Detailed Description

Definition at line 41 of file AlignerManager.hpp.

#include <AlignerManager.hpp>

Inheritance diagram for AlignerManager:

Public Member Functions
	AlignerManager (IAligner *aligner)
virtual	~AlignerManager ()
void	alignPartition (Partition partition, int startType)
void	setSequences (Sequence seq0, Sequence seq1, int i0, int j0, int i1, int j1, FILE *stats=NULL)
	Defines the partition that must be processed.
void	unsetSequences ()
	Clear all sequence strucutures.
void	setRecurrenceType (int recurrenceType)
	Defines that the first column must be initialized with a pre-defined column.
void	setBlockPruning (bool blockPruning)
	Defines if the aligner may do the block pruning optimization.
void	setSpecialRowsPartition (SpecialRowsPartition *specialRowsPartition)
	Defines the grid dimension of the grid, if capabilities_t::dispatch_block_scores is SUPPORTED.
void	setBestScoreList (BestScoreList *bestScoreList, const int bestScoreLocation=AT_NOWHERE)
	Defines the list to store the best scores.
void	setGoalScore (int goalScore, const int goalScoreLocation=AT_NOWHERE)
	Whenever the aligner finds the goal score, the processing must stop.
void	setLastColumnReader (SeekableCellsReader *lastColumnReader)
	Defines the previous special rows partition containing the rows to be matched against the last column/rows.
void	setLastRowReader (SeekableCellsReader *lastRowReader)
	Defines the previous special rows partition containing the rows to be matched against the last column/rows.
void	unsetGoalScore ()
	Do not find best score.
void	setBlocksFile (BlocksFile *blocksFile)
	Defines the file to store the best score of each block.
void	setSpecialRowInterval (const int specialRowInterval)
	Defines the minimum distance (in rows) between two special rows.
void	setPenalties (const int match, const int mismatch, const int gapOpen, const int gapExtension)
	Defines the variable penalty functions to be aligned.
void	setSuperPartition (Partition superPartition)
	Sets the super-partition being aligned to be returned by the IManager::getSuperPartition() method.
void	unsetSuperPartition ()
	Resets the super-partition.
const crosspoint_t	getNextCrosspoint () const
	Defines the callback function that will be called whenever the dispatchRow method is called for the last row.
bool	isFoundCrosspoint () const
	Return true if the next crosspoint was found.
int	getRecurrenceType () const
int	getSpecialRowInterval () const
int	getSpecialColumnInterval () const
int	getFirstColumnInitType ()
	Returns the initialization type of the first column.
int	getFirstRowInitType ()
	Returns the initialization type of the first row.
Partition	getSuperPartition ()
	Returns the super partition that includes all sub partitions being aligned.
void	receiveFirstRow (cell_t *buffer, int len)
	Receives the first row of the partition.
void	receiveFirstColumn (cell_t *buffer, int len)
	Receives the first column of the partition.
void	dispatchColumn (int j, const cell_t *buffer, int len)
	Notifies to the MASA framework that some cells of a column has been processed.
void	dispatchRow (int i, const cell_t *buffer, int len)
	Notifies to the MASA framework that some cells of a row has been processed.
void	dispatchScore (score_t score, int bx=-1, int by=-1)
	Notifies to the MASA framework that a new score has been computed.
bool	mustContinue ()
bool	mustDispatchLastCell ()
bool	mustDispatchLastRow ()
bool	mustDispatchLastColumn ()
bool	mustDispatchSpecialRows ()
bool	mustDispatchSpecialColumns ()
bool	mustDispatchScores ()
bool	mustPruneBlocks ()
score_t	getBestScoreLastColumn () const
score_t	getBestScoreLastRow () const
Private Member Functions
void	stopAligner ()
	Stops the execution of the aligner.
int	findBestCell (const cell_t *buffer, int len)
match_result_t	findGoalCell (const cell_t buffer, cell_t base, int len, CellsReader *cellsReader)
match_result_t	findFullGap (int len, bool openGap, SeekableCellsReader *cellsReader)
void	setFirstColumnSource (SeekableCellsReader *firstColumnReader)
	Defines that the first column must be initialized with a customized column.
void	setFirstRowSource (SeekableCellsReader *firstColumnReader)
	Defines that the first row must be initialized with a pre-defined row.
void	setLastColumnDestination (CellsWriter *lastColumnWriter)
	Defines the destination of the last column.
void	setLastRowDestination (CellsWriter *lastRowWriter)
Private Attributes
bool	active
IAligner *	aligner
	The aligner object that executes the SW computation.
Partition	partition
	The partition that is being aligned.
SeekableCellsReader *	lastColumnReader
	The reader that provides the last column saved in memory/disk.
SeekableCellsReader *	lastRowReader
	The reader that provides the last rows saved in memory/disk.
cell_t *	baseColumn
	Vector that store the temporary cells for the matching procedures.
cell_t *	baseRow
	Vector that store the temporary cells for the matching procedures.
const score_params_t *	score_params
	Math/mismatch/gaps parameters.
int	startType
	The start type of the partition.
int	match
	Match Score.
int	mismatch
	Mismatch Score.
int	gapOpen
	Gap opening penalty.
int	gapExtension
	Gap extension penalty.
SeekableCellsReader *	firstColumnReader
	First column blocking buffer.
SeekableCellsReader *	firstRowReader
	First row blocking buffer.
CellsWriter *	lastColumnWriter
	Last column blocking buffer.
CellsWriter *	lastRowWriter
	Last row blocking buffer.
SpecialRowsPartition *	specialRowsPartition
	Partition where the Special Rows are stored.
BestScoreList *	bestScoreList
	List with the best scores.
int	goalScore
	The aligner must stop whenever it finds the goal score.
int	goalScoreLocation
	Where to check the goal score.
bool	foundCrosspoint
	Indicates if the next crosspoint has already been found.
crosspoint_t	nextCrosspoint
	The crosspoint found by the matching procedure or the goal score.
BlocksFile *	blocksFile
int	bestScoreLocation
	Where to check best score.
int	lastColumnPos
	Column tracking position for the dispatching procedure.
int	lastRowPos
	Row tracking position for the dispatching procedure.
int	blockPruning
	Callback for the last rows.
int	recurrenceType
	required recurrence type (SMITH_WATERMAN or NEEDLEMAN_WUNSCH)
int	specialRowInterval
	minimum distance between two special rows
FILE *	firstRowFile
	File where the first row is stored.
int	firstColumnInitType
	First row tracking position for the receive procedure.
int	firstRowInitType
	true if first row is gapped
score_t	bestScoreLastColumn
	true if first columns is gapped
score_t	bestScoreLastRow
int	seq0_offset
	defines how many nucleotides were trimmed from the sequence 0
int	seq1_offset
	defines how many nucleotides were trimmed from the sequence 1
Partition	superPartition
	Partition that holds all sub-partitions.

