Detailed Description

Abstract class that processes diagonal of blocks.

This class implements some common behavior to simplify the implementation of diagonal aligners. Use the AbstractDiagonalAligner if you want to compute all blocks inside the diagonal at once inside the architecture hardware/software. Differently from the AbstractBlockAligner, the AbstractDiagonalAligner does not use an AbstractBlockProcessor object, what means that the Aligner must compute the blocks by themselves.

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

Memory related methods: get/set methods that obtain the results from the specific architecture, such as block scores and special rows/columns.
Iteration methods: responsible to execute the diagonal iterations. The diagonals are numbered from 0. Generically speaking, diagonal with number $d$ is expected to compute all blocks $(bx,by)$ such that $bx+by=d$ is true.

The memory related methods are called considering the order of the executed iteration, so we guarantee that a special row/column will only be issued when it is already computed.

Definition at line 56 of file AbstractDiagonalAligner.hpp.

#include <AbstractDiagonalAligner.hpp>

Inheritance diagram for AbstractDiagonalAligner:

List of all members.

Public Member Functions
	AbstractDiagonalAligner ()
	AbstractDiagonalAligner constructor.
virtual	~AbstractDiagonalAligner ()
	AbstractDiagonalAligner destructor.
virtual void	alignPartition (Partition partition)
	Aligns the given partition, processing it by antidiagonals.
virtual void	clearStatistics ()
virtual void	printInitialStatistics (FILE *file)
	Empty stub for the superclass virtual method.
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 width used range.
virtual long long	getProcessedCells ()
	Returns the number of processed cells since the last call to AbstractDiagonalAligner::clearStatistics method.
virtual const char *	getProgressString () const
	MASA-Core prints this string periodically.
Protected Member Functions
virtual int	getGridWidth (int width)=0
	Returns the number of horizontal blocks that the grid must have for a given width partition.
virtual int	getBlockHeight ()=0
	Returns the default height of each block.
virtual const cell_t *	getSpecialRow (int j, int len)=0
	Returns the bottom-most cells of a block computed from the previous computed diagonal.
virtual const cell_t *	getLastRow (int j, int len)=0
	Returns the cells in the interval $[j,j+len)$ of the bottom-most row.
virtual const cell_t *	getLastColumn (int i, int len)=0
	Returns the cells in the interval $[i,i+len)$ of the bottom-most row.
virtual const score_t *	getBlockScores ()=0
	Returns the best scores of the blocks from the last computed diagonal.
virtual void	setFirstRow (const cell_t *cells, int j, int len)=0
	Initializes the cells in the range $[j,j+len)$ of the first row.
virtual void	setFirstColumn (const cell_t *cells, int i, int len)=0
	Initializes the cells in the range $[i,i+len)$ of the first column.
virtual void	clearPrunedBlocks (int b0, int b1)=0
	Clear the rows of the pruned blocks, in range $[b0,b1)$.
virtual void	initializeDiagonals ()=0
	Executes initialization procedures before the first diagonal be processed.
virtual void	processDiagonal (int diagonal, int windowLeft, int windowRight)=0
	Executes one diagonal with the blocks from $[windowLeft, windowRight]$.
virtual void	finalizeDiagonals ()=0
	Executes finalization procedures after the last diagonal is processed.
Partition	getPartition () const
	Returns the partition currently being processed.
Private Member Functions
Grid *	configureGrid (Partition partition)
	Configures the grid for the given partition.
void	prepareIterations ()
	Configures the grid and initializes other structures before the beginning of the diagonal iterations.
void	processNextIteration ()
	Processes the next diagonal and loads/flushes the rows and columns necessary for the MASA-Core integration.
bool	hasMoreIterations ()
	Tests if we have more diagonals to be processed.
void	finalizeIterations ()
	Finalizes the execution of the partition.
void	flushSpecialRows ()
	Iterates on the blocks and check if any of them must flush its last row in the disk.
void	flushLastRow ()
	This function reads a chunk of the last row from the aligner and dispatch it to the MASA-Core.
void	flushLastColumn ()
	This function reads a chunk of the last column from the aligner and dispatch it to the MASA-Core.
void	flushLastCell ()
	This function reads the bottom-left cell from aligner and dispatch it to the MASA-Core.
void	flushBlockScores ()
	This function reads the block scores from aligner and dispatch them to the MASA-Core.
void	loadFirstRow ()
	Initialize the first row of the aligner with the cells received from the MASA-Core.
void	loadFirstColumn ()
	Initialize the first column of the aligner with the cells received from the MASA-Core.
bool	isSpecialRow (int by)
	Defines if the blocks in row $by$ must flush their last row.
void	pruneBlocks ()
	Updates the pruning window accordingly to the last block scores.
Private Attributes
cell_t *	h_loadColumn
	Vector used to store the cells of the first column.
int	gridWidth
	number of columns of blocks
int	gridHeight
	number of rows of blocks
int	externalDiagonalCount
	Number of external diagonals to be processed in the current partition.
int	currentExternalDiagonal
	The id of the current external diagonal being processed.
Partition	partition
	The partition currently being processed.
BlockPruningDiagonal *	pruner
	Block Pruner object.
int	windowStart
	First block of non-pruned window.
int	windowEnd
	Last block of non-pruned window.
int	statTotalBlocks
	Total number of blocks containing in the grid.
int	statPrunedBlocksLeft
	Number of pruned blocks in the left side of the grid.
int	statPrunedBlocksRight
	Number of pruned blocks in the left side of the grid.
long long	statTotalCells
	Total number of cells in the grid.
int	statMinGridWidth
	Maintains the minimum gridWidth used.
int	statMaxGridWidth
	Maintains the maximum gridWidth used.

