Detailed Description

Abstract class that processes blocks individually considering some schedule mechanism.

This class implements some common behavior to simplify the implementation of block aligners. These aligners process blocks individually using a customized schedule mechanism that processes block through an AbstractBlockProcessor object.

Use the AbstractBlockProcessor if you want to create a CPU block scheduler that processes a single block in the specific hardware/software architecture.

In order to extend an AbstractDiagonalAligner, the class must implement two methods.

scheduleBlocks: schedules the block executions using a customized mechanism.
alignBlock: responsible to receive/dispatch data from/to MASA-Core and call the processBlock for each block. These procedures must be aware of the schedule mechanism in order to avoid unsafe calls to MASA-Core.

Definition at line 56 of file AbstractBlockAligner.hpp.

#include <AbstractBlockAligner.hpp>

Inheritance diagram for AbstractBlockAligner:

List of all members.

Public Member Functions
	AbstractBlockAligner (AbstractBlockProcessor blockProcessor=NULL, BlockAlignerParameters params=NULL)
	Constructor.
virtual	~AbstractBlockAligner ()
	Destructor.
virtual void	initialize ()
	Initializes the Aligner before the execution of the alignment procedure.
virtual void	alignPartition (Partition partition)
	Aligns the given partition, processing it block by block using a customized scheduler.
virtual void	finalize ()
	Finalizes the execution of this IAligner.
virtual aligner_capabilities_t	getCapabilities ()
	Returns the capabilities of the aligner.
virtual const score_params_t *	getScoreParameters ()
	Returns the match/mismatch parameters and the gap penalties used by this IAligner.
virtual IAlignerParameters *	getParameters ()
	Get the command line parameters of the IAligner class.
virtual void	setSequences (const char seq0, const char seq1, int seq0_len, int seq1_len)
	This method is called in the beginning of each stage to inform the aligner about the sequence to be aligned.
virtual void	unsetSequences ()
	Defines that the sequence will not be used anymore and the Aligner should deallocate the memory used for them.
virtual void	clearStatistics ()
virtual void	printInitialStatistics (FILE *file)
	Prints the runtime parameters.
virtual void	printStageStatistics (FILE *file)
	Empty stub for the superclass virtual method.
virtual void	printFinalStatistics (FILE *file)
	Empty stub for the superclass virtual method.
virtual void	printStatistics (FILE *file)
	Prints the pruning statistics and grid used range.
virtual const char *	getProgressString () const
	Returns a string that will be appended into some intermediate statistics information of stage 1.
virtual long long	getProcessedCells ()
	Returns the number of cells that have been processed since the last call to clearStatistics.
Protected Member Functions
virtual void	scheduleBlocks (int grid_width, int grid_height)=0
	Schedules all the blocks for execution.
virtual void	alignBlock (int bx, int by, int i0, int j0, int i1, int j1)=0
	This method is called by AbstractBlockAligner::alignBlock(int,int) with additional information about block coordinates.
void	ignoreBlock (int bx, int by)
	Ignore the computation of a block.
bool	isBlockPruned (int bx, int by) const
	Check for pruned blocks.
virtual void	increaseBlockStat (const bool pruned)
	Increased statistics about block processing.
void	alignBlock (int bx, int by)
	This method aligns block (bx,by).
bool	processBlock (int bx, int by, int i0, int j0, int i1, int j1)
	This method calls AbstractBlockProcessor::processBlock(int,int,int,int,int,int,int) to execute the recurrence relation for a block.
bool	isSpecialRow (int by)
	Indicates if the blocks on row $by$ must dispatch its last row.
bool	isSpecialColumn (int by)
	Indicates if the blocks on column $bx$ must dispatch its last column.
void	setPreferredSizes (int preferredBlockSize, int preferredGridSize)
	Defines the preferred size of a block and the preferred number of blocks in the grid.
virtual void	allocateStructures ()
	Allocate vectors after sequence is set.
virtual void	deallocateStructures ()
	Deallocate vectors after sequence is unset.
Protected Attributes
cell_t **	row
	Chunk of rows used to pass cells from up to bottom blocks.
cell_t **	col
	Chunk of columns used to pass cells from left to right blocks.
Private Member Functions
Grid *	configureGrid (Partition partition)
	Configures the grid for the given partition.
void	pruningUpdate (int bx, int by, int score)
	Updates the pruning status accordingly to the block score.
Private Attributes
BlockAlignerParameters *	params
	Parameter used in this aligner.
score_t **	grid_scores
	Stores the score of each grid.
AbstractBlockProcessor *	blockProcessor
	Processor that computes a single block.
BlockPruningGenericN2 *	blockPruner
	Block Pruner object.
int	preferredBlockSize
	Preferred maximum size of a block.
int	preferredGridSize
	Preferred minimum grid size.
int	statMinBlockWidth
	Maintains the minimum blockWidth used.
int	statMaxBlockWidth
	Maintains the maximum blockWidth used.
int	statMinBlockHeight
	Maintains the minimum blockHeight used.
int	statMaxBlockHeight
	Maintains the maximum blockHeight used.
int	statMinGridWidth
	Maintains the minimum gridWidth used.
int	statMaxGridWidth
	Maintains the maximum gridWidth used.
int	statMinGridHeight
	Maintains the minimum gridHeight used.
int	statMaxGridHeight
	Maintains the maximum gridHeight used.
int	statTotalBlocks
	Total number of blocks processed in the grid.
int	statPrunedBlocks
	Number of pruned blocks.
score_params_t	score_params
	Score parameters.

