org.obolibrary.robot

Class DiffOperation

java.lang.Object

org.obolibrary.robot.DiffOperation

public class DiffOperation
extends Object

Get the differences between two ontology files.

Author:

James A. Overton

Constructor Summary

Constructors

Constructor and Description
DiffOperation()

Method Summary

Modifier and Type	Method and Description
static String	addLabels(IOHelper ioHelper, Map<org.semanticweb.owlapi.model.IRI,String> labels, String axiom) Deprecated. This functionality is now provided by the owl-diff library and no longer used to format results in DiffOperation.
static String	addLabels(Map<org.semanticweb.owlapi.model.IRI,String> labels, String axiom) Deprecated. This functionality is now provided by the owl-diff library and no longer used to format results in DiffOperation.
static boolean	compare(org.semanticweb.owlapi.model.OWLOntology ontology1, org.semanticweb.owlapi.model.OWLOntology ontology2, IOHelper ioHelper, Writer writer, Map<String,String> options) Given two ontologies, a Writer, and a set of diff options, get their differences and write then to the writer.
static boolean	compare(org.semanticweb.owlapi.model.OWLOntology ontology1, org.semanticweb.owlapi.model.OWLOntology ontology2, Writer writer) Given two ontologies and a Writer, get their differences and write then to the writer.
static boolean	equals(org.semanticweb.owlapi.model.OWLOntology ontology1, org.semanticweb.owlapi.model.OWLOntology ontology2) Given two ontologies, compare their sets of axioms, annotations, imports, and ontology IDs, returning true if they are identical and false otherwise.
static Set<String>	getAxiomStrings(org.semanticweb.owlapi.model.OWLOntology ontology) Deprecated. This functionality is no longer used within DiffOperation.
static Map<String,String>	getDefaultOptions() Return default diff options.

Methods inherited from class java.lang.Object

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

Constructor Detail

DiffOperation

public DiffOperation()

Method Detail

getDefaultOptions

public static Map<String,String> getDefaultOptions()

Return default diff options.

Returns:

diff options

equals

public static boolean equals(org.semanticweb.owlapi.model.OWLOntology ontology1,
                             org.semanticweb.owlapi.model.OWLOntology ontology2)

Given two ontologies, compare their sets of axioms, annotations, imports, and ontology IDs, returning true if they are identical and false otherwise.

Parameters:

ontology1 - the first ontology

ontology2 - the second ontology

Returns:

true if the ontologies are the same, false otherwise

compare

public static boolean compare(org.semanticweb.owlapi.model.OWLOntology ontology1,
                              org.semanticweb.owlapi.model.OWLOntology ontology2,
                              Writer writer)
                       throws IOException

Given two ontologies and a Writer, get their differences and write then to the writer. The ontologies are not changed.

Parameters:

ontology1 - the first ontology

ontology2 - the second ontology

writer - the Writer for the report, or null

Returns:

true if the ontologies are the same, false otherwise

Throws:

IOException - on writer failure

compare

public static boolean compare(org.semanticweb.owlapi.model.OWLOntology ontology1,
                              org.semanticweb.owlapi.model.OWLOntology ontology2,
                              IOHelper ioHelper,
                              Writer writer,
                              Map<String,String> options)
                       throws IOException

Given two ontologies, a Writer, and a set of diff options, get their differences and write then to the writer. The ontologies are not changed.

Parameters:

ontology1 - the first ontology

ontology2 - the second ontology

ioHelper - IOHelper to use for prefixes

writer - the Writer for the report, or null

options - diff options

Returns:

true if the ontologies are the same, false otherwise

Throws:

IOException - on writer failure

addLabels

@Deprecated
public static String addLabels(Map<org.semanticweb.owlapi.model.IRI,String> labels,
                                           String axiom)

Deprecated. This functionality is now provided by the owl-diff library and no longer used to format results in DiffOperation.

Given a map from IRIs to labels and an axiom string, add labels next to any IRIs in the string, shorten OBO IRIs, and return the updated string.

Parameters:

labels - a map from IRIs to label strings

axiom - a string representation of an OWLAxiom

Returns:

a string with labels inserted next to IRIs

addLabels

@Deprecated
public static String addLabels(IOHelper ioHelper,
                                           Map<org.semanticweb.owlapi.model.IRI,String> labels,
                                           String axiom)

Deprecated. This functionality is now provided by the owl-diff library and no longer used to format results in DiffOperation.

Given an IOHelper to get short form of IRIs, a map from IRIs to labels, and an axiom string, add labels next to any IRIs in the string, shorten OBO IRIs, and return the updated string.

Parameters:

ioHelper - IOHelper to use for prefixes

labels - a map from IRIs to label strings

axiom - a string representation of an OWLAxiom

Returns:

a string with labels inserted next to CURIEs

getAxiomStrings

@Deprecated
public static Set<String> getAxiomStrings(org.semanticweb.owlapi.model.OWLOntology ontology)

Deprecated. This functionality is no longer used within DiffOperation.

Given an ontology, return a list of strings for all the axioms of that ontology.

Parameters:

ontology - the ontology to use

Returns:

a set of strings, one for each axiom in the ontology