Index

A C E F G I N O R S T W
All Classes and Interfaces|All Packages|Serialized Form

A

addRange(int, String, String, int, int) - Method in class org.incenp.obofoundry.dicer.IDPolicy

Adds a pre-defined range.

addRange(String, String, int) - Method in class org.incenp.obofoundry.dicer.IDPolicy

Adds a new range to this policy.

ALLOCATEDTO_IRI - Static variable in class org.incenp.obofoundry.dicer.Constants

The property that associates an ID range to a user name.

C

Constants - Class in org.incenp.obofoundry.dicer

Constants used throughout the package.

Constants() - Constructor for class org.incenp.obofoundry.dicer.Constants

E

exists(String) - Method in interface org.incenp.obofoundry.dicer.IExistenceChecker

Checks whether the given identifier already exists.

exists(String) - Method in class org.incenp.obofoundry.dicer.OWLExistenceChecker

F

findAnyRange(List<String>) - Method in class org.incenp.obofoundry.dicer.IDPolicy

Finds a range allocated to any of the given users.

findIDPolicyFile() - Static method in class org.incenp.obofoundry.dicer.IDPolicyHelper

Finds an ID policy file in the current directory.

findOpenRange(int) - Method in class org.incenp.obofoundry.dicer.IDPolicy

Finds an available range with the given size in the policy.

findRange(String) - Method in class org.incenp.obofoundry.dicer.IDPolicy

Finds the range allocated to a given user.

fromOntology(OWLOntology) - Method in class org.incenp.obofoundry.dicer.IDPolicyReader

Extracts an ID policy from the given ontology.

G

getAnyRange(List<String>) - Method in class org.incenp.obofoundry.dicer.IDPolicy

Gets a range allocated to any of the given users.

getComment() - Method in class org.incenp.obofoundry.dicer.IDRange

Gets the comment associated with the range, if any.

getFormat() - Method in class org.incenp.obofoundry.dicer.IDPolicy

Gets a format string suitable to mind IDs conforming to this policy.

getFormat() - Method in class org.incenp.obofoundry.dicer.IDRange

Gets a format string suitable to mind IDs conforming to the policy this range belongs to.

getID() - Method in class org.incenp.obofoundry.dicer.IDRange

Gets the numerical identifier for this range.

getLowerBound() - Method in class org.incenp.obofoundry.dicer.IDRange

Gets the lower bound (inclusive) of the range.

getMaxUpperBound() - Method in class org.incenp.obofoundry.dicer.IDPolicy

Gets the highest possible upper bound for IDs in this policy.

getName() - Method in class org.incenp.obofoundry.dicer.IDPolicy

Gets the name of the ontology this policy is intended for.

getName() - Method in class org.incenp.obofoundry.dicer.IDRange

Gets the name of the user this range is allocated to.

getPrefix() - Method in class org.incenp.obofoundry.dicer.IDPolicy

Gets the prefix IRI for IDs to be created with this policy.

getPrefixName() - Method in class org.incenp.obofoundry.dicer.IDPolicy

Gets the prefix name for IDs to be created with this policy.

getRange(String) - Method in class org.incenp.obofoundry.dicer.IDPolicy

Gets the range allocated to a given user.

getRange(String, String[], String) - Static method in class org.incenp.obofoundry.dicer.IDPolicyHelper

Gets the ID range allocated to the given user according to the ID policy.

getRangeFor(String) - Method in class org.incenp.obofoundry.dicer.IDPolicy

Deprecated.

Use findRange(String) or getRange(String) instead.

getRangesByID() - Method in class org.incenp.obofoundry.dicer.IDPolicy

Gets all the ID ranges defined in this policy, sorted by their IDs.

getRangesByLowerBound() - Method in class org.incenp.obofoundry.dicer.IDPolicy

Gets all the ID ranges defined in this policy, sorted by the lower bound of each range.

getSize() - Method in class org.incenp.obofoundry.dicer.IDRange

Gets the number of IDs available in this range.

getUnallocatedRanges() - Method in class org.incenp.obofoundry.dicer.IDPolicy

Gets all the non-allocated ranges in this policy, sorted by the lower bound of each range.

getUpperBound() - Method in class org.incenp.obofoundry.dicer.IDRange

Gets the upper bound (exclusive) of the range.

getWidth() - Method in class org.incenp.obofoundry.dicer.IDPolicy

Gets the number of digits that IDs to be created with this policy should have.

I

IAutoIDGenerator - Interface in org.incenp.obofoundry.dicer

An object that generates automatic IDs for ontological entities.

IDDIGITS_IRI - Static variable in class org.incenp.obofoundry.dicer.Constants

The property that defines the number of digits that IDs created according to a given policy should have.

IDException - Exception Class in org.incenp.obofoundry.dicer

Base class for all exceptions from the Dicer library.

IDException(String, Object...) - Constructor for exception class org.incenp.obofoundry.dicer.IDException

Creates a new instance with the specified error message.

IDNotFoundException - Exception Class in org.incenp.obofoundry.dicer

An exception that is thrown when an ID cannot be found for any reason.

IDNotFoundException(String, Object...) - Constructor for exception class org.incenp.obofoundry.dicer.IDNotFoundException

Creates a new instance with the specified error message.

IDPolicy - Class in org.incenp.obofoundry.dicer

Represents a comprehensive ID range policy, that both describes the expected format of ID and allocates ranges to users.

