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.gui.structurechooser.PDBStructureChooserQuerySource;
34 import jalview.gui.structurechooser.StructureChooserQuerySource;
35 import jalview.gui.structurechooser.ThreeDBStructureChooserQuerySource;
36 import jalview.jbgui.FilterOption;
37 import jalview.ws.params.InvalidArgumentException;
39 import java.util.Collection;
40 import java.util.Vector;
42 import org.testng.annotations.AfterMethod;
43 import org.testng.annotations.BeforeClass;
44 import org.testng.annotations.BeforeMethod;
45 import org.testng.annotations.Test;
47 import junit.extensions.PA;
49 public class StructureChooserTest
52 @BeforeClass(alwaysRun = true)
53 public void setUpJvOptionPane()
55 JvOptionPane.setInteractiveMode(false);
56 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
61 @BeforeMethod(alwaysRun = true)
62 public void setUp() throws Exception
64 seq = new Sequence("PDB|4kqy|4KQY|A", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1,
66 seq.createDatasetSequence();
67 for (int x = 1; x < 5; x++)
69 DBRefEntry dbRef = new DBRefEntry();
70 dbRef.setAccessionId("XYZ_" + x);
74 PDBEntry dbRef = new PDBEntry();
77 Vector<PDBEntry> pdbIds = new Vector<>();
83 @AfterMethod(alwaysRun = true)
84 public void tearDown() throws Exception
89 @SuppressWarnings("deprecation")
90 @Test(groups = { "Functional" })
91 public void buildQueryTest()
93 System.out.println("seq >>>> " + seq);
95 StructureChooserQuerySource scquery = StructureChooserQuerySource.getQuerySourceFor(new SequenceI[] { seq});
96 assertTrue(scquery instanceof PDBStructureChooserQuerySource);
97 String query = scquery.buildQuery(seq);
98 assertEquals("pdb_id:1tim", query);
99 seq.getAllPDBEntries().clear();
100 query = scquery.buildQuery(seq);
102 "text:XYZ_1 OR text:XYZ_2 OR text:XYZ_3 OR text:XYZ_4 OR text:4kqy",
105 query = scquery.buildQuery(seq);
106 System.out.println(query);
107 assertEquals("text:4kqy", query);
109 DBRefEntry uniprotDBRef = new DBRefEntry();
110 uniprotDBRef.setAccessionId("P12345");
111 uniprotDBRef.setSource(DBRefSource.UNIPROT);
112 seq.addDBRef(uniprotDBRef);
114 DBRefEntry pdbDBRef = new DBRefEntry();
115 pdbDBRef.setAccessionId("1XYZ");
116 pdbDBRef.setSource(DBRefSource.PDB);
117 seq.addDBRef(pdbDBRef);
119 for (int x = 1; x < 5; x++)
121 DBRefEntry dbRef = new DBRefEntry();
122 dbRef.setAccessionId("XYZ_" + x);
125 System.out.println("");
126 System.out.println(seq.getDBRefs());
127 System.out.println(query);
128 query = scquery.buildQuery(seq);
130 "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
134 @Test(groups = { "Functional" })
135 public void populateFilterComboBoxTest() throws InterruptedException
137 SequenceI[] selectedSeqs = new SequenceI[] { seq };
138 StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
139 sc.populateFilterComboBox(false, false);
140 int optionsSize = sc.getCmbFilterOption().getItemCount();
141 assertEquals(2, optionsSize); // if structures are not discovered then don't
142 // populate filter options
144 sc.populateFilterComboBox(true, false);
145 optionsSize = sc.getCmbFilterOption().getItemCount();
146 assertTrue(optionsSize > 3); // if structures are found, filter options
147 // should be populated
149 sc.populateFilterComboBox(true, true);
150 assertTrue(sc.getCmbFilterOption().getSelectedItem() != null);
151 FilterOption filterOpt = (FilterOption) sc.getCmbFilterOption()
153 assertEquals("Cached Structures", filterOpt.getName());
156 @Test(groups = { "Network" })
157 public void fetchStructuresInfoTest()
159 SequenceI[] selectedSeqs = new SequenceI[] { seq };
160 StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
161 sc.fetchStructuresMetaData();
162 Collection<FTSData> ss = (Collection<FTSData>) PA.getValue(sc,
163 "discoveredStructuresSet");
165 assertTrue(ss.size() > 0);
169 @Test(groups = { "Functional" })
170 public void sanitizeSeqNameTest()
172 String name = "ab_cdEF|fwxyz012349";
173 assertEquals(name, PDBStructureChooserQuerySource.sanitizeSeqName(name));
175 // remove a [nn] substring
176 name = "abcde12[345]fg";
177 assertEquals("abcde12fg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
179 // remove characters other than a-zA-Z0-9 | or _
180 name = "ab[cd],.\t£$*!- \\\"@:e";
181 assertEquals("abcde", PDBStructureChooserQuerySource.sanitizeSeqName(name));
183 name = "abcde12[345a]fg";
184 assertEquals("abcde12345afg", PDBStructureChooserQuerySource.sanitizeSeqName(name));