/usr/include/libMems-1.6/libMems/RepeatMatchList.h is in libmems-1.6-dev 1.6.0+4725-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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* $Id: MatchList.h,v 1.10 2004/03/01 02:40:08 darling Exp $
* This file is copyright 2002-2007 Aaron Darling and authors listed in the AUTHORS file.
* This file is licensed under the GPL.
* Please see the file called COPYING for licensing details.
* **************
******************************************************************************/
#ifndef _RepeatMatchList_h_
#define _RepeatMatchList_h_
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#include <iostream>
#include <list>
#include "libMems/SortedMerList.h"
#include "libGenome/gnSequence.h"
#include "libMems/Match.h"
#include "libMems/MatchList.h"
//#include <valarray>
namespace mems {
// punt: Need to subclass AbstractMatchList, which can be a MatchList or RepeatMatchList
class RepeatMatchList : public MatchList {
public:
RepeatMatchList();
RepeatMatchList( const RepeatMatchList& ml );
void LoadSequences( std::ostream* log_stream );
void LoadSMLs( uint mer_size, std::ostream* log_stream );
/**
* Reads a MatchList from an input stream
* Sequence and SML file names are read into the seq_filename
* and sml_filename vectors, but the actual files are not
* opened. The calling function should load them after
* using this method.
* @param match_stream The input stream to read from
*/
void ReadList( std::istream& match_stream );
/**
* Writes a MatchList to the designated output stream
* @param match_stream The output stream to write to
*/
void WriteList( std::ostream& match_stream ) const;
//vector<string> sml_filename; /**< The file names of the sorted mer list for each sequence, may be empty or null */
//vector<string> seq_filename; /**< The file names of the sequence data, may be empty or null */
//vector<SortedMerList*> sml_table; /**< The sorted mer list associated with each sequence, may be empty or null */
//vector<genome::gnSequence*> seq_table; /**< The actual sequences associated with the matches stored in this list. Should not be empty or null. */
protected:
};
} // namespace mems
#endif
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