Interface IndexStore

All Known Implementing Classes:
BioIndex, EmblCDROMIndexStore, TabIndexStore

public interface IndexStore
This defines the objects that IndexedSequenceDB uses to store all of the database state, such as name, format, sequence builder and the actual file offsets. You should only ever have to instantiate an implementation of this. Don't call any of the inerface methods directly. They are intended for IndexedSequenceDB, not you. In general, these objects should be transactional. Calls to store should add the index to temporary storage. When commit is invoked, these indices should all be added to the permanent storage. When rollback is invoked, these indexes should be discarded. If commit fails for any reason, it should leave the permanent storage in the pre-commit status.
Author:
Matthew Pocock
  • Method Details

    • store

      Add the Index to the store.

      This method should be transactional. If the store fails, the IndexStore should be left in its original state.

      If the file of the Index is not known yet, it is the responsibility of the IndexStore to add it to the set returned by getFiles.

      Parameters:
      indx - the Index to add
      Throws:
      IllegalIDException - if the index has an invalid ID field
      BioException - if the store failed
    • commit

      void commit() throws BioException
      Commit the stored indices to permanent storage.
      Throws:
      BioException - if for any reason the commit fails
    • rollback

      void rollback()
      Discard all uncommited changes.
    • fetch

      Fetch an Index based upon an ID.
      Parameters:
      id - The ID of the sequence Index to retrieve
      Throws:
      IllegalIDException - if the ID couldn't be found
      BioException - if the fetch fails in the underlying storage mechanism
    • getName

      Retrieve the name of this store. This will be reflected as the name of the IndexedSequenceDB.
      Returns:
      the String name of the index
    • getIDs

      Retrieve the set of all current IDs.

      This set should either be immutable, or modifiable totally separately from the IndexStore.

      Returns:
      a Set of all legal IDs
    • getFiles

      Retrieve the Set of files that are currently indexed.
    • getFormat

      Retrieve the format of the index file.

      This set should either be immutable, or modifiable totally separately from the IndexStore.

      Returns:
      a Set of all indexed files
    • getSBFactory

      Retrieve the SequenceBuilderFactory used to build Sequence instances.
      Returns:
      the associated SequenceBuilderFactory
    • getSymbolParser

      Retrieve the symbol parser used to turn the sequence characters into Symobl objects.
      Returns:
      the associated SymbolParser