de.bioforscher.singa.structure.algorithms.superimposition.consensus

Class ConsensusBuilder.Builder

java.lang.Object

de.bioforscher.singa.structure.algorithms.superimposition.consensus.ConsensusBuilder.Builder

All Implemented Interfaces:

ConsensusBuilder.AtomStep, ConsensusBuilder.InputStep, ConsensusBuilder.ParameterStep

Enclosing class:

ConsensusBuilder

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

Constructor Summary

Constructors

Constructor and Description
Builder()

Method Summary

Modifier and Type	Method and Description
ConsensusBuilder.ParameterStep	alignWithinClusters(boolean alignWithinClusters)
ConsensusBuilder.ParameterStep	atomFilter(Predicate<Atom> atomFilter) Defines the StructuralEntityFilter.AtomFilter to be used during consensus calculation.
ConsensusBuilder.ParameterStep	clusterCutoff(double clusterCutoff)
ConsensusBuilder.ParameterStep	idealSuperimposition(boolean idealSuperimposition)
ConsensusBuilder.AtomStep	inputStructuralMotifs(List<StructuralMotif> structuralMotifs) Defines the input StructuralMotifs for the ConsensusAlignment.
ConsensusBuilder.ParameterStep	representationSchemeType(RepresentationSchemeType representationSchemeType) Defines a RepresentationSchemeType to be used during consensus calculation.
ConsensusAlignment	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

Constructor Detail

Builder

public Builder()

Method Detail

inputStructuralMotifs

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

Description copied from interface: ConsensusBuilder.InputStep

Defines the input StructuralMotifs for the ConsensusAlignment.

Specified by:

inputStructuralMotifs in interface ConsensusBuilder.InputStep

Parameters:

structuralMotifs - The input StructuralMotifs to be used.

Returns:

The ConsensusBuilder.AtomStep to define RepresentationSchemeType or StructuralEntityFilter.AtomFilter.

representationSchemeType

public ConsensusBuilder.ParameterStep representationSchemeType(RepresentationSchemeType representationSchemeType)

Description copied from interface: ConsensusBuilder.AtomStep

Defines a RepresentationSchemeType to be used during consensus calculation. This is exclusive to the definition of an StructuralEntityFilter.AtomFilter.

Specified by:

representationSchemeType in interface ConsensusBuilder.AtomStep

Parameters:

representationSchemeType - The RepresentationSchemeType to be used.

Returns:

The ConsensusBuilder.ParameterStep to define additional parameters.

atomFilter

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

Description copied from interface: ConsensusBuilder.AtomStep

Defines the StructuralEntityFilter.AtomFilter to be used during consensus calculation. This is exclusive to the definition of a RepresentationSchemeType.

Specified by:

atomFilter in interface ConsensusBuilder.AtomStep

Parameters:

atomFilter - The StructuralEntityFilter.AtomFilter to be used.

Returns:

The ConsensusBuilder.ParameterStep to define additional parameters.

run

public ConsensusAlignment run()

Description copied from interface: ConsensusBuilder.AtomStep

Creates a new ConsensusAlignment and starts the calculation.

Specified by:

run in interface ConsensusBuilder.AtomStep

Specified by:

run in interface ConsensusBuilder.ParameterStep

Returns:

A new ConsensusAlignment once calculation has finished.

clusterCutoff

public ConsensusBuilder.ParameterStep clusterCutoff(double clusterCutoff)

Specified by:

clusterCutoff in interface ConsensusBuilder.ParameterStep

idealSuperimposition

public ConsensusBuilder.ParameterStep idealSuperimposition(boolean idealSuperimposition)

Specified by:

idealSuperimposition in interface ConsensusBuilder.ParameterStep

alignWithinClusters

public ConsensusBuilder.ParameterStep alignWithinClusters(boolean alignWithinClusters)

Specified by:

alignWithinClusters in interface ConsensusBuilder.ParameterStep