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gnFASSource.h

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

/**
 *      gnFASSource reads and writes FastA files.
 * gnFASSource is used by gnSourceFactory to read files. 
 * Files can be written in the FastA file format by calling
 * gnFASSource::Write( mySpec, "C:\\myFasFile.fas");
 */

class GNDLLEXPORT gnFASSource : public gnFileSource
{
public:
        /**
         * Empty Constructor, does nothing.
         */
        gnFASSource();
        /**
         * Clone Constructor copies the specified gnFASSource.
         * @param s The gnFASSource to copy.
         */
        gnFASSource( const gnFASSource& s );
        /**
         * Destructor, frees memory.
         */
        ~gnFASSource();
        /**
         * Returns an exact copy of this class.
         */
        gnFASSource* Clone() const;

        uint32 GetContigListLength() const;
        boolean HasContig( const string& name ) const;
        uint32 GetContigID( const string& name ) 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 ) ;
        
        /**
         * Write the given gnSequence to a FastA file.
         * @param sequence The gnSequence to write out.
         * @param filename The name of the file to write.
         * @param write_coords If true each entry's name will be followed by the coordinates of the entry
         *                     in the context of the entrire file.
         * @param enforce_unique_names If true each entry's name will be recorded as they are written.  Each
         *                              successive duplicate name that is found will have an underscore and a
         *                                                 number appended to it, indicating the number of entries by the same
         *                                                         name which have already been written.
         *                             Turning this off will yield a slight performance improvement when writing
         *                             files with a large number of entries.  (More than 1000)
         * @throws A FileNotOpened() exception may be thrown.
         */
        static void Write(gnSequence& sequence, const string& filename, boolean write_coords = true, boolean enforce_unique_names = true);

        /**
         * Write the given gnSequence to an ostream.
         * @param sequence The gnSequence to write out.
         * @param m_ostream The output stream to write to.
         * @param write_coords If true each entry's name will be followed by the coordinates of the entry
         *                     in the context of the entrire file.
         * @param enforce_unique_names If true each entry's name will be recorded as they are written.  Each
         *                              successive duplicate name that is found will have an underscore and a
         *                                                 number appended to it, indicating the number of entries by the same
         *                                                         name which have already been written.
         *                             Turning this off will yield a slight performance improvement when writing
         *                             files with a large number of entries.  (More than 1000)
         */
        static void Write(gnSequence& sequence, ostream& m_ostream, boolean write_coords = true, boolean enforce_unique_names = true);

        /**
         * Deprecated - do not use.
         * Write the given source to a FastA file.
         * @param source The spec to write out.
         * @param filename The name of the file to write.
         */
        static boolean Write(gnBaseSource *source, 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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