gnStringSpec.cpp Source File

00001 
00002 // File:            gnStringSpec.cpp
00003 // Purpose:         implements gnContigSpec for strings
00004 // Description:     stores sequence in memory
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/gnStringSpec.h"
00015 #include <string>
00016 
00017 gnStringSpec::gnStringSpec()
00018 {
00019         Clear();
00020 }
00021 
00022 gnStringSpec::gnStringSpec( const string& m_string, gnSeqI start, gnSeqI endI, boolean revComp)
00023 {
00024         m_seqString = m_string;
00025         m_start = start;
00026         gnSeqI actual_len = m_seqString.length();
00027 
00028         //reverse comp has the end b.p. first, then start.  switch them.
00029         m_start = revComp ? endI : start;
00030         gnSeqI actual_end = revComp ? start : endI;
00031         //trim start and end down if they are too big.
00032         actual_end = actual_end < actual_len ? actual_end : actual_len -1;
00033         m_start = m_start < actual_len ? m_start : actual_len - 1;
00034         if(actual_len == 0)
00035                 m_start = 0;
00036         //if start is after end, we're using a circular sequence.
00037         m_circular = m_start > actual_end ? true : false;
00038         //if circular, the length will be different.
00039         m_length = m_circular ? (actual_len - m_start) + actual_end : actual_end - m_start + 1;
00040 
00041         m_reverseComplement = revComp;
00042         m_SourceContigIndex = ALL_CONTIGS;
00043 }
00044 
00045 gnStringSpec::gnStringSpec( const gnStringSpec& s )
00046 {
00047         m_seqString = s.m_seqString;
00048         m_sourceName = s.m_sourceName;
00049         m_name = s.m_name;
00050         m_start = s.m_start;
00051         m_length = s.m_length;
00052         m_reverseComplement = s.m_reverseComplement;
00053         m_circular = s.m_circular;
00054         m_SourceContigIndex = s.m_SourceContigIndex;
00055 }
00056 gnStringSpec::~gnStringSpec()
00057 {
00058         Clear();
00059 }
00060 void gnStringSpec::Clear()
00061 {
00062         gnContigSpec::Clear();
00063         m_seqString = "";
00064 }
00065 
00066 gnStringSpec* gnStringSpec::CloneRange( const gnSeqI startI, const gnSeqI len ) const{
00067         gnStringSpec* destSpec = new gnStringSpec();
00068         destSpec->m_seqString = m_seqString.substr(m_start + startI, len);
00069         destSpec->m_sourceName = m_sourceName;
00070         destSpec->m_name = m_name;
00071         destSpec->m_start = 0;
00072         destSpec->m_length = destSpec->m_seqString.length();
00073         destSpec->m_reverseComplement = m_reverseComplement;
00074         destSpec->m_circular = m_circular;
00075         destSpec->m_SourceContigIndex = m_SourceContigIndex;
00076         return destSpec;
00077 }