gnGBKSource.h Source File

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# gnGBKSource.h

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    00001
    00002 // File:            gnGBKSource.h
    00003 // Purpose:         Implements gnBaseSource for GenBank files
    00004 // Description:
    00005 // Changes:
    00006 // Version:         libGenome 0.1.0
    00007 // Author:          Aaron Darling
    00008 // Last Edited:     April 15, 2001, 10:34:50pm
    00009 // Modified by:
    00010 // Copyright:       (c) Aaron Darling
    00011 // Licenses:        Proprietary
    00013
    00014 #ifndef _gnGBKSource_h_
    00015 #define _gnGBKSource_h_
    00016
    00017 #include "gn/gnDefs.h"
    00018
    00019 #include <string>
    00020 #include <fstream>
    00021 #include <vector>
    00022 #include "gn/gnFileSource.h"
    00023 #include "gn/gnFileContig.h"
    00024 #include "gn/gnSourceSpec.h"
    00025 #include "gn/gnSequence.h"
    00026
    00027 const uint32 SEQ_COLUMN_WIDTH = 80;
    00028 const uint32 SEQ_HEADER_NAME_LENGTH = 11;
    00029 const uint32 SEQ_SUBTAG_COLUMN = 5;
    00030 const uint32 SEQ_LOCUS_CIRCULAR_COLUMN = 43;
    00031 const uint32 SEQ_LOCUS_NAME_COLUMN = 13;
    00032 const uint32 SEQ_LOCUS_NAME_LENGTH = 10;
    00033 const uint32 SEQ_LOCUS_SIZE_LENGTH = 7;
    00034 const uint32 SEQ_LOCUS_DNATYPE_OFFSET = 33;
    00035 const uint32 SEQ_LOCUS_DNATYPE_LENGTH = 7;
    00036 const uint32 SEQ_LOCUS_DIVCODE_OFFSET = 52;
    00037 const uint32 SEQ_LOCUS_DIVCODE_LENGTH = 3;
    00038 const uint32 SEQ_LOCUS_DATE_OFFSET = 62;
    00039 const uint32 SEQ_LOCUS_DATE_LENGTH = 11;
    00040 const uint32 SEQ_FEATURE_LOC_OFFSET = 21;
    00041 const uint32 SEQ_BASES_INDEX_END = 9;
    00042
    00050
    00051 class GNDLLEXPORT gnGBKSource : public gnFileSource
    00052 {
    00053 public:
    00057         gnGBKSource();
    00062         gnGBKSource( const gnGBKSource& s );
    00066         ~gnGBKSource();
    00070         gnGBKSource* Clone() const;
    00071 // Contig Access methods
    00072         uint32 GetContigListLength() const;
    00073         boolean HasContig( const string& name ) const;
    00074         uint32 GetContigID( const string& name ) const;
    00075         string GetContigName( const uint32 i ) const;
    00076         gnSeqI GetContigSeqLength( const uint32 i ) const;
    00077
    00078         boolean SeqRead( const gnSeqI start, char* buf, uint32& bufLen, const uint32 contigI=ALL_CONTIGS );
    00079
    00086         static boolean Write(gnSequence& seq, const string& filename);
    00093         static boolean Write(gnBaseSource *source, const string& filename);
    00094         gnGenomeSpec *GetSpec() const;
    00095         gnFileContig* GetFileContig( const uint32 contigI ) const;
    00096 private:
    00097         boolean SeqSeek( const gnSeqI start, const uint32& contigI, uint64& startPos, uint64& readableBytes );
    00098         boolean SeqStartPos( const gnSeqI start, gnFileContig& contig, uint64& startPos, uint64& readableBytes );
    00099         boolean ParseStream( istream& fin );
    00100
    00101         static string& Filler(uint32 length);
    00102         static void FormatString(string& data, uint32 offset, uint32 width);
    00103         static void WriteHeader(gnMultiSpec* spec, const string& hdr, ofstream& m_ofstream);
    00104 //      gnSeqI m_seqLength;
    00105
    00106         gnGenomeSpec *m_spec;
    00107         vector< gnFileContig* > m_contigList;
    00108 };// class gnGBKSource
    00109 // Clone
    00110 inline
    00111 gnGBKSource* gnGBKSource::Clone() const
    00112 {
    00113         return new gnGBKSource( *this );
    00114 }
    00115 // Contig Access methods
    00116 inline
    00117 uint32 gnGBKSource::GetContigListLength() const
    00118 {
    00119         return m_contigList.size();
    00120 }
    00121 inline
    00122 boolean gnGBKSource::Write(gnBaseSource *source, const string& filename){
    00123         gnSequence gns(*source->GetSpec());
    00124         return Write(gns, filename);
    00125 }
    00126 inline
    00127 gnGenomeSpec *gnGBKSource::GetSpec() const{
    00128         return m_spec->Clone();
    00129 }
    00130
    00131 #endif
    00132         // _gnGBKSource_h_