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 javax.annotation.Nullable;
22 import java.util.Collection;
23
24 /**
25 * @author Paul
26 */
27 public interface OntologyTerm extends OntologyResource {
28
29 /**
30 * Obtain alternative IDs for this term.
31 */
32 Collection<String> getAlternativeIds();
33
34 /**
35 * Obtain all annotations for this term.
36 */
37 Collection<AnnotationProperty> getAnnotations();
38
39 /**
40 * Obtain all the annotations for a given property URI.
41 */
42 Collection<AnnotationProperty> getAnnotations( String propertyUri );
43
44 /**
45 * Obtain an annotation by property URI.
46 */
47 @Nullable
48 AnnotationProperty getAnnotation( String propertyUri );
49
50 /**
51 * Obtain the children of this term via subclasses and additional properties.
52 *
53 * @see #getChildren(boolean, boolean)
54 */
55 default Collection<OntologyTerm> getChildren( boolean direct ) {
56 return getChildren( direct, true, false );
57 }
58
59 default Collection<OntologyTerm> getChildren( boolean direct, boolean includeAdditionalProperties ) {
60 return getChildren( direct, includeAdditionalProperties, false );
61 }
62
63 /**
64 * Obtain the children of this term via subclass relationships and possibly some additional properties.
65 *
66 * @param direct return only the immediate children; if false, return all of them down to the leaves.
67 * @param includeAdditionalProperties include terms matched via additional properties
68 */
69 Collection<OntologyTerm> getChildren( boolean direct, boolean includeAdditionalProperties, boolean keepObsoletes );
70
71 default Collection<OntologyIndividual> getIndividuals() {
72 return getIndividuals( true );
73 }
74
75 Collection<OntologyIndividual> getIndividuals( boolean direct );
76
77 /**
78 * Note that any restriction superclasses are not returned, unless they are has_proper_part
79 *
80 * @param direct
81 * @return
82 */
83 default Collection<OntologyTerm> getParents( boolean direct ) {
84 return getParents( direct, true, false );
85 }
86
87 default Collection<OntologyTerm> getParents( boolean direct, boolean includeAdditionalProperties ) {
88 return getParents( direct, includeAdditionalProperties, false );
89 }
90
91 Collection<OntologyTerm> getParents( boolean direct, boolean includeAdditionalProperties, boolean keepObsoletes );
92
93 Collection<OntologyRestriction> getRestrictions();
94
95 /**
96 * @deprecated use {@link #getLabel()} instead.
97 */
98 @Deprecated
99 String getTerm();
100
101 boolean isRoot();
102
103 /**
104 * check to see if the term is obsolete, if it is it should not be used
105 *
106 * @deprecated use {@link #isObsolete()} instead
107 */
108 @Deprecated
109 boolean isTermObsolete();
110 }