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 0.5.1
    00007 // Author:          Aaron Darling
    00008 // Modified by:
    00009 // Copyright:       (c) Aaron Darling
    00010 // Licenses:        See COPYING file for details
    00011 /////////////////////////////////////////////////////////////////////////////
    00012
    00013 #ifndef _gnGBKSource_h_
    00014 #define _gnGBKSource_h_
    00015
    00016 #include "gn/gnDefs.h"
    00017
    00018 #include <string>
    00019 #include <fstream>
    00020 #include <vector>
    00021 #include "gn/gnFileSource.h"
    00022 #include "gn/gnFileContig.h"
    00023 #include "gn/gnSourceSpec.h"
    00024 #include "gn/gnSequence.h"
    00025
    00026 const uint32 SEQ_COLUMN_WIDTH = 80;
    00027 const uint32 SEQ_HEADER_NAME_LENGTH = 11;
    00028 const uint32 SEQ_SUBTAG_COLUMN = 5;
    00029 const uint32 SEQ_LOCUS_CIRCULAR_COLUMN = 43;
    00030 const uint32 SEQ_LOCUS_NAME_COLUMN = 13;
    00031 const uint32 SEQ_LOCUS_NAME_LENGTH = 10;
    00032 const uint32 SEQ_LOCUS_SIZE_LENGTH = 7;
    00033 const uint32 SEQ_LOCUS_DNATYPE_OFFSET = 33;
    00034 const uint32 SEQ_LOCUS_DNATYPE_LENGTH = 7;
    00035 const uint32 SEQ_LOCUS_DIVCODE_OFFSET = 52;
    00036 const uint32 SEQ_LOCUS_DIVCODE_LENGTH = 3;
    00037 const uint32 SEQ_LOCUS_DATE_OFFSET = 62;
    00038 const uint32 SEQ_LOCUS_DATE_LENGTH = 11;
    00039 const uint32 SEQ_FEATURE_LOC_OFFSET = 21;
    00040 const uint32 SEQ_BASES_INDEX_END = 9;
    00041
    00042 /**
    00043  *      gnGBKSource is a GenBank sequence file reader.
    00044  * This class reads and writes the GenBank file format.
    00045  * gnGBKSource is used by gnSourceFactory to read files and should only be used
    00046  * directly when writing out files in GBK file format by calling
    00047  * gnGBKSource::Write( mySpec, "C:\\mySeqFile.gbk");
    00048  */
    00049
    00050 class GNDLLEXPORT gnGBKSource : public gnFileSource
    00051 {
    00052 public:
    00053         /**
    00054          * Empty Constructor, does nothing.
    00055          */
    00056         gnGBKSource();
    00057         /**
    00058          * Clone Constructor copies the specified gnGBKSource.
    00059          * @param s The gnGBKSource to copy.
    00060          */
    00061         gnGBKSource( const gnGBKSource& s );
    00062         /**
    00063          * Destructor, frees memory.
    00064          */
    00065         ~gnGBKSource();
    00066         /**
    00067          * Returns an exact copy of this class.
    00068          */
    00069         gnGBKSource* Clone() const;
    00070 // Contig Access methods
    00071         uint32 GetContigListLength() const;
    00072         boolean HasContig( const string& name ) const;
    00073         uint32 GetContigID( const string& name ) const;
    00074         string GetContigName( const uint32 i ) const;
    00075         gnSeqI GetContigSeqLength( const uint32 i ) const;
    00076
    00077         boolean SeqRead( const gnSeqI start, char* buf, uint32& bufLen, const uint32 contigI=ALL_CONTIGS );
    00078
    00079         /**
    00080          * Writes the specified gnSequence to a .GBK file named "filename".
    00081          * @param seq The gnSequence to write out.
    00082          * @param filename The name of the file to write.
    00083          * @return True if successful, false otherwise.
    00084          */
    00085         static boolean Write(gnSequence& seq, const string& filename);
    00086         /**
    00087          * Writes the specified source to a .GBK file named "filename".
    00088          * @param source The source to write out.
    00089          * @param filename The name of the file to write.
    00090          * @return True if successful, false otherwise.
    00091          */
    00092         static boolean Write(gnBaseSource *source, const string& filename);
    00093         gnGenomeSpec *GetSpec() const;
    00094         gnFileContig* GetFileContig( const uint32 contigI ) const;
    00095 private:
    00096         boolean SeqSeek( const gnSeqI start, const uint32& contigI, uint64& startPos, uint64& readableBytes );
    00097         boolean SeqStartPos( const gnSeqI start, gnFileContig& contig, uint64& startPos, uint64& readableBytes );
    00098         boolean ParseStream( istream& fin );
    00099
    00100         static string& Filler(uint32 length);
    00101         static void FormatString(string& data, uint32 offset, uint32 width);
    00102         static void WriteHeader(gnMultiSpec* spec, const string& hdr, ofstream& m_ofstream);
    00103 //      gnSeqI m_seqLength;
    00104
    00105         gnGenomeSpec *m_spec;
    00106         vector< gnFileContig* > m_contigList;
    00107 };// class gnGBKSource
    00108 // Clone
    00109 inline
    00110 gnGBKSource* gnGBKSource::Clone() const
    00111 {
    00112         return new gnGBKSource( *this );
    00113 }
    00114 // Contig Access methods
    00115 inline
    00116 uint32 gnGBKSource::GetContigListLength() const
    00117 {
    00118         return m_contigList.size();
    00119 }
    00120 inline
    00121 boolean gnGBKSource::Write(gnBaseSource *source, const string& filename){
    00122         gnSequence gns(*source->GetSpec());
    00123         return Write(gns, filename);
    00124 }
    00125 inline
    00126 gnGenomeSpec *gnGBKSource::GetSpec() const{
    00127         return m_spec->Clone();
    00128 }
    00129
    00130 #endif
    00131         // _gnGBKSource_h_