Interface DataStoreFactory

    • Method Detail

      • getDataStore

        DataStore getDataStore​(java.io.File storeFile)
                        throws java.io.IOException
        Get a pre-built data store associated with a file.
        Parameters:
        storeFile - the File to map in as a data store
        Returns:
        the DataStore made by mapping the file
        Throws:
        java.io.IOException - if the file could not be mapped
      • buildDataStore

        DataStore buildDataStore​(java.io.File storeFile,
                                 SequenceDB seqDB,
                                 Packing packing,
                                 int wordLength,
                                 int threshold)
                          throws IllegalAlphabetException,
                                 java.io.IOException,
                                 BioException
        Build a new DataStore.
        Parameters:
        storeFile - the file to store the data store
        seqDB - the SequenceDB to store in the data store
        packing - the Packing used to bit-encode the sequences
        wordLength - the number of symbols per word
        threshold - the number of times a word must appear to be ignored
        Throws:
        IllegalAlphabetException - if the packing does not agree with the sequences
        BioException - if there is a problem building the data store
        java.io.IOException