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.jbgui.GStructureChooser.FilterOption;
36 import jalview.ws.params.InvalidArgumentException;
38 import java.util.Collection;
39 import java.util.Vector;
41 import org.testng.annotations.AfterMethod;
42 import org.testng.annotations.BeforeClass;
43 import org.testng.annotations.BeforeMethod;
44 import org.testng.annotations.Test;
46 import junit.extensions.PA;
48 public class StructureChooserTest
51 @BeforeClass(alwaysRun = true)
52 public void setUpJvOptionPane()
54 JvOptionPane.setInteractiveMode(false);
55 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
60 @BeforeMethod(alwaysRun = true)
61 public void setUp() throws Exception
63 seq = new Sequence("PDB|4kqy|4KQY|A", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1,
65 seq.createDatasetSequence();
66 for (int x = 1; x < 5; x++)
68 DBRefEntry dbRef = new DBRefEntry();
69 dbRef.setAccessionId("XYZ_" + x);
73 PDBEntry dbRef = new PDBEntry();
76 Vector<PDBEntry> pdbIds = new Vector<>();
82 @AfterMethod(alwaysRun = true)
83 public void tearDown() throws Exception
88 @SuppressWarnings("deprecation")
89 @Test(groups = { "Functional" })
90 public void buildQueryTest()
92 System.out.println("seq >>>> " + seq);
93 StructureChooserQuerySource scquery = StructureChooserQuerySource.getPDBfts();
94 String query = scquery.buildQuery(seq);
95 assertEquals("pdb_id:1tim", query);
96 seq.getAllPDBEntries().clear();
97 query = scquery.buildQuery(seq);
99 "text:XYZ_1 OR text:XYZ_2 OR text:XYZ_3 OR text:XYZ_4 OR text:4kqy",
102 query = scquery.buildQuery(seq);
103 System.out.println(query);
104 assertEquals("text:4kqy", query);
106 DBRefEntry uniprotDBRef = new DBRefEntry();
107 uniprotDBRef.setAccessionId("P12345");
108 uniprotDBRef.setSource(DBRefSource.UNIPROT);
109 seq.addDBRef(uniprotDBRef);
111 DBRefEntry pdbDBRef = new DBRefEntry();
112 pdbDBRef.setAccessionId("1XYZ");
113 pdbDBRef.setSource(DBRefSource.PDB);
114 seq.addDBRef(pdbDBRef);
116 for (int x = 1; x < 5; x++)
118 DBRefEntry dbRef = new DBRefEntry();
119 dbRef.setAccessionId("XYZ_" + x);
122 System.out.println("");
123 System.out.println(seq.getDBRefs());
124 System.out.println(query);
125 query = scquery.buildQuery(seq);
127 "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
131 @Test(groups = { "Functional" })
132 public void populateFilterComboBoxTest() throws InterruptedException
134 SequenceI[] selectedSeqs = new SequenceI[] { seq };
135 StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
136 sc.populateFilterComboBox(false, false);
137 int optionsSize = sc.getCmbFilterOption().getItemCount();
138 assertEquals(2, optionsSize); // if structures are not discovered then don't
139 // populate filter options
141 sc.populateFilterComboBox(true, false);
142 optionsSize = sc.getCmbFilterOption().getItemCount();
143 assertTrue(optionsSize > 3); // if structures are found, filter options
144 // should be populated
146 sc.populateFilterComboBox(true, true);
147 assertTrue(sc.getCmbFilterOption().getSelectedItem() != null);
148 FilterOption filterOpt = (FilterOption) sc.getCmbFilterOption()
150 assertEquals("Cached Structures", filterOpt.getName());
153 @Test(groups = { "Network" })
154 public void fetchStructuresInfoTest()
156 SequenceI[] selectedSeqs = new SequenceI[] { seq };
157 StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
158 sc.fetchStructuresMetaData();
159 Collection<FTSData> ss = (Collection<FTSData>) PA.getValue(sc,
160 "discoveredStructuresSet");
162 assertTrue(ss.size() > 0);
166 @Test(groups = { "Functional" })
167 public void sanitizeSeqNameTest()
169 String name = "ab_cdEF|fwxyz012349";
170 assertEquals(name, PDBStructureChooserQuerySource.sanitizeSeqName(name));
172 // remove a [nn] substring
173 name = "abcde12[345]fg";
174 assertEquals("abcde12fg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
176 // remove characters other than a-zA-Z0-9 | or _
177 name = "ab[cd],.\t£$*!- \\\"@:e";
178 assertEquals("abcde", PDBStructureChooserQuerySource.sanitizeSeqName(name));
180 name = "abcde12[345a]fg";
181 assertEquals("abcde12345afg", PDBStructureChooserQuerySource.sanitizeSeqName(name));