gnABISource.h Source File

00001 
00002 // File:            gnABISource.h
00003 // Purpose:         Implements gnBaseSource for ABI 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 _gnABISource_h_
00014 #define _gnABISource_h_
00015 
00016 #include "gn/gnDefs.h"
00017 
00018 #include <string>
00019 #include "gn/gnFileSource.h"
00020 #include "gn/gnFileContig.h"
00021 #include "gn/gnSourceSpec.h"
00022 #include "gn/gnFilter.h"
00023 
00027 class GNDLLEXPORT gnABISource : public gnFileSource
00028 {
00029 public:
00030         gnABISource();  
00035         gnABISource( const gnABISource& s );
00036         ~gnABISource();
00037         gnABISource* Clone() const;
00038 
00039         uint32 GetContigListLength() const;
00040         boolean HasContig( const string& name ) const;
00041         uint32 GetContigID( const string& name ) const;
00042         string GetContigName( uint32 i ) const;
00043         gnSeqI GetContigSeqLength( uint32 i ) const;
00044         gnFileContig* GetContig( const uint32 i ) const;
00045 
00046         boolean SeqRead( const gnSeqI start, char* buf, uint32& bufLen, const uint32 contigI=ALL_CONTIGS );
00047 
00054         static boolean Write(gnSequence& sequence, const string& filename);
00055         gnGenomeSpec *GetSpec() const;
00056 
00057         gnFileContig* GetFileContig( const uint32 contigI ) const;
00058 private:
00059         boolean SeqSeek( const gnSeqI start, const uint32& contigI, uint64& startPos, uint64& readableBytes );
00060         boolean SeqStartPos( const gnSeqI start, gnFileContig& contig, uint64& startPos, uint64& readableBytes );
00061         boolean ParseStream( istream& fin );
00062 
00063         gnGenomeSpec *m_spec;
00064         vector< gnFileContig* > m_contigList;   
00065 
00066 };// class gnABISource
00067 
00068 inline
00069 gnABISource* gnABISource::Clone() const
00070 {
00071         return new gnABISource( *this );
00072 }
00073 inline
00074 uint32 gnABISource::GetContigListLength() const
00075 {
00076         return m_contigList.size();
00077 }
00078 inline
00079 gnGenomeSpec *gnABISource::GetSpec() const
00080 {
00081         return m_spec->Clone();
00082 }
00083 
00084 #endif
00085         // _gnABISource_h_