1 /*
2 * The basecode project
3 *
4 * Copyright (c) 2007-2019 Columbia University
5 *
6 * Licensed under the Apache License, Version 2.0 (the "License");
7 * you may not use this file except in compliance with the License.
8 * You may obtain a copy of the License at
9 *
10 * http://www.apache.org/licenses/LICENSE-2.0
11 *
12 * Unless required by applicable law or agreed to in writing, software
13 * distributed under the License is distributed on an "AS IS" BASIS,
14 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
15 * See the License for the specific language governing permissions and
16 * limitations under the License.
17 *
18 */
19 package ubic.basecode.ontology.model;
20
21 import java.util.Collection;
22
23 /**
24 * @author Paul
25 */
26 public interface OntologyTerm extends OntologyResource {
27
28 Collection<String> getAlternativeIds();
29
30 Collection<AnnotationProperty> getAnnotations();
31
32 Collection<OntologyTerm> getChildren( boolean direct );
33
34 /**
35 * @param direct return only the immediate children; if false, return all of them down to the leaves.
36 * @param includePartOf include terms matched via
37 * @return
38 */
39 Collection<OntologyTerm> getChildren( boolean direct, boolean includePartOf );
40
41 String getComment();
42
43 Collection<OntologyIndividual> getIndividuals();
44
45 Collection<OntologyIndividual> getIndividuals( boolean direct );
46
47 String getLocalName();
48
49 Object getModel();
50
51 /**
52 * Note that any restriction superclasses are not returned, unless they are has_proper_part
53 *
54 * @param direct
55 * @return
56 */
57 Collection<OntologyTerm> getParents( boolean direct );
58
59 Collection<OntologyTerm> getParents( boolean direct, boolean includePartOf );
60
61 Collection<OntologyRestriction> getRestrictions();
62
63 String getTerm();
64
65 @Override
66 String getUri();
67
68 boolean isRoot();
69
70 /**
71 * check to see if the term is obsolete, if it is it should not be used
72 */
73 boolean isTermObsolete();
74 }