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gnContigSpec.h

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/////////////////////////////////////////////////////////////////////////////
// File:            gnContigSpec.h
// Purpose:         Abstract Contig Spec class
// Description:     Defines an interface for contig specs
// Changes:        
// Version:         libGenome 0.5.1 
// Author:          Aaron Darling 
// Modified by:     
// Copyright:       (c) Aaron Darling 
// Licenses:        See COPYING file for details 
/////////////////////////////////////////////////////////////////////////////
#ifndef _gnContigSpec_h_
#define _gnContigSpec_h_

#include "gn/gnDefs.h"

#include <vector>
#include <string>

#include "gn/gnBaseSpec.h"
#include "gn/gnBaseFeature.h"
#include "gn/gnDebug.h"
/**
 * gnContigSpec is an interface for classes which store contigs, or reads,
 * of DNA or protein sequence
 */
class GNDLLEXPORT gnContigSpec : public gnBaseSpec
{
public:
        gnContigSpec(){}
        /**
         * Destructor, frees memory.
         */
        virtual ~gnContigSpec(){}
        virtual gnContigSpec* Clone() const = 0;
        virtual gnContigSpec* CloneRange( const uint32 startI, const uint32 len ) const = 0;
        /**
         * Get the name of the source associated with this spec.
         * @return The source name or an empty string if none exists.
         */
        virtual string GetSourceName() const;
        /**
         * Get the base pair index where this contig starts inside of the sequence data.
         * @return The starting base pair.
         */
        virtual gnSeqI GetStart() const;
        /**
         * Get the length of this contig inside of the sequence data.
         * @return This contigs length.
         */
        virtual gnSeqI GetLength() const;
        /**
         * Get the length of the source for this spec.
         * @return The source length.
         */
        virtual gnSeqI GetSourceLength() const = 0;
        /**
         * Returns this contig's index in its source sequence.
         * @return This contig's index in the source sequence.
         */
        virtual uint32 GetSourceContigIndex() const;
        /**
         * Sets the name of the source associated with this contig.
         * @param sourceName The new name.
         * @return True if successful.
         */
        virtual void SetSourceName( const string& sourceName );
        /**
         * Sets the starting base pair to read from in the contig's sequence.
         * This does not affect the actual sequence data but only where to begin
         * using it in this contig.
         * @param start The new starting base pair.
         * @return True if successful.
         */
        virtual void SetStart( const gnSeqI start );
        /**
         * Sets the length of reads into this sequence.
         * This does not affect the actual sequence data but only how much of it
         * is used in this contig.
         * @param len The new sequence length.
         * @return True if successful.
         */
        virtual void SetLength( const gnSeqI len );
        /**
         * Sets this contig's index in its source sequence.
         * @param contigI This contig's index in the source sequence.
         */
        virtual void SetSourceContigIndex( const uint32 contigI );
        /**
         * Sets the reverse complement bit for this contig.
         * This routine will translate the start index to the reverse base pair.
         * @param value True for reverse complement, false otherwise.
         * @return True if successful.
         */
        virtual void SetReverseComplement( const boolean value );

        virtual void CropStart( gnSeqI cropLen );
        virtual void CropEnd( gnSeqI cropLen );

        virtual boolean SeqRead(const gnSeqI start, gnSeqC* buf, uint32& bufLen, const uint32 contigI ) const;
        virtual void Clear();
protected:
        gnSeqI m_start;  //start within the genome.
        gnSeqI m_length;
        uint32 m_SourceContigIndex;

        /**
         * all derived classes must implement this!
         * it simply reads the specified bases into buf, disregarding circularity and reverse complement.
         */
        virtual boolean Read(const gnSeqI start, gnSeqC* buf, uint32& bufLen ) const = 0;

private:

}; // class gnContigSpec


inline
string gnContigSpec::GetSourceName() const{
        return m_sourceName;
}
inline
void gnContigSpec::SetSourceName(const string& sourceName){
        m_sourceName = sourceName;
}

inline
gnSeqI gnContigSpec::GetStart() const
{
        return m_start;
}
inline
gnSeqI gnContigSpec::GetLength() const
{
        return m_length;
}
// SET
inline
void gnContigSpec::SetStart( const gnSeqI start )
{
        m_start = start;
}
inline
void gnContigSpec::SetLength( const gnSeqI len )
{
        m_length = len;
}
inline
uint32 gnContigSpec::GetSourceContigIndex() const{
        return m_SourceContigIndex;
}
inline
void gnContigSpec::SetSourceContigIndex( const uint32 contigI ){
        m_SourceContigIndex = contigI;
}

#endif
        // _gnContigSpec_h_

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