* the resulting gnStringSpec. You must delete the copy when you
* are finished with it.
* @param startI The first base pair to copy
* @param len The length of the piece to copy
* @return A copy of the gnStringSpec containing only the specified bases
*/
virtual gnStringSpec* CloneRange( const gnSeqI startI, const gnSeqI len ) const;
protected:
virtual boolean Read(const gnSeqI start, gnSeqC* buf, gnSeqI& bufLen ) const;
std::string m_seqString;
}; // class gnStringSpec
inline
gnStringSpec* gnStringSpec::Clone() const
{
return new gnStringSpec( *this );
}
inline
gnSeqI gnStringSpec::GetSourceLength() const{
return m_seqString.length();
}
inline
gnBaseSource* gnStringSpec::GetSource() const
{
return NULL;
}
inline
boolean gnStringSpec::Read(const gnSeqI start, gnSeqC* buf, gnSeqI& bufLen) const{
memcpy(buf, m_seqString.data() + start, bufLen);
return true;
}
} // end namespace genome
#endif
// _gnStringSpec_h_
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