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;
35 import java.util.Collection;
36 import java.util.Vector;
38 import org.testng.annotations.AfterMethod;
39 import org.testng.annotations.BeforeClass;
40 import org.testng.annotations.BeforeMethod;
41 import org.testng.annotations.Test;
43 import junit.extensions.PA;
45 public class StructureChooserTest
48 @BeforeClass(alwaysRun = true)
49 public void setUpJvOptionPane()
51 JvOptionPane.setInteractiveMode(false);
52 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
57 @BeforeMethod(alwaysRun = true)
58 public void setUp() throws Exception
60 seq = new Sequence("PDB|4kqy|4KQY|A", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1,
62 seq.createDatasetSequence();
63 for (int x = 1; x < 5; x++)
65 DBRefEntry dbRef = new DBRefEntry();
66 dbRef.setAccessionId("XYZ_" + x);
70 PDBEntry dbRef = new PDBEntry();
73 Vector<PDBEntry> pdbIds = new Vector<>();
79 @AfterMethod(alwaysRun = true)
80 public void tearDown() throws Exception
85 @Test(groups = { "Functional" })
86 public void buildQueryTest()
88 String query = StructureChooser.buildQuery(seq);
89 assertEquals("pdb_id:1tim", query);
90 System.out.println("seq >>>> " + seq);
91 seq.getAllPDBEntries().clear();
92 query = StructureChooser.buildQuery(seq);
94 "text:XYZ_1 OR text:XYZ_2 OR text:XYZ_3 OR text:XYZ_4 OR text:4kqy",
97 query = StructureChooser.buildQuery(seq);
98 assertEquals("text:4kqy", query);
100 DBRefEntry uniprotDBRef = new DBRefEntry();
101 uniprotDBRef.setAccessionId("P12345");
102 uniprotDBRef.setSource(DBRefSource.UNIPROT);
103 seq.addDBRef(uniprotDBRef);
105 DBRefEntry pdbDBRef = new DBRefEntry();
106 pdbDBRef.setAccessionId("1XYZ");
107 pdbDBRef.setSource(DBRefSource.PDB);
108 seq.addDBRef(pdbDBRef);
110 for (int x = 1; x < 5; x++)
112 DBRefEntry dbRef = new DBRefEntry();
113 dbRef.setAccessionId("XYZ_" + x);
116 query = StructureChooser.buildQuery(seq);
118 "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
122 @Test(groups = { "Functional" })
123 public void populateFilterComboBoxTest() throws InterruptedException
125 SequenceI[] selectedSeqs = new SequenceI[] { seq };
126 StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
127 sc.populateFilterComboBox(false, false);
128 int optionsSize = sc.getCmbFilterOption().getItemCount();
129 assertEquals(2, optionsSize); // if structures are not discovered then don't
130 // populate filter options
132 sc.populateFilterComboBox(true, false);
133 optionsSize = sc.getCmbFilterOption().getItemCount();
134 assertTrue(optionsSize > 3); // if structures are found, filter options
135 // should be populated
137 sc.populateFilterComboBox(true, true);
138 assertTrue(sc.getCmbFilterOption().getSelectedItem() != null);
139 FilterOption filterOpt = (FilterOption) sc.getCmbFilterOption()
141 assertEquals("Cached Structures", filterOpt.getName());
144 @Test(groups = { "Network" })
145 public void fetchStructuresInfoTest()
147 SequenceI[] selectedSeqs = new SequenceI[] { seq };
148 StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
149 sc.fetchStructuresMetaData();
150 Collection<FTSData> ss = (Collection<FTSData>) PA.getValue(sc,
151 "discoveredStructuresSet");
153 assertTrue(ss.size() > 0);
157 @Test(groups = { "Functional" })
158 public void sanitizeSeqNameTest()
160 String name = "ab_cdEF|fwxyz012349";
161 assertEquals(name, StructureChooser.sanitizeSeqName(name));
163 // remove a [nn] substring
164 name = "abcde12[345]fg";
165 assertEquals("abcde12fg", StructureChooser.sanitizeSeqName(name));
167 // remove characters other than a-zA-Z0-9 | or _
168 name = "ab[cd],.\t£$*!- \\\"@:e";
169 assertEquals("abcde", StructureChooser.sanitizeSeqName(name));
171 name = "abcde12[345a]fg";
172 assertEquals("abcde12345afg", StructureChooser.sanitizeSeqName(name));