de.bioforscher.singa.structure.algorithms.superimposition.affinity

Class AffinityAlignment

java.lang.Object

de.bioforscher.singa.structure.algorithms.superimposition.affinity.AffinityAlignment

public class AffinityAlignment
extends Object

An affinity alignment of same-sized StructuralMotifs can be used to cluster them according their geometric similarity in a multi-structure alignment manner. NOTE: Copies of given StructuralMotifs will be used, so original structures are not altered.

Author:

fk

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static interface	AffinityAlignment.AtomStep
static class	AffinityAlignment.Builder
static interface	AffinityAlignment.InputStep
static interface	AffinityAlignment.ParameterStep

Method Summary

Modifier and Type	Method and Description
static AffinityAlignment.InputStep	create()
Map<StructuralMotif,List<StructuralMotif>>	getClusters()
LabeledSymmetricMatrix<StructuralMotif>	getDistanceMatrix()
double	getSelfDissimilarity()
double	getSilhouetteCoefficient()
void	writeClusters(Path outputPath) Writes the created clusters to the specified Path.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

create

public static AffinityAlignment.InputStep create()

getDistanceMatrix

public LabeledSymmetricMatrix<StructuralMotif> getDistanceMatrix()

getSelfDissimilarity

public double getSelfDissimilarity()

getSilhouetteCoefficient

public double getSilhouetteCoefficient()

getClusters

public Map<StructuralMotif,List<StructuralMotif>> getClusters()

writeClusters

public void writeClusters(Path outputPath)
                   throws IOException

Writes the created clusters to the specified Path.

Parameters:

outputPath - the desired output Path

Throws:

IOException - If the path cannot be written to.