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/*****************************************************************************
* *
* PLAST : Parallel Local Alignment Search Tool *
* Version 2.3, released November 2015 *
* Copyright (c) 2009-2015 Inria-Cnrs-Ens *
* *
* PLAST is free software; you can redistribute it and/or modify it under *
* the Affero GPL ver 3 License, that is compatible with the GNU General *
* Public License *
* *
* This program is distributed in the hope that it will be useful, *
* but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* Affero GPL ver 3 License for more details. *
*****************************************************************************/
#include <database/impl/BlastdbFileIndexReader.hpp>
#include <database/impl/DatabaseUtility.hpp>
#include <misc/api/PlastStrings.hpp>
#include <os/impl/CommonOsImpl.hpp>
#include <os/impl/DefaultOsFactory.hpp>
#include <misc/api/macros.hpp>
#define DEBUG(a) //printf a
using namespace std;
using namespace dp;
using namespace os::impl;
using namespace database::impl;
/********************************************************************************/
namespace database { namespace impl {
/********************************************************************************/
/*********************************************************************
** METHOD :
** PURPOSE :
** INPUT :
** OUTPUT :
** RETURN :
** REMARKS :
*********************************************************************/
BlastdbFileIndexReader::BlastdbFileIndexReader (const char* filename)
: _filename(filename),_version(0),
_dbKind (IDatabaseQuickReader::ENUM_UNKNOWN),
_title(""),_timestamp(""),
_dataSize(0), _nbSequences(0), _maxSeqSize(0),_startIndexOffsetTable(0),
_sequenceFilesize(0),_startSequenceIndex(0), _data(NULL)
{
u_int32_t foundPoint;
foundPoint = std::string(filename).find_last_of(".");
_filenameWithoutExt = std::string(filename).substr(0,foundPoint);
/** Open the File index depending of the extension nin = Nucleotides, pin = Protein*/
DatabaseLookupType::QuickReaderType_e databaseType;
databaseType = DatabaseLookupType::quickReaderType(filename);
_fileindex = DefaultFactory::fileMem().newFile (filename);
if ((databaseType == DatabaseLookupType::ENUM_BLAST_PIN)||(databaseType == DatabaseLookupType::ENUM_BLAST_PAL))
_dbKind = IDatabaseQuickReader::ENUM_AMINO_ACID;
else if ((databaseType == DatabaseLookupType::ENUM_BLAST_NIN)||(databaseType == DatabaseLookupType::ENUM_BLAST_NAL))
_dbKind = IDatabaseQuickReader::ENUM_NUCLOTID;
else
_dbKind = IDatabaseQuickReader::ENUM_UNKNOWN;
}
/*********************************************************************
** METHOD :
** PURPOSE :
** INPUT :
** OUTPUT :
** RETURN :
** REMARKS :
*********************************************************************/
BlastdbFileIndexReader::~BlastdbFileIndexReader ()
{
delete (_fileindex);
}
/*********************************************************************
** METHOD :
** PURPOSE :
** INPUT :
** OUTPUT :
** RETURN :
** REMARKS :
*********************************************************************/
void BlastdbFileIndexReader::read ()
{
u_int32_t templength=0;
u_int32_t index=0;
_data = _fileindex->getData();
_dataSize = 0;
_nbSequences = 0;
/** We read the 3 first 32 bytes in order to get :
* Version : Int32
* Database Type : Int32
* Title Length : Int32. */
index=3;
_version = _data[index];
index+=4;
_dbKind = (_data[index]==0) ? IDatabaseQuickReader::ENUM_NUCLOTID : IDatabaseQuickReader::ENUM_AMINO_ACID;;
index++;
/** Read the title length */
templength = CHAR_TO_INT32(_data[index],_data[index+1],_data[index+2],_data[index+3]);
index+=4;
/** Read the timestamp length */
index+=templength;
templength = CHAR_TO_INT32(_data[index],_data[index+1],_data[index+2],_data[index+3]);
index+=4;
/** We read the 4 next 32 bytes in order to get :
* Sequences number : Int32
* Data size : Int64
* Sequence max size : Int32. */
index+=templength;
_nbSequences = CHAR_TO_INT32(_data[index],_data[index+1],_data[index+2],_data[index+3]);
index+=4;
_dataSize = CHAR_TO_INT64(_data[index+7],_data[index+6],_data[index+5],_data[index+4],
_data[index+3],_data[index+2], _data[index+1],_data[index+0]);
index+=8;
_maxSeqSize = CHAR_TO_INT32(_data[index],_data[index+1],_data[index+2],_data[index+3]);
index+=4;
/** Save the index to start to read the offset table */
_startIndexOffsetTable = index;
/** Read the last offset of the offset sequence table to get the sequence file size */
index+=2*((_nbSequences+1)*4)-4;
_sequenceFilesize = CHAR_TO_INT32(_data[index],_data[index+1],_data[index+2],_data[index+3]);
}
/********************************************************************************/
} } /* end of namespaces. */
/********************************************************************************/
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