2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
23 import static org.testng.AssertJUnit.assertEquals;
24 import static org.testng.AssertJUnit.assertNotNull;
25 import static org.testng.AssertJUnit.assertTrue;
27 import jalview.datamodel.DBRefEntry;
28 import jalview.datamodel.DBRefSource;
29 import jalview.datamodel.PDBEntry;
30 import jalview.datamodel.Sequence;
31 import jalview.datamodel.SequenceI;
32 import jalview.fts.api.FTSData;
33 import jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient;
34 import jalview.fts.threedbeacons.TDBeaconsFTSRestClientTest;
35 import jalview.gui.structurechooser.PDBStructureChooserQuerySource;
36 import jalview.gui.structurechooser.StructureChooserQuerySource;
37 import jalview.gui.structurechooser.ThreeDBStructureChooserQuerySource;
38 import jalview.jbgui.FilterOption;
39 import jalview.ws.params.InvalidArgumentException;
41 import java.util.Collection;
42 import java.util.Vector;
44 import org.testng.annotations.AfterMethod;
45 import org.testng.annotations.BeforeClass;
46 import org.testng.annotations.BeforeMethod;
47 import org.testng.annotations.Test;
49 import junit.extensions.PA;
51 public class StructureChooserTest
54 @BeforeClass(alwaysRun = true)
55 public void setUpJvOptionPane()
57 JvOptionPane.setInteractiveMode(false);
58 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
63 @BeforeMethod(alwaysRun = true)
64 public void setUp() throws Exception
66 seq = new Sequence("PDB|4kqy|4KQY|A", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1,
68 seq.createDatasetSequence();
69 for (int x = 1; x < 5; x++)
71 DBRefEntry dbRef = new DBRefEntry();
72 dbRef.setAccessionId("XYZ_" + x);
76 PDBEntry dbRef = new PDBEntry();
79 Vector<PDBEntry> pdbIds = new Vector<>();
84 // Uniprot sequence for 3D-Beacons mocks
85 upSeq = new Sequence("P38398",
86 "MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRS\n"
87 + "LQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNRAKRLLQSEPEN\n"
88 + "PSLQETSLSVQLSNLGTVRTLRTKQRIQPQKTSVYIELGSDSSEDTVNKATYCSVGDQELLQITPQGTRDEI\n"
89 + "SLDSAKKAACEFSETDVTNTEHHQPSNNDLNTTEKRAAERHPEKYQGSSVSNLHVEPCGTNTHASSLQHENS\n"
90 + "SLLLTKDRMNVEKAEFCNKSKQPGLARSQHNRWAGSKETCNDRRTPSTEKKVDLNADPLCERKEWNKQKLPC\n"
91 + "SENPRDTEDVPWITLNSSIQKVNEWFSRSDELLGSDDSHDGESESNAKVADVLDVLNEVDEYSGSSEKIDLL\n"
92 + "ASDPHEALICKSERVHSKSVESNIEDKIFGKTYRKKASLPNLSHVTENLIIGAFVTEPQIIQERPLTNKLKR\n"
93 + "KRRPTSGLHPEDFIKKADLAVQKTPEMINQGTNQTEQNGQVMNITNSGHENKTKGDSIQNEKNPNPIESLEK\n"
94 + "ESAFKTKAEPISSSISNMELELNIHNSKAPKKNRLRRKSSTRHIHALELVVSRNLSPPNCTELQIDSCSSSE\n"
95 + "EIKKKKYNQMPVRHSRNLQLMEGKEPATGAKKSNKPNEQTSKRHDSDTFPELKLTNAPGSFTKCSNTSELKE\n"
96 + "FVNPSLPREEKEEKLETVKVSNNAEDPKDLMLSGERVLQTERSVESSSISLVPGTDYGTQESISLLEVSTLG\n"
97 + "KAKTEPNKCVSQCAAFENPKGLIHGCSKDNRNDTEGFKYPLGHEVNHSRETSIEMEESELDAQYLQNTFKVS\n"
98 + "KRQSFAPFSNPGNAEEECATFSAHSGSLKKQSPKVTFECEQKEENQGKNESNIKPVQTVNITAGFPVVGQKD\n"
99 + "KPVDNAKCSIKGGSRFCLSSQFRGNETGLITPNKHGLLQNPYRIPPLFPIKSFVKTKCKKNLLEENFEEHSM\n"
100 + "SPEREMGNENIPSTVSTISRNNIRENVFKEASSSNINEVGSSTNEVGSSINEIGSSDENIQAELGRNRGPKL\n"
