gnSEQSource.h Source File

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