Class SimpleSeqSimilaritySearchSubHit

    • Constructor Detail

      • SimpleSeqSimilaritySearchSubHit

        public SimpleSeqSimilaritySearchSubHit​(double score,
                                               double eValue,
                                               double pValue,
                                               int queryStart,
                                               int queryEnd,
                                               StrandedFeature.Strand queryStrand,
                                               int subjectStart,
                                               int subjectEnd,
                                               StrandedFeature.Strand subjectStrand,
                                               Alignment alignment,
                                               Annotation annotation)
        Creates a new SimpleSeqSimilaritySearchSubHit 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.