Package | Description |
---|---|
de.unibi.citec.tcs.alignment |
This package contains the actual AlignmentAlgorithms as well as their return
classes.
|
de.unibi.citec.tcs.alignment.visualization | |
de.unibi.citec.tcs.alignment.wrappers |
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 |
StrictLocalAlignmentFullAlgorithm.transformToResult(EnumMap<AbstractLocalAlignmentAlgorithm.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!
|
AlignmentPath |
StrictAlignmentFullAlgorithm.transformToResult(StrictAlignmentFullAlgorithm.FullMatrixEntry[][] alignmentMatrix,
Sequence a,
Sequence b)
This method should not be called from outside!
|
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 |
---|---|
static void |
Visualization.createHTMLs(AlignmentPath[][] alignments,
ArrayList<String> usedKeys,
String datasetName,
String savePath,
String[] programNames,
ExternalContent[] extContent,
boolean upperTriangle)
Visualizes given alignments in clear and adaptable tables.
|
static Map<Double,Integer[]> |
Utils.rgbColorsForAlignments(AlignmentPath[][] alignments)
Calculates a color scheme for all alignment scores (for form.html).
|
static Map<String,Map<Double,Integer[]>> |
Utils.rgbColorsForKeys(AlignmentPath[][] alignments)
Calculates a color scheme for all keys over all alignments.
|
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, 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