Package | Description |
---|---|
de.citec.tcs.alignment |
This module defines the interface for AlignmentAlgorithms as
well as some helper 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!
The subclass specifies the entry (i+1,0) of the alignment matrix with
this method given the entry (i,0).
|
SoftPathModel.SoftMatrixEntry |
SoftAlignmentSamplingAlgorithm.createDelInitial(SoftPathModel.SoftMatrixEntry delOld,
int i,
double delLocal)
This method should not be called from outside!
The subclass specifies the entry (i+1,0) of the alignment matrix with
this method given the entry (i,0).
|
SoftPathModel.SoftMatrixEntry |
SoftAlignmentFullAlgorithm.createInitial()
This method should not be called from outside!
The subclass specifies the entry (0,0) of the alignment matrix with this
method.
|
SoftPathModel.SoftMatrixEntry |
SoftAlignmentSamplingAlgorithm.createInitial()
This method should not be called from outside!
The subclass specifies the entry (0,0) of the alignment matrix with this
method.
|
SoftPathModel.SoftMatrixEntry |
SoftAlignmentFullAlgorithm.createInsInitial(SoftPathModel.SoftMatrixEntry insOld,
int j,
double insLocal)
This method should not be called from outside!
The subclass specifies the entry (0,j+1) of the alignment matrix with
this method given the entry (0,j).
|
SoftPathModel.SoftMatrixEntry |
SoftAlignmentSamplingAlgorithm.createInsInitial(SoftPathModel.SoftMatrixEntry insOld,
int j,
double insLocal)
This method should not be called from outside!
The subclass specifies the entry (0,j+1) of the alignment matrix with
this method given the entry (0,j).
|
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!
The subclass specifies the entry (i+1,j+1) of the alignment matrix with
this method given the entries (i,j+1) (deletion), (i+1,j) (insertion) and
(i,j) (replacement).
|
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!
The subclass specifies the entry (i+1,j+1) of the alignment matrix with
this method given the entries (i,j+1) (deletion), (i+1,j) (insertion) and
(i,j) (replacement).
|
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!
The subclass specifies the entry (i+1,0) of the alignment matrix with
this method given the entry (i,0).
|
SoftPathModel.SoftMatrixEntry |
SoftAlignmentSamplingAlgorithm.createDelInitial(SoftPathModel.SoftMatrixEntry delOld,
int i,
double delLocal)
This method should not be called from outside!
The subclass specifies the entry (i+1,0) of the alignment matrix with
this method given the entry (i,0).
|
SoftPathModel.SoftMatrixEntry |
SoftAlignmentFullAlgorithm.createInsInitial(SoftPathModel.SoftMatrixEntry insOld,
int j,
double insLocal)
This method should not be called from outside!
The subclass specifies the entry (0,j+1) of the alignment matrix with
this method given the entry (0,j).
|
SoftPathModel.SoftMatrixEntry |
SoftAlignmentSamplingAlgorithm.createInsInitial(SoftPathModel.SoftMatrixEntry insOld,
int j,
double insLocal)
This method should not be called from outside!
The subclass specifies the entry (0,j+1) of the alignment matrix with
this method given the entry (0,j).
|
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!
The subclass specifies the entry (i+1,j+1) of the alignment matrix with
this method given the entries (i,j+1) (deletion), (i+1,j) (insertion) and
(i,j) (replacement).
|
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!
The subclass specifies the entry (i+1,j+1) of the alignment matrix with
this method given the entries (i,j+1) (deletion), (i+1,j) (insertion) and
(i,j) (replacement).
|
SoftPathModel |
SoftAlignmentFullAlgorithm.transformToResult(SoftPathModel.SoftMatrixEntry[][] 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.
|
PathList |
SoftAlignmentSamplingAlgorithm.transformToResult(SoftPathModel.SoftMatrixEntry[][] 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.
|
Constructor and Description |
---|
SoftPathModel(AlignmentSpecification specification,
Sequence left,
Sequence right,
double distance,
double beta,
SoftPathModel.SoftMatrixEntry[][] pathMatrix) |
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/