Interface SeqSimilaritySearchSubHit

All Superinterfaces:
Annotatable, Changeable
All Known Implementing Classes:
SequenceDBSearchSubHit, SimpleSeqSimilaritySearchSubHit

public interface SeqSimilaritySearchSubHit extends Annotatable
Objects of this type represent one particular sub-hit (one concrete sequence stretch within a sequence and associated information) from a sequence similarity search hit.
Author:
Gerald Loeffler, Keith James
  • Field Details

  • Method Details

    • getScore

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

      double getPValue()
      Return the P-value of this sub-hit.
      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

      double getEValue()
      Return the E-value of this sub-hit.
      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.
    • getQueryStart

      Return the start position of the sub-hit in the query sequence.
      Returns:
      an int.
    • getQueryEnd

      Return the end position of the sub-hit in the query sequence.
      Returns:
      an int.
    • getQueryStrand

      Return the strand of the sub-hit with respect to the query sequence. This may be null for protein sequences.
      Returns:
      a Strand.
    • getSubjectStart

      Return the start position of the sub-hit in the subject sequence.
      Returns:
      an int.
    • getSubjectEnd

      Return the start position of the sub-hit in the subject sequence.
      Returns:
      an int.
    • getSubjectStrand

      Return the strand of the sub-hit with respect to the subject sequence. This may be null for protein sequences.
      Returns:
      a Strand.
    • getAlignment

      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.
      Returns:
      the alignment of the query sequence against this hit sequence.