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java.lang.Objectorg.biojava.bio.dp.twohead.LightPairDPCursor
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.
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 |
protected BackPointer[][][] bPointers
protected int numStates
protected double[] zeroCol
protected BackPointer[] emptyBP
protected int[] depth
protected EmissionCache eCache
Constructor Detail |
public LightPairDPCursor(SymbolList seq1, SymbolList seq2, int depth1, int depth2, int numStates, EmissionCache eCache) throws IllegalSymbolException
seq1
- Description of Parameterseq2
- Description of Parameterdepth1
- Description of Parameterdepth2
- Description of ParameternumStates
- Description of ParametereCache
- Description of Parameter
IllegalSymbolException
- Description of ExceptionMethod Detail |
public int[] getDepth()
getDepth
in interface PairDPCursor
public boolean hasNext()
hasNext
in interface PairDPCursor
public Cell[][] press()
press
in interface PairDPCursor
public void next(Cell[][] cells) throws IllegalSymbolException
next
in interface PairDPCursor
cells
- Description of Parameter
IllegalSymbolException
- Description of Exception
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