org.biojava.bio.dp.twohead
Class LightPairDPCursor

java.lang.Object
  extended byorg.biojava.bio.dp.twohead.LightPairDPCursor
All Implemented Interfaces:
PairDPCursor

public class LightPairDPCursor
extends java.lang.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

Field Summary
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
LightPairDPCursor(SymbolList seq1, SymbolList seq2, int depth1, int depth2, int numStates, EmissionCache eCache)
          Constructor for the LightPairDPCursor object
 
Method Summary
 int[] getDepth()
          Gets the Depth attribute of the LightPairDPCursor object
 boolean hasNext()
          Description of the Method
 void next(Cell[][] cells)
          Description of the Method
 Cell[][] press()
          Description of the Method
 
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 - Description of Parameter
seq2 - Description of Parameter
depth1 - Description of Parameter
depth2 - Description of Parameter
numStates - Description of Parameter
eCache - Description of Parameter
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()
Description of the Method

Specified by:
hasNext in interface PairDPCursor
Returns:
Description of the Returned Value

press

public Cell[][] press()
Description of the Method

Specified by:
press in interface PairDPCursor
Returns:
Description of the Returned Value

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