Constructor & Destructor Documentation

AlignerManager::AlignerManager ( IAligner * aligner )

Definition at line 31 of file AlignerManager.cpp.

AlignerManager::~AlignerManager ( ) [virtual]

Definition at line 74 of file AlignerManager.cpp.

Member Function Documentation

void AlignerManager::alignPartition	(	Partition	partition,
		int	startType
	)

Definition at line 91 of file AlignerManager.cpp.

void AlignerManager::dispatchColumn	(	int	j,
		const cell_t *	buffer,
		int	len
	)		`[virtual]`

Notifies to the MASA framework that some cells of a column has been processed.

This function must be called serially for each column. For example, the invocation of dispatchColumn(50000, vector, 100) will dispatch the first 100 cells of the column 50000 to MASA, and the cells are read from the vector[0..99] elements. After this, a call to dispatchColumn(50000, vector, 50) will dispatch the next 50 cells of the same column 5000, and the cells are read from the vector[0..49] elements.

Parameters:

j	the column to be dispatched.
buffer	the vector containing the data (starting from cell 0).
len	the number of cells that will be read from the vector.

Implements IManager.

Definition at line 334 of file AlignerManager.cpp.

void AlignerManager::dispatchRow	(	int	i,
		const cell_t *	buffer,
		int	len
	)		`[virtual]`

Notifies to the MASA framework that some cells of a row has been processed.

This function must be called serially for each row, analogous to the AbstractAligner::dispatchLastColumn method.

Parameters:

i	the row to be dispatched.
buffer	the vector containing the data (starting from cell 0).
len	the number of cells that will be read from the vector.

Implements IManager.

