Package org.biojava.bio.program.ssaha

Class HitMerger

java.lang.Object
org.biojava.bio.program.ssaha.HitMerger
All Implemented Interfaces:
SearchListener
public class HitMerger extends Object implements SearchListener
A listener that merges overlapping hits and culls all hits under a given length.
Author:
Matthew Pocock

  • Constructor Details

    • 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 Details

    • startSearch

      public void startSearch(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(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