Constructor & Destructor Documentation

AbstractDiagonalAligner::AbstractDiagonalAligner ( )

AbstractDiagonalAligner constructor.

Definition at line 40 of file AbstractDiagonalAligner.cpp.

AbstractDiagonalAligner::~AbstractDiagonalAligner ( ) [virtual]

AbstractDiagonalAligner destructor.

Definition at line 48 of file AbstractDiagonalAligner.cpp.

Member Function Documentation

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

Aligns the given partition, processing it by antidiagonals.

Parameters:

partition partition to be aligned.

See also:: IAligner::alignPartition

Implements IAligner.

Definition at line 59 of file AbstractDiagonalAligner.cpp.

virtual void AbstractDiagonalAligner::clearPrunedBlocks	(	int	b0,
		int	b1
	)		`[protected, pure virtual]`

Clear the rows of the pruned blocks, in range $[b0,b1)$.

The rows must be cleared with very small numbers (-INF) in order to avoid garbage data in the special rows or in future non-pruned blocks that may use the same area in memory.

Parameters:

b0	first block to be cleared (inclusive).
b1	last block to be cleared (exclusive)

void AbstractDiagonalAligner::clearStatistics ( ) [virtual]

clear all internal statistics of the aligner.

Implements IAligner.

Definition at line 203 of file AbstractDiagonalAligner.cpp.

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

Configures the grid for the given partition.

Parameters:

partition partition to be aligned.

Definition at line 183 of file AbstractDiagonalAligner.cpp.

virtual void AbstractDiagonalAligner::finalizeDiagonals ( ) [protected, pure virtual]

Executes finalization procedures after the last diagonal is processed.

void AbstractDiagonalAligner::finalizeIterations ( ) [private]

Finalizes the execution of the partition.

Definition at line 172 of file AbstractDiagonalAligner.cpp.

void AbstractDiagonalAligner::flushBlockScores ( ) [private]

This function reads the block scores from aligner and dispatch them to the MASA-Core.

Definition at line 392 of file AbstractDiagonalAligner.cpp.

void AbstractDiagonalAligner::flushLastCell ( ) [private]

This function reads the bottom-left cell from aligner and dispatch it to the MASA-Core.

Definition at line 375 of file AbstractDiagonalAligner.cpp.

void AbstractDiagonalAligner::flushLastColumn ( ) [private]

This function reads a chunk of the last column from the aligner and dispatch it to the MASA-Core.

This method is called once for each external diagonal, since the last block is always calculating a new chunk of the last column.

Definition at line 358 of file AbstractDiagonalAligner.cpp.

void AbstractDiagonalAligner::flushLastRow ( ) [private]

This function reads a chunk of the last row from the aligner and dispatch it to the MASA-Core.

This method is called multiple times during the last external diagonals, since each of the bottom-most blocks calculates a range of the last row.

Definition at line 325 of file AbstractDiagonalAligner.cpp.

void AbstractDiagonalAligner::flushSpecialRows ( ) [private]

Iterates on the blocks and check if any of them must flush its last row in the disk.

If so, the row is copied from the aligner and dispatched to the MASA-Core. Note that the blocks are disposed in a diagonal, so there may be a maximum of one block per special row.

Definition at line 286 of file AbstractDiagonalAligner.cpp.

virtual int AbstractDiagonalAligner::getBlockHeight ( ) [protected, pure virtual]

Returns the default height of each block.

All the blocks will have the same height except the bottom most rows, that may be truncated.

Returns:: the default height of each block.

virtual const score_t* AbstractDiagonalAligner::getBlockScores ( ) [protected, pure virtual]

Returns the best scores of the blocks from the last computed diagonal.

Returns:: the best scores of each blocks (ordered from left to right).

virtual int AbstractDiagonalAligner::getGridWidth ( int width ) [protected, pure virtual]

Returns the number of horizontal blocks that the grid must have for a given width partition.

Parameters:

width the width of the partition to be aligned.

Returns:: the recommended grid width for that partition.

virtual const cell_t* AbstractDiagonalAligner::getLastColumn	(	int	i,
		int	len
	)		`[protected, pure virtual]`

Returns the cells in the interval $[i,i+len)$ of the bottom-most row.

