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 /**
33 * Obtain the children of this term via subclasses and additional properties.
34 *
35 * @see #getChildren(boolean, boolean)
36 */
37 default Collection<OntologyTerm> getChildren( boolean direct ) {
38 return getChildren( direct, true, false );
39 }
40
41 default Collection<OntologyTerm> getChildren( boolean direct, boolean includeAdditionalProperties ) {
42 return getChildren( direct, includeAdditionalProperties, false );
43 }
44
45 /**
46 * Obtain the children of this term via subclass relationships and possibly some additional properties.
47 *
48 * @param direct return only the immediate children; if false, return all of them down to the leaves.
49 * @param includeAdditionalProperties include terms matched via additional properties
50 */
51 Collection<OntologyTerm> getChildren( boolean direct, boolean includeAdditionalProperties, boolean keepObsoletes );
52
53 String getComment();
54
55 default Collection<OntologyIndividual> getIndividuals() {
56 return getIndividuals( true );
57 }
58
59 Collection<OntologyIndividual> getIndividuals( boolean direct );
60
61 String getLocalName();
62
63 Object getModel();
64
65 /**
66 * Note that any restriction superclasses are not returned, unless they are has_proper_part
67 *
68 * @param direct
69 * @return
70 */
71 default Collection<OntologyTerm> getParents( boolean direct ) {
72 return getParents( direct, true, false );
73 }
74
75 default Collection<OntologyTerm> getParents( boolean direct, boolean includeAdditionalProperties ) {
76 return getParents( direct, includeAdditionalProperties, false );
77 }
78
79 Collection<OntologyTerm> getParents( boolean direct, boolean includeAdditionalProperties, boolean keepObsoletes );
80
81 Collection<OntologyRestriction> getRestrictions();
82
83 /**
84 * @deprecated use {@link #getLabel()} instead.
85 */
86 @Deprecated
87 String getTerm();
88
89 boolean isRoot();
90
91 /**
92 * check to see if the term is obsolete, if it is it should not be used
93 *
94 * @deprecated use {@link #isObsolete()} instead
95 */
96 @Deprecated
97 boolean isTermObsolete();
98 }