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gnFASSource.h

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// File:            gnFASSource.h
// Purpose:         Implements gnBaseSource for .FAS files
// Description:     
// Changes:        
// Version:         libGenome 0.1.0 
// Author:          Aaron Darling 
// Last Edited:     April 15, 2001, 10:34:50pm 
// Modified by:     
// Copyright:       (c) Aaron Darling 
// Licenses:        Proprietary 
#ifndef _gnFASSource_h_
#define _gnFASSource_h_

#include "gn/gnDefs.h"

#include <string>
#include <fstream>
#include <vector>
#include "gn/gnFileSource.h"
#include "gn/gnSequence.h"

#define FAS_LINE_WIDTH 80


class GNDLLEXPORT gnFASSource : public gnFileSource
{
public:
        gnFASSource();
        gnFASSource( const gnFASSource& s );
        ~gnFASSource();
        gnFASSource* Clone() const;

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

        boolean SeqRead( const gnSeqI start, char* buf, uint32& bufLen, const uint32 contigI=ALL_CONTIGS ) ;
        
        static void Write(gnSequence& sequence, const string& filename, boolean write_coords = true, boolean enforce_unique_names = true);

        static void Write(gnSequence& sequence, ostream& m_ostream, boolean write_coords = true, boolean enforce_unique_names = true);

        static boolean Write(gnBaseSource *source, const string& filename);
//      /**
//       * deprecated - do not use
//       * Writes the given spec to a FastA file named "filename".
//       * @param spec The spec to write out.
//       * @param filename The name of the file to write.
//       * @return True if successful, false otherwise.
//       */
//      static boolean Write(gnGenomeSpec *spec, 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 );
        
        vector< gnFileContig* > m_contigList;
};// class gnFASSource

inline
gnFASSource* gnFASSource::Clone() const
{
        return new gnFASSource( *this );
}

inline
uint32 gnFASSource::GetContigListLength() const
{
        return m_contigList.size();
}

#endif
        // _gnFASSource_h_

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