1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
|
/*
* Copyright (c) 2006 Genome Research Limited.
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU Library General Public License as published
* by the Free Software Foundation; either version 2 of the License or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Library General Public License for more details.
*
* You should have received a copy of the GNU Library General Public License
* along with this program; see the file COPYING.LIB. If not, write to
* the Free Software Foundation Inc., 59 Temple Place - Suite 330,
* Boston, MA 02111-1307 USA
*/
package org.gmod.schema.dao;
import org.gmod.schema.cv.Cv;
import org.gmod.schema.cv.CvTerm;
import org.gmod.schema.general.DbXRef;
import org.gmod.schema.utils.CountedName;
import java.util.List;
public interface CvDaoI extends BaseDaoI {
/**
* Get a CV by id
*
* @param id the cv id (primary key)
* @return the corresponding Cv, or null
*/
public abstract Cv getCvById(int id);
// TODO Should this return a list or just one?
/**
* Retrieve a controlled vocabulary by its name
*
* @param name the name to lookup
* @return the List<Cv> of matches, or null
*/
public abstract List<Cv> getCvByName(String name);
/**
* Retrieve a CvTerm by id
*
* @param id then cvterm id (primary key)
* @return the corresponding CvTerm, or null
*/
public abstract CvTerm getCvTermById(int id);
// TODO Should this return a list or just one?
/**
* Retrieve a named CvTerm from a given Cv
*
* @param cvTermName the name of the cvterm
* @param cv the controlled vocabulary this cvterm is part of
* @return a (possibly empty) list of matching cvterms
*/
public abstract List<CvTerm> getCvTermByNameInCv(String cvTermName, Cv cv);
/**
* Retrieve a CvTerm from the Gene Ontology
*
* @param value the
* @return the corresponding CvTerm, or null
*/
public abstract CvTerm getGoCvTermByAcc(String value);
/**
* Retrieve a CvTerm from the Gene Ontology via it's database entry
*
* @param id the database name eg GO:123456
* @return the corresponding CvTerm, or null
*/
public abstract CvTerm getGoCvTermByAccViaDb(final String id);
/**
* Retrieve all CvTerms
* @return a list of all cvterms
*/
public abstract List<CvTerm> getCvTerms();
/**
* Retrieve a named CvTerm from a given Cv
*
* @param cvTermName the name of the cvterm
* @param name the controlled vocabulary name this cvterm could be part of
* @return a (possibly empty) cvterm
*/
public abstract CvTerm getCvTermByNameAndCvName(String cvTermName, String name);
/**
* Get a CvTerm by DbXRef
*
* @param dbXRef the DbXRef
* @return the corresponding CvTerm, or null
*/
public abstract CvTerm getCvTermByDbXRef(DbXRef dbXRef);
public boolean existsNameInOntology(String name, Cv ontology);
public List<String> getPossibleMatches(String search, Cv cv, int limit);
public List<CountedName> getAllTermsInCvWithCount(Cv cv);
}
|
