org.biojava.bio.program.ssaha
Class CompactedDataStore

java.lang.Object
  extended byorg.biojava.bio.program.ssaha.CompactedDataStore
All Implemented Interfaces:
DataStore

public class CompactedDataStore
extends java.lang.Object
implements DataStore

An implementation of DataStore that will map onto a file using the NIO constructs. You should obtain one of these by using the methods in MappedDataStoreFactory.

Author:
Matthew Pocock, Thomas Down

Method Summary
 void fireHits(int word, int offset, SearchListener listener)
           
 FiniteAlphabet getAlphabet()
          The alphabet of symbol lists that can be searched against this DataStore.
 void search(java.lang.String seqID, SymbolList symList, SearchListener listener)
          Search the DataStore with a symbol list.
 java.lang.String seqNameForID(int id)
          Resolve an ID to a sequence name.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Method Detail

getAlphabet

public FiniteAlphabet getAlphabet()
Description copied from interface: DataStore
The alphabet of symbol lists that can be searched against this DataStore.

Specified by:
getAlphabet in interface DataStore
Returns:
a FiniteAlphabet search types of SymbolList

search

public void search(java.lang.String seqID,
                   SymbolList symList,
                   SearchListener listener)
Description copied from interface: DataStore
Search the DataStore with a symbol list.

Specified by:
search in interface DataStore
Parameters:
seqID - the ID to report the symbol list by e.g. 'test' or 'foo1'
symList - the symbol list to search with
listener - the listener to inform of hits

seqNameForID

public java.lang.String seqNameForID(int id)
Description copied from interface: DataStore
Resolve an ID to a sequence name.

Specified by:
seqNameForID in interface DataStore
Parameters:
id - the int number of the sequence name to resolve
Returns:
the name of that sequence as a String

fireHits

public void fireHits(int word,
                     int offset,
                     SearchListener listener)