libMems/FileSML.h

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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();
        
        virtual void LoadFile(const std::string& fname);
        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:
        virtual void OpenForWriting( boolean truncate = false );
        virtual boolean WriteHeader();
        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;        
        std::vector< int64 > seq_coords;        
};

// 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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