org.biojava.bio.dp.twohead
Class AbstractMatrixPairDPCursor

java.lang.Object
  extended by 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

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