Constructor & Destructor Documentation

AbstractBlockAligner::AbstractBlockAligner	(	AbstractBlockProcessor *	blockProcessor = `NULL`,
		BlockAlignerParameters *	params = `NULL`
	)

Constructor.

AbstractBlockAligner Constructor.

Parameters:

blockProcessor	the block processor to be used. If NULL, the default processor will be used.
params	the aligner parameters. If NULL, the default param class will be used.

Definition at line 73 of file AbstractBlockAligner.cpp.

AbstractBlockAligner::~AbstractBlockAligner ( ) [virtual]

Destructor.

AbstractBlockAligner destructor.

Definition at line 119 of file AbstractBlockAligner.cpp.

Member Function Documentation

virtual void AbstractBlockAligner::alignBlock	(	int	bx,
		int	by,
		int	i0,
		int	j0,
		int	i1,
		int	j1
	)		`[protected, pure virtual]`

This method is called by AbstractBlockAligner::alignBlock(int,int) with additional information about block coordinates.

Then, this method must receive/dispatch rows and columns from/to MASA-Core and call the processBlock(int,int,int,int,int,int) method.

Parameters:

bx	horizontal block coordinate
by	vertical block coordinate
i0	vertical first row of the block
j0	horizontal first column of the block
i1	vertical last row of the block
j1	horizontal last column of the block

void AbstractBlockAligner::alignBlock	(	int	bx,
		int	by
	)		`[protected]`

This method aligns block (bx,by).

This method calls the AbstractBlockAligner::alignBlock(int,int,int,int,int,int) with additional information about block coordinates.

Parameters:

bx	horizontal coordinate of the block in the grid
by	vertical coordinate of the block in the grid

Definition at line 338 of file AbstractBlockAligner.cpp.

void AbstractBlockAligner::alignPartition ( Partition partition ) [virtual]

Aligns the given partition, processing it block by block using a customized scheduler.

Parameters:

partition partition to be aligned.

See also:: IAligner::alignPartition

Implements IAligner.

Definition at line 276 of file AbstractBlockAligner.cpp.

void AbstractBlockAligner::allocateStructures ( ) [protected, virtual]

Allocate vectors after sequence is set.

Definition at line 536 of file AbstractBlockAligner.cpp.

void AbstractBlockAligner::clearStatistics ( ) [virtual]

clear all internal statistics of the aligner.

Implements IAligner.

Definition at line 492 of file AbstractBlockAligner.cpp.

Grid * AbstractBlockAligner::configureGrid ( Partition partition ) [private]

Configures the grid for the given partition.

Parameters:

partition partition to be aligned.

Definition at line 198 of file AbstractBlockAligner.cpp.

void AbstractBlockAligner::deallocateStructures ( ) [protected, virtual]

Deallocate vectors after sequence is unset.

Definition at line 573 of file AbstractBlockAligner.cpp.

void AbstractBlockAligner::finalize ( ) [virtual]

Finalizes the execution of this IAligner.

Use this method to free any allocated memory during the life time of the IAligner.

Implements IAligner.

Definition at line 187 of file AbstractBlockAligner.cpp.

aligner_capabilities_t AbstractBlockAligner::getCapabilities ( ) [virtual]

Returns the capabilities of the aligner.

Returns:: the capabilities.

