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

Class SequenceAlignmentCluster

  • All Implemented Interfaces:
    java.lang.Cloneable
    public class SequenceAlignmentCluster
extends java.lang.Object
implements java.lang.Cloneable
    Represents a cluster of equivalent sequences

    • Method Detail

      • isPseudoStoichiometric

        public boolean isPseudoStoichiometric()

      • getMinSequenceIdentity

        public double getMinSequenceIdentity()

      • setMinSequenceIdentity

        public void setMinSequenceIdentity​(double minSequenceIdentity)

      • getMaxSequenceIdentity

        public double getMaxSequenceIdentity()

      • setMaxSequenceIdentity

        public void setMaxSequenceIdentity​(double maxSequenceIdentity)

      • addUniqueSequenceList

        public void addUniqueSequenceList​(UniqueSequenceList sequenceList)

      • getSequenceCount

        public int getSequenceCount()
        Returns:
        the number of sequences which have been added to this cluster

      • getSequenceAlignmentLength

        public int getSequenceAlignmentLength()

      • getUniqueSequenceList

        public java.util.List<UniqueSequenceList> getUniqueSequenceList()

      • getChainIds

        public java.util.List<java.lang.String> getChainIds()

      • getModelNumbers

        public java.util.List<java.lang.Integer> getModelNumbers()

      • getStructureIds

        public java.util.List<java.lang.Integer> getStructureIds()

      • getAlignedCalphaAtoms

        public java.util.List<Atom[]> getAlignedCalphaAtoms()

      • identityMatch

        public boolean identityMatch​(Atom[] cAlphaAtoms,
                             java.lang.String chainId,
                             int modelNumber,
                             int structureId,
                             java.lang.String sequence)
        Match a sequence to this cluster at 100% identity. If the given sequence matches the cluster seed (100%), then performs an alignment to the seed and adds it to the unique sequence list.
        Parameters:
        cAlphaAtoms -
        chainId -
        modelNumber -
        structureId -
        sequence -
        Returns:

      • clone

        public java.lang.Object clone()
        Overrides:
        clone in class java.lang.Object

      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object