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.
21 package jalview.controller;
23 import static org.testng.AssertJUnit.assertEquals;
24 import static org.testng.AssertJUnit.assertTrue;
26 import jalview.analysis.Finder;
27 import jalview.api.AlignViewControllerI;
28 import jalview.api.FeatureColourI;
29 import jalview.api.FinderI;
30 import jalview.datamodel.Alignment;
31 import jalview.datamodel.SearchResults;
32 import jalview.datamodel.SearchResultsI;
33 import jalview.datamodel.Sequence;
34 import jalview.datamodel.SequenceFeature;
35 import jalview.datamodel.SequenceGroup;
36 import jalview.datamodel.SequenceI;
37 import jalview.gui.AlignFrame;
38 import jalview.gui.JvOptionPane;
39 import jalview.io.DataSourceType;
40 import jalview.io.FileLoader;
41 import jalview.schemes.FeatureColour;
43 import java.awt.Color;
44 import java.util.Arrays;
45 import java.util.BitSet;
47 import org.testng.annotations.BeforeClass;
48 import org.testng.annotations.Test;
50 public class AlignViewControllerTest
53 @BeforeClass(alwaysRun = true)
54 public void setUpJvOptionPane()
56 JvOptionPane.setInteractiveMode(false);
57 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
60 @Test(groups = "Functional")
61 public void testFindColumnsWithFeature()
63 SequenceI seq1 = new Sequence("seq1", "-a-MMMaaaaaaaaaaaaaaaa");
64 SequenceI seq2 = new Sequence("seq2", "aa--aMM-MMMMMaaaaaaaaaa");
65 SequenceI seq3 = new Sequence("seq3", "abcab-caD-aaMMMMMaaaaa");
66 SequenceI seq4 = new Sequence("seq4", "abc--abcaaaaaaaaaaaaaa");
69 * features start/end are base 1
71 seq1.addSequenceFeature(new SequenceFeature("Metal", "desc", 2, 4, 0f,
73 seq1.addSequenceFeature(new SequenceFeature("Helix", "desc", 1, 15, 0f,
75 seq2.addSequenceFeature(new SequenceFeature("Metal", "desc", 4, 10,
78 seq3.addSequenceFeature(new SequenceFeature("Metal", "desc", 11, 15,
80 // disulfide bond is a 'contact feature' - only select its 'start' and 'end'
81 seq3.addSequenceFeature(new SequenceFeature("disulfide bond", "desc",
85 * select the first five columns --> Metal in seq1 cols 4-5
87 SequenceGroup sg = new SequenceGroup();
88 sg.setStartRes(0); // base 0
90 sg.addSequence(seq1, false);
91 sg.addSequence(seq2, false);
92 sg.addSequence(seq3, false);
93 sg.addSequence(seq4, false);
96 * set features visible on a viewport as only visible features are selected
98 AlignFrame af = new AlignFrame(new Alignment(new SequenceI[] { seq1,
99 seq2, seq3, seq4 }), 100, 100);
100 af.getFeatureRenderer().findAllFeatures(true);
102 AlignViewController avc = new AlignViewController(af, af.getViewport(),
105 BitSet bs = new BitSet();
106 int seqCount = avc.findColumnsWithFeature("Metal", sg, bs);
107 assertEquals(1, seqCount);
108 assertEquals(2, bs.cardinality());
109 assertTrue(bs.get(3)); // base 0
110 assertTrue(bs.get(4));
113 * select the first seven columns: Metal in seq1 cols 4-6, seq2 cols 6-7
117 seqCount = avc.findColumnsWithFeature("Metal", sg, bs);
118 assertEquals(2, seqCount);
119 assertEquals(4, bs.cardinality());
120 assertTrue(bs.get(3));
121 assertTrue(bs.get(4));
122 assertTrue(bs.get(5));
123 assertTrue(bs.get(6));
126 * select column 14: Metal in seq3 only
131 seqCount = avc.findColumnsWithFeature("Metal", sg, bs);
132 assertEquals(1, seqCount);
133 assertEquals(1, bs.cardinality());
134 assertTrue(bs.get(13));
137 * select columns 18-20: no Metal feature
142 seqCount = avc.findColumnsWithFeature("Metal", sg, bs);
143 assertEquals(0, seqCount);
144 assertEquals(0, bs.cardinality());
147 * threshold Metal to hide where score < 5
148 * seq1 feature in columns 4-6 is hidden
149 * seq2 feature in columns 6-7 is shown
151 FeatureColourI fc = new FeatureColour(Color.red, Color.blue, 0f, 10f);
152 fc.setAboveThreshold(true);
154 af.getFeatureRenderer().setColour("Metal", fc);
158 seqCount = avc.findColumnsWithFeature("Metal", sg, bs);
159 assertEquals(1, seqCount);
160 assertEquals(2, bs.cardinality());
161 assertTrue(bs.get(5));
162 assertTrue(bs.get(6));
165 * columns 11-13 should not match disulfide bond at 8/12
170 seqCount = avc.findColumnsWithFeature("disulfide bond", sg, bs);
171 assertEquals(0, seqCount);
172 assertEquals(0, bs.cardinality());
175 * columns 6-18 should match disulfide bond at columns 9, 14
180 seqCount = avc.findColumnsWithFeature("disulfide bond", sg, bs);
181 assertEquals(1, seqCount);
182 assertEquals(2, bs.cardinality());
183 assertTrue(bs.get(8));
184 assertTrue(bs.get(13));
187 * look for a feature that isn't there
192 seqCount = avc.findColumnsWithFeature("Pfam", sg, bs);
193 assertEquals(0, seqCount);
194 assertEquals(0, bs.cardinality());
198 * shameless copy of test data from findFeature for testing mark columns from
201 @Test(groups = "Functional")
202 public void testSelectColumnsWithHighlight()
204 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
205 "seq1 aMMMaaaaaaaaaaaaaaaa\n" + "seq2 aaaMMMMMMMaaaaaaaaaa\n"
206 + "seq3 aaaaaaaaaaMMMMMaaaaa\n"
207 + "seq4 aaaaaaaaaaaaaaaaaaaa\n", DataSourceType.PASTE);
209 SearchResultsI sr = new SearchResults();
210 SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray();
211 SequenceI seq1 = sqs[0];
212 SequenceI seq2 = sqs[1];
213 SequenceI seq3 = sqs[2];
214 SequenceI seq4 = sqs[3];
217 * features start/end are base 1
219 sr.addResult(seq1, 2, 4);
220 sr.addResult(seq2, 4, 10);
221 sr.addResult(seq3, 11, 15);
224 * test Match/Find works first
226 FinderI f = new Finder(af.getViewport().getAlignment());
227 f.findAll("M+", null, true, false);
229 "Finder found different set of results to manually created SearchResults",
230 sr, f.getSearchResults());
233 * now check simple mark columns from find operation
235 af.getViewport().setSearchResults(sr);
236 AlignViewControllerI avc = af.avc;
238 avc.markHighlightedColumns(false, false, false);
239 assertTrue("Didn't select highlighted columns", Arrays.deepEquals(af
240 .getViewport().getColumnSelection().getSelectedRanges()
241 .toArray(), new int[][] { { 1, 14 } }));