gnBaseSource.h Source File

00001 
00002 // File:            gnBaseSource.h
00003 // Purpose:         Abstract source class
00004 // Description:     Basic interface to all source objects
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 _gnBaseSource_h_
00014 #define _gnBaseSource_h_
00015 
00016 #include "gn/gnDefs.h"
00017 
00018 #include <string>
00019 
00020 #include "gn/gnClone.h"
00021 class gnGenomeSpec;
00022 class gnFilter;
00023 
00032 class GNDLLEXPORT gnBaseSource : public gnClone
00033 {
00034 public:
00035         gnBaseSource(){}
00039         virtual ~gnBaseSource(){}
00040         virtual gnBaseSource* Clone() const = 0;
00041 
00050         virtual void Open( string openString ) = 0;
00056         virtual void Open() = 0;
00061         virtual void Close() = 0;
00067         virtual string GetOpenString() const = 0;
00068 
00073         virtual uint32 GetContigListLength() const = 0;
00080         virtual boolean HasContig( const string& name ) const = 0;
00088         virtual uint32 GetContigID( const string& name ) const = 0;
00095         virtual string GetContigName( const uint32 i ) const = 0;
00101         virtual gnSeqI GetContigSeqLength( const uint32 i ) const = 0;
00102 
00107         virtual const gnFilter* GetFilter() const = 0;
00113         virtual void SetFilter( gnFilter* filter ) = 0;
00114 
00125         virtual boolean Read( const uint64 pos, char* buf, uint32& len) = 0;
00139         virtual boolean SeqRead( const gnSeqI start, char* buf, uint32& bufLen, const uint32 contigI=ALL_CONTIGS ) = 0;
00146         virtual gnGenomeSpec *GetSpec() const = 0;
00147 private:
00148 };// class gnBaseSource
00149 
00150 #endif
00151         // _gnBaseSource_h_