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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. *
*****************************************************************************/
/** \file AminoAcidDatabaseQuickReader.hpp
* \brief IDatabaseQuickReader implementation for amino acid database.
* \date 07/11/2011
* \author edrezen
*/
#ifndef _AMINO_ACID_DATABASE_QUICK_READER_HPP_
#define _AMINO_ACID_DATABASE_QUICK_READER_HPP_
/********************************************************************************/
#include <database/api/IDatabaseQuickReader.hpp>
/********************************************************************************/
namespace database {
/** \brief Implementation of concepts related to genomic databases. */
namespace impl {
/********************************************************************************/
/** \brief Implementation of IDatabaseQuickReader for amino acid database.
*
* This class takes a IDatabaseQuickReader instance as a reference (reference supposed
* to point to a nucleotide database). The different getters are then proxies to the
* reference. Most of the getters return the same information than the referenced instance
* but note for instance the 'getDataSize' method that divides by 3 the data size (which
* means that 3 nucleotides are needed to code an amino acid).
*
* This class is a Proxy Design Pattern.
*/
class AminoAcidDatabaseQuickReader : public IDatabaseQuickReader
{
public:
/** Constructor.
* \param[in] ref : a IDatabaseQuickReader instance on a nucleotide database.
*/
AminoAcidDatabaseQuickReader (IDatabaseQuickReader* ref) : _ref(0) { setRef (ref); }
/** Destructor. */
virtual ~AminoAcidDatabaseQuickReader () { setRef (0); }
/** \copydoc IDatabaseQuickReader::read */
void read (u_int64_t maxblocksize) { _ref->read (maxblocksize); }
/** \copydoc IDatabaseQuickReader::getUri */
std::string& getUri () { return _ref->getUri(); }
/** \copydoc IDatabaseQuickReader::getTotalSize */
u_int64_t getTotalSize () { return _ref->getTotalSize(); }
/** Returns the total read size (including only sequences data). This is the data size of the nucleotide
* reference divided by 3.
* \return the total size.
*/
u_int64_t getDataSize () { return _ref->getDataSize() / 3; }
/** \copydoc IDatabaseQuickReader::getNbSequences */
u_int32_t getNbSequences () { return _ref->getNbSequences(); }
/** \copydoc IDatabaseQuickReader::getOffsets */
std::vector<u_int64_t>& getOffsets () { return _ref->getOffsets(); }
/** Returns the kind of database (ADN or protein).
* \return always ENUM_AMINO_ACID.
*/
DatabaseKind_e getKind () { return ENUM_AMINO_ACID; }
/** Max block size of a bank. */
u_int64_t getMaxBlockSize() { return _ref->getMaxBlockSize(); }
/** */
dp::IProperties* getProperties () { return _ref->getProperties(); }
/** \copydoc IDatabaseQuickReader::load */
int load (const std::string& uri) { return _ref->load (uri); }
/** \copydoc IDatabaseQuickReader::save */
int save (const std::string& uri) { return _ref->save (uri); }
private:
/** Referenced nucleotide instance. */
IDatabaseQuickReader* _ref;
/** Smart setter for the _ref attribute. */
void setRef (IDatabaseQuickReader* ref) { SP_SETATTR(ref); }
};
/********************************************************************************/
} } /* end of namespaces. */
/********************************************************************************/
#endif /* _AMINO_ACID_DATABASE_QUICK_READER_HPP_ */
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