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/*******************************************************************************
* $Id: Match.cpp,v 1.9 2004/03/01 02:40:08 darling Exp $
* This file is copyright 2002-2007 Aaron Darling and authors listed in the AUTHORS file.
* Please see the file called COPYING for licensing, copying, and modification
* Please see the file called COPYING for licensing details.
* **************
******************************************************************************/
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#include "libMems/RepeatMatch.h"
#include "libGenome/gnException.h"
#include "libGenome/gnDebug.h"
namespace mems {
RepeatMatch::RepeatMatch() : MatchHashEntry()
{
}
RepeatMatch::~RepeatMatch(){
}
void RepeatMatch::FromSeq( uint32 match_id, uint32 seq_id )
{
// unsure what to do with this: (it doesn't compile)
// this->m_seq_id.insert( match_id, seq_id);
}
uint32 RepeatMatch::SeqId( uint32 match_id )
{
return this->m_seq_id.at(match_id);
}
std::ostream& operator<<(std::ostream& os, const RepeatMatch& mhe){ //write to stream.
os << mhe.Length();
for(uint32 i=0; i < mhe.SeqCount(); i++)
{
//if ( mhe.Start(i) <
os << '\t' << mhe.Start(i);
}
return os;
}
} // namespace mems
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