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

Class UniqueSequenceList

  • All Implemented Interfaces:
    java.lang.Cloneable
    public class UniqueSequenceList
extends java.lang.Object
implements java.lang.Cloneable
    Bean for a single sequence. These are intended to be unique sequences (100% id) as an imput to clustering.

    • Constructor Detail

      • UniqueSequenceList

        public UniqueSequenceList​(Atom[] cAlphaAtoms,
                          java.lang.String chainId,
                          int modelNumber,
                          int structureId,
                          java.lang.String seqResSequence)

    • Method Detail

      • isMatch

        public boolean isMatch​(Atom[] caAlphaAtoms)
        Return true is the sequence and residues numbers of the passed in array of atoms matches those of this unique sequence list
        Parameters:
        caAlphaAtoms -
        Returns:

      • getChainId

        public java.lang.String getChainId()

      • getModelNumber

        public int getModelNumber()

      • getStructureId

        public int getStructureId()

      • getCalphaAtoms

        public Atom[] getCalphaAtoms()

      • getSeqResSequence

        public java.lang.String getSeqResSequence()

      • setSequenceString

        public void setSequenceString​(java.lang.String sequenceString)
        Parameters:
        sequenceString - the sequenceString to set

      • getAlignment1

        public java.util.List<java.lang.Integer> getAlignment1()
        Returns:
        the alignment1

      • setAlignment1

        public void setAlignment1​(java.util.List<java.lang.Integer> alignment1)
        Parameters:
        alignment1 - the alignment1 to set

      • getAlignment2

        public java.util.List<java.lang.Integer> getAlignment2()
        Returns:
        the alignment2

      • setAlignment2

        public void setAlignment2​(java.util.List<java.lang.Integer> alignment2)
        Parameters:
        alignment2 - the alignment2 to set

      • clone

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

      • getSequenceString

        public static java.lang.String getSequenceString​(Atom[] caAlphaAtoms)

      • toString

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