1. Project Clover database Fri Dec 6 2024 13:47:14 GMT
  2. Package jalview.util

File DBRefUtilsTest.java

 

Code metrics

0
121
9
1
305
207
9
0.07
13.44
9
1

Classes

Class
Line #
Actions
DBRefUtilsTest 42 121 9
1.0100%
 

Contributing tests

This file is covered by 8 tests. .

Source view

1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
7    * Jalview is free software: you can redistribute it and/or
8    * modify it under the terms of the GNU General Public License
9    * as published by the Free Software Foundation, either version 3
10    * of the License, or (at your option) any later version.
11    *
12    * Jalview is distributed in the hope that it will be useful, but
13    * WITHOUT ANY WARRANTY; without even the implied warranty
14    * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15    * PURPOSE. See the GNU General Public License for more details.
16    *
17    * You should have received a copy of the GNU General Public License
18    * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19    * The Jalview Authors are detailed in the 'AUTHORS' file.
20    */
21    package jalview.util;
22   
23    import static org.testng.AssertJUnit.assertEquals;
24    import static org.testng.AssertJUnit.assertNull;
25    import static org.testng.AssertJUnit.assertSame;
26    import static org.testng.AssertJUnit.assertTrue;
27   
28    import jalview.datamodel.DBRefEntry;
29    import jalview.datamodel.DBRefSource;
30    import jalview.datamodel.Mapping;
31    import jalview.datamodel.PDBEntry;
32    import jalview.datamodel.Sequence;
33    import jalview.datamodel.SequenceI;
34    import jalview.gui.JvOptionPane;
35   
36    import java.util.Arrays;
37    import java.util.List;
38   
39    import org.testng.annotations.BeforeClass;
40    import org.testng.annotations.Test;
41   
 
42    public class DBRefUtilsTest
43    {
44   
 
45  1 toggle @BeforeClass(alwaysRun = true)
46    public void setUpJvOptionPane()
47    {
48  1 JvOptionPane.setInteractiveMode(false);
49  1 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
50    }
51   
52    /**
53    * Test the method that selects DBRefEntry items whose source is in a supplied
54    * list
55    */
 
56  1 toggle @Test(groups = { "Functional" })
57    public void testSelectRefs()
58    {
59  1 assertNull(DBRefUtils.selectRefs(null, null));
60  1 assertNull(DBRefUtils.selectRefs(null, DBRefSource.CODINGDBS));
61   
62  1 DBRefEntry ref1 = new DBRefEntry("EMBL", "1.2", "A12345");
63  1 DBRefEntry ref2 = new DBRefEntry("UNIPROT", "1.2", "A12346");
64    // Source is converted to upper-case by this constructor!
65  1 DBRefEntry ref3 = new DBRefEntry("Uniprot", "1.2", "A12347");
66  1 List<DBRefEntry> dbrefs = Arrays
67    .asList(new DBRefEntry[]
68    { ref1, ref2, ref3 });
69  1 String[] sources = new String[] { "EMBL", "UNIPROT" };
70   
71  1 List<DBRefEntry> selected = DBRefUtils.selectRefs(dbrefs, sources);
72  1 assertEquals(3, selected.size());
73  1 assertSame(ref1, selected.get(0));
74  1 assertSame(ref2, selected.get(1));
75  1 assertSame(ref3, selected.get(2));
76   
77  1 sources = new String[] { "EMBL" };
78  1 selected = DBRefUtils.selectRefs(dbrefs, sources);
79  1 assertEquals(1, selected.size());
80  1 assertSame(ref1, selected.get(0));
81   
82  1 sources = new String[] { "UNIPROT" };
83  1 selected = DBRefUtils.selectRefs(dbrefs, sources);
84  1 assertEquals(2, selected.size());
85  1 assertSame(ref2, selected.get(0));
86  1 assertSame(ref3, selected.get(1));
87   
88  1 sources = new String[] { "EMBLCDS" };
89  1 selected = DBRefUtils.selectRefs(dbrefs, sources);
90  1 assertNull(selected);
91   
92  1 sources = new String[] { "embl", "uniprot" };
93  1 selected = DBRefUtils.selectRefs(dbrefs, sources);
94  1 assertEquals(3, selected.size());
95  1 assertSame(ref1, selected.get(0));
96  1 assertSame(ref2, selected.get(1));
97  1 assertSame(ref3, selected.get(2));
98    }
99   
100    /**
101    * Test the method that converts (currently three) database names to a
102    * canonical name (not case-sensitive)
103    */
 
