Package org.biojava.bio.search

Interface BlastLikeSearchFilter

  • All Superinterfaces:
    Serializable
    All Known Implementing Classes:
    BlastLikeSearchFilter.AbstractBlastLikeSearchFilter, BlastLikeSearchFilter.ByHitProperty, BlastLikeSearchFilter.BySearchProperty, BlastLikeSearchFilter.BySubHitProperty, BlastLikeSearchFilter.Not
    public interface BlastLikeSearchFilter
extends Serializable
    A SearchContentHandler class that implements filtering in chains of SearchContentHandler instances.

    The SearchContentHandler organise Blast-like searches as a hierarchy of search/hit/subhit. Each search is conducted with a single query sequence. Hits of the query sequence are reported against different target sequences. The hit is further subdivided into one of more subhits which represent the positions within the target sequence that alignments of the query sequence were achieved against the query sequence (e.g. HSPs).

    This implementation depends on the a well ordered use of the SearchContentHandler interface. In particular, it requires that search/hit/subhit properties are reported immediately following the associated startSearch/startHit/startSubHit call. For example, search properties should not be reported following the corresponding startHit() call.

    Semantics of this interface
    BlastLikeSearchFilters test different levels of the SearchContentHandler property hierarchy and each filter should be seen as being applied when a full set of events from that level is received. So the ByHitProperty filter is applied when endHit() is called and determines whether all events received between startHit() and endHit() are to be passed on or discarded.

    Some keys used by SearchContentHandlers
    SearchProperties

    KEY_QUERY_ID String. Value from setQueryID
    queryDescription String. FASTA description line
    program String. variant of BLAST used
    version software version

    HitProperties

    subjectId String. Identity of subject (target) sequence.
    subjectSequenceLength String representation of integer value
    subjectDescription String.

    SubHitProperties

    bitScore String representation of real value
    queryStrand plus/minus
    percentageIdentity String representation of real value
    querySequenceEnd String representation of integer value
    expectValue String representation of real value
    subjectStrand plus/minus
    subjectSequenceEnd String representation of integer value
    numberOfPositives String representation of integer value
    score String representation of integer value
    subjectSequence String representation of sequence
    alignmentSize String representation of integer value
    querySequenceStart String representation of integer value
    subjectSequenceStart String representation of integer value
    numberOfIdentities String representation of integer value
    querySequence String representation of sequence
    Author:
    David Huen

    • Method Detail

      • accept

        TriState accept()
        returns a TriState indicating the current outcome of evaluating this filter. This is usually the outcome saved when evaluate(FilteringContentHandler fch) was called.

      • evaluate

        void evaluate​(BlastLikeSearchFilter.Node fch)
        computes the outcome of this filter on the specified node and stores it. This method is only exposed to permit it to be included in an interface. Users should not use it.

      • reset

        void reset()
        resets the internal state of this filter including any cached evaluations. This method is only exposed to permit it to be included in an interface. Users should not use it.