Class HitMerger

  • All Implemented Interfaces:
    SearchListener

    public class HitMerger
    extends java.lang.Object
    implements SearchListener
    A listener that merges overlapping hits and culls all hits under a given length.
    Author:
    Matthew Pocock
    • Constructor Summary

      Constructors 
      Constructor Description
      HitMerger​(SearchListener delegate, int minLength)
      Build a new HitMerger that will pass events on to a delegate.
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void endSearch​(java.lang.String seqID)
      Indicates that a sequence has been searched against a DataStore.
      void hit​(int hitID, int queryOffset, int hitOffset, int hitLength)
      There has been a hit between the query sequence and a database sequence.
      void startSearch​(java.lang.String seqID)
      Indicates that a sequence is about to be searched against a DataStore.
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Constructor Detail

      • HitMerger

        public HitMerger​(SearchListener delegate,
                         int minLength)
        Build a new HitMerger that will pass events on to a delegate.
        Parameters:
        delegate - the SearchListener to inform of all merged and filtered hits
        minLength - the minimum length a hit must reach to be passed on
    • Method Detail

      • startSearch

        public void startSearch​(java.lang.String seqID)
        Description copied from interface: SearchListener
        Indicates that a sequence is about to be searched against a DataStore.
        Specified by:
        startSearch in interface SearchListener
        Parameters:
        seqID - the id of the sequence to be searched
      • hit

        public void hit​(int hitID,
                        int queryOffset,
                        int hitOffset,
                        int hitLength)
        Description copied from interface: SearchListener
        There has been a hit between the query sequence and a database sequence.
        Specified by:
        hit in interface SearchListener
        Parameters:
        hitID - the number of the sequence hit; resolvable by String id = DataStore.seqNameForID(hitID)
        queryOffset - the offset into the query sequence
        hitOffset - the offset into the sequence hit in the database
        hitLength - the number of symbols hit
      • endSearch

        public void endSearch​(java.lang.String seqID)
        Description copied from interface: SearchListener
        Indicates that a sequence has been searched against a DataStore.
        Specified by:
        endSearch in interface SearchListener
        Parameters:
        seqID - the id of the sequence to be searched