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

Class AffinityAlignment.Builder

java.lang.Object

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

All Implemented Interfaces:

AffinityAlignment.AtomStep, AffinityAlignment.InputStep, AffinityAlignment.ParameterStep

Enclosing class:

AffinityAlignment

public static class AffinityAlignment.Builder
extends Object
implements AffinityAlignment.InputStep, AffinityAlignment.AtomStep, AffinityAlignment.ParameterStep

Method Summary

Modifier and Type	Method and Description
AffinityAlignment.ParameterStep	alignWithinClusters(boolean alignWithinClusters)
AffinityAlignment.ParameterStep	atomFilter(Predicate<Atom> atomFilter) Defines the StructuralEntityFilter.AtomFilter to be used for the computed alignments.
AffinityAlignment.ParameterStep	idealSuperimposition(boolean idealSuperimposition)
AffinityAlignment.AtomStep	inputStructuralMotifs(List<StructuralMotif> structuralMotifs)
AffinityAlignment.ParameterStep	representationSchemeType(RepresentationSchemeType representationSchemeType) Defines a RepresentationSchemeType to be used for the computed alignments.
AffinityAlignment	run() Creates a new ConsensusAlignment and starts the calculation.

Methods inherited from class java.lang.Object

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

Method Detail

inputStructuralMotifs

public AffinityAlignment.AtomStep inputStructuralMotifs(List<StructuralMotif> structuralMotifs)

Specified by:

inputStructuralMotifs in interface AffinityAlignment.InputStep

representationSchemeType

public AffinityAlignment.ParameterStep representationSchemeType(RepresentationSchemeType representationSchemeType)

Description copied from interface: AffinityAlignment.AtomStep

Defines a RepresentationSchemeType to be used for the computed alignments. This is exclusive to the definition of an StructuralEntityFilter.AtomFilter.

Specified by:

representationSchemeType in interface AffinityAlignment.AtomStep

Parameters:

representationSchemeType - The RepresentationSchemeType to be used.

Returns:

The ConsensusBuilder.ParameterStep to define additional parameters.

atomFilter

public AffinityAlignment.ParameterStep atomFilter(Predicate<Atom> atomFilter)

Description copied from interface: AffinityAlignment.AtomStep

Defines the StructuralEntityFilter.AtomFilter to be used for the computed alignments. This is exclusive to the definition of a RepresentationSchemeType.

Specified by:

atomFilter in interface AffinityAlignment.AtomStep

Parameters:

atomFilter - The StructuralEntityFilter.AtomFilter to be used.

Returns:

The ConsensusBuilder.ParameterStep to define additional parameters.

run

public AffinityAlignment run()

Description copied from interface: AffinityAlignment.AtomStep

Creates a new ConsensusAlignment and starts the calculation.

Specified by:

run in interface AffinityAlignment.AtomStep

Specified by:

run in interface AffinityAlignment.ParameterStep

Returns:

A new ConsensusAlignment once calculation has finished.

idealSuperimposition

public AffinityAlignment.ParameterStep idealSuperimposition(boolean idealSuperimposition)

Specified by:

idealSuperimposition in interface AffinityAlignment.ParameterStep

alignWithinClusters

public AffinityAlignment.ParameterStep alignWithinClusters(boolean alignWithinClusters)

Specified by:

alignWithinClusters in interface AffinityAlignment.ParameterStep