Package | Description |
---|---|
de.unibi.citec.tcs.alignment |
This package contains the actual AlignmentAlgorithms as well as their return
classes.
|
Modifier and Type | Class and Description |
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class |
AbstractGapAlignmentAlgorithm<X extends AlignmentMatrixEntry,R>
This is an abstract super class for GapAlignmentAlgorithms that provides a
generic implementation of the dynamic programming needed to efficiently
calculate the alignment.
|
Modifier and Type | Class and Description |
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static class |
SoftAlignmentScoreAlgorithm.ScoreEntry |
static class |
SoftPathModel.SoftMatrixEntry |
static class |
StrictAlignmentFullAlgorithm.FullMatrixEntry |
static class |
StrictAlignmentScoreAlgorithm.ScoreEntry |
static class |
StrictAllOptimalAlgorithm.FullMatrixEntry |
Modifier and Type | Method and Description |
---|---|
X[][] |
AbstractGapAlignmentAlgorithm.getLastAlignmentMatrix()
The last matrix that was calculated using this algorithm.
|
Modifier and Type | Method and Description |
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abstract R |
AbstractGapAlignmentAlgorithm.transformToResult(X[][] alignmentMatrix,
Sequence a,
Sequence b)
This method should not be called from outside!
The subclass uses this method to transform the alignment matrix and the
input sequences to the actual alignment result.
|
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