gnFileContig.cpp Source File

00001 
00002 // File:            gnFileContig.h
00003 // Purpose:         File Position holder.
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/gnFileContig.h"
00014 #include <iostream>
00015 
00016 gnFileContig::gnFileContig()
00017 {
00018         Clear();
00019 }
00020 gnFileContig::gnFileContig( string nameStr, const uint64 s, const uint64 e )
00021 {
00022         Clear();
00023         m_name = nameStr;
00024         m_fileStartEnd.first = s;
00025         m_fileStartEnd.second = e;
00026 }
00027 gnFileContig::gnFileContig( const gnFileContig& fc )
00028 {
00029         m_name = fc.m_name;
00030         m_seqLength = fc.m_seqLength;
00031         m_fileStartEnd = fc.m_fileStartEnd;
00032         for( uint32 i=0; i < CONTIG_SECTION_SIZE; ++i )
00033                 m_startEndArray[i] = fc.m_startEndArray[i];
00034         m_repeatSeqGap = fc.m_repeatSeqGap;
00035         m_repeatSeqGapSize = fc.m_repeatSeqGapSize;
00036 }
00037 gnFileContig::~gnFileContig()
00038 {
00039 }
00040 void gnFileContig::Clear()
00041 {
00042         m_name = "";
00043         m_seqLength = 0;
00044         m_fileStartEnd = pair<uint64,uint64>(0,0);
00045         for( uint32 i=0; i < CONTIG_SECTION_SIZE; ++i )
00046                 m_startEndArray[i] = pair<uint64,uint64>(0,0);
00047         m_repeatSeqGap = false;
00048         m_repeatSeqGapSize = pair<uint64,uint64>(0,0);
00049 }
00050 
00051 boolean gnFileContig::SetRepeatSeqSize( const uint64 seqSize )
00052 {
00053         if( !m_repeatSeqGap )
00054                 return false;
00055         if( m_repeatSeqGapSize.first == seqSize )
00056                 return true;
00057         if( m_repeatSeqGapSize.first == 0 )
00058         {
00059                 m_repeatSeqGapSize.first = seqSize;
00060                 return true;
00061         }
00062         m_repeatSeqGap = false;
00063         return false;
00064 }
00065 boolean gnFileContig::SetRepeatGapSize( const uint64 gapSize )
00066 {
00067         if( !m_repeatSeqGap )
00068                 return false;
00069         if( m_repeatSeqGapSize.second == gapSize )
00070                 return true;
00071         if( m_repeatSeqGapSize.second == 0 )
00072         {
00073                 m_repeatSeqGapSize.second = gapSize;
00074                 return true;
00075         }
00076         m_repeatSeqGap = false;
00077         return false;
00078 }