101 + "NAMLRLGVLQPEVYKQSLPGSNCKHPEIKKQEYEEVVQTVNTDFSPYLISDNLEQPMGSSHASQVCSETPDD\n"
102 + "LLDDGEIKEDTSFAENDIKESSAVFSKSVQKGELSRSPSPFTHTHLAQGYRRGAKKLESSEENLSSEDEELP\n"
103 + "CFQHLLFGKVNNIPSQSTRHSTVATECLSKNTEENLLSLKNSLNDCSNQVILAKASQEHHLSEETKCSASLF\n"
104 + "SSQCSELEDLTANTNTQDPFLIGSSKQMRHQSESQGVGLSDKELVSDDEERGTGLEENNQEEQSMDSNLGEA\n"
105 + "ASGCESETSVSEDCSGLSSQSDILTTQQRDTMQHNLIKLQQEMAELEAVLEQHGSQPSNSYPSIISDSSALE\n"
106 + "DLRNPEQSTSEKAVLTSQKSSEYPISQNPEGLSADKFEVSADSSTSKNKEPGVERSSPSKCPSLDDRWYMHS\n"
107 + "CSGSLQNRNYPSQEELIKVVDVEEQQLEESGPHDLTETSYLPRQDLEGTPYLESGISLFSDDPESDPSEDRA\n"
108 + "PESARVGNIPSSTSALKVPQLKVAESAQSPAAAHTTDTAGYNAMEESVSREKPELTASTERVNKRMSMVVSG\n"
109 + "LTPEEFMLVYKFARKHHITLTNLITEETTHVVMKTDAEFVCERTLKYFLGIAGGKWVVSYFWVTQSIKERKM\n"
110 + "LNEHDFEVRGDVVNGRNHQGPKRARESQDRKIFRGLEICCYGPFTNMPTDQLEWMVQLCGASVVKELSSFTL\n"
111 + "GTGVHPIVVVQPDAWTEDNGFHAIGQMCEAPVVTREWVLDSVALYQCQELDTYLIPQIPHSHY\n"
114 upSeq.createDatasetSequence();
115 upSeq.setDescription("Breast cancer type 1 susceptibility protein");
116 upSeq.addDBRef(new DBRefEntry("UNIPROT","0","P38398",null,true));
119 @AfterMethod(alwaysRun = true)
120 public void tearDown() throws Exception
126 @SuppressWarnings("deprecation")
127 @Test(groups = { "Functional" })
128 public void buildQueryTest()
130 System.out.println("seq >>>> " + seq);
132 StructureChooserQuerySource scquery = StructureChooserQuerySource.getQuerySourceFor(new SequenceI[] { seq});
133 assertTrue(scquery instanceof PDBStructureChooserQuerySource);
134 String query = scquery.buildQuery(seq);
135 assertEquals("pdb_id:1tim", query);
136 seq.getAllPDBEntries().clear();
137 query = scquery.buildQuery(seq);
139 "text:XYZ_1 OR text:XYZ_2 OR text:XYZ_3 OR text:XYZ_4 OR text:4kqy",
142 query = scquery.buildQuery(seq);
143 System.out.println(query);
144 assertEquals("text:4kqy", query);
146 DBRefEntry uniprotDBRef = new DBRefEntry();
147 uniprotDBRef.setAccessionId("P12345");
148 uniprotDBRef.setSource(DBRefSource.UNIPROT);
149 seq.addDBRef(uniprotDBRef);
151 DBRefEntry pdbDBRef = new DBRefEntry();
152 pdbDBRef.setAccessionId("1XYZ");
153 pdbDBRef.setSource(DBRefSource.PDB);
154 seq.addDBRef(pdbDBRef);
156 for (int x = 1; x < 5; x++)
158 DBRefEntry dbRef = new DBRefEntry();
159 dbRef.setAccessionId("XYZ_" + x);
162 System.out.println("");
163 System.out.println(seq.getDBRefs());
164 System.out.println(query);
165 query = scquery.buildQuery(seq);
167 "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
171 @SuppressWarnings("deprecation")
172 @Test(groups = { "Functional" })
173 public void buildThreeDBQueryTest()
175 System.out.println("seq >>>> " + upSeq);
176 TDBeaconsFTSRestClientTest.setMock();
177 StructureChooserQuerySource scquery = StructureChooserQuerySource.getQuerySourceFor(new SequenceI[] { upSeq});
178 assertTrue(scquery instanceof ThreeDBStructureChooserQuerySource);
179 String query = scquery.buildQuery(upSeq);
180 assertEquals("P38398", query);
182 // query shouldn't change regardless of additional entries
183 // because 3DBeacons requires canonical entries.
