Package org.biojava.bio.dp.twohead

Class MatrixPairDPCursor

java.lang.Object

org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor

org.biojava.bio.dp.twohead.MatrixPairDPCursor

All Implemented Interfaces:

PairDPCursor

public class MatrixPairDPCursor
extends AbstractMatrixPairDPCursor

Author:

Matthew Pocock

Field Summary

Fields inherited from class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor

bPointers, columns, depth, eCache, emissions, emptyBP, numStates, pos, seqs, sMatrix, zeroCol

Constructor Summary

Constructors

Constructor	Description
MatrixPairDPCursor(SymbolList seq1, SymbolList seq2, int depth1, int depth2, PairDPMatrix matrix, EmissionCache eCache)

Method Summary

Modifier and Type	Method	Description
boolean	hasNext()	test wether the cursor can be advanced further
void	next(Cell[][] cells)	retrieve the next block of cells

Methods inherited from class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor

getDepth, press

Methods inherited from class java.lang.Object

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

Constructor Detail

MatrixPairDPCursor

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

Throws:

IllegalSymbolException

Method Detail

hasNext

public boolean hasNext()

Description copied from interface: PairDPCursor

test wether the cursor can be advanced further

next

public void next(Cell[][] cells)

Description copied from interface: PairDPCursor

retrieve the next block of cells