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gnGBKSource.h

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

#ifndef _gnGBKSource_h_
#define _gnGBKSource_h_

#include "gn/gnDefs.h"

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

const uint32 SEQ_COLUMN_WIDTH = 80;
const uint32 SEQ_HEADER_NAME_LENGTH = 11;
const uint32 SEQ_SUBTAG_COLUMN = 5;
const uint32 SEQ_LOCUS_CIRCULAR_COLUMN = 43;
const uint32 SEQ_LOCUS_NAME_COLUMN = 13;
const uint32 SEQ_LOCUS_NAME_LENGTH = 10;
const uint32 SEQ_LOCUS_SIZE_LENGTH = 7;
const uint32 SEQ_LOCUS_DNATYPE_OFFSET = 33;
const uint32 SEQ_LOCUS_DNATYPE_LENGTH = 7;
const uint32 SEQ_LOCUS_DIVCODE_OFFSET = 52;
const uint32 SEQ_LOCUS_DIVCODE_LENGTH = 3;
const uint32 SEQ_LOCUS_DATE_OFFSET = 62;
const uint32 SEQ_LOCUS_DATE_LENGTH = 11;
const uint32 SEQ_FEATURE_LOC_OFFSET = 21;
const uint32 SEQ_BASES_INDEX_END = 9;

/**
 *      gnGBKSource is a GenBank sequence file reader.
 * This class reads and writes the GenBank file format.
 * gnGBKSource is used by gnSourceFactory to read files and should only be used
 * directly when writing out files in GBK file format by calling
 * gnGBKSource::Write( mySpec, "C:\\mySeqFile.gbk");
 */

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

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

        /**
         * Writes the specified gnSequence to a .GBK file named "filename".
         * @param seq The gnSequence to write out.
         * @param filename The name of the file to write.
         * @return True if successful, false otherwise.
         */
        static boolean Write(gnSequence& seq, const string& filename);
        /**
         * Writes the specified source to a .GBK file named "filename".
         * @param source The source to write out.
         * @param filename The name of the file to write.
         * @return True if successful, false otherwise.
         */
        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 );

        static string& Filler(uint32 length);
        static void FormatString(string& data, uint32 offset, uint32 width);
        static void WriteHeader(gnMultiSpec* spec, const string& hdr, ofstream& m_ofstream);
//      gnSeqI m_seqLength;
        
        gnGenomeSpec *m_spec;
        vector< gnFileContig* > m_contigList;   
};// class gnGBKSource
// Clone        
inline
gnGBKSource* gnGBKSource::Clone() const
{
        return new gnGBKSource( *this );
}
// Contig Access methods        
inline
uint32 gnGBKSource::GetContigListLength() const
{
        return m_contigList.size();
}
inline
boolean gnGBKSource::Write(gnBaseSource *source, const string& filename){
        gnSequence gns(*source->GetSpec());
        return Write(gns, filename);
}
inline
gnGenomeSpec *gnGBKSource::GetSpec() const{
        return m_spec->Clone();
}

#endif
        // _gnGBKSource_h_

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