gnContigSpec.cpp Source File

00001 
00002 // File:            gnContigSpec.cpp
00003 // Purpose:         Abstract Contig Spec class
00004 // Description:     Defines an interface for contig specs
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 
00014 #include "gn/gnContigSpec.h"
00015 #include "gn/gnFilter.h"
00016 
00017 void gnContigSpec::CropStart( gnSeqI cropLen ){
00018         m_start = m_reverseComplement ? (GetSourceLength() + m_start - cropLen) % GetSourceLength() : (m_start + cropLen) % GetSourceLength();
00019         m_length -= cropLen;
00020         return;
00021 }
00022 
00023 void gnContigSpec::CropEnd( gnSeqI cropLen ){
00024         m_length -= cropLen;
00025 }
00026 
00027 void gnContigSpec::SetReverseComplement( const boolean value )
00028 {
00029         //translate coordinates if revComp has changed.
00030         if((m_reverseComplement != value) && (m_length > 0))
00031                 m_start = (m_start + m_length) % GetSourceLength();
00032         m_reverseComplement = value;
00033 }
00034 
00035 boolean gnContigSpec::SeqRead(const gnSeqI start, gnSeqC* buf, uint32& bufLen, const uint32 contigI ) const{
00036         boolean success;
00037         bufLen = bufLen < m_length - start? bufLen : m_length - start;  //trim the read down to size.
00038         gnSeqI readable = bufLen;
00039         gnSeqI read_start = start;      // coordinate translation
00040 
00041         if(contigI == ALL_CONTIGS)
00042                 read_start = m_reverseComplement ? (m_start - start - readable + GetSourceLength()) % GetSourceLength() : start + m_start;
00043 
00044         success = Read(read_start, buf, readable);
00045 
00046         if(m_circular){
00047                 gnSeqI beginread = bufLen - readable;  //read whatever couldn't be read before
00048                 read_start = m_reverseComplement ? (m_start - readable + GetSourceLength()) % GetSourceLength() : m_start;
00049                 success = Read(read_start , buf + readable, beginread);
00050                 readable += beginread;
00051         }
00052 
00053         bufLen = readable;
00054 
00055         if(m_reverseComplement)
00056                 gnFilter::DNAComplementFilter()->ReverseFilter(&buf, bufLen);
00057 
00058         return success;
00059 }
00060 
00061 void gnContigSpec::Clear(){
00062         gnBaseSpec::Clear();
00063         m_start = 0;
00064         m_length = 0;
00065         m_SourceContigIndex = ALL_CONTIGS;
00066 }