Package org.biojava.bio.seq.db

Class EmblCDROMIndexStore

  • All Implemented Interfaces:
    IndexStore
    public class EmblCDROMIndexStore
extends Object
implements IndexStore

    EmblCDROMIndexStores implement a read-only IndexStore backed by EMBL CD-ROM format binary indices. The required index files are typically named "division.lkp" and "entrynam.idx". As an IndexStore performs lookups by sequence ID, the index files "acnum.trg" and "acnum.hit" (which store additional accession number data) are not used.

    The sequence IDs are found using a binary search via a pointer into the index file. The whole file is not read unless a request for all the IDs is made using the getIDs() method. The set of IDs is then cached after the first pass. This class also has a close() method to free resources associated with the underlying RandomAccessFile.

    The binary index files may be created using the EMBOSS programs dbifasta, dbiblast, dbiflat or dbigcg. The least useful from the BioJava perspective is dbigcg because we do not have a SequenceFormat implementation for GCG format files.

    The Index instances returned by this class do not have the record length set because this information is not available in the binary index. The value -1 is used instead, as described in the Index interface.

    Since:
    1.2
    Author:
    Keith James

    • Constructor Detail

      • EmblCDROMIndexStore

        public EmblCDROMIndexStore​(File divisionLkp,
                           File entryNamIdx,
                           SequenceFormat format,
                           SequenceBuilderFactory factory,
                           SymbolTokenization parser)
                    throws IOException
        Creates a new EmblCDROMIndexStore backed by a random access binary index.
        Parameters:
        divisionLkp - a File containing the master index.
        entryNamIdx - a File containing the sequence IDs and offsets.
        format - a SequenceFormat.
        factory - a SequenceBuilderFactory.
        parser - a SymbolTokenization.
        Throws:
        IOException - if an error occurs.

      • EmblCDROMIndexStore

        public EmblCDROMIndexStore​(File pathPrefix,
                           File divisionLkp,
                           File entryNamIdx,
                           SequenceFormat format,
                           SequenceBuilderFactory factory,
                           SymbolTokenization parser)
                    throws IOException
        Creates a new EmblCDROMIndexStore backed by a random access binary index.
        Parameters:
        pathPrefix - a File containing the abstract path to be appended to sequence database filenames retrieved from the binary index.
        divisionLkp - a File containing the master index.
        entryNamIdx - a File containing the sequence IDs and offsets.
        format - a SequenceFormat.
        factory - a SequenceBuilderFactory.
        parser - a SymbolTokenization.
        Throws:
        IOException - if an error occurs.

    • Method Detail

      • getPathPrefix

        public File getPathPrefix()
        getPathPrefix returns the abstract path currently being appended to the raw sequence database filenames extracted from the binary index. This value defaults to the empty abstract path.
        Returns:
        a File.

      • setPathPrefix

        public void setPathPrefix​(File pathPrefix)
        setPathPrefix sets the abstract path to be appended to sequence database filenames retrieved from the binary index. E.g. if the binary index refers to the database as 'SWALL' and the pathPrefix is set to "/usr/local/share/data/seq/", then the IndexStore will know the database path as "/usr/local/share/data/seq/swall" and any Index instances produced by the store will return the latter path when their getFile() method is called. This value defaults to the empty abstract path.
        Parameters:
        pathPrefix - a File prefix specifying the abstract path to append.

      • getName

        public String getName()
        getName returns the database name as defined within the EMBL CD-ROM index.
        Specified by:
        getName in interface IndexStore
        Returns:
        a String value.

      • commit

        public void commit()
            throws BioException
        commit commits changes. As EMBL CD-ROM indices are read-only, this implementation throws a BioException.
        Specified by:
        commit in interface IndexStore
        Throws:
        BioException - if an error occurs.

      • rollback

        public void rollback()
        rollback rolls back changes made since the last commit. As EMBL CD-ROM indices are read-only, this implementation does nothing.
        Specified by:
        rollback in interface IndexStore

      • getIDs

        public Set getIDs()
        Description copied from interface: IndexStore
        Retrieve the set of all current IDs.

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

        Specified by:
        getIDs in interface IndexStore
        Returns:
        a Set of all legal IDs

      • getFormat

        public SequenceFormat getFormat()
        Description copied from interface: IndexStore
        Retrieve the format of the index file.

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

        Specified by:
        getFormat in interface IndexStore
        Returns:
        a Set of all indexed files

      • close

        public void close()
           throws IOException
        close closes the underlying EntryNamRandomAccess which in turn closes the lower level RandomAccessFile. This frees the resources associated with the file.
        Throws:
        IOException - if an error occurs.