Package org.biojava.bio.search

Interface SeqSimilaritySearchHit

All Superinterfaces:
Annotatable, Changeable
All Known Implementing Classes:
SequenceDBSearchHit, SimpleSeqSimilaritySearchHit
public interface SeqSimilaritySearchHit extends Annotatable
Objects of this type represent one particular hit (sequence and associated information) from a sequence similarity search.
Author:
Gerald Loeffler, Keith James

  • Field Details

  • Method Details

    • getScore

      double getScore()
      Return the overall score of this hit in the units defined by the search algorithm.
      Returns:
      the overall score of this hit. This is a mandatory piece of information and hence may not be NaN.

    • getPValue

      double getPValue()
      Return the overall P-value of this hit.
      Returns:
      the overall P-value of this 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

      double getEValue()
      Return the overall E-value of this hit.
      Returns:
      the overall E-value of this 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.

    • getQueryStart

      int getQueryStart()
      Return the start position of the first sub-hit in the query sequence.
      Returns:
      an int.

    • getQueryEnd

      int getQueryEnd()
      Return the end position of the last sub-hit in the query sequence.
      Returns:
      an int.

    • getQueryStrand

      StrandedFeature.Strand getQueryStrand()
      Return the strand of the hit with respect to the query sequence. If the sub-hits are not all on the same strand this should return the unknown strand. This may be null for protein sequences.
      Returns:
      a Strand.

    • getSubjectStart

      int getSubjectStart()
      Return the start position of the first sub-hit in the subject sequence.
      Returns:
      an int.

    • getSubjectEnd

      int getSubjectEnd()
      Return the end position of the last sub-hit in the subject sequence.
      Returns:
      an int.

    • getSubjectStrand

      StrandedFeature.Strand getSubjectStrand()
      Return the strand of the sub-hit with respect to the subject sequence. If the sub-hits are not all on the same strand this should return the unknown strand. This may be null for protein sequences.
      Returns:
      a Strand.

    • getSubjectID

      String getSubjectID()
      The sequence identifier of this hit within the sequence database against which the search was performed.
      Returns:
      the (unique) sequence identifier for this hit, valid within the sequence database against which this search was performed. Never returns null.

    • getSubHits

      List getSubHits()
      Return all sub-hits for this sequence similarity search hit. The sub-hits contain concrete alignments (and scores) for sequence stretches from the sequence of this hit. The sub-hits in the list returned by this method are sorted from best to worst.
      Returns:
      a List of SeqSimilaritySearchSubHit objects containing all sub-hits for this hit. Never returns null and the List is guaranteed to contain at least one entry.