/usr/include/libMems-1.6/libMems/DNAFileSML.h is in libmems-1.6-dev 1.6.0+4725-4.
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: DNAFileSML.h,v 1.6 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 _DNAFileSML_h_
#define _DNAFileSML_h_
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#include "libMems/FileSML.h"
namespace mems {
/**
* The seed pattern for DNA SMLs must be palindromic
*/
class DNAFileSML : public FileSML
{
public:
DNAFileSML();
/**
* Load or create a DNAFileSML ()
* Attempts to load a DNA sorted mer list from the named file if it exists.
* If the given file does not exist it creates an empty DNAFileSML with
* the supplied translation table and alphabet bit size.
* @param fname The name of the file to create.
* @param table The array used to translate characters into binary code
* @param alpha_bits The number of bits each character consumes in binary
*/
DNAFileSML(const std::string& fname, const uint8* table = SortedMerList::BasicDNATable(), const uint32 alpha_bits = DNA_ALPHA_BITS);
DNAFileSML(const SortedMerList& sa);
DNAFileSML& operator=(const DNAFileSML& msa );
DNAFileSML* Clone() const;
virtual uint64 GetMer(gnSeqI position) const;
virtual uint32 FormatVersion();
virtual uint64 GetSeedMer( gnSeqI offset ) const;
protected:
virtual void FillSML(const genome::gnSequence& seq, std::vector<bmer>& sml_array);
virtual uint32 CalculateMaxMerSize() const;
virtual uint64 GetNeededMemory(gnSeqI len);
};
// version 3 was original DNAFileSML format
// version 4 was introduction of inexact seeds
// version 5 was fix in header struct for 64-bit seed size
inline
uint32 DNAFileSML::FormatVersion(){
static uint32 f_version = 5;
return f_version;
}
}
#endif //_DNAFileSML_h_
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