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.datamodel.Alignment;
30 import jalview.datamodel.SearchResults;
31 import jalview.datamodel.SearchResultsI;
32 import jalview.datamodel.Sequence;
33 import jalview.datamodel.SequenceFeature;
34 import jalview.datamodel.SequenceGroup;
35 import jalview.datamodel.SequenceI;
36 import jalview.gui.AlignFrame;
37 import jalview.gui.JvOptionPane;
38 import jalview.io.DataSourceType;
39 import jalview.io.FileLoader;
40 import jalview.schemes.FeatureColour;
42 import java.awt.Color;
43 import java.util.Arrays;
44 import java.util.BitSet;
46 import org.testng.annotations.BeforeClass;
47 import org.testng.annotations.Test;
49 public class AlignViewControllerTest
52 @BeforeClass(alwaysRun = true)
53 public void setUpJvOptionPane()
55 JvOptionPane.setInteractiveMode(false);
56 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
59 @Test(groups = "Functional")
60 public void testFindColumnsWithFeature()
62 SequenceI seq1 = new Sequence("seq1", "-a-MMMaaaaaaaaaaaaaaaa");
63 SequenceI seq2 = new Sequence("seq2", "aa--aMM-MMMMMaaaaaaaaaa");
64 SequenceI seq3 = new Sequence("seq3", "abcab-caD-aaMMMMMaaaaa");
65 SequenceI seq4 = new Sequence("seq4", "abc--abcaaaaaaaaaaaaaa");
68 * features start/end are base 1
70 seq1.addSequenceFeature(new SequenceFeature("Metal", "desc", 2, 4, 0f,
72 seq1.addSequenceFeature(new SequenceFeature("Helix", "desc", 1, 15, 0f,
74 seq2.addSequenceFeature(new SequenceFeature("Metal", "desc", 4, 10,
77 seq3.addSequenceFeature(new SequenceFeature("Metal", "desc", 11, 15,
79 // disulfide bond is a 'contact feature' - only select its 'start' and 'end'
80 seq3.addSequenceFeature(new SequenceFeature("disulfide bond", "desc",
84 * select the first five columns --> Metal in seq1 cols 4-5
86 SequenceGroup sg = new SequenceGroup();
87 sg.setStartRes(0); // base 0
89 sg.addSequence(seq1, false);
90 sg.addSequence(seq2, false);
91 sg.addSequence(seq3, false);
92 sg.addSequence(seq4, false);
95 * set features visible on a viewport as only visible features are selected
97 AlignFrame af = new AlignFrame(new Alignment(new SequenceI[] { seq1,
98 seq2, seq3, seq4 }), 100, 100);
99 af.getFeatureRenderer().findAllFeatures(true);
101 AlignViewController avc = new AlignViewController(af, af.getViewport(),
104 BitSet bs = new BitSet();
105 int seqCount = avc.findColumnsWithFeature("Metal", sg, bs);
106 assertEquals(1, seqCount);
107 assertEquals(2, bs.cardinality());
108 assertTrue(bs.get(3)); // base 0
109 assertTrue(bs.get(4));
112 * select the first seven columns: Metal in seq1 cols 4-6, seq2 cols 6-7
116 seqCount = avc.findColumnsWithFeature("Metal", sg, bs);
117 assertEquals(2, seqCount);
118 assertEquals(4, bs.cardinality());
119 assertTrue(bs.get(3));
120 assertTrue(bs.get(4));
121 assertTrue(bs.get(5));
122 assertTrue(bs.get(6));
125 * select column 14: Metal in seq3 only
130 seqCount = avc.findColumnsWithFeature("Metal", sg, bs);
131 assertEquals(1, seqCount);
132 assertEquals(1, bs.cardinality());
133 assertTrue(bs.get(13));
136 * select columns 18-20: no Metal feature
141 seqCount = avc.findColumnsWithFeature("Metal", sg, bs);
142 assertEquals(0, seqCount);
143 assertEquals(0, bs.cardinality());
146 * threshold Metal to hide where score < 5
147 * seq1 feature in columns 4-6 is hidden
148 * seq2 feature in columns 6-7 is shown
150 FeatureColourI fc = new FeatureColour(Color.red, Color.blue, 0f, 10f);
151 fc.setAboveThreshold(true);
153 af.getFeatureRenderer().setColour("Metal", fc);
157 seqCount = avc.findColumnsWithFeature("Metal", sg, bs);
158 assertEquals(1, seqCount);
159 assertEquals(2, bs.cardinality());
160 assertTrue(bs.get(5));
161 assertTrue(bs.get(6));
164 * columns 11-13 should not match disulfide bond at 8/12
169 seqCount = avc.findColumnsWithFeature("disulfide bond", sg, bs);
170 assertEquals(0, seqCount);
171 assertEquals(0, bs.cardinality());
174 * columns 6-18 should match disulfide bond at columns 9, 14
179 seqCount = avc.findColumnsWithFeature("disulfide bond", sg, bs);
180 assertEquals(1, seqCount);
181 assertEquals(2, bs.cardinality());
182 assertTrue(bs.get(8));
183 assertTrue(bs.get(13));
186 * look for a feature that isn't there
191 seqCount = avc.findColumnsWithFeature("Pfam", sg, bs);
192 assertEquals(0, seqCount);
193 assertEquals(0, bs.cardinality());
197 * shameless copy of test data from findFeature for testing mark columns from
200 @Test(groups = "Functional")
201 public void testSelectColumnsWithHighlight()
203 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
204 "seq1 aMMMaaaaaaaaaaaaaaaa\n" + "seq2 aaaMMMMMMMaaaaaaaaaa\n"
205 + "seq3 aaaaaaaaaaMMMMMaaaaa\n"
206 + "seq4 aaaaaaaaaaaaaaaaaaaa\n", DataSourceType.PASTE);
208 SearchResultsI sr = new SearchResults();
209 SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray();
210 SequenceI seq1 = sqs[0];
211 SequenceI seq2 = sqs[1];
212 SequenceI seq3 = sqs[2];
213 SequenceI seq4 = sqs[3];
216 * features start/end are base 1
218 sr.addResult(seq1, 2, 4);
219 sr.addResult(seq2, 4, 10);
220 sr.addResult(seq3, 11, 15);
223 * test Match/Find works first
225 Finder f = new Finder(af.getViewport().getAlignment(), null);
227 f.setCaseSensitive(true);
230 "Finder found different set of results to manually created SearchResults",
231 sr, f.getSearchResults());
234 * now check simple mark columns from find operation
236 af.getViewport().setSearchResults(sr);
237 AlignViewControllerI avc = af.avc;
239 avc.markHighlightedColumns(false, false, false);
240 assertTrue("Didn't select highlighted columns", Arrays.deepEquals(af
241 .getViewport().getColumnSelection().getSelectedRanges()
242 .toArray(), new int[][] { { 1, 14 } }));