gnABISource.cpp 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, 11:13:00pm 
00009 // Modified by:     
00010 // Copyright:       (c) Aaron Darling 
00011 // Licenses:        Proprietary 
00013 #include "gn/gnABISource.h"
00014 
00015 gnABISource::gnABISource()
00016 {
00017         m_openString = "";
00018         m_pFilter = gnFilter::fullDNASeqFilter();
00019 }
00020 gnABISource::gnABISource( const gnABISource& s ) : gnFileSource(s)
00021 {
00022         vector< gnFileContig* >::const_iterator iter = s.m_contigList.begin();
00023         for( ; iter != s.m_contigList.end(); ++iter )
00024         {
00025                 m_contigList.push_back( *iter );
00026         }
00027 }
00028 gnABISource::~gnABISource()
00029 {
00030         m_ifstream.close();
00031         vector< gnFileContig* >::iterator iter = m_contigList.begin();
00032         for( ; iter != m_contigList.end(); ++iter )
00033         {
00034                 gnFileContig* fg = *iter;
00035                 *iter = 0;
00036                 delete fg;
00037         }
00038 }
00039 
00040 // Contig Access methods        
00041 boolean gnABISource::HasContig( const string& name ) const
00042 {
00043         vector< gnFileContig* const>::iterator iter = m_contigList.begin();
00044         for( ; iter != m_contigList.end(); ++iter )
00045         {
00046                 if( name == (*iter)->GetName() )
00047                         return true;
00048         }
00049         return false;
00050 }
00051 uint32 gnABISource::GetContigID( const string& name ) const
00052 {
00053         vector< gnFileContig* const>::iterator iter = m_contigList.begin();
00054         for( ; iter != m_contigList.end(); ++iter )
00055         {
00056                 if( name == (*iter)->GetName() )
00057                         return iter - m_contigList.begin();
00058         }
00059         return ALL_CONTIGS;
00060 }
00061 
00062 string gnABISource::GetContigName( uint32 i ) const{
00063         if( i < m_contigList.size() ){
00064                 return m_contigList[i]->GetName();
00065         }
00066         return "";
00067 }
00068 
00069 gnSeqI gnABISource::GetContigSeqLength( uint32 i ) const{
00070         if( i < m_contigList.size() )
00071         {
00072                 return m_contigList[i]->GetSeqLength();
00073         }else if( i == ALL_CONTIGS){
00074                 gnSeqI seqlen = 0;
00075                 for(int j=0; j < m_contigList.size(); j++)
00076                         seqlen += m_contigList[j]->GetSeqLength();
00077                 return seqlen;
00078         }
00079         return GNSEQI_ERROR;
00080 }
00081 
00082 boolean gnABISource::SeqRead( const gnSeqI start, char* buf, uint32& bufLen, const uint32 contigI )
00083 {
00084         return false;
00085 }
00086 
00087 boolean gnABISource::SeqSeek( const gnSeqI start, const uint32& contigI, uint64& startPos, uint64& readableBytes ){
00088         return SeqStartPos( start, *(m_contigList[contigI]), startPos, readableBytes );
00089 }
00090 
00091 boolean gnABISource::SeqStartPos( const gnSeqI start, gnFileContig& contig, uint64& startPos, uint64& readableBytes )
00092 {
00093         return false;
00094 }
00095 
00096 gnFileContig* gnABISource::GetFileContig( const uint32 contigI ) const{
00097         if(m_contigList.size() > contigI)
00098                 return m_contigList[contigI];
00099         return NULL;
00100 }
00101  
00102 boolean gnABISource::ParseStream( istream& fin )
00103 {
00104         return false;
00105 }