gnBaseSource.h Source File

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# gnBaseSource.h

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    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_