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java.lang.Objectorg.biojava.bio.program.ssaha.CompactedDataStore
public class CompactedDataStore
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.
Method Summary | |
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void |
fireHits(int word,
int offset,
SearchListener listener)
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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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Method Detail |
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public FiniteAlphabet getAlphabet()
DataStore
getAlphabet
in interface DataStore
public void search(java.lang.String seqID, SymbolList symList, SearchListener listener)
DataStore
search
in interface DataStore
seqID
- the ID to report the symbol list by e.g. 'test' or 'foo1'symList
- the symbol list to search withlistener
- the listener to inform of hitspublic java.lang.String seqNameForID(int id)
DataStore
seqNameForID
in interface DataStore
id
- the int number of the sequence name to resolve
public void fireHits(int word, int offset, SearchListener listener)
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