See also:: aligner_capabilities_t

Implements IAligner.

Definition at line 128 of file AbstractBlockAligner.cpp.

IAlignerParameters * AbstractBlockAligner::getParameters ( ) [virtual]

Get the command line parameters of the IAligner class.

The IAlignerParameters interface is used by MASA to present extra command line parameters to each IAligner subclass. Be warned that the MASA-Core is responsible to present all the command line options, so, any attempt to modify the command line parameters must be done by the IAlignerParameters class, otherwise the behavior of the entire MASA-Core may be compromised. The AbstractAlignerParameters implements the base operations of the IAlignerParameters interface.

Returns:: The customized parameters for this IAligner.

See also:: The IAlignerParameters class presents the details to customize these parameters.

Implements IAligner.

Definition at line 164 of file AbstractBlockAligner.cpp.

long long AbstractBlockAligner::getProcessedCells ( ) [virtual]

Returns the number of cells that have been processed since the last call to clearStatistics.

Returns:: the number of processed cells.

Implements IAligner.

Definition at line 529 of file AbstractBlockAligner.cpp.

const char * AbstractBlockAligner::getProgressString ( ) const [virtual]

Returns a string that will be appended into some intermediate statistics information of stage 1.

Basically, the aligner should present how many steps have been calculated, giving an idea of conclusion percentage, and some quick information about pruning status. All the string should reside in a line (around 80 characters).

Returns:: a single line progress strings without '\n'.

Implements IAligner.

Definition at line 522 of file AbstractBlockAligner.cpp.

const score_params_t * AbstractBlockAligner::getScoreParameters ( ) [virtual]

Returns the match/mismatch parameters and the gap penalties used by this IAligner.

Returns:: the score parameters of this IAligner.

Implements IAligner.

Definition at line 157 of file AbstractBlockAligner.cpp.

void AbstractBlockAligner::ignoreBlock	(	int	bx,
		int	by
	)		`[protected]`

Ignore the computation of a block.

This method must be called for statistical purposes only.

Parameters:

bx	horizontal block coordinate
by	vertical block coordinate

Definition at line 397 of file AbstractBlockAligner.cpp.

void AbstractBlockAligner::increaseBlockStat ( const bool pruned ) [protected, virtual]

Increased statistics about block processing.

Parameters:

pruned indicates if the block was pruned.

Definition at line 405 of file AbstractBlockAligner.cpp.

void AbstractBlockAligner::initialize ( ) [virtual]

Initializes the Aligner before the execution of the alignment procedure.

The IManager associated with this IAligner may only be called to obtain the command line parameters, specially the AbstractAlignerParameters::getForkId() in multi-process executions.

The IManager is not set and must not be queried. The initialize() method is called only once per process. Here, we may initialize the hardware and allocate some global structures that are not associated with the sequence sizes.

The initialize() method will be called once for each MASA stage and the sequences will not be changed until the finalize method be called. Meanwhile, the alignPartition() method may be called multiple times before the finalize() method is called.

The initialize() method may be used to process and allocated the sequences in memory. Note that the MASA stages may change the direction of the sequences, so consider that each call to the initialize method will change the sequence data.

Implements IAligner.

Definition at line 176 of file AbstractBlockAligner.cpp.

bool AbstractBlockAligner::isBlockPruned	(	int	bx,
		int	by
	)		const `[protected]`

Check for pruned blocks.

Returns true if block (bx, by) can be pruned.

Parameters:

bx	horizontal block coordinate
by	vertical block coordinate

Returns:: true if the block can be pruned

Parameters:

bx	horizontal block coordinate
by	vertical block coordinate

Returns:: pruned status of the block.

Definition at line 610 of file AbstractBlockAligner.cpp.

bool AbstractBlockAligner::isSpecialColumn ( int bx ) [protected]

Indicates if the blocks on column $bx$ must dispatch its last column.

Parameters:

bx	the column of blocks.

Returns:: true if the last column of the block will be stored (special column).

Definition at line 448 of file AbstractBlockAligner.cpp.

bool AbstractBlockAligner::isSpecialRow ( int by ) [protected]

Indicates if the blocks on row $by$ must dispatch its last row.

Parameters:

by	the row of blocks.

Returns:: true if the last row of the block will be stored (special row).

Definition at line 419 of file AbstractBlockAligner.cpp.

void AbstractBlockAligner::printFinalStatistics ( FILE * file ) [virtual]

Empty stub for the superclass virtual method.

