gnFileSource.h Source File

00001 
00002 // File:            gnFileSource.h
00003 // Purpose:         Implements gnBaseSource for .File 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 _gnFileSource_h_
00014 #define _gnFileSource_h_
00015 
00016 #include "gn/gnDefs.h"
00017 
00018 #include <string>
00019 #include <fstream>
00020 #include "gn/gnBaseSource.h"
00021 #include "gn/gnFileContig.h"
00022 #include "gn/gnException.h"
00023 
00028 class GNDLLEXPORT gnFileSource : public gnBaseSource
00029 {
00030 public:
00031         gnFileSource(){}
00032         gnFileSource(const gnFileSource& gnfs);
00033         virtual ~gnFileSource(){}
00034         virtual gnFileSource* Clone() const = 0;
00035         // Open, Close  
00036         virtual void Open( string openString );
00037         virtual void Open();
00038         virtual void Close();
00039         virtual string GetOpenString() const ;
00040           // Filter
00041         virtual const gnFilter* GetFilter() const ;
00042         virtual void SetFilter( gnFilter* filter );
00043 
00044         virtual boolean Read( const uint64 pos, char* buf, uint32& bufLen );
00049         virtual gnFileContig* GetFileContig( const uint32 contigI ) const = 0;
00050 protected:
00051         string m_openString;
00052         ifstream m_ifstream;
00053         const gnFilter* m_pFilter;
00054         gnNewlineType m_newlineType;
00055         uint32 m_newlineSize;
00056 private:
00057         virtual boolean ParseStream( istream& fin ) = 0;
00058 };// class gnFileSource
00059 
00060 inline
00061 string gnFileSource::GetOpenString( ) const
00062 {
00063         return m_openString;
00064 }
00065 // Filter
00066 inline
00067 const gnFilter* gnFileSource::GetFilter() const
00068 {
00069         return m_pFilter;
00070 }
00071 
00072 inline
00073 void gnFileSource::SetFilter( gnFilter* filter )
00074 {
00075         if(filter == NULL){
00076                 Throw_gnEx(NullPointer());
00077         }
00078         m_pFilter = filter;
00079 }
00080 
00081 #endif
00082         // _gnFileSource_h_