Package | Description |
---|---|
de.unibi.citec.tcs.alignment |
This package contains the actual AlignmentAlgorithms as well as their return
classes.
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de.unibi.citec.tcs.alignment.visualization |
Modifier and Type | Method and Description |
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AlignmentPath |
Operation.getPath() |
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 |
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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 |
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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.
|
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