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
    • Field Detail

      • HOMOLOGY_FEATURE_TYPE

        public static final java.lang.String HOMOLOGY_FEATURE_TYPE
        HOMOLOGY_FEATURE_TYPE is the type String used by BlastLikeHomologyBuilder when creating HomologyFeatures. This is the String which is returned when an HomologyFeature's getType() method is called.
        See Also:
        Constant Field Values
    • Constructor Detail

      • BlastLikeHomologyBuilder

        public BlastLikeHomologyBuilder​(java.util.List target)
        Creates a new BlastLikeHomologyBuilder which will instantiate Homology objects into the List target.
        Parameters:
        target - a List.
    • Method Detail

      • setQueryID

        public void setQueryID​(java.lang.String queryID)
        Description copied from interface: SearchContentHandler
        setQueryID identifies the query sequence by a name, ID or URN.
        Specified by:
        setQueryID in interface SearchContentHandler
        Parameters:
        queryID - a String which should be an unique identifer for the sequence.
      • getMoreSearches

        public boolean getMoreSearches()
        Description copied from interface: SearchContentHandler
        getMoreSearches returns the state of the SearchContentHandler with respect to further searches from its data source. Used for handling streams of search results.
        Specified by:
        getMoreSearches in interface SearchContentHandler
        Returns:
        a boolean value.
      • setMoreSearches

        public void setMoreSearches​(boolean value)
        Description copied from interface: SearchContentHandler
        setMoreSearches sets the state of the SearchContentHandler's expectation of receiving more results. Used for handling streams of search results.
        Specified by:
        setMoreSearches in interface SearchContentHandler
        Parameters:
        value - a boolean value.
      • startHeader

        public void startHeader()
        Description copied from interface: SearchContentHandler
        The startHeader method indicates the start of a formatted header. This usually contains information relevant to the search as a whole.
        Specified by:
        startHeader in interface SearchContentHandler
      • startHit

        public void startHit()
        Description copied from interface: SearchContentHandler
        The startHit method indicates the start of a formatted hit. This could be a single line, or a block of lines.
        Specified by:
        startHit in interface SearchContentHandler
      • startSubHit

        public void startSubHit()
        Description copied from interface: SearchContentHandler
        The startSubHit method indicates the start of a formatted subhit. There may be zero or more of these per hit.
        Specified by:
        startSubHit in interface SearchContentHandler
      • addSearchProperty

        public void addSearchProperty​(java.lang.Object key,
                                      java.lang.Object value)
        Description copied from interface: SearchContentHandler
        The addSearchProperty method adds a key/value pair containing some property of the overall search result.
        Specified by:
        addSearchProperty in interface SearchContentHandler
        Parameters:
        key - an Object.
        value - an Object.
      • addHitProperty

        public void addHitProperty​(java.lang.Object key,
                                   java.lang.Object value)
        Description copied from interface: SearchContentHandler
        The addHitProperty method adds a key/value pair containing some property of a particular hit.
        Specified by:
        addHitProperty in interface SearchContentHandler
        Parameters:
        key - an Object.
        value - an Object.
      • addSubHitProperty

        public void addSubHitProperty​(java.lang.Object key,
                                      java.lang.Object value)
        Description copied from interface: SearchContentHandler
        The addSubHitProperty method adds a key/value pair containing some property of a particular subhit.
        Specified by:
        addSubHitProperty in interface SearchContentHandler
        Parameters:
        key - an Object.
        value - an Object.