Definition at line 374 of file AlignerManager.cpp.

void AlignerManager::dispatchScore	(	score_t	score,
		int	bx = `-1`,
		int	by = `-1`
	)		`[virtual]`

Notifies to the MASA framework that a new score has been computed.

This method may be called as many times it is necessary, and the best score will be calculated among all calls of this method.

If the Aligner supports the aligner_capabilities_t::dispatch_block_scores capability, them it must dispatch the score with the bx, by parameters set to the block indices and this method must be called only once for each block.

Parameters:

score	the score to be dispatched
bx	the block position in the horizontal direction, starting from 0 up to AbstractAligner::getGridWidth() minus 1.
by	the block position in the vertical direction, starting from 0 up to AbstractAligner::getGridHeight() minus 1.

Implements IManager.

Definition at line 411 of file AlignerManager.cpp.

int AlignerManager::findBestCell	(	const cell_t *	buffer,
		int	len
	)		`[private]`

Definition at line 611 of file AlignerManager.cpp.

match_result_t AlignerManager::findFullGap	(	int	len,
		bool	openGap,
		SeekableCellsReader *	cellsReader
	)		`[private]`

Definition at line 658 of file AlignerManager.cpp.

match_result_t AlignerManager::findGoalCell	(	const cell_t *	buffer,
		cell_t *	base,
		int	len,
		CellsReader *	cellsReader
	)		`[private]`

Definition at line 625 of file AlignerManager.cpp.

score_t AlignerManager::getBestScoreLastColumn ( ) const

Definition at line 720 of file AlignerManager.cpp.

score_t AlignerManager::getBestScoreLastRow ( ) const

Definition at line 724 of file AlignerManager.cpp.

int AlignerManager::getFirstColumnInitType ( ) [virtual]

Returns the initialization type of the first column.

Possible values are

INIT_WITH_CUSTOM_DATA: the first column must be initialized with custom data that can only be obtained by the AbstractAligner::receiveFirstColumn method.
INIT_WITH_GAPS: the first column must be initialized considering gaps. The initialization equation is:

$\begin{eqnarray*}H_{0,0} &=& 0 \\ H_{k,0} &=& -k.G_{ext}-G_{open} \\ F_{k,0} &=& -\infty \end{eqnarray*}$
INIT_WITH_GAPS_OPENED: the first column must be initialized considering gaps, but without gap opening penalty. The initialization equation is:

$\begin{eqnarray*}H_{k,0} &=& -k.G_{ext} \\ F_{k,0} &=& -\infty \end{eqnarray*}$
INIT_WITH_ZEROES: the first column must be initialized considering zero values. The initialization equation is:

$\begin{eqnarray*}H_{k,0} &=& 0 \\ F_{k,0} &=& -\infty \end{eqnarray*}$

The initialization data of all types may be obtained by the AbstractAligner::receiveFirstColumn method, but the subclass of AbstractAligner may implement the initialization functions using some architectural dependent code (for example, using vectorial hardware instructions).

Returns:: the initialization type.

Implements IManager.

Definition at line 542 of file AlignerManager.cpp.

int AlignerManager::getFirstRowInitType ( ) [virtual]

Returns the initialization type of the first row.

Possible values are

INIT_WITH_CUSTOM_DATA: the first row must be initialized with custom data that can only be obtained by the AbstractAligner::receiveFirstRow method.
INIT_WITH_GAPS: the first column must be initialized considering gaps. The initialization equation is:

$\begin{eqnarray*}H_{0,0} &=& 0 \\ H_{0,k} &=& -k.G_{ext}-G_{open} \\ F_{0,k} &=& -\infty \end{eqnarray*}$
INIT_WITH_GAPS_OPENED: the first column must be initialized considering gaps, but without gap opening penalty. The initialization equation is:

$\begin{eqnarray*}H_{0,k} &=& -k.G_{ext} \\ F_{0,k} &=& -\infty \end{eqnarray*}$
INIT_WITH_ZEROES: the first row must be initialized considering zero values. The initialization equation is:

$\begin{eqnarray*}H_{0,k} &=& 0 \\ F_{0,k} &=& -\infty \end{eqnarray*}$

The initialization data of all types may be obtained by the AbstractAligner::receiveFirstRow method, but the subclass of AbstractAligner may implement the initialization functions using some architectural dependent code (for example, using vectorial hardware instructions).

Returns:: the initialization type.

Implements IManager.

