Package org.biojava.bio.seq.db

Class EmblCDROMIndexStore

java.lang.Object
org.biojava.bio.seq.db.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 Details

    • 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 Details

    • 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.

    • store

      public void store(Index index) throws IllegalIDException, BioException
      store adds an Index to the store. As EMBL CD-ROM indices are read-only, this implementation throws a BioException.
      Specified by:
      store in interface IndexStore
      Parameters:
      index - an Index.
      Throws:
      IllegalIDException - if an error occurs.
      BioException - if an error occurs.

    • 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

    • fetch

      public Index fetch(String id) throws IllegalIDException, BioException
      Description copied from interface: IndexStore
      Fetch an Index based upon an ID.
      Specified by:
      fetch in interface IndexStore
      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

    • 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

    • getFiles

      public Set getFiles()
      Description copied from interface: IndexStore
      Retrieve the Set of files that are currently indexed.
      Specified by:
      getFiles in interface IndexStore

    • 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

    • getSBFactory

      public SequenceBuilderFactory getSBFactory()
      Description copied from interface: IndexStore
      Retrieve the SequenceBuilderFactory used to build Sequence instances.
      Specified by:
      getSBFactory in interface IndexStore
      Returns:
      the associated SequenceBuilderFactory

    • getSymbolParser

      public SymbolTokenization getSymbolParser()
      Description copied from interface: IndexStore
      Retrieve the symbol parser used to turn the sequence characters into Symobl objects.
      Specified by:
      getSymbolParser in interface IndexStore
      Returns:
      the associated SymbolParser

    • 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.