This method is called immediately after finalize(), allowing the aligner to print some finalization information.

Parameters:

file	The log file where the statistics will be written.

Implements IAligner.

Definition at line 516 of file AbstractBlockAligner.cpp.

void AbstractBlockAligner::printInitialStatistics ( FILE * file ) [virtual]

Prints the runtime parameters.

Parameters:

file	handler to print out the statistics.

See also:: IAligner::printInitialStatistics

Implements IAligner.

Definition at line 478 of file AbstractBlockAligner.cpp.

void AbstractBlockAligner::printStageStatistics ( FILE * file ) [virtual]

Empty stub for the superclass virtual method.

This method is called immediately after onSequenceChange(), allowing the aligner to print some information before a new stage.

Parameters:

file	The log file where the statistics will be written.

Implements IAligner.

Definition at line 510 of file AbstractBlockAligner.cpp.

void AbstractBlockAligner::printStatistics ( FILE * file ) [virtual]

Prints the pruning statistics and grid used range.

Parameters:

file	handler to print out the statistics.

See also:: IAligner::printStatistics

Implements IAligner.

Definition at line 457 of file AbstractBlockAligner.cpp.

bool AbstractBlockAligner::processBlock	(	int	bx,
		int	by,
		int	i0,
		int	j0,
		int	i1,
		int	j1
	)		`[protected]`

This method calls AbstractBlockProcessor::processBlock(int,int,int,int,int,int,int) to execute the recurrence relation for a block.

Parameters:

bx	horizontal block coordinate
by	vertical block coordinate
i0	vertical first row of the block
j0	horizontal first column of the block
i1	vertical last row of the block
j1	horizontal last column of the block
true	if the block was processed or false if it was pruned.

Definition at line 362 of file AbstractBlockAligner.cpp.

void AbstractBlockAligner::pruningUpdate	(	int	bx,
		int	by,
		int	score
	)		`[private]`

Updates the pruning status accordingly to the block score.

Parameters:

bx	horizontal block coordinate
by	vertical block coordinate
score	the score of block at coordinate $(bx,by)$

Definition at line 621 of file AbstractBlockAligner.cpp.

virtual void AbstractBlockAligner::scheduleBlocks	(	int	grid_width,
		int	grid_height
	)		`[protected, pure virtual]`

Schedules all the blocks for execution.

As soon as one block is ready to be executed, this method must call the AbstractBlockAligner::alignBlock(int,int) function in order to prepare this block for real execution.

Parameters:

grid_width	width of the grid in blocks.
grid_height	height of the grid in blocks.

void AbstractBlockAligner::setPreferredSizes	(	int	preferredBlockSize,
		int	preferredGridSize
	)		`[protected]`

Defines the preferred size of a block and the preferred number of blocks in the grid.

Defines the preferred block/grid sizes.

This values are used as a hint for the automatic grid/block configuration.

Parameters:

preferredBlockSize	the preferred maximum size of a block. Must be greater than 0.
preferredGridSize	the preferred minimum grid size. Must be greater than 0.

Used as a hint.

Parameters:

preferredBlockSize	the preferred maximum size of a block.
preferredGridSize	the preferred minimum grid size.

Definition at line 633 of file AbstractBlockAligner.cpp.

void AbstractBlockAligner::setSequences	(	const char *	seq0,
		const char *	seq1,
		int	seq0_len,
		int	seq1_len
	)		`[virtual]`

This method is called in the beginning of each stage to inform the aligner about the sequence to be aligned.

The MASA stages alternates the direction of the sequences in each stage, possibly trimming if the beginning and end of the sequences will not be used in this stage. So consider that each call to the onSequenceChange() method may completely change the sequence data for the further calls to alignPartition.

Note that the seq0_len and seq1_len parameters are not the sizes of the original sequences, but the sizes of the trimmed sequences.

Parameters:

seq0	trimmed vertical sequence data
seq1	trimmed horizontal sequence data
seq0_len	length of the trimmed vertical sequence.
seq1_len	length of the trimmed horizontal sequence.

Implements IAligner.

Definition at line 261 of file AbstractBlockAligner.cpp.

void AbstractBlockAligner::unsetSequences ( ) [virtual]

Defines that the sequence will not be used anymore and the Aligner should deallocate the memory used for them.

This method is called in the end of each stage.

Implements IAligner.

Definition at line 265 of file AbstractBlockAligner.cpp.