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

Class SequenceAlignmentCluster

java.lang.Object
org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster
All Implemented Interfaces:
Cloneable
public class SequenceAlignmentCluster extends Object implements Cloneable
Represents a cluster of equivalent sequences

  • Constructor Details

  • Method Details

    • 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 List<UniqueSequenceList> getUniqueSequenceList()

    • getChainIds

      public List<String> getChainIds()

    • getModelNumbers

      public List<Integer> getModelNumbers()

    • getStructureIds

      public List<Integer> getStructureIds()

    • getAlignedCalphaAtoms

      public List<Atom[]> getAlignedCalphaAtoms()

    • identityMatch

      public boolean identityMatch(Atom[] cAlphaAtoms, String chainId, int modelNumber, int structureId, 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:

    • getPairwiseAlignment

      public PairwiseAlignment getPairwiseAlignment(SequenceAlignmentCluster other)

    • clone

      public Object clone()
      Overrides:
      clone in class Object

    • toString

      public String toString()
      Overrides:
      toString in class Object