Definition at line 561 of file AlignerManager.cpp.

const crosspoint_t AlignerManager::getNextCrosspoint ( ) const

Defines the callback function that will be called whenever the dispatchRow method is called for the last row.

Parameters:

processLastRowFunction	the callback function. Defines the callback function that will be called whenever the dispatchColumn method is called for the last column.
processLastColumnFunction	the callback function. Defines the callback function that will be called whenever the dispatchScore method is called.
processBlockFunction	the callback function. Defines the callback function that will be called whenever the dispatchScore method is called for the last cell (right-bottom most cell).
processLastCellFunction	the callback function. Return the next crosspoint found by the matching procedure or by the goal score. If it was not found, the returned crosspoint score is -INF.

Definition at line 593 of file AlignerManager.cpp.

int AlignerManager::getRecurrenceType ( ) const [virtual]

Returns:: the recurrence type of the alignment. Possible values are SMITH_WATERMAN and NEEDLEMAN_WUNSCH.

Implements IManager.

Definition at line 508 of file AlignerManager.cpp.

int AlignerManager::getSpecialColumnInterval ( ) const [virtual]

Returns:: the minimum distance between two special columns, or 0 if it must not save special columns.

Implements IManager.

Definition at line 519 of file AlignerManager.cpp.

int AlignerManager::getSpecialRowInterval ( ) const [virtual]

Returns:: the minimum distance between two special rows, or 0 if it must not save special rows.

Implements IManager.

Definition at line 515 of file AlignerManager.cpp.

Partition AlignerManager::getSuperPartition ( ) [virtual]

Returns the super partition that includes all sub partitions being aligned.

This method must be used only by block pruning algorithms in order to obtain the corner coordinates of the matrix.

A super partition is a set of many smaller partitions and this occurs in two situations. The first is when we are running stage1 in a multiprocess environment, where we have one sub partition for each process. The second situation happens when the aligner cannot handle the full size of the matrix, so the partition is split in parts smaller than the max sequence size capability of the aligner.

Returns:: the super partition.

Implements IManager.

Definition at line 268 of file AlignerManager.cpp.

bool AlignerManager::isFoundCrosspoint ( ) const

Return true if the next crosspoint was found.

Definition at line 607 of file AlignerManager.cpp.

bool AlignerManager::mustContinue ( ) [virtual]

Returns:: true if the execution must continue.

Implements IManager.

Definition at line 527 of file AlignerManager.cpp.

bool AlignerManager::mustDispatchLastCell ( ) [virtual]

Returns:: true if the last cell must be dispatched.

Implements IManager.

Definition at line 455 of file AlignerManager.cpp.

bool AlignerManager::mustDispatchLastColumn ( ) [virtual]

Returns:: true if the last column must be dispatched.

Implements IManager.

Definition at line 475 of file AlignerManager.cpp.

bool AlignerManager::mustDispatchLastRow ( ) [virtual]

Returns:: true if the last row must be dispatched.

Implements IManager.

Definition at line 463 of file AlignerManager.cpp.

bool AlignerManager::mustDispatchScores ( ) [virtual]

Returns:: true if intermediate scores must be dispatched.

Implements IManager.

Definition at line 501 of file AlignerManager.cpp.

bool AlignerManager::mustDispatchSpecialColumns ( ) [virtual]

Returns:: true if special columns must be dispatched.

Implements IManager.

Definition at line 494 of file AlignerManager.cpp.

bool AlignerManager::mustDispatchSpecialRows ( ) [virtual]

Returns:: true if special rows must be dispatched.

Implements IManager.

Definition at line 487 of file AlignerManager.cpp.

bool AlignerManager::mustPruneBlocks ( ) [virtual]

Returns:: true if block pruning optimization may be used.

Implements IManager.

Definition at line 535 of file AlignerManager.cpp.

void AlignerManager::receiveFirstColumn	(	cell_t *	buffer,
		int	len
	)		`[virtual]`

Receives the first column of the partition.

This function may block until all the requested data is ready. So prefer to read data in chunks instead of reading the full first row. The data will be stored from 0 to len-1 positions of the vector passed in the parameters.

Parameters:

buffer	the vector where the first column data will be stored.
len	the number of cells that will be read.

Implements IManager.

Definition at line 318 of file AlignerManager.cpp.

void AlignerManager::receiveFirstRow	(	cell_t *	buffer,
		int	len
	)		`[virtual]`

Receives the first row of the partition.

