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gnStringSpec.h

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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 
/////////////////////////////////////////////////////////////////////////////
#ifndef _gnStringSpec_h_
#define _gnStringSpec_h_

#include "gn/gnDefs.h"

#include <string>
#include "gn/gnContigSpec.h"
#include "gn/gnBaseSource.h"

/**
 * 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 string.
         * A circular spec will be created if the end index is greater than the start.
         * @param m_string The string to read base pairs from.
         * @param startI The index to start reading base pairs from the string.
         * @param endI The index to stop reading base pairs from the string.
         * @param revComp True if the sequence is read reverse complement.
         */
        gnStringSpec( const 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;
        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;
}

#endif
        // _gnStringSpec_h_

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