Package org.biojava.bio.dp.twohead

Class AbstractMatrixPairDPCursor

java.lang.Object

org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor

All Implemented Interfaces:

PairDPCursor

Direct Known Subclasses:

BackMatrixPairDPCursor, MatrixPairDPCursor

public abstract class AbstractMatrixPairDPCursor
extends Object
implements PairDPCursor

Author:

Matthew Pocock

Field Summary

Fields

Modifier and Type	Field	Description
protected BackPointer[][][]	bPointers
protected double[][][]	columns
protected int[]	depth
protected EmissionCache	eCache
protected double[][][]	emissions
protected BackPointer[]	emptyBP
protected int	numStates
protected int[]	pos
protected SymbolList[]	seqs
protected double[][][]	sMatrix
protected double[]	zeroCol

Constructor Summary

Constructors

Constructor	Description
AbstractMatrixPairDPCursor(SymbolList seq1, SymbolList seq2, int start1, int start2, int depth1, int depth2, PairDPMatrix matrix, EmissionCache eCache)

Method Summary

Modifier and Type	Method	Description
int[]	getDepth()	retrieve the depth of this cursor
Cell[][]	press()	press out a new correctly sized cell array

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.biojava.bio.dp.twohead.PairDPCursor

hasNext, next

Field Detail

pos

protected int[] pos

seqs

protected SymbolList[] seqs

columns

protected double[][][] columns

bPointers

protected BackPointer[][][] bPointers

emissions

protected double[][][] emissions

numStates

protected int numStates

zeroCol

protected double[] zeroCol

emptyBP

protected BackPointer[] emptyBP

depth

protected int[] depth

sMatrix

protected double[][][] sMatrix

eCache

protected EmissionCache eCache

Constructor Detail

AbstractMatrixPairDPCursor

public AbstractMatrixPairDPCursor(SymbolList seq1,
                                  SymbolList seq2,
                                  int start1,
                                  int start2,
                                  int depth1,
                                  int depth2,
                                  PairDPMatrix matrix,
                                  EmissionCache eCache)
                           throws IllegalSymbolException

Throws:

IllegalSymbolException

Method Detail

getDepth

public int[] getDepth()

Description copied from interface: PairDPCursor

retrieve the depth of this cursor

Specified by:

getDepth in interface PairDPCursor

press

public Cell[][] press()

Description copied from interface: PairDPCursor

press out a new correctly sized cell array

Specified by:

press in interface PairDPCursor