IDPolicy(String) - Constructor for class org.incenp.obofoundry.dicer.IDPolicy

Creates a new policy for a typical OBO ontology.

IDPolicy(String, int) - Constructor for class org.incenp.obofoundry.dicer.IDPolicy

Creates a new policy for a typical OBO ontology, with a custom ID width.

IDPolicy(String, String, String, int) - Constructor for class org.incenp.obofoundry.dicer.IDPolicy

Creates a new custom policy.

IDPolicyHelper - Class in org.incenp.obofoundry.dicer

A class of helper methods to work with ID policies.

IDPolicyHelper() - Constructor for class org.incenp.obofoundry.dicer.IDPolicyHelper

IDPolicyReader - Class in org.incenp.obofoundry.dicer

A class to read an ID policy from an ontology file.

IDPolicyReader() - Constructor for class org.incenp.obofoundry.dicer.IDPolicyReader

IDPolicyWriter - Class in org.incenp.obofoundry.dicer

A class to serialise an ID policy to file.

IDPolicyWriter() - Constructor for class org.incenp.obofoundry.dicer.IDPolicyWriter

IDPREFIX_IRI - Static variable in class org.incenp.obofoundry.dicer.Constants

The property that defines the IRI prefix that a policy is intended for.

IDRange - Class in org.incenp.obofoundry.dicer

Represents an ID range in an ID policy.

IDRange(int, String, String, int, int, IDPolicy) - Constructor for class org.incenp.obofoundry.dicer.IDRange

Creates a range with an optional comment.

IDRangeNotFoundException - Exception Class in org.incenp.obofoundry.dicer

An exception that is thrown when a requested range cannot be found in a ID policy.

IDRangeNotFoundException() - Constructor for exception class org.incenp.obofoundry.dicer.IDRangeNotFoundException

Creates a new instance with a generic error message.

IDRangeNotFoundException(String) - Constructor for exception class org.incenp.obofoundry.dicer.IDRangeNotFoundException

Creates a new instance with the name of the unfound range.

IDRangeNotFoundException(String, Object...) - Constructor for exception class org.incenp.obofoundry.dicer.IDRangeNotFoundException

Creates a new instance with the specified error message.

IDSFOR_IRI - Static variable in class org.incenp.obofoundry.dicer.Constants

The property that defines the prefix name of a ID policy.

IExistenceChecker - Interface in org.incenp.obofoundry.dicer

An interface to check whether a given identifier is already in use.

InvalidIDPolicyException - Exception Class in org.incenp.obofoundry.dicer

An exception that is thrown when a ID policy is invalid.

InvalidIDPolicyException(String, Object...) - Constructor for exception class org.incenp.obofoundry.dicer.InvalidIDPolicyException

Creates a new instance with the specified error message.

N

nextID() - Method in interface org.incenp.obofoundry.dicer.IAutoIDGenerator

Generates a new automatic ID.

nextID() - Method in class org.incenp.obofoundry.dicer.RandomizedIDGenerator

nextID() - Method in class org.incenp.obofoundry.dicer.SequentialIDGenerator

O

org.incenp.obofoundry.dicer - package org.incenp.obofoundry.dicer

OWLExistenceChecker - Class in org.incenp.obofoundry.dicer

An IExistenceChecker implementation that uses a OWLSignature object as the backend.

OWLExistenceChecker(OWLSignature) - Constructor for class org.incenp.obofoundry.dicer.OWLExistenceChecker

Creates a new instance.

R

RandomizedIDGenerator - Class in org.incenp.obofoundry.dicer

Generates numerical IDs within a given range.

RandomizedIDGenerator(String, int, int, IExistenceChecker) - Constructor for class org.incenp.obofoundry.dicer.RandomizedIDGenerator

Creates a new instance.

RandomizedIDGenerator(IDRange, IExistenceChecker) - Constructor for class org.incenp.obofoundry.dicer.RandomizedIDGenerator

Creates a new instance from a IDRange object.

read(String) - Method in class org.incenp.obofoundry.dicer.IDPolicyReader

Parses the given file into an ID policy.

S

SequentialIDGenerator - Class in org.incenp.obofoundry.dicer

Generates numerical IDs sequentially within a given range.

SequentialIDGenerator(String, int, int, IExistenceChecker) - Constructor for class org.incenp.obofoundry.dicer.SequentialIDGenerator

Creates a new instance.

SequentialIDGenerator(IDRange, IExistenceChecker) - Constructor for class org.incenp.obofoundry.dicer.SequentialIDGenerator

Creates a new instance from a IDRange object.

T

toString() - Method in class org.incenp.obofoundry.dicer.IDRange

W

write(IDPolicy, File) - Method in class org.incenp.obofoundry.dicer.IDPolicyWriter

Writes a policy to a file.

write(IDPolicy, OutputStream) - Method in class org.incenp.obofoundry.dicer.IDPolicyWriter

Writes a policy to a stream.

write(IDPolicy, Writer) - Method in class org.incenp.obofoundry.dicer.IDPolicyWriter

Writes a policy to a Writer object.

write(IDPolicy, String) - Method in class org.incenp.obofoundry.dicer.IDPolicyWriter

Writes a policy to a file.

A C E F G I N O R S T W
All Classes and Interfaces|All Packages|Serialized Form