Class HitMerger

    • 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​(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