Class CompactedDataStore

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

public class CompactedDataStore extends 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 Details

    • 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(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 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)