Package | Description |
---|---|
de.citec.tcs.alignment |
This module defines the interface for AlignmentAlgorithms as
well as some helper classes.
|
de.citec.tcs.alignment.adp |
This package contains a more general approach to construct
AlignmentAlgorithms by relying on the theoretical concept of Algebraic
Dynamic Programming (ADP) as developed by Giegerich et al.
|
de.citec.tcs.alignment.visualization |
This module contains means to visualize AlignmentPaths.
|
de.citec.tcs.alignment.wrappers |
This module contains some wrappers to make usage of the
TCSAlignmentToolbox easier.
|
Modifier and Type | Method and Description |
---|---|
AlignmentPath |
Operation.getPath() |
AlignmentPath |
StrictDTWFullAlgorithm.transformToResult(double[][] dtwMatrix,
Sequence a,
Sequence b)
This method has to be implemented by sub classes to transform
a calculated dynamic programming matrix to a valid result of
that implementation.
|
AlignmentPath |
StrictAffineAlignmentFullAlgorithm.transformToResult(EnumMap<AbstractAffineAlignmentAlgorithm.Recurrence,double[][]> dp_tables,
double[][] compareMatrix,
double[] deletionMatrix,
double[] insertionMatrix,
double[] skipDeletionMatrix,
double[] skipInsertionMatrix,
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.
|
AlignmentPath |
StrictAlignmentFullAlgorithm.transformToResult(StrictAlignmentFullAlgorithm.FullMatrixEntry[][] 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.
|
Modifier and Type | Method and Description |
---|---|
List<AlignmentPath> |
PathMap.getAllPaths()
Returns all paths stored in this map in order of their score (from
good/low to bad/high).
|
List<AlignmentPath> |
PathMap.getPaths(double score)
Returns all paths with the given score.
|
List<AlignmentPath> |
PathMap.removeValues(double score)
Removes all AlignmentPaths with the given score from the map and returns
them.
|
Modifier and Type | Method and Description |
---|---|
void |
PathMap.put(AlignmentPath path)
Adds a new AlignmentPath to this map.
|
Constructor and Description |
---|
Operation(Node left,
Node right,
OperationType type,
AlignmentPath path)
This constructs an Operation within an AlignmentPath.
|
Modifier and Type | Method and Description |
---|---|
AlignmentPath |
StrictADPFullAlgorithm.transformToResult(EnumMap<N,double[][]> dpTables,
double[][] compareMatrix,
double[] deletionMatrix,
double[] insertionMatrix,
double[] skipDeletionMatrix,
double[] skipInsertionMatrix,
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.
|
Modifier and Type | Method and Description |
---|---|
String |
AbstractVisualizer.getVisualizationData(AlignmentPath path)
Returns the visualization as string.
|
void |
AbstractVisualizer.visualize(AlignmentPath path,
File file)
Returns the visualization as string.
|
void |
HTMLVisualizer.visualize(AlignmentPath path,
OutputStream out)
A visualization in this sense is some arbitrary data that can be written
to an output stream and is created from an AlignmentPath.
|
void |
StringVisualizer.visualize(AlignmentPath path,
OutputStream out)
A visualization in this sense is some arbitrary data that can be written
to an output stream and is created from an AlignmentPath.
|
void |
Visualizer.visualize(AlignmentPath path,
OutputStream out)
A visualization in this sense is some arbitrary data that can be written
to an output stream and is created from an AlignmentPath.
|
void |
AbstractVisualizer.visualize(AlignmentPath path,
String file)
Returns the visualization as string.
|
void |
HTMLVisualizer.visualizeMatrix(AlignmentPath[][] paths,
String[] names,
File outDir,
boolean verbose)
This takes a full or sparse matrix of AlignmentPaths and provides HTML
output for it.
|
void |
HTMLVisualizer.visualizeMatrix(AlignmentPath[][] paths,
String[] leftNames,
String[] rightNames,
File outDir,
boolean verbose)
This takes a full or sparse matrix of AlignmentPaths and provides HTML
output for it.
|
Modifier and Type | Method and Description |
---|---|
static double[][] |
VectorialSequences.getDifference(AlignmentPath path)
Returns the difference at each operation of the given AlignmentPath.
|
static double[][][] |
VectorialSequences.getExtensions(AlignmentPath path)
Returns the sequence extensions modelled by this AlignmentPath.
|
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