gnFASSource.h Source File

00001 
00002 // File:            gnFASSource.h
00003 // Purpose:         Implements gnBaseSource for .FAS 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 #ifndef _gnFASSource_h_
00014 #define _gnFASSource_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/gnSequence.h"
00023 
00024 #define FAS_LINE_WIDTH 80
00025 
00032 
00033 class GNDLLEXPORT gnFASSource : public gnFileSource
00034 {
00035 public:
00039         gnFASSource();
00044         gnFASSource( const gnFASSource& s );
00048         ~gnFASSource();
00052         gnFASSource* Clone() const;
00053 
00054         uint32 GetContigListLength() const;
00055         boolean HasContig( const string& nameStr ) const;
00056         uint32 GetContigID( const string& nameStr ) const;
00057         string GetContigName( const uint32 i ) const;
00058         gnSeqI GetContigSeqLength( const uint32 i ) const;
00059         gnFileContig* GetContig( const uint32 i ) const;
00060 
00061         boolean SeqRead( const gnSeqI start, char* buf, uint32& bufLen, const uint32 contigI=ALL_CONTIGS ) ;
00062         
00077         static void Write(gnSequence& sequence, const string& filename, boolean write_coords = true, boolean enforce_unique_names = true);
00078 
00092         static void Write(gnSequence& sequence, ostream& m_ostream, boolean write_coords = true, boolean enforce_unique_names = true);
00093 
00100         static boolean Write(gnBaseSource *source, const string& filename);
00101 //      /**
00102 //       * deprecated - do not use
00103 //       * Writes the given spec to a FastA file named "filename".
00104 //       * @param spec The spec to write out.
00105 //       * @param filename The name of the file to write.
00106 //       * @return True if successful, false otherwise.
00107 //       */
00108 //      static boolean Write(gnGenomeSpec *spec, const string& filename);
00109         gnGenomeSpec *GetSpec() const;
00110         
00111         gnFileContig* GetFileContig( const uint32 contigI ) const;
00112 private:
00113         boolean SeqSeek( const gnSeqI start, const uint32 contigI, uint64& startPos, uint64& readableBytes );
00114         boolean SeqStartPos( const gnSeqI start, gnFileContig& contig, uint64& startPos, uint64& readableBytes );
00115         boolean ParseStream( istream& fin );
00116         
00117         vector< gnFileContig* > m_contigList;
00118 };// class gnFASSource
00119 
00120 inline
00121 gnFASSource* gnFASSource::Clone() const
00122 {
00123         return new gnFASSource( *this );
00124 }
00125 
00126 inline
00127 uint32 gnFASSource::GetContigListLength() const
00128 {
00129         return m_contigList.size();
00130 }
00131 
00132 #endif
00133         // _gnFASSource_h_