This function may block until all the requested data is ready. So prefer to read data in chunks instead of reading the full first row. The data will be stored from 0 to len-1 positions of the vector passed in the parameters.

Parameters:

buffer	the vector where the first row data will be stored.
len	the number of cells that will be read.

Implements IManager.

Definition at line 326 of file AlignerManager.cpp.

void AlignerManager::setBestScoreList	(	BestScoreList *	bestScoreList,
		const int	bestScoreLocation = `AT_NOWHERE`
	)

Defines the list to store the best scores.

Parameters:

bestScoreList	the list to store the best scores.
bestScoreLocation	where to check for best score.

Definition at line 565 of file AlignerManager.cpp.

void AlignerManager::setBlockPruning ( bool blockPruning )

Defines if the aligner may do the block pruning optimization.

Since there are situations that the block pruning is not permitted, so the aligner must respect when blockPruning is false.

Parameters:

blockPruning true if the aligner may prune blocks.

Definition at line 195 of file AlignerManager.cpp.

void AlignerManager::setBlocksFile ( BlocksFile * blocksFile )

Defines the file to store the best score of each block.

Parameters:

blocksFile the file to store the scores.

Definition at line 575 of file AlignerManager.cpp.

void AlignerManager::setFirstColumnSource ( SeekableCellsReader * firstColumnReader ) [private]

Defines that the first column must be initialized with a customized column.

The column is loaded from a Blocking Buffer, so consider that the buffer will block the process if the requested data is not fully ready. So, the buffer must be read in chunks, in order to not block the entire execution.

Parameters:

firstColumnBuffer the blocking buffer that will contain the first column data.

Definition at line 216 of file AlignerManager.cpp.

void AlignerManager::setFirstRowSource ( SeekableCellsReader * firstColumnReader ) [private]

Defines that the first row must be initialized with a pre-defined row.

Parameters:

firstRowGapped	If true, than the cells must be initialized considering gaps, otherwise the cells must be initialized with zeros. See AbstractAligner::getFirstRowInitType for the initialization functions. Defines that the first row must be initialized with a customized row. The column is loaded from a FILE.
firstRow	the file that contains the first column data.

Definition at line 247 of file AlignerManager.cpp.

void AlignerManager::setGoalScore	(	int	goalScore,
		const int	goalScoreLocation = `AT_NOWHERE`
	)

Whenever the aligner finds the goal score, the processing must stop.

Definition at line 579 of file AlignerManager.cpp.

void AlignerManager::setLastColumnDestination ( CellsWriter * lastColumnWriter ) [private]

Defines the destination of the last column.

The column is stored in a Blocking Buffer, so consider that the buffer will block the process if the buffer is full.

Parameters:

lastColumnBuffer the buffer that will receive the data of the last column.

Definition at line 263 of file AlignerManager.cpp.

void AlignerManager::setLastColumnReader ( SeekableCellsReader * lastColumnReader )

Defines the previous special rows partition containing the rows to be matched against the last column/rows.

Definition at line 288 of file AlignerManager.cpp.

void AlignerManager::setLastRowDestination ( CellsWriter * lastRowWriter ) [private]

Definition at line 284 of file AlignerManager.cpp.

void AlignerManager::setLastRowReader ( SeekableCellsReader * lastRowReader )

Defines the previous special rows partition containing the rows to be matched against the last column/rows.

Definition at line 292 of file AlignerManager.cpp.

void AlignerManager::setPenalties	(	const int	match,
		const int	mismatch,
		const int	gapOpen,
		const int	gapExtension
	)

Defines the variable penalty functions to be aligned.

Parameters:

match	Match score
mismatch	Mismatch score
gapOpen	Gap opening penalty
gapExtension	Gap extension penalty

Definition at line 549 of file AlignerManager.cpp.

void AlignerManager::setRecurrenceType ( int recurrenceType )

Defines that the first column must be initialized with a pre-defined column.

Parameters:

firstColumnGapped	If true, than the cells must be initialized considering gaps, otherwise the cells must be initialized with zeros. See AbstractAligner::getFirstColumnInitType for the initialization functions. Defines the recurrence type of the execution.
recurrenceType	can be SMITH_WATERMAN or NEEDLEMAN_WUNSCH.

