---

gnABISource.h

Go to the documentation of this file.

/////////////////////////////////////////////////////////////////////////////
// File:            gnABISource.h
// Purpose:         Implements gnBaseSource for ABI files
// Description:     
// Changes:        
// Version:         libGenome 0.5.1 
// Author:          Aaron Darling 
// Modified by:     
// Copyright:       (c) Aaron Darling 
// Licenses:        See COPYING file for details 
/////////////////////////////////////////////////////////////////////////////
#ifndef _gnABISource_h_
#define _gnABISource_h_

#include "gn/gnDefs.h"

#include <string>
#include "gn/gnFileSource.h"
#include "gn/gnFileContig.h"
#include "gn/gnSourceSpec.h"
#include "gn/gnFilter.h"

/**
 * gnABISource is not implemented.
 */
class GNDLLEXPORT gnABISource : public gnFileSource
{
public:
        gnABISource();  
        /**
         * Clone Constructor copies the specified gnSEQSource.
         * @param s The gnABISource to copy.
         */
        gnABISource( const gnABISource& s );
        ~gnABISource();
        gnABISource* Clone() const;

        uint32 GetContigListLength() const;
        boolean HasContig( const string& name ) const;
        uint32 GetContigID( const string& name ) const;
        string GetContigName( uint32 i ) const;
        gnSeqI GetContigSeqLength( uint32 i ) const;
        gnFileContig* GetContig( const uint32 i ) const;

        boolean SeqRead( const gnSeqI start, char* buf, uint32& bufLen, const uint32 contigI=ALL_CONTIGS );

        /**
         * Writes the specified gnSequence to an ABI file named "filename".
         * @param sequence The gnSequence to write out.
         * @param filename The name of the file to write.
         * @return True if successful, false otherwise.
         */
        static boolean Write(gnSequence& sequence, const string& filename);
        gnGenomeSpec *GetSpec() const;

        gnFileContig* GetFileContig( const uint32 contigI ) const;
private:
        boolean SeqSeek( const gnSeqI start, const uint32& contigI, uint64& startPos, uint64& readableBytes );
        boolean SeqStartPos( const gnSeqI start, gnFileContig& contig, uint64& startPos, uint64& readableBytes );
        boolean ParseStream( istream& fin );

        gnGenomeSpec *m_spec;
        vector< gnFileContig* > m_contigList;   

};// class gnABISource

inline
gnABISource* gnABISource::Clone() const
{
        return new gnABISource( *this );
}
inline
uint32 gnABISource::GetContigListLength() const
{
        return m_contigList.size();
}
inline
gnGenomeSpec *gnABISource::GetSpec() const
{
        return m_spec->Clone();
}

#endif
        // _gnABISource_h_

---