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.jbgui.GStructureChooser.FilterOption;
34 import jalview.ws.params.InvalidArgumentException;
36 import java.util.Collection;
37 import java.util.Vector;
39 import org.testng.annotations.AfterMethod;
40 import org.testng.annotations.BeforeClass;
41 import org.testng.annotations.BeforeMethod;
42 import org.testng.annotations.Test;
44 import junit.extensions.PA;
46 public class StructureChooserTest
49 @BeforeClass(alwaysRun = true)
50 public void setUpJvOptionPane()
52 JvOptionPane.setInteractiveMode(false);
53 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
58 @BeforeMethod(alwaysRun = true)
59 public void setUp() throws Exception
61 seq = new Sequence("PDB|4kqy|4KQY|A", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1,
63 seq.createDatasetSequence();
64 for (int x = 1; x < 5; x++)
66 DBRefEntry dbRef = new DBRefEntry();
67 dbRef.setAccessionId("XYZ_" + x);
71 PDBEntry dbRef = new PDBEntry();
74 Vector<PDBEntry> pdbIds = new Vector<>();
80 @AfterMethod(alwaysRun = true)
81 public void tearDown() throws Exception
86 @Test(groups = { "Functional" })
87 public void buildQueryTest()
89 String query = StructureChooser.buildQuery(seq);
90 assertEquals("pdb_id:1tim", query);
91 System.out.println("seq >>>> " + seq);
92 seq.getAllPDBEntries().clear();
93 query = StructureChooser.buildQuery(seq);
95 "text:XYZ_1 OR text:XYZ_2 OR text:XYZ_3 OR text:XYZ_4 OR text:4kqy",
98 query = StructureChooser.buildQuery(seq);
99 assertEquals("text:4kqy", query);
101 DBRefEntry uniprotDBRef = new DBRefEntry();
102 uniprotDBRef.setAccessionId("P12345");
103 uniprotDBRef.setSource(DBRefSource.UNIPROT);
104 seq.addDBRef(uniprotDBRef);
106 DBRefEntry pdbDBRef = new DBRefEntry();
107 pdbDBRef.setAccessionId("1XYZ");
108 pdbDBRef.setSource(DBRefSource.PDB);
109 seq.addDBRef(pdbDBRef);
111 for (int x = 1; x < 5; x++)
113 DBRefEntry dbRef = new DBRefEntry();
114 dbRef.setAccessionId("XYZ_" + x);
117 query = StructureChooser.buildQuery(seq);
119 "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
123 @Test(groups = { "Functional" })
124 public void populateFilterComboBoxTest() throws InterruptedException
126 SequenceI[] selectedSeqs = new SequenceI[] { seq };
127 StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
128 sc.populateFilterComboBox(false, false);
129 int optionsSize = sc.getCmbFilterOption().getItemCount();
130 assertEquals(2, optionsSize); // if structures are not discovered then don't
131 // populate filter options
133 sc.populateFilterComboBox(true, false);
134 optionsSize = sc.getCmbFilterOption().getItemCount();
135 assertTrue(optionsSize > 3); // if structures are found, filter options
136 // should be populated
138 sc.populateFilterComboBox(true, true);
139 assertTrue(sc.getCmbFilterOption().getSelectedItem() != null);
140 FilterOption filterOpt = (FilterOption) sc.getCmbFilterOption()
142 assertEquals("Cached Structures", filterOpt.getName());
145 @Test(groups = { "Network" })
146 public void fetchStructuresInfoTest()
148 SequenceI[] selectedSeqs = new SequenceI[] { seq };
149 StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
150 sc.fetchStructuresMetaData();
151 Collection<FTSData> ss = (Collection<FTSData>) PA.getValue(sc,
152 "discoveredStructuresSet");
154 assertTrue(ss.size() > 0);
158 @Test(groups = { "Functional" })
159 public void sanitizeSeqNameTest()
161 String name = "ab_cdEF|fwxyz012349";
162 assertEquals(name, StructureChooser.sanitizeSeqName(name));
164 // remove a [nn] substring
165 name = "abcde12[345]fg";
166 assertEquals("abcde12fg", StructureChooser.sanitizeSeqName(name));
168 // remove characters other than a-zA-Z0-9 | or _
169 name = "ab[cd],.\t£$*!- \\\"@:e";
170 assertEquals("abcde", StructureChooser.sanitizeSeqName(name));
172 name = "abcde12[345a]fg";
173 assertEquals("abcde12345afg", StructureChooser.sanitizeSeqName(name));