/usr/include/libMems-1.6/libMems/FileSML.h is in libmems-1.6-dev 1.6.0+4725-4build1.
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: FileSML.h,v 1.11 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 _FileSML_h_
#define _FileSML_h_
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#pragma warning(push)
#pragma warning(disable : 4996)
#pragma warning(pop)
#include "libGenome/gnSequence.h"
#include "libMems/SortedMerList.h"
#include <boost/iostreams/device/mapped_file.hpp>
#include <fstream>
#include <vector>
#include <string>
namespace mems {
//sequence database size will be
//base_count / 4 + base_count * 12 bytes
#define DEFAULT_MEMORY_MINIMUM 20971520 //~20 Megabytes
class FileSML : public SortedMerList
{
public:
FileSML() : SortedMerList() {
// file_mutex = new wxMutex();
};
FileSML& operator=(const FileSML& sa);
virtual FileSML* Clone() const = 0;
virtual void Clear();
/**
* Loads an existing sorted mer list from a file on disk.
* @param fname The name of the file to load
* @throws FileNotOpened thrown if the file could not be opened
* @throws FileUnreadable thrown if the file was corrupt or not a sorted mer list
*/
virtual void LoadFile(const std::string& fname);
/**
* Creates large sorted mer lists which do not fit entirely in memory.
* BigCreate uses an external mergesort to create large sorted mer lists.
* It will divide the data a number of times specified by the split_levels
* parameter. Each split is written to temp files on disk and merged.
* @param seq The sequence to create an SML for.
* @param split_levels The number of times to divide the sequence in half.
* @param mersize The size of the mers to sort on.
* @see FileSML::Create
*/
virtual void BigCreate(const genome::gnSequence& seq, const uint32 split_levels, const uint32 mersize = DNA_MER_SIZE);
virtual void Create(const genome::gnSequence& seq, const uint64 seed );
virtual boolean Read(std::vector<bmer>& readVector, gnSeqI size, gnSeqI offset = 0);
virtual void Merge(SortedMerList& sa, SortedMerList& sa2);
virtual bmer operator[]( gnSeqI index );
virtual gnSeqI UniqueMerCount();
virtual void SetDescription(const std::string& d);
virtual void SetID(const sarID_t d);
virtual uint32 FormatVersion();
static uint64 MemoryMinimum();
virtual void RadixSort(std::vector<bmer>& s_array);
void dmCreate(const genome::gnSequence& seq, const uint64 seed);
static void registerTempPath( const std::string& tmp_path );
static const char* getTempPath( int pathI );
static int getTempPathCount();
const std::vector< int64 >& getUsedCoordinates() const { return seq_coords; };
protected:
/**
* Reopens the sarfile fstream in read/write mode
* @throws FileNotOpened thrown if the file could not be opened for writing
*/
virtual void OpenForWriting( boolean truncate = false );
/**
* Writes the SML header to disk
* @throws FileNotOpened thrown if the file could not be opened for writing
* @throws IOStreamFailed thrown if an error occurred writing the data
*/
virtual boolean WriteHeader();
/**
* Calculates and returns the amount of memory needed to create a sorted
* mer list for a sequence of the specified length.
* @param len The length of the sequence
* @return The amount of memory needed in bytes.
*/
virtual uint64 GetNeededMemory(gnSeqI len) = 0;
std::string filename;
std::fstream sarfile;
uint64 sarray_start_offset;
boost::iostreams::mapped_file_source sardata;
smlSeqI_t* base(){ return (smlSeqI_t*)(sardata.data()+sarray_start_offset); }
static char** tmp_paths; /**< paths to scratch disk space that can be used for an external sort */
std::vector< int64 > seq_coords; /**< If Ns are masked, contains coordinates of regions without Ns */
};
// versions 2 and 5 were previous
// jump to 100 to avoid confusion with DNAFileSML
inline
uint32 FileSML::FormatVersion(){
static uint32 f_version = 100;
return f_version;
}
inline
uint64 FileSML::MemoryMinimum(){
static uint32 m_minimum = DEFAULT_MEMORY_MINIMUM;
return m_minimum;
}
void maskNNNNN( const genome::gnSequence& in_seq, genome::gnSequence& out_seq, std::vector< int64 >& seq_coords, int mask_n_length );
}
#endif //_FileSML_h_
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