Field Summary

Constructor Summary

Method Summary

• Methods inherited from class java.lang.Object

  clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

• STORE_NAME

  public static final String STORE_NAME

  STORE_NAME is the key used to identify the arbitrary name of the store in the OBDA config.dat files.

  See Also:

  Constant Field Values

• SEQUENCE_FORMAT

  public static final String SEQUENCE_FORMAT

  SEQUENCE_FORMAT is the key used to identify the format of the indexed sequence files represented by the store in the OBDA config.dat files.

  See Also:

  Constant Field Values

• PRIMARY_KEY_NAME

  public static final String PRIMARY_KEY_NAME

  PRIMARY_KEY_NAME is the key used to identify the primary namespace in the OBDA config.dat files.

  See Also:

  Constant Field Values

• KEYS

  public static final String KEYS

  KEYS is the key used to identify the secondary namespaces in the OBDA config.dat files.

  See Also:

  Constant Field Values

• META_DATA_TYPE

  public static final AnnotationType META_DATA_TYPE

  AnnotationType that all meta-data files should fit.

Constructor Detail

• BioStoreFactory

  public BioStoreFactory()

  Creates a new BioStoreFactory.

Method Detail

• setStoreName

  public void setStoreName​(String name)

  setStoreName sets the name to be given to the new index.

  Parameters:

  name - a String.

• getStoreName

  public String getStoreName()

  getStoreName returns the name to be given to the new index.

  Returns:

  a String.

• setStoreLocation

  public void setStoreLocation​(File storeLoc)

  setStoreLocation sets the directory of the new index.

  Parameters:

  storeLoc - a File.

• getStoreLocation

  public File getStoreLocation()

  getStoreLocation returns the directory of the bew index.

  Returns:

  a File.

• setSequenceFormat

  public void setSequenceFormat​(LifeScienceIdentifier format)

  setSequenceFormat sets the sequence format name which will be indicated in the index.

  Parameters:

  format - a LifeScienceIdentifier which must be one of those mandated by the OBDA flatfile indexing specification.

• getSequenceFormat

  public LifeScienceIdentifier getSequenceFormat()

  getSequenceFormat returns the current sequence format name.

  Returns:

  a LifeScienceIdentifier.

• setPrimaryKey

  public void setPrimaryKey​(String primaryKey)

  setPrimaryKey sets the primary identifier namespace.

  Parameters:

  primaryKey - a String.

• getPrimaryKey

  public String getPrimaryKey()

  getPrimaryKey returns the primary identifier namespace.

  Returns:

  a String.

• addKey

  public void addKey​(String keyName,
                     int length)

  addKey adds a new identifier namespace.

  Parameters:

  keyName - a String.

  length - an int indicating the byte length of the key records.

• getKeys

  public Set getKeys()

• removeKey

  public void removeKey​(String keyName)

  removeKey removes the specified key.

  Parameters:

  keyName - a String.

• createBioStore

  public BioStore createBioStore()
                          throws BioException

  createBioStore creates a BioStore reflecting the current state of the factory and returns a reference to it.

  Returns:

  a BioStore.

  Throws:

  BioException - if an error occurs.

• makeConfigFile

  public static File makeConfigFile​(File storeLoc)
                             throws IOException

  makeConfigFile returns a file which represents an OBDA "config.dat" in the specified index directory.

  Parameters:

  storeLoc - a File indicating the index directory.

  Returns:

  a File representing "config.dat".

  Throws:

  IOException - if an error occurs.

• makePrimaryKeyFile

  public static File makePrimaryKeyFile​(File storeLoc,
                                        String key)
                                 throws IOException

  makePrimaryKeyFile returns a file which represents an OBDA "key_<primary namespace>.key" primary key file on the specified index directory.

  Parameters:

  storeLoc - a File indicating the parent path.

  key - a String primary key namespace.

  Returns:

  a File representing a "key_<primary namespace>.key".

  Throws:

  IOException - if an error occurs.

• makeSecondaryFile

  public static File makeSecondaryFile​(File storeLoc,
                                       String key)
                                throws IOException

  makeSecondaryFile returns a file which represents an OBDA "id_<secondary namespace>.index" secondary key file on the specified.

  Parameters:

  storeLoc - a File indicating the parent path.

  key - a String secondary key namespace.

  Returns:

  a File representing an "id_<secondary namespace>.index" file.

  Throws:

  IOException - if an error occurs.

• calculatePrimRecLen

  public static int calculatePrimRecLen​(int idLen)

  calculatePrimRecLen calculates the byte length of primary namespace records.

  Parameters:

  idLen - an int the number of bytes required to hold the primary namespace ID.

  Returns:

  an int record length in bytes.

• calculateSecRecLen

  public static int calculateSecRecLen​(int idLen,
                                       String primaryKey,
                                       Map keys)

  calculateSecRecLen calculates the byte length of secondary namespace records.

  Parameters:

  idLen - an int the number of bytes required to hold the secondary namespace ID.

  primaryKey - a String the primary namespace ID.

  keys - a Map of secondary keys to their byte lengths.

  Returns:

  an int record length in bytes.