184 upSeq.getAllPDBEntries().clear();
185 query = scquery.buildQuery(upSeq);
186 assertEquals("P38398", query);
187 upSeq.setDBRefs(null);
188 query = scquery.buildQuery(upSeq);
190 * legacy projects/datasets will not have canonical flags set for uniprot dbrefs
191 * graceful behaviour would be to
192 * - pick one ? not possible
193 * - iterate through all until a 200 is obtained ?
194 * ---> ideal but could be costly
195 * ---> better to do a direct retrieval from uniprot to work out which is the canonical identifier..
196 * ----> need a test to check that accessions can be promoted to canonical!
198 assertEquals(null, query);
202 // DBRefEntry uniprotDBRef = new DBRefEntry();
203 // uniprotDBRef.setAccessionId("P12345");
204 // uniprotDBRef.setSource(DBRefSource.UNIPROT);
205 // upSeq.addDBRef(uniprotDBRef);
207 // DBRefEntry pdbDBRef = new DBRefEntry();
208 // pdbDBRef.setAccessionId("1XYZ");
209 // pdbDBRef.setSource(DBRefSource.PDB);
210 // upSeq.addDBRef(pdbDBRef);
212 // for (int x = 1; x < 5; x++)
214 // DBRefEntry dbRef = new DBRefEntry();
215 // dbRef.setAccessionId("XYZ_" + x);
216 // seq.addDBRef(dbRef);
218 // System.out.println("");
219 // System.out.println(seq.getDBRefs());
220 // System.out.println(query);
221 // query = scquery.buildQuery(seq);
223 // "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
228 @Test(groups = { "Functional" })
229 public void populateFilterComboBoxTest() throws InterruptedException
231 SequenceI[] selectedSeqs = new SequenceI[] { seq };
232 StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
233 sc.populateFilterComboBox(false, false);
234 int optionsSize = sc.getCmbFilterOption().getItemCount();
235 assertEquals(2, optionsSize); // if structures are not discovered then don't
236 // populate filter options
238 sc.populateFilterComboBox(true, false);
239 optionsSize = sc.getCmbFilterOption().getItemCount();
240 assertTrue(optionsSize > 3); // if structures are found, filter options
241 // should be populated
243 sc.populateFilterComboBox(true, true);
244 assertTrue(sc.getCmbFilterOption().getSelectedItem() != null);
245 FilterOption filterOpt = (FilterOption) sc.getCmbFilterOption()
247 assertEquals("Cached Structures", filterOpt.getName());
250 @Test(groups = { "Network" })
251 public void fetchStructuresInfoTest()
253 SequenceI[] selectedSeqs = new SequenceI[] { seq };
254 StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
255 sc.fetchStructuresMetaData();
256 Collection<FTSData> ss = (Collection<FTSData>) PA.getValue(sc,
257 "discoveredStructuresSet");
259 assertTrue(ss.size() > 0);
263 @Test(groups = { "Functional" })
264 public void sanitizeSeqNameTest()
266 String name = "ab_cdEF|fwxyz012349";
267 assertEquals(name, PDBStructureChooserQuerySource.sanitizeSeqName(name));
269 // remove a [nn] substring
270 name = "abcde12[345]fg";
271 assertEquals("abcde12fg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
273 // remove characters other than a-zA-Z0-9 | or _
274 name = "ab[cd],.\t£$*!- \\\"@:e";
275 assertEquals("abcde", PDBStructureChooserQuerySource.sanitizeSeqName(name));
277 name = "abcde12[345a]fg";
278 assertEquals("abcde12345afg", PDBStructureChooserQuerySource.sanitizeSeqName(name));