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java.lang.Objectorg.biojava.bio.dp.twohead.LightPairDPCursor
public class 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 | |
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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 | |
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LightPairDPCursor(SymbolList seq1,
SymbolList seq2,
int depth1,
int depth2,
int numStates,
EmissionCache eCache)
Constructor for the LightPairDPCursor object |
Method Summary | |
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int[] |
getDepth()
Gets the Depth attribute of the LightPairDPCursor object |
boolean |
hasNext()
Are there further Cells to be computed? |
void |
next(Cell[][] cells)
Description of the Method |
Cell[][] |
press()
Returns the minimal context of the DP matrix necessary to compute the value of a single point in that matrix. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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protected BackPointer[][][] bPointers
protected int numStates
protected double[] zeroCol
protected BackPointer[] emptyBP
protected int[] depth
protected EmissionCache eCache
Constructor Detail |
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public LightPairDPCursor(SymbolList seq1, SymbolList seq2, int depth1, int depth2, int numStates, EmissionCache eCache) throws IllegalSymbolException
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.
IllegalSymbolException
- Description of ExceptionMethod Detail |
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public int[] getDepth()
getDepth
in interface PairDPCursor
public boolean hasNext()
hasNext
in interface PairDPCursor
public Cell[][] press()
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.
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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