gnFileSource.cpp Source File

00001 
00002 // File:            gnFileSource.h
00003 // Purpose:         Implements generic gnBaseSource methods
00004 // Description:     Provides a general implementation for accessing DNA
00005 //                  sequence contig data files.
00006 // Changes:        
00007 // Version:         libGenome 0.1.0 
00008 // Author:          Aaron Darling 
00009 // Last Edited:     April 15, 2001, 11:13:00pm 
00010 // Modified by:     
00011 // Copyright:       (c) Aaron Darling 
00012 // Licenses:        Proprietary 
00014 #include "gn/gnFileSource.h"
00015 #include <fstream>
00016 #include "gn/gnFilter.h"
00017 
00018 //copy constructor
00019 gnFileSource::gnFileSource(const gnFileSource& gnfs){
00020         m_openString = gnfs.m_openString;
00021         m_pFilter = gnfs.m_pFilter;
00022         m_newlineType = gnfs.m_newlineType;
00023         m_newlineSize = gnfs.m_newlineSize;
00024         m_ifstream.open( m_openString.c_str(), ios::in | ios::binary );
00025         if( !m_ifstream.is_open() )
00026                 m_ifstream.clear();
00027 }
00028 
00029 // Open, Close  
00030 void gnFileSource::Open( string openString )
00031 {
00032         m_ifstream.open(openString.c_str(), ios::in | ios::binary );
00033         if( m_ifstream.is_open() )
00034         {
00035                 m_openString = openString;
00036                 if( ParseStream(m_ifstream) )
00037                 {
00038                         ;
00039                 }
00040                 else{
00041                         m_ifstream.clear();
00042                         m_ifstream.close();
00043                 }
00044         }else{
00045                 m_ifstream.clear();
00046                 Throw_gnEx(FileNotOpened());
00047         }
00048 }
00049 void gnFileSource::Open( )
00050 {
00051         m_ifstream.open( m_openString.c_str(), ios::in | ios::binary );
00052         if( !m_ifstream.is_open() ){
00053                 m_ifstream.clear();
00054                 Throw_gnEx(FileNotOpened());
00055         }
00056 }
00057 void gnFileSource::Close()
00058 {
00059         m_ifstream.close();
00060         if( m_ifstream.is_open() )
00061                 Throw_gnEx(IOStreamFailed());
00062 }
00063 
00064 boolean gnFileSource::Read( const uint64 pos, char* buf, uint32& bufLen) 
00065 {
00066         m_ifstream.seekg(pos, ios::beg);
00067         m_ifstream.read(buf, bufLen);
00068         if(m_ifstream.fail()){
00069                 m_ifstream.clear();
00070                 return false;
00071         }
00072         return true;
00073 }