org.biojava.bio.dp.twohead

Class LightPairDPCursor

java.lang.Object

org.biojava.bio.dp.twohead.LightPairDPCursor

All Implemented Interfaces:

PairDPCursor

public class LightPairDPCursor
extends Object
implements PairDPCursor

A LIGHT implementation of PairDPCursor.

This object manages memory that is linear on the length of the shortest sequence. It does not maintain any data beyond that necessary for the next round of calcCell invocations.

Author:

Matthew Pocock, David Huen (fixes for magical state)

Field Summary

Fields

Modifier and Type	Field and Description
protected BackPointer[][][]	bPointers Description of the Field
protected int[]	depth Description of the Field
protected EmissionCache	eCache Description of the Field
protected BackPointer[]	emptyBP Description of the Field
protected int	numStates Description of the Field
protected double[]	zeroCol Description of the Field

Constructor Summary

Constructors

Constructor and Description
LightPairDPCursor(SymbolList seq1, SymbolList seq2, int depth1, int depth2, int numStates, EmissionCache eCache) Constructor for the LightPairDPCursor object

Method Summary

Methods

Modifier and Type	Method and Description
int[]	getDepth() Gets the Depth attribute of the LightPairDPCursor object
boolean	hasNext() Are there further Cells to be computed?
void	next(Cell[][] cells) Description of the Method
Cell[][]	press() Returns the minimal context of the DP matrix necessary to compute the value of a single point in that matrix.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

bPointers

protected BackPointer[][][] bPointers

Description of the Field

numStates

protected int numStates

Description of the Field

zeroCol

protected double[] zeroCol

Description of the Field

emptyBP

protected BackPointer[] emptyBP

Description of the Field

depth

protected int[] depth

Description of the Field

eCache

protected EmissionCache eCache

Description of the Field

Constructor Detail

LightPairDPCursor

public LightPairDPCursor(SymbolList seq1,
                 SymbolList seq2,
                 int depth1,
                 int depth2,
                 int numStates,
                 EmissionCache eCache)
                  throws IllegalSymbolException

Constructor for the LightPairDPCursor object

Parameters:

seq1 - First sequence in this twohead DP.

seq2 - Second sequence in this twohead DP.

depth1 - The number of bases of context required in first sequence to compute DP matrix at a point (= max advance in first sequence + 1).

depth2 - The number of bases of context required in second sequence to compute DP matrix at a point (= max advance in second sequence + 1).

numStates - Total number of states in model.

eCache - Emission cache to be used with this run.

Throws:

IllegalSymbolException - Description of Exception

Method Detail

getDepth

public int[] getDepth()

Gets the Depth attribute of the LightPairDPCursor object

Specified by:

getDepth in interface PairDPCursor

Returns:

The Depth value

hasNext

public boolean hasNext()

Are there further Cells to be computed?

Specified by:

hasNext in interface PairDPCursor

Returns:

Description of the Returned Value

press

public Cell[][] press()

Returns the minimal context of the DP matrix necessary to compute the value of a single point in that matrix.

The Cell [][] array has the origin as the current point to be evaluated and successive rows/columns represent rows/columns backwards within the DP matrix.

Specified by:

press in interface PairDPCursor

Returns:

An array representing the immediate context around the element to be computed.

next

public void next(Cell[][] cells)
          throws IllegalSymbolException

Description of the Method

Specified by:

next in interface PairDPCursor

Parameters:

cells - Description of Parameter

Throws:

IllegalSymbolException - Description of Exception