Package | Description |
---|---|
de.citec.tcs.alignment |
This module defines the interface for AlignmentAlgorithms as
well as some helper 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 |
---|---|
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.
|
Copyright (C) 2013-2015 Benjamin Paaßen, 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 . This documentation is licensed under the conditions of CC-BY-SA 4.0: https://creativecommons.org/licenses/by-sa/4.0/