Package org.biojava.bio.search

Class SimpleSeqSimilaritySearchSubHit

java.lang.Object
org.biojava.utils.AbstractChangeable
org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
All Implemented Interfaces:
Annotatable, SeqSimilaritySearchSubHit, Changeable
public class SimpleSeqSimilaritySearchSubHit extends AbstractChangeable implements SeqSimilaritySearchSubHit

SimpleSeqSimilaritySearchSubHit objects represent sub-hits which make up a hit. In the case of Blast these correspond to HSPs.

Since:
1.1
Author:
Keith James, Gerald Loeffler

  • Field Details

  • Constructor Details

    • 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.

  • Method Details