Class SequenceDBSearchSubHit

    • Field Detail

      • annotationForwarder

        protected transient ChangeForwarder annotationForwarder
        Deprecated.
    • Constructor Detail

      • SequenceDBSearchSubHit

        public SequenceDBSearchSubHit​(double score,
                                      double eValue,
                                      double pValue,
                                      int queryStart,
                                      int queryEnd,
                                      StrandedFeature.Strand queryStrand,
                                      int subjectStart,
                                      int subjectEnd,
                                      StrandedFeature.Strand subjectStrand,
                                      Alignment alignment,
                                      Annotation annotation)
        Deprecated.
        Creates a new SequenceDBSearchSubHit object.
        Parameters:
        queryStart - an int value indicating the start coordinate of the hit on the query sequence.
        queryEnd - an int value indicating the end coordinate of the hit on the query sequence.
        queryStrand - a Strand object indicating the strand of the hit with respect to the query sequence, which may be null for protein similarities.
        subjectStart - an int value indicating the start coordinate of the hit on the subject sequence.
        subjectEnd - an int value indicating the end coordinate of the hit on the query sequence.
        subjectStrand - a Strand object indicating the strand of the hit with respect to the query sequence, which may be null for protein similarities.
        score - a double value; the score of the subhit, which may not be NaN.
        eValue - a double the E-value of the subhit, which may be NaN.
        pValue - a double value; the P-value of the hit, which may be NaN.
        alignment - an Alignment object containing the alignment described by the subhit region, which may not be null.
        annotation - an Annotation object, which may not be null.
    • Method Detail

      • getScore

        public double getScore()
        Deprecated.
        Description copied from interface: SeqSimilaritySearchSubHit
        Return the score of this sub-hit in the units defined by the search algorithm.
        Specified by:
        getScore in interface SeqSimilaritySearchSubHit
        Returns:
        the score of this sub-hit. This is a mandatory piece of information and hence may not be NaN.
      • getPValue

        public double getPValue()
        Deprecated.
        Description copied from interface: SeqSimilaritySearchSubHit
        Return the P-value of this sub-hit.
        Specified by:
        getPValue in interface SeqSimilaritySearchSubHit
        Returns:
        the P-value of this sub-hit. This is an optional (but desired) piece of information and implementations of this interface may return NaN if a P-value is not available for this hit.
      • getEValue

        public double getEValue()
        Deprecated.
        Description copied from interface: SeqSimilaritySearchSubHit
        Return the E-value of this sub-hit.
        Specified by:
        getEValue in interface SeqSimilaritySearchSubHit
        Returns:
        the E-value of this sub-hit. This is an optional (but desired) piece of information and implementations of this interface may return NaN if an E-value is not available for this hit.
      • getAlignment

        public Alignment getAlignment()
        Deprecated.
        Description copied from interface: SeqSimilaritySearchSubHit
        Return an alignment of (possibly part of) the query sequence against (possibly part of) this hit sequence. In this alignment, the query is identified by the label given by the static field QUERY_LABEL.
        Specified by:
        getAlignment in interface SeqSimilaritySearchSubHit
        Returns:
        the alignment of the query sequence against this hit sequence.
      • getAnnotation

        public Annotation getAnnotation()
        Deprecated.
        Description copied from interface: Annotatable
        Should return the associated annotation object.
        Specified by:
        getAnnotation in interface Annotatable
        Returns:
        an Annotation object, never null
      • equals

        public boolean equals​(java.lang.Object other)
        Deprecated.
        Overrides:
        equals in class java.lang.Object
      • hashCode

        public int hashCode()
        Deprecated.
        Overrides:
        hashCode in class java.lang.Object
      • toString

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

        protected ChangeSupport getChangeSupport​(ChangeType ct)
        Deprecated.
        Description copied from class: AbstractChangeable
        Called to retrieve the ChangeSupport for this object.

        Your implementation of this method should have the following structure:

         ChangeSupport cs = super.getChangeSupport(ct);
        
         if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
           someForwarder = new ChangeForwarder(...
        
           this.stateVariable.addChangeListener(someForwarder, VariableInterface.AChange);
         }
        
         return cs;
         
        It is usual for the forwarding listeners (someForwarder in this example) to be transient and lazily instantiated. Be sure to register & unregister the forwarder in the code that does the ChangeEvent handling in setter methods.
        Overrides:
        getChangeSupport in class AbstractChangeable