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