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 java.util.Collection;
28 import java.util.Vector;
30 import org.testng.annotations.AfterMethod;
31 import org.testng.annotations.BeforeClass;
32 import org.testng.annotations.BeforeMethod;
33 import org.testng.annotations.Test;
35 import jalview.datamodel.DBRefEntry;
36 import jalview.datamodel.DBRefSource;
37 import jalview.datamodel.PDBEntry;
38 import jalview.datamodel.Sequence;
39 import jalview.datamodel.SequenceI;
40 import jalview.fts.api.FTSData;
41 import jalview.jbgui.GStructureChooser.FilterOption;
42 import junit.extensions.PA;
44 public class StructureChooserTest
47 @BeforeClass(alwaysRun = true)
48 public void setUpJvOptionPane()
50 JvOptionPane.setInteractiveMode(false);
51 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
56 @BeforeMethod(alwaysRun = true)
57 public void setUp() throws Exception
59 seq = new Sequence("PDB|4kqy|4KQY|A", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1,
61 seq.createDatasetSequence();
62 for (int x = 1; x < 5; x++)
64 DBRefEntry dbRef = new DBRefEntry();
65 dbRef.setAccessionId("XYZ_" + x);
69 PDBEntry dbRef = new PDBEntry();
72 Vector<PDBEntry> pdbIds = new Vector<>();
78 @AfterMethod(alwaysRun = true)
79 public void tearDown() throws Exception
84 @Test(groups = { "Functional" })
85 public void buildQueryTest()
87 String query = StructureChooser.buildQuery(seq);
88 assertEquals("pdb_id:1tim", query);
89 System.out.println("seq >>>> " + seq);
90 seq.getAllPDBEntries().clear();
91 query = StructureChooser.buildQuery(seq);
93 "text:XYZ_1 OR text:XYZ_2 OR text:XYZ_3 OR text:XYZ_4 OR text:4kqy",
96 query = StructureChooser.buildQuery(seq);
97 assertEquals("text:4kqy", query);
99 DBRefEntry uniprotDBRef = new DBRefEntry();
100 uniprotDBRef.setAccessionId("P12345");
101 uniprotDBRef.setSource(DBRefSource.UNIPROT);
102 seq.addDBRef(uniprotDBRef);
104 DBRefEntry pdbDBRef = new DBRefEntry();
105 pdbDBRef.setAccessionId("1XYZ");
106 pdbDBRef.setSource(DBRefSource.PDB);
107 seq.addDBRef(pdbDBRef);
109 for (int x = 1; x < 5; x++)
111 DBRefEntry dbRef = new DBRefEntry();
112 dbRef.setAccessionId("XYZ_" + x);
115 query = StructureChooser.buildQuery(seq);
117 "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
121 @Test(groups = { "Functional" })
122 public void populateFilterComboBoxTest() throws InterruptedException
124 SequenceI[] selectedSeqs = new SequenceI[] { seq };
125 StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
126 sc.populateFilterComboBox(false, false);
127 int optionsSize = sc.getCmbFilterOption().getItemCount();
128 assertEquals(2, optionsSize); // if structures are not discovered then don't
129 // populate filter options
131 sc.populateFilterComboBox(true, false);
132 optionsSize = sc.getCmbFilterOption().getItemCount();
133 assertTrue(optionsSize > 3); // if structures are found, filter options
134 // should be populated
136 sc.populateFilterComboBox(true, true);
137 assertTrue(sc.getCmbFilterOption().getSelectedItem() != null);
138 FilterOption filterOpt = (FilterOption) sc.getCmbFilterOption()
140 assertEquals("Cached Structures", filterOpt.getName());
143 @Test(groups = { "Network" })
144 public void fetchStructuresInfoTest()
146 SequenceI[] selectedSeqs = new SequenceI[] { seq };
147 StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
148 sc.fetchStructuresMetaData();
149 Collection<FTSData> ss = (Collection<FTSData>) PA.getValue(sc,
150 "discoveredStructuresSet");
152 assertTrue(ss.size() > 0);
156 @Test(groups = { "Functional" })
157 public void sanitizeSeqNameTest()
159 String name = "ab_cdEF|fwxyz012349";
160 assertEquals(name, StructureChooser.sanitizeSeqName(name));
162 // remove a [nn] substring
163 name = "abcde12[345]fg";
164 assertEquals("abcde12fg", StructureChooser.sanitizeSeqName(name));
166 // remove characters other than a-zA-Z0-9 | or _
167 name = "ab[cd],.\t£$*!- \\\"@:e";
168 assertEquals("abcde", StructureChooser.sanitizeSeqName(name));
170 name = "abcde12[345a]fg";
171 assertEquals("abcde12345afg", StructureChooser.sanitizeSeqName(name));