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.assertTrue;
26 import jalview.datamodel.DBRefEntry;
27 import jalview.datamodel.DBRefSource;
28 import jalview.datamodel.PDBEntry;
29 import jalview.datamodel.Sequence;
30 import jalview.datamodel.SequenceI;
31 import jalview.jbgui.GStructureChooser.FilterOption;
33 import java.util.Vector;
35 import org.testng.annotations.AfterMethod;
36 import org.testng.annotations.BeforeMethod;
37 import org.testng.annotations.Test;
39 public class StructureChooserTest
43 @BeforeMethod(alwaysRun = true)
44 public void setUp() throws Exception
46 seq = new Sequence("PDB|4kqy|4KQY|A", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1,
48 seq.createDatasetSequence();
49 for (int x = 1; x < 5; x++)
51 DBRefEntry dbRef = new DBRefEntry();
52 dbRef.setAccessionId("XYZ_" + x);
56 PDBEntry dbRef = new PDBEntry();
59 Vector<PDBEntry> pdbIds = new Vector<PDBEntry>();
65 @AfterMethod(alwaysRun = true)
66 public void tearDown() throws Exception
71 @Test(groups = { "Functional" })
72 public void buildQueryTest()
74 String query = StructureChooser.buildQuery(seq);
75 assertEquals("pdb_id:1tim", query);
76 System.out.println("seq >>>> " + seq);
77 seq.getAllPDBEntries().clear();
78 query = StructureChooser.buildQuery(seq);
80 "text:XYZ_1 OR text:XYZ_2 OR text:XYZ_3 OR text:XYZ_4 OR text:4kqy",
83 query = StructureChooser.buildQuery(seq);
84 assertEquals("text:4kqy", query);
86 DBRefEntry uniprotDBRef = new DBRefEntry();
87 uniprotDBRef.setAccessionId("P12345");
88 uniprotDBRef.setSource(DBRefSource.UNIPROT);
89 seq.addDBRef(uniprotDBRef);
91 DBRefEntry pdbDBRef = new DBRefEntry();
92 pdbDBRef.setAccessionId("1XYZ");
93 pdbDBRef.setSource(DBRefSource.PDB);
94 seq.addDBRef(pdbDBRef);
96 for (int x = 1; x < 5; x++)
98 DBRefEntry dbRef = new DBRefEntry();
99 dbRef.setAccessionId("XYZ_" + x);
102 query = StructureChooser.buildQuery(seq);
104 "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
108 @Test(groups = { "Functional" })
109 public void populateFilterComboBoxTest() throws InterruptedException
111 SequenceI[] selectedSeqs = new SequenceI[] { seq };
112 StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
113 sc.populateFilterComboBox(false, false);
114 int optionsSize = sc.getCmbFilterOption().getItemCount();
115 assertEquals(3, optionsSize); // if structures are not discovered then don't
116 // populate filter options
118 sc.populateFilterComboBox(true, false);
119 optionsSize = sc.getCmbFilterOption().getItemCount();
120 assertTrue(optionsSize > 3); // if structures are found, filter options
121 // should be populated
123 sc.populateFilterComboBox(true, true);
124 assertTrue(sc.getCmbFilterOption().getSelectedItem() != null);
125 FilterOption filterOpt = (FilterOption) sc.getCmbFilterOption()
127 assertEquals("Cached PDB Entries", filterOpt.getName());
130 @Test(groups = { "Functional" })
131 public void fetchStructuresInfoTest()
133 SequenceI[] selectedSeqs = new SequenceI[] { seq };
134 StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
135 sc.fetchStructuresMetaData();
136 assertTrue(sc.getDiscoveredStructuresSet() != null);
137 assertTrue(sc.getDiscoveredStructuresSet().size() > 0);
141 @Test(groups = { "Functional" })
142 public void sanitizeSeqNameTest()
144 String name = "ab_cdEF|fwxyz012349";
145 assertEquals(name, StructureChooser.sanitizeSeqName(name));
147 // remove a [nn] substring
148 name = "abcde12[345]fg";
149 assertEquals("abcde12fg", StructureChooser.sanitizeSeqName(name));
151 // remove characters other than a-zA-Z0-9 | or _
152 name = "ab[cd],.\t£$*!- \\\"@:e";
153 assertEquals("abcde", StructureChooser.sanitizeSeqName(name));
155 name = "abcde12[345a]fg";
156 assertEquals("abcde12345afg", StructureChooser.sanitizeSeqName(name));