104  1 toggle @Test(groups = { "Functional" })
105    public void testGetCanonicalName()
106    {
107  1 assertNull(DBRefUtils.getCanonicalName(null));
108  1 assertEquals("", DBRefUtils.getCanonicalName(""));
109  1 assertEquals("PDB", DBRefUtils.getCanonicalName("pdb"));
110  1 assertEquals("PDB", DBRefUtils.getCanonicalName("Pdb"));
111  1 assertEquals("UNIPROT",
112    DBRefUtils.getCanonicalName("uniprotkb/swiss-prot"));
113  1 assertEquals("UNIPROT",
114    DBRefUtils.getCanonicalName("uniprotkb/trembl"));
115  1 assertEquals("UNIPROT",
116    DBRefUtils.getCanonicalName("UNIPROTKB/SWISS-PROT"));
117  1 assertEquals("UNIPROT",
118    DBRefUtils.getCanonicalName("UNIPROTKB/TREMBL"));
119  1 assertEquals("UNIPROTKB/SWISS-CHEESE",
120    DBRefUtils.getCanonicalName("UNIPROTKB/SWISS-CHEESE"));
121  1 assertEquals("ENSEMBL", DBRefUtils.getCanonicalName("Ensembl"));
122   
123    // these are not 'known' to Jalview
124  1 assertEquals("PFAM", DBRefUtils.getCanonicalName("PFAM"));
125  1 assertEquals("pfam", DBRefUtils.getCanonicalName("pfam"));
126   
127    }
128   
129    /**
130    * Test 'parsing' a DBRef - non PDB case
131    */
 
132  1 toggle @Test(groups = { "Functional" })
133    public void testParseToDbRef()
134    {
135  1 SequenceI seq = new Sequence("Seq1", "ABCD");
136  1 DBRefEntry ref = DBRefUtils.parseToDbRef(seq, "EMBL", "1.2", "a7890");
137  1 List<DBRefEntry> refs = seq.getDBRefs();
138  1 assertEquals(1, refs.size());
139  1 assertSame(ref, refs.get(0));
140  1 assertEquals("EMBL", ref.getSource());
141  1 assertEquals("1.2", ref.getVersion());
142  1 assertEquals("a7890", ref.getAccessionId());
143  1 assertTrue(seq.getAllPDBEntries().isEmpty());
144  1 SequenceI seq2 = new Sequence("Seq2", "ABCD");
145    // Check that whitespace doesn't confuse parseToDbRef
146  1 DBRefEntry ref2 = DBRefUtils.parseToDbRef(seq2, "EMBL", "1.2",
147    " a7890");
148  1 assertEquals(ref, ref2);
149    }
150   
151    /**
152    * Test 'parsing' a DBRef - Stockholm PDB format
153    */
 
154  1 toggle @Test(groups = { "Functional" })
155    public void testParseToDbRef_PDB()
156    {
157  1 SequenceI seq = new Sequence("Seq1", "ABCD");
158  1 DBRefEntry ref = DBRefUtils.parseToDbRef(seq, "pdb", "1.2",
159    "1WRI A; 7-80;");
160    // TODO: correct PDBEntry and PDB DBRef accessions need to be generated for
161    // PDB ref in Stockholm
162   
163  1 List<DBRefEntry> refs = seq.getDBRefs();
164  1 assertEquals(1, refs.size());
165  1 assertSame(ref, refs.get(0));
166  1 assertEquals("PDB", ref.getSource());
167  1 assertEquals("1.2", ref.getVersion());
168    // DBRef id is pdbId + chain code
169  1 assertEquals("1WRIA", ref.getAccessionId());
170  1 assertEquals(1, seq.getAllPDBEntries().size());
171  1 PDBEntry pdbRef = seq.getAllPDBEntries().get(0);
172  1 assertEquals("1WRI", pdbRef.getId());
173  1 assertNull(pdbRef.getFile());
174  1 assertEquals("A", pdbRef.getChainCode());
175  1 assertEquals("PDB", pdbRef.getType());
176    }
177   
178    /**
179    * Test the method that searches for matches references - case when we are
180    * matching a reference with no mappings
181    */
 
182  1 toggle @Test(groups = { "Functional" })
183    public void testSearchRefs_noMapping()
184    {
185  1 DBRefEntry target = new DBRefEntry("EMBL", "2", "A1234");
186   
187  1 DBRefEntry ref1 = new DBRefEntry("EMBL", "1", "A1234"); // matches
188    // constructor changes embl to EMBL
189  1 DBRefEntry ref2 = new DBRefEntry("embl", "1", "A1234"); // matches
190    // constructor does not upper-case accession id
191  1 DBRefEntry ref3 = new DBRefEntry("EMBL", "1", "a1234"); // no match
192  1 DBRefEntry ref4 = new DBRefEntry("EMBLCDS", "1", "A1234"); // no match
193    // ref5 matches although it has a mapping - ignored
194  1 DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1234");
195  1 ref5.setMap(
196    new Mapping(new MapList(new int[]
197    { 1, 1 }, new int[] { 1, 1 }, 1, 1)));
198   
199  1 List<DBRefEntry> matches = DBRefUtils
200    .searchRefs(Arrays.asList(new DBRefEntry[]
201    { ref1, ref2, ref3, ref4, ref5 }), target,
202    DBRefUtils.SEARCH_MODE_FULL);
203  1 assertEquals(3, matches.size());
204  1 assertSame(ref1, matches.get(0));
205  1 assertSame(ref2, matches.get(1));
206  1 assertSame(ref5, matches.get(2));
207    }
208   
209    /**
210    * Test the method that searches for matches references - case when we are
211    * matching a reference with a mapping
212    */
 
