AbstractMatrixPairDPCursor (biojava-legacy 1.9.7 API)

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 Details
- 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 Details
- AbstractMatrixPairDPCursor
  
  public AbstractMatrixPairDPCursor(SymbolList seq1, SymbolList seq2, int start1, int start2, int depth1, int depth2, PairDPMatrix matrix, EmissionCache eCache) throws IllegalSymbolException
  
  Throws:
  
  IllegalSymbolException
Method Details
- 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