org.biojava.bio.program.ssaha

Class CompactedDataStore

java.lang.Object

org.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

Modifier and Type	Method and Description
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)