213  1 toggle @Test(groups = { "Functional" })
214    public void testSearchRefs_withMapping()
215    {
216  1 DBRefEntry target = new DBRefEntry("EMBL", "2", "A1234");
217  1 final Mapping map1 = new Mapping(
218    new MapList(new int[]
219    { 1, 1 }, new int[] { 1, 1 }, 1, 1));
220  1 target.setMap(map1);
221   
222    // these all match target iff mappings match
223  1 DBRefEntry ref1 = new DBRefEntry("EMBL", "1", "A1234"); // no map: matches
224  1 DBRefEntry ref2 = new DBRefEntry("EMBL", "1", "A1234"); // =map: matches
225  1 final Mapping map2 = new Mapping(
226    new MapList(new int[]
227    { 1, 1 }, new int[] { 1, 1 }, 1, 1));
228  1 ref2.setMap(map2);
229   
230    // different map: no match
231  1 DBRefEntry ref3 = new DBRefEntry("EMBL", "1", "A1234");
232  1 final Mapping map3 = new Mapping(
233    new MapList(new int[]
234    { 1, 1 }, new int[] { 1, 1 }, 2, 2));
235  1 ref3.setMap(map3);
236   
237  1 List<DBRefEntry> matches = DBRefUtils
238    .searchRefs(Arrays.asList(new DBRefEntry[]
239    { ref1, ref2, ref3 }), target, DBRefUtils.SEARCH_MODE_FULL);
240  1 assertEquals(2, matches.size());
241  1 assertSame(ref1, matches.get(0));
242  1 assertSame(ref2, matches.get(1));
243    }
244   
245    /**
246    * Test the method that searches for matching references based on accession id
247    * only
248    */
 
249  1 toggle @Test(groups = { "Functional" })
250    public void testSearchRefs_accessionid()
251    {
252   
253  1 DBRefEntry ref1 = new DBRefEntry("Uniprot", "1", "A1234"); // matches
254  1 DBRefEntry ref2 = new DBRefEntry("embl", "1", "A1234"); // matches
255    // constructor does not upper-case accession id
256  1 DBRefEntry ref3 = new DBRefEntry("EMBL", "1", "a1234"); // no match
257  1 DBRefEntry ref4 = new DBRefEntry("EMBLCDS", "1", "A1235"); // no match
258    // ref5 matches although it has a mapping - ignored
259  1 DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1234");
260  1 ref5.setMap(
261    new Mapping(new MapList(new int[]
262    { 1, 1 }, new int[] { 1, 1 }, 1, 1)));
263   
264  1 List<DBRefEntry> dbrefs = Arrays
265    .asList(new DBRefEntry[]
266    { ref1, ref2, ref3, ref4, ref5 });
267  1 List<DBRefEntry> matches = DBRefUtils.searchRefs(dbrefs, "A1234");
268  1 assertEquals(3, matches.size());
269  1 assertSame(ref1, matches.get(0));
270  1 assertSame(ref2, matches.get(1));
271  1 assertSame(ref5, matches.get(2));
272    }
273   
274    /**
275    * Test the method that searches for matches references - case when we are
276    * matching a reference with null (any) accession id
277    */
 
278  1 toggle @Test(groups = { "Functional" })
279    public void testSearchRefs_wildcardAccessionid()
280    {
281  1 DBRefEntry target = new DBRefEntry("EMBL", "2", null);
282   
283  1 DBRefEntry ref1 = new DBRefEntry("EMBL", "1", "A1234"); // matches
284    // constructor changes embl to EMBL
285  1 DBRefEntry ref2 = new DBRefEntry("embl", "1", "A1235"); // matches
286    // constructor does not upper-case accession id
287  1 DBRefEntry ref3 = new DBRefEntry("EMBL", "1", "A1236"); // matches
288  1 DBRefEntry ref4 = new DBRefEntry("EMBLCDS", "1", "A1234"); // no match
289    // ref5 matches although it has a mapping - ignored
290  1 DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1237");
291  1 ref5.setMap(
292    new Mapping(new MapList(new int[]
293    { 1, 1 }, new int[] { 1, 1 }, 1, 1)));
294   
295  1 List<DBRefEntry> matches = DBRefUtils
296    .searchRefs(Arrays.asList(new DBRefEntry[]
297    { ref1, ref2, ref3, ref4, ref5 }), target,
298    DBRefUtils.SEARCH_MODE_FULL);
299  1 assertEquals(4, matches.size());
300  1 assertSame(ref1, matches.get(0));
301  1 assertSame(ref2, matches.get(1));
302  1 assertSame(ref3, matches.get(2));
303  1 assertSame(ref5, matches.get(3));
304    }
305    }