Definition at line 299 of file AlignerManager.cpp.

void AlignerManager::setSequences	(	Sequence *	seq0,
		Sequence *	seq1,
		int	i0,
		int	j0,
		int	i1,
		int	j1,
		FILE *	stats = `NULL`
	)

Defines the partition that must be processed.

Parameters:

i0	start row
j0	start column
i1	end row (exclusive)
j1	end column (exclusive)
start_type	The start type of the partition. See AbstractAligner::startType. Defines the sequences and the range of the sequences that will be aligned. This method also defines the range of the sequences that will be used in the alignPartitions. Note that the [i0,i1) and [j0,j1) are not the partition itself, but all the aligned partitions will reside inside this range. If the parameters $i0$ and $j0$ are positive, then the sequence data passed to the aligner is shifted, starting in positions $i0$ and $j0$. This allows the reduction of memory consumption, trimming the prefix of the sequences that would never be used (i.e. the memory may be allocated solely for the given sequence ranges.).
seq0	vertical sequence object.
seq1	horizontal sequence object.
i0	lowest position in seq0 that may be aligned.
j0	lowest position in seq1 that may be aligned.
i1	highest position in seq0 that may be aligned.
j1	highest position in seq1 that may be aligned.
stats	the statistics log file

Definition at line 173 of file AlignerManager.cpp.

void AlignerManager::setSpecialRowInterval ( const int specialRowInterval )

Defines the minimum distance (in rows) between two special rows.

Parameters:

specialRowInterval the minimum interval between special rows.

Definition at line 313 of file AlignerManager.cpp.

void AlignerManager::setSpecialRowsPartition ( SpecialRowsPartition * specialRowsPartition )

Defines the grid dimension of the grid, if capabilities_t::dispatch_block_scores is SUPPORTED.

Parameters:

width	the width of the grid.
height	the height of the grid. Defines the partition where the special rows will be stored.
specialRowsPartition	the special row partition.

Definition at line 306 of file AlignerManager.cpp.

void AlignerManager::setSuperPartition ( Partition superPartition )

Sets the super-partition being aligned to be returned by the IManager::getSuperPartition() method.

Parameters:

superPartition the super partition to be set.

See also:: IManager::getSuperPartition()

Definition at line 276 of file AlignerManager.cpp.

void AlignerManager::stopAligner ( ) [private]

Stops the execution of the aligner.

This makes the mustContinue() method to return false.

Definition at line 523 of file AlignerManager.cpp.

void AlignerManager::unsetGoalScore ( )

Do not find best score.

Definition at line 588 of file AlignerManager.cpp.

void AlignerManager::unsetSequences ( )

Clear all sequence strucutures.

Definition at line 186 of file AlignerManager.cpp.

void AlignerManager::unsetSuperPartition ( )

Resets the super-partition.

A reseted super-partition means that it will always be equal to the current aligned partition.

Definition at line 280 of file AlignerManager.cpp.

Member Data Documentation

bool AlignerManager::active [private]

Definition at line 272 of file AlignerManager.hpp.

IAligner* AlignerManager::aligner [private]

The aligner object that executes the SW computation.

Definition at line 275 of file AlignerManager.hpp.

cell_t* AlignerManager::baseColumn [private]

Vector that store the temporary cells for the matching procedures.

Definition at line 293 of file AlignerManager.hpp.

cell_t* AlignerManager::baseRow [private]

Vector that store the temporary cells for the matching procedures.

Definition at line 298 of file AlignerManager.hpp.

score_t AlignerManager::bestScoreLastColumn [private]

true if first columns is gapped

Definition at line 405 of file AlignerManager.hpp.

score_t AlignerManager::bestScoreLastRow [private]

Definition at line 406 of file AlignerManager.hpp.

BestScoreList* AlignerManager::bestScoreList [private]

List with the best scores.

Definition at line 339 of file AlignerManager.hpp.

int AlignerManager::bestScoreLocation [private]

Where to check best score.

Definition at line 357 of file AlignerManager.hpp.

int AlignerManager::blockPruning [private]

Callback for the last rows.

Callback for the last cells Callback for the scores Callback for the last score true if block must be pruned

Definition at line 378 of file AlignerManager.hpp.

BlocksFile* AlignerManager::blocksFile [private]

Definition at line 354 of file AlignerManager.hpp.

int AlignerManager::firstColumnInitType [private]

First row tracking position for the receive procedure.

