gnRAWSource.h Source File

00001 
00002 // File:            gnRAWSource.h
00003 // Purpose:         Implements gnBaseSource for raw data 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 _gnRAWSource_h_
00015 #define _gnRAWSource_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 
00035 
00036 class GNDLLEXPORT gnRAWSource : public gnFileSource
00037 {
00038 public:
00042         gnRAWSource();  
00047         gnRAWSource( const gnRAWSource& s );
00051         ~gnRAWSource();
00055         gnRAWSource* Clone() const;
00056 // Contig Access methods        
00057         uint32 GetContigListLength() const;
00058         boolean HasContig( const string& name ) const;
00059         uint32 GetContigID( const string& name ) const;
00060         string GetContigName( const uint32 i ) const;
00061         gnSeqI GetContigSeqLength( const uint32 i ) const;
00062 
00063         boolean SeqRead( const gnSeqI start, char* buf, uint32& bufLen, const uint32 contigI=ALL_CONTIGS );
00064 
00071         static boolean Write(gnSequence& sequence, const string& filename);
00078         static boolean Write(gnBaseSource *source, const string& filename);
00079         gnGenomeSpec *GetSpec() const;
00080         gnFileContig* GetFileContig( const uint32 contigI ) const;
00081 private:
00082         boolean SeqSeek( const gnSeqI start, const uint32& contigI, uint64& startPos, uint64& readableBytes );
00083         boolean SeqStartPos( const gnSeqI start, gnFileContig& contig, uint64& startPos, uint64& readableBytes );
00084         boolean ParseStream( istream& fin );
00085         
00086         gnFileContig* m_contig; 
00087         gnGenomeSpec* m_spec;
00088 };// class gnRAWSource
00089 // Clone        
00090 inline
00091 gnRAWSource* gnRAWSource::Clone() const
00092 {
00093         return new gnRAWSource( *this );
00094 }
00095 // Contig Access methods        
00096 inline
00097 uint32 gnRAWSource::GetContigListLength() const
00098 {
00099         return m_contig == NULL? 0 : 1;
00100 }
00101 inline
00102 boolean gnRAWSource::Write(gnBaseSource *source, const string& filename){
00103         gnSequence gns(*source->GetSpec());
00104         return Write(gns, filename);
00105 }
00106 
00107 #endif
00108         // _gnRAWSource_h_