Parameters:

i	the start column of the cells to be returned.
len	the number of cells to be returned.

Returns:: the vector containing the special cells.

virtual const cell_t* AbstractDiagonalAligner::getLastRow	(	int	j,
		int	len
	)		`[protected, pure virtual]`

Returns the cells in the interval $[j,j+len)$ of the bottom-most row.

Parameters:

l	the start column of the cells to be returned.
len	the number of cells to be returned.

Returns:: the vector containing the special cells.

Partition AbstractDiagonalAligner::getPartition ( ) const [protected]

Returns the partition currently being processed.

Returns:: the partition currently being processed.

Definition at line 484 of file AbstractDiagonalAligner.cpp.

long long AbstractDiagonalAligner::getProcessedCells ( ) [virtual]

Returns the number of processed cells since the last call to AbstractDiagonalAligner::clearStatistics method.

Returns:: number of processed cells

Implements IAligner.

Definition at line 260 of file AbstractDiagonalAligner.cpp.

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

MASA-Core prints this string periodically.

Returns:: the string to be printed.

Implements IAligner.

Definition at line 268 of file AbstractDiagonalAligner.cpp.

virtual const cell_t* AbstractDiagonalAligner::getSpecialRow	(	int	j,
		int	len
	)		`[protected, pure virtual]`

Returns the bottom-most cells of a block computed from the previous computed diagonal.

The block cells range is in the interval $[j,j+len)$. Since we are processing in diagonals, only one block can reside in this range. The cells will be saved in a special row by MASA-Core.

Parameters:

j	the start column of the cells to be returned.
len	the number of cells to be returned.

Returns:: the vector containing the special cells.

bool AbstractDiagonalAligner::hasMoreIterations ( ) [private]

Tests if we have more diagonals to be processed.

Returns:: true if we have more diagonals.

Definition at line 165 of file AbstractDiagonalAligner.cpp.

virtual void AbstractDiagonalAligner::initializeDiagonals ( ) [protected, pure virtual]

Executes initialization procedures before the first diagonal be processed.

bool AbstractDiagonalAligner::isSpecialRow ( int by ) [private]

Defines if the blocks in row $by$ must flush their last row.

The top-most and bottom-most rows are never special rows.

Parameters:

by	the block's row id

Returns:: true if the blocks inr row $by$ must save their last row.

Definition at line 466 of file AbstractDiagonalAligner.cpp.

void AbstractDiagonalAligner::loadFirstColumn ( ) [private]

Initialize the first column of the aligner with the cells received from the MASA-Core.

The first column is read in chunks, which size is defined by the getBlockHeight() function.

Definition at line 433 of file AbstractDiagonalAligner.cpp.

void AbstractDiagonalAligner::loadFirstRow ( ) [private]

Initialize the first row of the aligner with the cells received from the MASA-Core.

The first row is read all at once.

Definition at line 409 of file AbstractDiagonalAligner.cpp.

void AbstractDiagonalAligner::prepareIterations ( ) [private]

Configures the grid and initializes other structures before the beginning of the diagonal iterations.

Definition at line 76 of file AbstractDiagonalAligner.cpp.

void AbstractDiagonalAligner::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 228 of file AbstractDiagonalAligner.cpp.

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

Empty stub for the superclass virtual method.

clear all internal statistics of the aligner.

Implements IAligner.

Definition at line 216 of file AbstractDiagonalAligner.cpp.

void AbstractDiagonalAligner::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 222 of file AbstractDiagonalAligner.cpp.

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

Prints the pruning statistics and grid width used range.

Parameters:

file	handler to print out the statistics.

See also:: IAligner::printStatistics

Implements IAligner.

Definition at line 236 of file AbstractDiagonalAligner.cpp.

virtual void AbstractDiagonalAligner::processDiagonal	(	int	diagonal,
		int	windowLeft,
		int	windowRight
	)		`[protected, pure virtual]`

Executes one diagonal with the blocks from $[windowLeft, windowRight]$.

The diagonals are numbered from 0, but the first diagonal (0) is not expected to compute any block. Diagonal 1 is expected to compute block $(0,0)$, diagonal 2 is expected to compute blocks $(1,0)$ and $(0,1)$, and so on. Generically speaking, diagonal $d$ is expected to compute all blocks $(bx,by)$ that $bx+by=d$.

Parameters:

diagonal	the diagonal number to be processed.
windowLeft	the first block to be processed (inclusive).
windowRight	the last block to be processed (inclusive).

void AbstractDiagonalAligner::processNextIteration ( ) [private]

Processes the next diagonal and loads/flushes the rows and columns necessary for the MASA-Core integration.

Definition at line 110 of file AbstractDiagonalAligner.cpp.

void AbstractDiagonalAligner::pruneBlocks ( ) [private]

Updates the pruning window accordingly to the last block scores.

Definition at line 491 of file AbstractDiagonalAligner.cpp.