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;
32 import java.util.Vector;
34 import org.testng.annotations.AfterMethod;
35 import org.testng.annotations.BeforeMethod;
36 import org.testng.annotations.Test;
38 public class StructureChooserTest
42 @BeforeMethod(alwaysRun = true)
43 public void setUp() throws Exception
45 seq = new Sequence("PDB|4kqy|4KQY|A", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1,
47 seq.setDatasetSequence(seq);
48 for (int x = 1; x < 5; x++)
50 DBRefEntry dbRef = new DBRefEntry();
51 dbRef.setAccessionId("XYZ_" + x);
55 PDBEntry dbRef = new PDBEntry();
58 Vector<PDBEntry> pdbIds = new Vector<PDBEntry>();
64 @AfterMethod(alwaysRun = true)
65 public void tearDown() throws Exception
70 @Test(groups = { "Functional" })
71 public void buildQueryTest()
73 String query = StructureChooser.buildQuery(seq);
74 assertEquals("pdb_id:1tim", query);
75 System.out.println("seq >>>> " + seq);
76 seq.getAllPDBEntries().clear();
77 query = StructureChooser.buildQuery(seq);
79 "text:XYZ_1 OR text:XYZ_2 OR text:XYZ_3 OR text:XYZ_4 OR text:4kqy",
82 query = StructureChooser.buildQuery(seq);
83 assertEquals("text:4kqy", query);
85 DBRefEntry uniprotDBRef = new DBRefEntry();
86 uniprotDBRef.setAccessionId("P12345");
87 uniprotDBRef.setSource(DBRefSource.UNIPROT);
88 seq.addDBRef(uniprotDBRef);
90 DBRefEntry pdbDBRef = new DBRefEntry();
91 pdbDBRef.setAccessionId("1XYZ");
92 pdbDBRef.setSource(DBRefSource.PDB);
93 seq.addDBRef(pdbDBRef);
95 for (int x = 1; x < 5; x++)
97 DBRefEntry dbRef = new DBRefEntry();
98 dbRef.setAccessionId("XYZ_" + x);
101 query = StructureChooser.buildQuery(seq);
103 "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
107 @Test(groups = { "Functional" })
108 public void populateFilterComboBoxTest()
110 SequenceI[] selectedSeqs = new SequenceI[] { seq };
111 StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
112 sc.populateFilterComboBox();
113 int optionsSize = sc.getCmbFilterOption().getItemCount();
114 assertEquals(3, optionsSize); // if structures are not discovered then don't
115 // populate filter options
117 sc.setStructuresDiscovered(true);
118 sc.populateFilterComboBox();
122 } catch (InterruptedException e)
126 optionsSize = sc.getCmbFilterOption().getItemCount();
127 assertTrue(optionsSize > 3); // if structures are found, filter options
128 // should be populated
131 @Test(groups = { "Functional" })
132 public void fetchStructuresInfoTest()
134 SequenceI[] selectedSeqs = new SequenceI[] { seq };
135 StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
136 sc.fetchStructuresMetaData();
137 assertTrue(sc.getDiscoveredStructuresSet() != null);
138 assertTrue(sc.getDiscoveredStructuresSet().size() > 0);
142 @Test(groups = { "Functional" })
143 public void sanitizeSeqNameTest()
145 String name = "ab_cdEF|fwxyz012349";
146 assertEquals(name, StructureChooser.sanitizeSeqName(name));
148 // remove a [nn] substring
149 name = "abcde12[345]fg";
150 assertEquals("abcde12fg", StructureChooser.sanitizeSeqName(name));
152 // remove characters other than a-zA-Z0-9 | or _
153 name = "ab[cd],.\t£$*!- \\\"@:e";
154 assertEquals("abcde", StructureChooser.sanitizeSeqName(name));
156 name = "abcde12[345a]fg";
157 assertEquals("abcde12345afg", StructureChooser.sanitizeSeqName(name));