Package 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
- Author:
- Matthew Pocock
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Field Summary
FieldsModifier and TypeFieldDescriptionprotected BackPointer[][][]
protected double[][][]
protected int[]
protected EmissionCache
protected double[][][]
protected BackPointer[]
protected int
protected int[]
protected SymbolList[]
protected double[][][]
protected double[]
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Constructor Summary
ConstructorsConstructorDescriptionAbstractMatrixPairDPCursor
(SymbolList seq1, SymbolList seq2, int start1, int start2, int depth1, int depth2, PairDPMatrix matrix, EmissionCache eCache) -
Method Summary
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
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Field Details
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pos
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seqs
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columns
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bPointers
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emissions
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numStates
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zeroCol
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emptyBP
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depth
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sMatrix
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eCache
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Constructor Details
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AbstractMatrixPairDPCursor
public AbstractMatrixPairDPCursor(SymbolList seq1, SymbolList seq2, int start1, int start2, int depth1, int depth2, PairDPMatrix matrix, EmissionCache eCache) throws IllegalSymbolException - Throws:
IllegalSymbolException
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Method Details
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getDepth
Description copied from interface:PairDPCursor
retrieve the depth of this cursor- Specified by:
getDepth
in interfacePairDPCursor
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press
Description copied from interface:PairDPCursor
press out a new correctly sized cell array- Specified by:
press
in interfacePairDPCursor
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