Class BlastLikeHomologyBuilder

  • All Implemented Interfaces:
    SearchContentHandler

    public class BlastLikeHomologyBuilder
    extends ViewSequenceFactory
    implements SearchContentHandler

    BlastLikeHomologyBuilder populates a List with Homology instances created from SAX events supplied via a SeqSimilarityAdapter. The SAX events should describe elements conforming to the BioJava BlastLikeDataSetCollection DTD. Suitable sources are BlastLikeSAXParser or FastaSAXParser. Annotated ViewSequences wrapping both query and subject sequences are created and populated with HomologyFeatures. See the documentation of Homology and HomologyFeature.

    As SimpleHomologyFeatures are created on views of the query and subject sequences, both query and subject should be nucleotide sequences (SimpleHomologyFeature extends StrandedFeature.). This limits the searches currently handled to BLASTN, TBLASTX and Fasta DNA.

    Since:
    1.2
    Author:
    Keith James, Greg Cox
    • Constructor Summary

      Constructors 
      Constructor Description
      BlastLikeHomologyBuilder​(java.util.List target)
      Creates a new BlastLikeHomologyBuilder which will instantiate Homology objects into the List target.
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void addHitProperty​(java.lang.Object key, java.lang.Object value)
      The addHitProperty method adds a key/value pair containing some property of a particular hit.
      void addSearchProperty​(java.lang.Object key, java.lang.Object value)
      The addSearchProperty method adds a key/value pair containing some property of the overall search result.
      void addSubHitProperty​(java.lang.Object key, java.lang.Object value)
      The addSubHitProperty method adds a key/value pair containing some property of a particular subhit.
      void endHeader()
      The endHeader method indicates the end of a formatted header.
      void endHit()
      The endHit method indicates the end of a formatted hit.
      void endSearch()
      The endSearch method indicates the end of useful search information.
      void endSubHit()
      The endSubHit method indicates the end of a formatted subhit.
      boolean getMoreSearches()
      getMoreSearches returns the state of the SearchContentHandler with respect to further searches from its data source.
      void setMoreSearches​(boolean value)
      setMoreSearches sets the state of the SearchContentHandler's expectation of receiving more results.
      void setQueryID​(java.lang.String queryID)
      setQueryID identifies the query sequence by a name, ID or URN.
      void startHeader()
      The startHeader method indicates the start of a formatted header.
      void startHit()
      The startHit method indicates the start of a formatted hit.
      void startSearch()
      The startSearch method indicates the start of useful search information.
      void startSubHit()
      The startSubHit method indicates the start of a formatted subhit.
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait