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;
24 import static org.testng.Assert.assertNotEquals;
26 import jalview.bin.Cache;
27 import jalview.bin.Jalview;
28 import jalview.datamodel.Sequence;
29 import jalview.datamodel.SequenceI;
30 import jalview.io.DataSourceType;
31 import jalview.io.FileLoader;
32 import jalview.viewmodel.ViewportRanges;
34 import org.testng.annotations.BeforeMethod;
35 import org.testng.annotations.Test;
37 public class AlignmentPanelTest
39 SequenceI seq1 = new Sequence(
41 "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
43 SequenceI seq2 = new Sequence(
45 "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
47 SequenceI seq3 = new Sequence(
49 "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
51 SequenceI seq4 = new Sequence(
53 "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
55 SequenceI seq5 = new Sequence(
57 "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
59 SequenceI seq6 = new Sequence(
61 "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
63 SequenceI seq7 = new Sequence(
65 "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
67 SequenceI seq8 = new Sequence(
69 "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
71 SequenceI seq9 = new Sequence(
73 "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
75 SequenceI seq10 = new Sequence(
77 "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
79 SequenceI seq11 = new Sequence(
81 "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
83 SequenceI seq12 = new Sequence(
85 "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
87 SequenceI seq13 = new Sequence(
89 "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
91 SequenceI seq14 = new Sequence(
93 "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
95 SequenceI seq15 = new Sequence(
97 "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
99 SequenceI seq16 = new Sequence(
101 "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
103 SequenceI seq17 = new Sequence(
105 "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
107 SequenceI seq18 = new Sequence(
109 "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
111 SequenceI seq19 = new Sequence(
113 "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
115 SequenceI seq20 = new Sequence(
117 "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
119 SequenceI seq21 = new Sequence(
121 "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
123 SequenceI seq22 = new Sequence(
125 "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
127 SequenceI seq23 = new Sequence(
129 "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
133 @BeforeMethod(alwaysRun = true)
136 Jalview.main(new String[] { "-nonews", "-props",
137 "test/jalview/testProps.jvprops" });
139 Cache.applicationProperties.setProperty("SHOW_IDENTITY",
140 Boolean.TRUE.toString());
141 af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
142 DataSourceType.FILE);
145 * wait for Consensus thread to complete
149 while (af.getViewport().getConsensusSeq() == null)
154 } catch (InterruptedException e)
163 * Test side effect that end residue is set correctly by setScrollValues, with
164 * or without hidden columns
166 @Test(groups = "Functional")
167 public void TestSetScrollValues()
169 ViewportRanges ranges = af.getViewport().getRanges();
170 af.alignPanel.setScrollValues(0, 0);
172 int oldres = ranges.getEndRes();
173 af.alignPanel.setScrollValues(-1, 5);
175 // setting -ve x value does not change residue
176 assertEquals(ranges.getEndRes(), oldres);
178 af.alignPanel.setScrollValues(0, 5);
180 // setting 0 as x value does not change residue
181 assertEquals(ranges.getEndRes(), oldres);
183 af.alignPanel.setScrollValues(5, 5);
184 // setting x value to 5 extends endRes by 5 residues
185 assertEquals(ranges.getEndRes(), oldres + 5);
187 // scroll to position after hidden columns sets endres to oldres (width) +
190 af.getViewport().hideColumns(30, 50);
191 af.alignPanel.setScrollValues(scrollpos, 5);
192 assertEquals(ranges.getEndRes(), oldres + scrollpos);
194 // scroll to position within hidden columns, still sets endres to oldres +
196 // not sure if this is actually correct behaviour but this is what Jalview
199 af.getViewport().showAllHiddenColumns();
200 af.getViewport().hideColumns(30, 50);
201 af.alignPanel.setScrollValues(scrollpos, 5);
202 assertEquals(ranges.getEndRes(), oldres + scrollpos);
204 // scroll to position within <width> distance of the end of the alignment
205 // endRes should be set to width of alignment - 1
207 af.getViewport().showAllHiddenColumns();
208 af.alignPanel.setScrollValues(scrollpos, 5);
209 assertEquals(ranges.getEndRes(), af.getViewport()
210 .getAlignment().getWidth() - 1);
212 // now hide some columns, and scroll to position within <width>
213 // distance of the end of the alignment
214 // endRes should be set to width of alignment - 1 - the number of hidden
216 af.getViewport().hideColumns(30, 50);
217 af.alignPanel.setScrollValues(scrollpos, 5);
218 assertEquals(ranges.getEndRes(), af.getViewport()
219 .getAlignment().getWidth() - 1 - 21); // 21 is the number of hidden
224 * Test that update layout reverts to original (unwrapped) values for endRes
225 * and endSeq when switching from wrapped to unwrapped mode (JAL-2739)
227 @Test(groups = "Functional")
228 public void TestUpdateLayout_endRes()
230 // get details of original alignment dimensions
231 ViewportRanges ranges = af.getViewport().getRanges();
232 int endres = ranges.getEndRes();
235 af.alignPanel.getAlignViewport().setWrapAlignment(true);
236 af.alignPanel.updateLayout();
239 assertNotEquals(ranges.getEndRes(), endres);
242 af.alignPanel.getAlignViewport().setWrapAlignment(false);
243 af.alignPanel.updateLayout();
245 // endRes and endSeq back to original values
246 assertEquals(ranges.getEndRes(), endres);