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 java.lang.Object
- implements PairDPCursor
- Author:
- Matthew Pocock
Method Summary |
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 |
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
AbstractMatrixPairDPCursor
public AbstractMatrixPairDPCursor(SymbolList seq1,
SymbolList seq2,
int start1,
int start2,
int depth1,
int depth2,
PairDPMatrix matrix,
EmissionCache eCache)
throws IllegalSymbolException
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