org.biojava.bio.program.ssaha
Interface SearchListener

All Known Implementing Classes:
HitMerger, SearchListener.Echo, SearchListener.FilterByLength, SearchListener.Tee, SearchListener.Wrapper

public interface SearchListener

The interface used to inform interested parties that some sequence has been searched and something found.

The callbacks will always be called in the order startSearch, hit, endSearch, during which time there may be multiple hit calls. The seqID of startSearch and endSearch will match. After this, a new startSearch may begin. These events will usually originate from the search method of DataStore.

Author:
Matthew Pocock

Nested Class Summary
static class SearchListener.Echo
          A SearchListener that prints events out to a PrintStream.
static class SearchListener.FilterByLength
          A simple listener that filters out all hits that are too short.
static class SearchListener.Tee
          A SearchListener that passes events on to two delegate listeners.
static class SearchListener.Wrapper
          A simple wrapper implementation.
 
Method Summary
 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.
 

Method Detail

startSearch

void startSearch(java.lang.String seqID)
Indicates that a sequence is about to be searched against a DataStore.

Parameters:
seqID - the id of the sequence to be searched

endSearch

void endSearch(java.lang.String seqID)
Indicates that a sequence has been searched against a DataStore.

Parameters:
seqID - the id of the sequence to be searched

hit

void hit(int hitID,
         int queryOffset,
         int hitOffset,
         int hitLength)
There has been a hit between the query sequence and a database sequence.

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