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.
    Matthew Pocock
    • Method Detail

      • store

        void store​(Index indx)
            throws IllegalIDException,
        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.

        indx - the Index to add
        IllegalIDException - if the index has an invalid ID field
        BioException - if the store failed
      • rollback

        void rollback()
        Discard all uncommited changes.
      • getName

        String getName()
        Retrieve the name of this store. This will be reflected as the name of the IndexedSequenceDB.
        the String name of the index
      • getIDs

        Set getIDs()
        Retrieve the set of all current IDs.

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

        a Set of all legal IDs
      • getFiles

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

        SequenceFormat getFormat()
        Retrieve the format of the index file.

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

        a Set of all indexed files
      • getSBFactory

        SequenceBuilderFactory getSBFactory()
        Retrieve the SequenceBuilderFactory used to build Sequence instances.
        the associated SequenceBuilderFactory
      • getSymbolParser

        SymbolTokenization getSymbolParser()
        Retrieve the symbol parser used to turn the sequence characters into Symobl objects.
        the associated SymbolParser