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 |
---|---|
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 |
---|---|
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 |
---|---|
abstract R |
AbstractGapAlignmentAlgorithm.transformToResult(X[][] alignmentMatrix,
Sequence a,
Sequence b)
This method should not be called from outside!
|
Copyright (C) 2013, 2014 Benjamin Paaßen, Charlie Krüger, Georg Zentgraf, AG Theoretical Computer Science, Centre of Excellence Cognitive Interaction Technology (CITEC), University of Bielefeld, licensed under the AGPL v. 3: http://openresearch.cit-ec.de/projects/tcs