org.biojava.bio.program.ssaha
Class SearchListener.Wrapper
java.lang.Object
org.biojava.bio.program.ssaha.SearchListener.Wrapper
- All Implemented Interfaces:
- SearchListener
- Direct Known Subclasses:
- SearchListener.FilterByLength
- Enclosing interface:
- SearchListener
public abstract static class SearchListener.Wrapper
- extends java.lang.Object
- implements SearchListener
A simple wrapper implementation.
Extend this and over-ride any of the interface methods to implement
SearchListeners that filter hits before passing them on to an
underlying listener.
You can modify the search events the delegate sees by over-riding any of
the SearchListener methods, modify the arguments
and then call the method on super with the new arguments.
You can drop hits by just not passing them onto the delegate using
super.hits().
Note: Be sure to maintain the nesting of start/stop search and
hit, or you will confuse the delegate.
- Since:
- 1.4
- Author:
- Matthew Pocock
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. |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
SearchListener.Wrapper
public SearchListener.Wrapper(SearchListener delegate)
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
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
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 sequencehitOffset
- the offset into the sequence hit in the databasehitLength
- the number of symbols hit