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.Assert.assertEquals;
25 import jalview.bin.Cache;
26 import jalview.bin.Jalview;
27 import jalview.datamodel.Sequence;
28 import jalview.datamodel.SequenceI;
29 import jalview.io.DataSourceType;
30 import jalview.io.FileLoader;
32 import org.testng.annotations.BeforeMethod;
33 import org.testng.annotations.Test;
35 public class AlignmentPanelTest
37 SequenceI seq1 = new Sequence(
39 "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
41 SequenceI seq2 = new Sequence(
43 "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
45 SequenceI seq3 = new Sequence(
47 "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
49 SequenceI seq4 = new Sequence(
51 "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
53 SequenceI seq5 = new Sequence(
55 "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
57 SequenceI seq6 = new Sequence(
59 "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
61 SequenceI seq7 = new Sequence(
63 "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
65 SequenceI seq8 = new Sequence(
67 "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
69 SequenceI seq9 = new Sequence(
71 "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
73 SequenceI seq10 = new Sequence(
75 "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
77 SequenceI seq11 = new Sequence(
79 "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
81 SequenceI seq12 = new Sequence(
83 "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
85 SequenceI seq13 = new Sequence(
87 "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
89 SequenceI seq14 = new Sequence(
91 "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
93 SequenceI seq15 = new Sequence(
95 "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
97 SequenceI seq16 = new Sequence(
99 "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
101 SequenceI seq17 = new Sequence(
103 "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
105 SequenceI seq18 = new Sequence(
107 "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
109 SequenceI seq19 = new Sequence(
111 "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
113 SequenceI seq20 = new Sequence(
115 "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
117 SequenceI seq21 = new Sequence(
119 "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
121 SequenceI seq22 = new Sequence(
123 "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
125 SequenceI seq23 = new Sequence(
127 "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
131 @BeforeMethod(alwaysRun = true)
134 Jalview.main(new String[] { "-nonews", "-props",
135 "test/jalview/testProps.jvprops" });
137 Cache.applicationProperties.setProperty("SHOW_IDENTITY",
138 Boolean.TRUE.toString());
139 af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
140 DataSourceType.FILE);
143 * wait for Consensus thread to complete
147 while (af.getViewport().getConsensusSeq() == null)
152 } catch (InterruptedException e)
161 * Test side effect that end residue is set correctly by setScrollValues, with
162 * or without hidden columns
164 @Test(groups = "Functional")
165 public void TestSetScrollValues()
167 int oldres = af.getViewport().getEndRes();
168 af.alignPanel.setScrollValues(-1, 5);
170 // setting -ve x value does not change residue
171 assertEquals(af.getViewport().getEndRes(), oldres);
173 af.alignPanel.setScrollValues(0, 5);
175 // setting 0 as x value does not change residue
176 assertEquals(af.getViewport().getEndRes(), oldres);
178 af.alignPanel.setScrollValues(5, 5);
179 // setting x value to 5 extends endRes by 5 residues
180 assertEquals(af.getViewport().getEndRes(), oldres + 5);
182 // scroll to position after hidden columns sets endres to oldres (width) +
185 af.getViewport().hideColumns(30, 50);
186 af.alignPanel.setScrollValues(scrollpos, 5);
187 assertEquals(af.getViewport().getEndRes(), oldres + scrollpos);
189 // scroll to position within hidden columns, still sets endres to oldres +
191 // not sure if this is actually correct behaviour but this is what Jalview
194 af.getViewport().showAllHiddenColumns();
195 af.getViewport().hideColumns(30, 50);
196 af.alignPanel.setScrollValues(scrollpos, 5);
197 assertEquals(af.getViewport().getEndRes(), oldres + scrollpos);
199 // scroll to position within <width> distance of the end of the alignment
200 // endRes should be set to width of alignment - 1
202 af.getViewport().showAllHiddenColumns();
203 af.alignPanel.setScrollValues(scrollpos, 5);
204 assertEquals(af.getViewport().getEndRes(), af.getViewport()
205 .getAlignment().getWidth() - 1);
207 // now hide some columns, and scroll to position within <width>
208 // distance of the end of the alignment
209 // endRes should be set to width of alignment - 1 - the number of hidden
211 af.getViewport().hideColumns(30, 50);
212 af.alignPanel.setScrollValues(scrollpos, 5);
213 assertEquals(af.getViewport().getEndRes(), af.getViewport()
214 .getAlignment().getWidth() - 1 - 21); // 21 is the number of hidden