Package org.biojava.bio.dp.twohead
Class LightPairDPCursor
java.lang.Object
org.biojava.bio.dp.twohead.LightPairDPCursor
- All Implemented Interfaces:
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, David Huen (fixes for magical state)
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Field Summary
FieldsModifier and TypeFieldDescriptionprotected BackPointer[][][]
Description of the Fieldprotected int[]
Description of the Fieldprotected EmissionCache
Description of the Fieldprotected BackPointer[]
Description of the Fieldprotected int
Description of the Fieldprotected double[]
Description of the Field -
Constructor Summary
ConstructorsConstructorDescriptionLightPairDPCursor
(SymbolList seq1, SymbolList seq2, int depth1, int depth2, int numStates, EmissionCache eCache) Constructor for the LightPairDPCursor object -
Method Summary
Modifier and TypeMethodDescriptionint[]
getDepth()
Gets the Depth attribute of the LightPairDPCursor objectboolean
hasNext()
Are there further Cells to be computed?void
Description of the MethodCell[][]
press()
Returns the minimal context of the DP matrix necessary to compute the value of a single point in that matrix.
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Field Details
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bPointers
Description of the Field -
numStates
Description of the Field -
zeroCol
Description of the Field -
emptyBP
Description of the Field -
depth
Description of the Field -
eCache
Description of the Field
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Constructor Details
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LightPairDPCursor
public LightPairDPCursor(SymbolList seq1, SymbolList seq2, int depth1, int depth2, int numStates, EmissionCache eCache) throws IllegalSymbolException Constructor for the LightPairDPCursor object- Parameters:
seq1
- First sequence in this twohead DP.seq2
- Second sequence in this twohead DP.depth1
- The number of bases of context required in first sequence to compute DP matrix at a point (= max advance in first sequence + 1).depth2
- The number of bases of context required in second sequence to compute DP matrix at a point (= max advance in second sequence + 1).numStates
- Total number of states in model.eCache
- Emission cache to be used with this run.- Throws:
IllegalSymbolException
- Description of Exception
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Method Details
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getDepth
Gets the Depth attribute of the LightPairDPCursor object- Specified by:
getDepth
in interfacePairDPCursor
- Returns:
- The Depth value
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hasNext
Are there further Cells to be computed?- Specified by:
hasNext
in interfacePairDPCursor
- Returns:
- Description of the Returned Value
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press
Returns the minimal context of the DP matrix necessary to compute the value of a single point in that matrix.The Cell [][] array has the origin as the current point to be evaluated and successive rows/columns represent rows/columns backwards within the DP matrix.
- Specified by:
press
in interfacePairDPCursor
- Returns:
- An array representing the immediate context around the element to be computed.
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next
Description of the Method- Specified by:
next
in interfacePairDPCursor
- Parameters:
cells
- Description of Parameter- Throws:
IllegalSymbolException
- Description of Exception
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