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/*
Ray -- Parallel genome assemblies for parallel DNA sequencing
Copyright (C) 2011, 2012, 2013 Sébastien Boisvert
http://DeNovoAssembler.SourceForge.Net/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, version 3 of the 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
GNU General Public License for more details.
You have received a copy of the GNU General Public License
along with this program (gpl-3.0.txt).
see <http://www.gnu.org/licenses/>
*/
#ifndef _ExtensionElement
#define _ExtensionElement
#include <code/SequencesIndexer/PairedRead.h>
#include <code/SequencesLoader/Read.h>
#include <code/Mock/Parameters.h>
#include <RayPlatform/memory/MyAllocator.h>
/*
* An extension element is a read mapped on an
* extension for an MPI rank.
*
* \author Sébastien Boisvert
*/
class ExtensionElement{
PairedRead m_pairedRead;
Read m_read;
int m_position;
uint16_t m_strandPosition;
char m_strand;
bool m_hasPairedRead;
uint8_t m_type;
bool m_canMove;
/** the overall agreement of this molecular target */
uint16_t m_agreement;
uint8_t m_numberOfTries;
bool m_activated;
public:
void setStrandPosition(int a);
int getStrandPosition();
void setStartingPosition(int a);
void setStrand(char a);
void setPairedRead(PairedRead a);
void setType(int a);
bool hasPairedRead();
void setSequence(const char*a,MyAllocator*b);
int getPosition();
char getStrand();
PairedRead*getPairedRead();
void getSequence(char*sequence,Parameters*p);
int getReadLength();
bool isLeftEnd();
bool isRightEnd();
int getType();
void removeSequence();
void constructor();
bool canMove();
void freezePlacement();
void increaseAgreement();
int getAgreement();
void deactivate();
void activate();
bool isActive()const;
int getNumberOfTries()const;
void increaseNumberOfTries();
} ATTRIBUTE_PACKED;
#endif
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