Package | Description |
---|---|
de.unibi.citec.tcs.alignment |
This package contains the actual AlignmentAlgorithms as well as their return
classes.
|
Modifier and Type | Method and Description |
---|---|
SoftPathModel.SoftMatrixEntry |
SoftAlignmentFullAlgorithm.createDelInitial(SoftPathModel.SoftMatrixEntry delOld,
int i,
double delLocal)
This method should not be called from outside!
|
SoftPathModel.SoftMatrixEntry |
SoftAlignmentSamplingAlgorithm.createDelInitial(SoftPathModel.SoftMatrixEntry delOld,
int i,
double delLocal)
This method should not be called from outside!
|
SoftPathModel.SoftMatrixEntry |
SoftAlignmentFullAlgorithm.createInitial()
This method should not be called from outside!
|
SoftPathModel.SoftMatrixEntry |
SoftAlignmentSamplingAlgorithm.createInitial()
This method should not be called from outside!
|
SoftPathModel.SoftMatrixEntry |
SoftAlignmentFullAlgorithm.createInsInitial(SoftPathModel.SoftMatrixEntry insOld,
int j,
double insLocal)
This method should not be called from outside!
|
SoftPathModel.SoftMatrixEntry |
SoftAlignmentSamplingAlgorithm.createInsInitial(SoftPathModel.SoftMatrixEntry insOld,
int j,
double insLocal)
This method should not be called from outside!
|
SoftPathModel.SoftMatrixEntry |
SoftAlignmentFullAlgorithm.createNewEntry(SoftPathModel.SoftMatrixEntry delOld,
SoftPathModel.SoftMatrixEntry insOld,
SoftPathModel.SoftMatrixEntry repOld,
int i,
int j,
double delLocal,
double insLocal,
double repLocal)
This method should not be called from outside!
|
SoftPathModel.SoftMatrixEntry |
SoftAlignmentSamplingAlgorithm.createNewEntry(SoftPathModel.SoftMatrixEntry delOld,
SoftPathModel.SoftMatrixEntry insOld,
SoftPathModel.SoftMatrixEntry repOld,
int i,
int j,
double delLocal,
double insLocal,
double repLocal)
This method should not be called from outside!
|
SoftPathModel.SoftMatrixEntry[][] |
SoftPathModel.getPathMatrix()
This is the dynamic programming matrix calculated by a
SoftAlignmentAlgorithm.
|
Modifier and Type | Method and Description |
---|---|
SoftPathModel.SoftMatrixEntry |
SoftAlignmentFullAlgorithm.createDelInitial(SoftPathModel.SoftMatrixEntry delOld,
int i,
double delLocal)
This method should not be called from outside!
|
SoftPathModel.SoftMatrixEntry |
SoftAlignmentSamplingAlgorithm.createDelInitial(SoftPathModel.SoftMatrixEntry delOld,
int i,
double delLocal)
This method should not be called from outside!
|
SoftPathModel.SoftMatrixEntry |
SoftAlignmentFullAlgorithm.createInsInitial(SoftPathModel.SoftMatrixEntry insOld,
int j,
double insLocal)
This method should not be called from outside!
|
SoftPathModel.SoftMatrixEntry |
SoftAlignmentSamplingAlgorithm.createInsInitial(SoftPathModel.SoftMatrixEntry insOld,
int j,
double insLocal)
This method should not be called from outside!
|
SoftPathModel.SoftMatrixEntry |
SoftAlignmentFullAlgorithm.createNewEntry(SoftPathModel.SoftMatrixEntry delOld,
SoftPathModel.SoftMatrixEntry insOld,
SoftPathModel.SoftMatrixEntry repOld,
int i,
int j,
double delLocal,
double insLocal,
double repLocal)
This method should not be called from outside!
|
SoftPathModel.SoftMatrixEntry |
SoftAlignmentSamplingAlgorithm.createNewEntry(SoftPathModel.SoftMatrixEntry delOld,
SoftPathModel.SoftMatrixEntry insOld,
SoftPathModel.SoftMatrixEntry repOld,
int i,
int j,
double delLocal,
double insLocal,
double repLocal)
This method should not be called from outside!
|
SoftPathModel |
SoftAlignmentFullAlgorithm.transformToResult(SoftPathModel.SoftMatrixEntry[][] alignmentMatrix,
Sequence a,
Sequence b)
This method should not be called from outside!
|
PathList |
SoftAlignmentSamplingAlgorithm.transformToResult(SoftPathModel.SoftMatrixEntry[][] alignmentMatrix,
Sequence a,
Sequence b)
This method should not be called from outside!
|
Constructor and Description |
---|
SoftPathModel(AlignmentSpecification specification,
Sequence left,
Sequence right,
double score,
double beta,
SoftPathModel.SoftMatrixEntry[][] pathMatrix) |
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