gnSEQSource.h Source File

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# gnSEQSource.h

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    00001
    00002 // File:            gnSEQSource.h
    00003 // Purpose:         Implements gnBaseSource for .SEQ 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 _gnSEQSource_h_
    00015 #define _gnSEQSource_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
    00034
    00035 class GNDLLEXPORT gnSEQSource : public gnFileSource
    00036 {
    00037 public:
    00041         gnSEQSource();
    00046         gnSEQSource( const gnSEQSource& s );
    00050         ~gnSEQSource();
    00054         gnSEQSource* Clone() const;
    00055 // Contig Access methods
    00056         uint32 GetContigListLength() const;
    00057         boolean HasContig( const string& name ) const;
    00058         uint32 GetContigID( const string& name ) const;
    00059         string GetContigName( const uint32 i ) const;
    00060         gnSeqI GetContigSeqLength( const uint32 i ) const;
    00061
    00062         boolean SeqRead( const gnSeqI start, char* buf, uint32& bufLen, const uint32 contigI=ALL_CONTIGS );
    00063
    00070         static boolean Write(gnSequence& sequence, const string& filename);
    00077         static boolean Write(gnBaseSource *source, const string& filename);
    00084         static boolean Write(gnGenomeSpec *spec, const string& filename);
    00085         gnGenomeSpec *GetSpec() const;
    00086         gnFileContig* GetFileContig( const uint32 contigI ) const;
    00087 private:
    00088         boolean SeqSeek( const gnSeqI start, const uint32& contigI, uint64& startPos, uint64& readableBytes );
    00089         boolean SeqStartPos( const gnSeqI start, gnFileContig& contig, uint64& startPos, uint64& readableBytes );
    00090         boolean ParseStream( istream& fin );
    00091
    00092         static string& Filler(uint32 length);
    00093         static void FormatString(string& data, uint32 offset, uint32 width);
    00094         static void BaseCount(const string& bases, gnSeqI& a_count, gnSeqI& c_count, gnSeqI& g_count, gnSeqI& t_count, gnSeqI& other_count);
    00095 //      gnSeqI m_seqLength;
    00096
    00097         gnGenomeSpec *m_spec;
    00098         vector< gnFileContig* > m_contigList;
    00099 };// class gnSEQSource
    00100 // Clone
    00101 inline
    00102 gnSEQSource* gnSEQSource::Clone() const
    00103 {
    00104         return new gnSEQSource( *this );
    00105 }
    00106 // Contig Access methods
    00107 inline
    00108 uint32 gnSEQSource::GetContigListLength() const
    00109 {
    00110         return m_contigList.size();
    00111 }
    00112 inline
    00113 boolean gnSEQSource::Write(gnSequence& sequence, const string& filename){
    00114         return Write(sequence.GetSpec(), filename);
    00115 }
    00116 inline
    00117 boolean gnSEQSource::Write(gnBaseSource *source, const string& filename){
    00118         return Write(source->GetSpec(), filename);
    00119 }
    00120 inline
    00121 gnGenomeSpec *gnSEQSource::GetSpec() const{
    00122         return m_spec->Clone();
    00123 }
    00124
    00125 #endif
    00126         // _gnSEQSource_h_
    00127