Class QsAlignResult


  • public class QsAlignResult
    extends java.lang.Object
    Result of a Quaternary Structure Alignment QsAlign. The QsAlignResult holds the original inputs of the algorithm and the results and scores of the alignment.
    Since:
    5.0.0
    Author:
    Aleix Lafita
    • Constructor Summary

      Constructors 
      Constructor Description
      QsAlignResult​(java.util.List<Subunit> subunits1, java.util.List<Subunit> subunits2)
      The Constructor of the result takes the same inputs as the QsAlign algorithm.
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      Atom[] getAlignedAtomsForSubunits1​(int index)  
      Atom[] getAlignedAtomsForSubunits2​(int index)  
      java.util.List<Subunit> getAlignedSubunits1()
      Return the aligned subunits of the first Subunit group, in the alignment order.
      java.util.List<Subunit> getAlignedSubunits2()
      Return the aligned subunits of the second Subunit group, in the alignment order.
      MultipleAlignment getAlignment()
      The alignment that specifies the residue equivalencies of the equivalent Subunits.
      QsRelation getRelation()
      The quaternary structure relation QsRelation between the two groups of Subunits.
      double getRmsd()
      The RMSD between the equivalent residues of the equivalent Subunits after superposition of the Subunit groups.
      java.util.Map<java.lang.Integer,​java.lang.Integer> getSubunitMap()
      Map of Subunit equivalencies from the first to the second group.
      java.util.List<Subunit> getSubunits1()
      Original Subunits of the first group.
      java.util.List<Subunit> getSubunits2()
      Original Subunits of the second group.
      javax.vecmath.Matrix4d getTransform()
      The transformation 4D matrix that needs to be applied to the second group of Subunits to superimpose them onto the first group of Subunits, given the equivalent residues in the SubunitCluster and the Subunit equivalencies.
      int length()
      The length of the alignment is the number of Subunit equivalencies it contains.
      void setAlignment​(MultipleAlignment alignment)
      The alignment that specifies the residue equivalencies of the equivalent Subunits.
      void setClusters​(java.util.List<SubunitCluster> clusters)  
      void setRelation​(QsRelation relation)
      The quaternary structure relation QsRelation between the two groups of Subunits.
      void setSubunitMap​(java.util.Map<java.lang.Integer,​java.lang.Integer> subunitMap)
      Map of Subunit equivalencies from the first to the second group.
      java.lang.String toString()  
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
    • Constructor Detail

      • QsAlignResult

        public QsAlignResult​(java.util.List<Subunit> subunits1,
                             java.util.List<Subunit> subunits2)
        The Constructor of the result takes the same inputs as the QsAlign algorithm.
        Parameters:
        subunits1 -
        subunits2 -
    • Method Detail

      • getSubunits1

        public java.util.List<Subunit> getSubunits1()
        Original Subunits of the first group.
        Returns:
        an unmodifiable view of the original List
      • getSubunits2

        public java.util.List<Subunit> getSubunits2()
        Original Subunits of the second group.
        Returns:
        an unmodifiable view of the original List
      • getSubunitMap

        public java.util.Map<java.lang.Integer,​java.lang.Integer> getSubunitMap()
        Map of Subunit equivalencies from the first to the second group.
        Returns:
        an unmodifiable view of the original Map
      • setSubunitMap

        public void setSubunitMap​(java.util.Map<java.lang.Integer,​java.lang.Integer> subunitMap)
        Map of Subunit equivalencies from the first to the second group.
        Parameters:
        subunitMap -
      • length

        public int length()
        The length of the alignment is the number of Subunit equivalencies it contains. This is equivalent to the size of the Subunit Map.
        Returns:
        length of the alignment
      • getTransform

        public javax.vecmath.Matrix4d getTransform()
        The transformation 4D matrix that needs to be applied to the second group of Subunits to superimpose them onto the first group of Subunits, given the equivalent residues in the SubunitCluster and the Subunit equivalencies.

        This is equivalent to multipleAlignment.getBlockSet(0).getTransformations().get(1).

        Returns:
        Matrix4d
      • getRmsd

        public double getRmsd()
        The RMSD between the equivalent residues of the equivalent Subunits after superposition of the Subunit groups. This is equivalent to multipleAlignment.getScore(MultipleAlignmentScorer.RMSD).
        Returns:
        rmsd
      • getRelation

        public QsRelation getRelation()
        The quaternary structure relation QsRelation between the two groups of Subunits.
        Returns:
        relation
      • setRelation

        public void setRelation​(QsRelation relation)
        The quaternary structure relation QsRelation between the two groups of Subunits.
        Parameters:
        relation -
      • getAlignment

        public MultipleAlignment getAlignment()
        The alignment that specifies the residue equivalencies of the equivalent Subunits.
        Returns:
        alignment as a MultipleAlignment object
      • setAlignment

        public void setAlignment​(MultipleAlignment alignment)
        The alignment that specifies the residue equivalencies of the equivalent Subunits.
        Parameters:
        alignment - a MultipleAlignment object
      • getAlignedSubunits1

        public java.util.List<Subunit> getAlignedSubunits1()
        Return the aligned subunits of the first Subunit group, in the alignment order.
        Returns:
        a List of Subunits in the alignment order
      • getAlignedSubunits2

        public java.util.List<Subunit> getAlignedSubunits2()
        Return the aligned subunits of the second Subunit group, in the alignment order.
        Returns:
        a List of Subunits in the alignment order
      • setClusters

        public void setClusters​(java.util.List<SubunitCluster> clusters)
      • getAlignedAtomsForSubunits1

        public Atom[] getAlignedAtomsForSubunits1​(int index)
      • getAlignedAtomsForSubunits2

        public Atom[] getAlignedAtomsForSubunits2​(int index)
      • toString

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