Package org.biojava.bio.search

Class SequenceDBSearchSubHit

    • 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.