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 Alignments.
|
de.citec.tcs.alignment.wrappers |
This module contains some wrappers to make usage of the
TCSAlignmentToolbox easier.
|
Modifier and Type | Method and Description |
---|---|
Alignment<X,Y> |
StrictDTWFullAlgorithm.transformToResult(double[][] dtwMatrix,
double[][] repCosts,
double[][] delRepCosts,
double[][] insRepCosts,
List<X> a,
List<Y> b) |
Alignment<X,Y> |
StrictAlignmentFullAlgorithm.transformToResult(double[][] alignMat,
double[][] repCosts,
double[] delCosts,
double[] insCosts,
List<X> a,
List<Y> b) |
Modifier and Type | Method and Description |
---|---|
List<Alignment<X,Y>> |
AlignmentMap.getAlignments(double score)
Returns all Alignments for the given score.
|
List<Alignment<X,Y>> |
AlignmentMap.getAllAlignments()
Returns all Alignments stored in this map in order of their score (from good/low to
bad/high).
|
List<Alignment<X,Y>> |
AlignmentMap.removeAlignments(double score)
Removes all Alignments with the given score from the map and returns them.
|
Modifier and Type | Method and Description |
---|---|
void |
AlignmentMap.put(Alignment<X,Y> path)
Adds a new Alignment to this map.
|
Constructor and Description |
---|
Alignment(Alignment<X,Y> copy)
A copy constructor.
|
Modifier and Type | Method and Description |
---|---|
Alignment<X,Y> |
StrictADPFullAlgorithm.transformToResult(EnumMap<N,double[][]> dpTables,
EnumMap<OperationType,double[][]> repMatrices,
EnumMap<OperationType,double[]> delVectors,
EnumMap<OperationType,double[]> insVectors,
List<X> a,
List<Y> b) |
Alignment<X,Y> |
SparseStrictADPFullAlgorithm.transformToResult(EnumMap<N,SparseAbstractADPAlgorithm.SparseMatrix> dpTables,
EnumMap<OperationType,SparseAbstractADPAlgorithm.SparseMatrix> repMatrices,
EnumMap<OperationType,double[]> delVectors,
EnumMap<OperationType,double[]> insVectors,
List<X> a,
List<Y> b) |
Modifier and Type | Method and Description |
---|---|
void |
CharacterVisualizer.visualize(Alignment<Character,Character> alignment,
OutputStream out) |
void |
StringVisualizer.visualize(Alignment<X,Y> path,
OutputStream out) |
void |
Visualizer.visualize(Alignment<X,Y> alignment,
OutputStream out)
Visualize the given Alignment and write the resulting data to the given OutputStream.
|
void |
HTMLVisualizer.visualize(Alignment<X,Y> alignment,
OutputStream out) |
static <X,Y> String |
VisualizerUtils.visualize(Visualizer<X,Y> visualizer,
Alignment<X,Y> alignment)
Visualize the given Alignment and write the resulting data to a String.
|
static <X,Y> void |
VisualizerUtils.visualize(Visualizer<X,Y> visualizer,
Alignment<X,Y> alignment,
File out)
Visualize the given Alignment and write the resulting data to the given File.
|
static <X,Y> void |
VisualizerUtils.visualize(Visualizer<X,Y> visualizer,
Alignment<X,Y> alignment,
String out)
Visualize the given Alignment and write the resulting data to the given File.
|
static <X,Y> void |
VisualizerUtils.visualize(Visualizer<X,Y> visualizer,
Alignment<X,Y> alignment,
Writer out)
Visualize the given Alignment and write the resulting data to the given Writer.
|
void |
HTMLVisualizer.visualizeMatrix(Alignment[][] alignments,
String[] names,
File outDir)
This takes a full or sparse matrix of Alignments and provides HTML
output for it.
|
void |
HTMLVisualizer.visualizeMatrix(Alignment[][] alignments,
String[] leftNames,
String[] rightNames,
File outDir)
This takes a full or sparse matrix of Alignments and provides HTML
output for it.
|
Modifier and Type | Method and Description |
---|---|
static double[][] |
VectorialSequences.getDifference(Alignment<Node,Node> path)
Returns the difference at each operation of the given AlignmentPath.
|
static double[][][] |
VectorialSequences.getExtensions(Alignment<Node,Node> path)
Returns the sequence extensions modelled by this AlignmentPath.
|
Copyright (C) 2016 Benjamin Paaßen, 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/