Class ClusterMerger
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- org.biojava.nbio.structure.symmetry.core.ClusterMerger
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public class ClusterMerger extends java.lang.Object
Merges clusters based on their sequence identity. This class does the actual agglomerative clustering calculation, whileSequenceAlignmentCluster
stores the results.
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Constructor Summary
Constructors Constructor Description ClusterMerger(java.util.List<SequenceAlignmentCluster> clusters, QuatSymmetryParameters parameters)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
calcPairwiseAlignments()
Aligns all pairs of input clusters, calculating their pairwise alignmentsjava.util.List<SequenceAlignmentCluster>
getMergedClusters(double sequenceIdentityCutoff)
Combine clusters based on the given sequence identity
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Constructor Detail
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ClusterMerger
public ClusterMerger(java.util.List<SequenceAlignmentCluster> clusters, QuatSymmetryParameters parameters)
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Method Detail
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calcPairwiseAlignments
public void calcPairwiseAlignments()
Aligns all pairs of input clusters, calculating their pairwise alignments
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getMergedClusters
public java.util.List<SequenceAlignmentCluster> getMergedClusters(double sequenceIdentityCutoff)
Combine clusters based on the given sequence identity- Parameters:
sequenceIdentityCutoff
-- Returns:
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