Uses of Class
org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster

Packages that use SequenceAlignmentCluster

Package	Description
org.biojava.nbio.structure.symmetry.core

Uses of SequenceAlignmentCluster in org.biojava.nbio.structure.symmetry.core

Methods in org.biojava.nbio.structure.symmetry.core that return SequenceAlignmentCluster

Modifier and Type	Method and Description
SequenceAlignmentCluster	PairwiseAlignment.getCluster1()
SequenceAlignmentCluster	PairwiseAlignment.getCluster2()

Methods in org.biojava.nbio.structure.symmetry.core that return types with arguments of type SequenceAlignmentCluster

Modifier and Type	Method and Description
List<SequenceAlignmentCluster>	ClusterMerger.getMergedClusters(double sequenceIdentityCutoff) Combine clusters based on the given sequence identity
List<SequenceAlignmentCluster>	ProteinSequenceClusterer.getSequenceAlignmentClusters()
List<SequenceAlignmentCluster>	ChainClusterer.getSequenceAlignmentClusters()
List<SequenceAlignmentCluster>	ClusterProteinChains.getSequenceAlignmentClusters(double sequenceIdentityThreshold) Get a non-redundent set of clusters for a given sequence cutoff

Methods in org.biojava.nbio.structure.symmetry.core with parameters of type SequenceAlignmentCluster

Modifier and Type	Method and Description
PairwiseAlignment	SequenceAlignmentCluster.getPairwiseAlignment(SequenceAlignmentCluster other)

Method parameters in org.biojava.nbio.structure.symmetry.core with type arguments of type SequenceAlignmentCluster

Modifier and Type	Method and Description
static void	ProteinSequenceClusterer.sortSequenceClustersBySize(List<SequenceAlignmentCluster> clusters)

Constructors in org.biojava.nbio.structure.symmetry.core with parameters of type SequenceAlignmentCluster

Constructor and Description
PairwiseAlignment(SequenceAlignmentCluster cluster1, SequenceAlignmentCluster cluster2)

Constructor parameters in org.biojava.nbio.structure.symmetry.core with type arguments of type SequenceAlignmentCluster

Constructor and Description
ChainClusterer(List<SequenceAlignmentCluster> seqClusters)
ClusterMerger(List<SequenceAlignmentCluster> clusters, QuatSymmetryParameters parameters)