First column tracking position for the receive procedure

Definition at line 395 of file AlignerManager.hpp.

SeekableCellsReader* AlignerManager::firstColumnReader [private]

First column blocking buffer.

Definition at line 324 of file AlignerManager.hpp.

FILE* AlignerManager::firstRowFile [private]

File where the first row is stored.

Definition at line 387 of file AlignerManager.hpp.

int AlignerManager::firstRowInitType [private]

true if first row is gapped

Definition at line 400 of file AlignerManager.hpp.

SeekableCellsReader* AlignerManager::firstRowReader [private]

First row blocking buffer.

Definition at line 327 of file AlignerManager.hpp.

bool AlignerManager::foundCrosspoint [private]

Indicates if the next crosspoint has already been found.

Definition at line 348 of file AlignerManager.hpp.

int AlignerManager::gapExtension [private]

Gap extension penalty.

Definition at line 321 of file AlignerManager.hpp.

int AlignerManager::gapOpen [private]

Gap opening penalty.

Definition at line 318 of file AlignerManager.hpp.

int AlignerManager::goalScore [private]

The aligner must stop whenever it finds the goal score.

Definition at line 342 of file AlignerManager.hpp.

int AlignerManager::goalScoreLocation [private]

Where to check the goal score.

Definition at line 345 of file AlignerManager.hpp.

int AlignerManager::lastColumnPos [private]

Column tracking position for the dispatching procedure.

Definition at line 360 of file AlignerManager.hpp.

SeekableCellsReader* AlignerManager::lastColumnReader [private]

The reader that provides the last column saved in memory/disk.

Definition at line 283 of file AlignerManager.hpp.

CellsWriter* AlignerManager::lastColumnWriter [private]

Last column blocking buffer.

Definition at line 330 of file AlignerManager.hpp.

int AlignerManager::lastRowPos [private]

Row tracking position for the dispatching procedure.

Definition at line 363 of file AlignerManager.hpp.

SeekableCellsReader* AlignerManager::lastRowReader [private]

The reader that provides the last rows saved in memory/disk.

Definition at line 288 of file AlignerManager.hpp.

CellsWriter* AlignerManager::lastRowWriter [private]

Last row blocking buffer.

Definition at line 333 of file AlignerManager.hpp.

int AlignerManager::match [private]

Match Score.

Definition at line 312 of file AlignerManager.hpp.

int AlignerManager::mismatch [private]

Mismatch Score.

Definition at line 315 of file AlignerManager.hpp.

crosspoint_t AlignerManager::nextCrosspoint [private]

The crosspoint found by the matching procedure or the goal score.

Definition at line 351 of file AlignerManager.hpp.

Partition AlignerManager::partition [private]

The partition that is being aligned.

Definition at line 278 of file AlignerManager.hpp.

int AlignerManager::recurrenceType [private]

required recurrence type (SMITH_WATERMAN or NEEDLEMAN_WUNSCH)

Definition at line 381 of file AlignerManager.hpp.

const score_params_t* AlignerManager::score_params [private]

Math/mismatch/gaps parameters.

Definition at line 301 of file AlignerManager.hpp.

int AlignerManager::seq0_offset [private]

defines how many nucleotides were trimmed from the sequence 0

Definition at line 417 of file AlignerManager.hpp.

int AlignerManager::seq1_offset [private]

defines how many nucleotides were trimmed from the sequence 1

Definition at line 419 of file AlignerManager.hpp.

int AlignerManager::specialRowInterval [private]

minimum distance between two special rows

Definition at line 384 of file AlignerManager.hpp.

SpecialRowsPartition* AlignerManager::specialRowsPartition [private]

Partition where the Special Rows are stored.

Definition at line 336 of file AlignerManager.hpp.

int AlignerManager::startType [private]

The start type of the partition.

Possible values are: TYPE_MATCH, TYPE_GAP_1 or TYPE_GAP_2. When set to the TYPE_GAP_1 or TYPE_GAP_2, the initialization of the first row/column must be done without the gap opening penalty.

Definition at line 309 of file AlignerManager.hpp.

Partition AlignerManager::superPartition [private]

Partition that holds all sub-partitions.

If there are no sub-partition, this is the single partition being aligned.

Definition at line 425 of file AlignerManager.hpp.

The documentation for this class was generated from the following files:

Detailed Description

Public Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation