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AlignViewControllerTest | 50 | 98 | 3 |
1 | /* | |
2 | * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) | |
3 | * Copyright (C) $$Year-Rel$$ The Jalview Authors | |
4 | * | |
5 | * This file is part of Jalview. | |
6 | * | |
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. | |
11 | * | |
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. | |
16 | * | |
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. | |
20 | */ | |
21 | package jalview.controller; | |
22 | ||
23 | import static org.testng.AssertJUnit.assertEquals; | |
24 | import static org.testng.AssertJUnit.assertTrue; | |
25 | ||
26 | import java.awt.Color; | |
27 | import java.util.Arrays; | |
28 | import java.util.BitSet; | |
29 | ||
30 | import org.testng.annotations.BeforeClass; | |
31 | import org.testng.annotations.Test; | |
32 | ||
33 | import jalview.analysis.Finder; | |
34 | import jalview.api.AlignViewControllerI; | |
35 | import jalview.api.FeatureColourI; | |
36 | import jalview.api.FinderI; | |
37 | import jalview.datamodel.Alignment; | |
38 | import jalview.datamodel.SearchResults; | |
39 | import jalview.datamodel.SearchResultsI; | |
40 | import jalview.datamodel.Sequence; | |
41 | import jalview.datamodel.SequenceFeature; | |
42 | import jalview.datamodel.SequenceGroup; | |
43 | import jalview.datamodel.SequenceI; | |
44 | import jalview.gui.AlignFrame; | |
45 | import jalview.gui.JvOptionPane; | |
46 | import jalview.io.DataSourceType; | |
47 | import jalview.io.FileLoader; | |
48 | import jalview.schemes.FeatureColour; | |
49 | ||
50 | public class AlignViewControllerTest | |
51 | { | |
52 | ||
53 | 1 | @BeforeClass(alwaysRun = true) |
54 | public void setUpJvOptionPane() | |
55 | { | |
56 | 1 | JvOptionPane.setInteractiveMode(false); |
57 | 1 | JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); |
58 | } | |
59 | ||
60 | 1 | @Test(groups = "Functional") |
61 | public void testFindColumnsWithFeature() | |
62 | { | |
63 | 1 | SequenceI seq1 = new Sequence("seq1", "-a-MMMaaaaaaaaaaaaaaaa"); |
64 | 1 | SequenceI seq2 = new Sequence("seq2", "aa--aMM-MMMMMaaaaaaaaaa"); |
65 | 1 | SequenceI seq3 = new Sequence("seq3", "abcab-caD-aaMMMMMaaaaa"); |
66 | 1 | SequenceI seq4 = new Sequence("seq4", "abc--abcaaaaaaaaaaaaaa"); |
67 | ||
68 | /* | |
69 | * features start/end are base 1 | |
70 | */ | |
71 | 1 | seq1.addSequenceFeature( |
72 | new SequenceFeature("Metal", "desc", 2, 4, 0f, null)); | |
73 | 1 | seq1.addSequenceFeature( |
74 | new SequenceFeature("Helix", "desc", 1, 15, 0f, null)); | |
75 | 1 | seq2.addSequenceFeature( |
76 | new SequenceFeature("Metal", "desc", 4, 10, 10f, null)); | |
77 | 1 | seq3.addSequenceFeature( |
78 | new SequenceFeature("Metal", "desc", 11, 15, 10f, null)); | |
79 | // disulfide bond is a 'contact feature' - only select its 'start' and 'end' | |
80 | 1 | seq3.addSequenceFeature( |
81 | new SequenceFeature("disulfide bond", "desc", 8, 12, 0f, null)); | |
82 | ||
83 | /* | |
84 | * select the first five columns --> Metal in seq1 cols 4-5 | |
85 | */ | |
86 | 1 | SequenceGroup sg = new SequenceGroup(); |
87 | 1 | sg.setStartRes(0); // base 0 |
88 | 1 | sg.setEndRes(4); |
89 | 1 | sg.addSequence(seq1, false); |
90 | 1 | sg.addSequence(seq2, false); |
91 | 1 | sg.addSequence(seq3, false); |
92 | 1 | sg.addSequence(seq4, false); |
93 | ||
94 | /* | |
95 | * set features visible on a viewport as only visible features are selected | |
96 | */ | |
97 | 1 | AlignFrame af = new AlignFrame( |
98 | new Alignment(new SequenceI[] | |
99 | { seq1, seq2, seq3, seq4 }), 100, 100); | |
100 | 1 | af.getFeatureRenderer().findAllFeatures(true); |
101 | ||
102 | 1 | AlignViewController avc = new AlignViewController(af, af.getViewport(), |
103 | af.alignPanel); | |
104 | ||
105 | 1 | BitSet bs = new BitSet(); |
106 | 1 | int seqCount = avc.findColumnsWithFeature("Metal", sg, bs); |
107 | 1 | assertEquals(1, seqCount); |
108 | 1 | assertEquals(2, bs.cardinality()); |
109 | 1 | assertTrue(bs.get(3)); // base 0 |
110 | 1 | assertTrue(bs.get(4)); |
111 | ||
112 | /* | |
113 | * select the first seven columns: Metal in seq1 cols 4-6, seq2 cols 6-7 | |
114 | */ | |
115 | 1 | sg.setEndRes(6); |
116 | 1 | bs.clear(); |
117 | 1 | seqCount = avc.findColumnsWithFeature("Metal", sg, bs); |
118 | 1 | assertEquals(2, seqCount); |
119 | 1 | assertEquals(4, bs.cardinality()); |
120 | 1 | assertTrue(bs.get(3)); |
121 | 1 | assertTrue(bs.get(4)); |
122 | 1 | assertTrue(bs.get(5)); |
123 | 1 | assertTrue(bs.get(6)); |
124 | ||
125 | /* | |
126 | * select column 14: Metal in seq3 only | |
127 | */ | |
128 | 1 | sg.setStartRes(13); |
129 | 1 | sg.setEndRes(13); |
130 | 1 | bs.clear(); |
131 | 1 | seqCount = avc.findColumnsWithFeature("Metal", sg, bs); |
132 | 1 | assertEquals(1, seqCount); |
133 | 1 | assertEquals(1, bs.cardinality()); |
134 | 1 | assertTrue(bs.get(13)); |
135 | ||
136 | /* | |
137 | * select columns 18-20: no Metal feature | |
138 | */ | |
139 | 1 | sg.setStartRes(17); |
140 | 1 | sg.setEndRes(19); |
141 | 1 | bs.clear(); |
142 | 1 | seqCount = avc.findColumnsWithFeature("Metal", sg, bs); |
143 | 1 | assertEquals(0, seqCount); |
144 | 1 | assertEquals(0, bs.cardinality()); |
145 | ||
146 | /* | |
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 | |
150 | */ | |
151 | 1 | FeatureColourI fc = new FeatureColour(null, Color.red, Color.blue, null, |
152 | 0f, 10f); | |
153 | 1 | fc.setAboveThreshold(true); |
154 | 1 | fc.setThreshold(5f); |
155 | 1 | af.getFeatureRenderer().setColour("Metal", fc); |
156 | 1 | sg.setStartRes(0); |
157 | 1 | sg.setEndRes(6); |
158 | 1 | bs.clear(); |
159 | 1 | seqCount = avc.findColumnsWithFeature("Metal", sg, bs); |
160 | 1 | assertEquals(1, seqCount); |
161 | 1 | assertEquals(2, bs.cardinality()); |
162 | 1 | assertTrue(bs.get(5)); |
163 | 1 | assertTrue(bs.get(6)); |
164 | ||
165 | /* | |
166 | * columns 11-13 should not match disulfide bond at 8/12 | |
167 | */ | |
168 | 1 | sg.setStartRes(10); |
169 | 1 | sg.setEndRes(12); |
170 | 1 | bs.clear(); |
171 | 1 | seqCount = avc.findColumnsWithFeature("disulfide bond", sg, bs); |
172 | 1 | assertEquals(0, seqCount); |
173 | 1 | assertEquals(0, bs.cardinality()); |
174 | ||
175 | /* | |
176 | * columns 6-18 should match disulfide bond at columns 9, 14 | |
177 | */ | |
178 | 1 | sg.setStartRes(5); |
179 | 1 | sg.setEndRes(17); |
180 | 1 | bs.clear(); |
181 | 1 | seqCount = avc.findColumnsWithFeature("disulfide bond", sg, bs); |
182 | 1 | assertEquals(1, seqCount); |
183 | 1 | assertEquals(2, bs.cardinality()); |
184 | 1 | assertTrue(bs.get(8)); |
185 | 1 | assertTrue(bs.get(13)); |
186 | ||
187 | /* | |
188 | * look for a feature that isn't there | |
189 | */ | |
190 | 1 | sg.setStartRes(0); |
191 | 1 | sg.setEndRes(19); |
192 | 1 | bs.clear(); |
193 | 1 | seqCount = avc.findColumnsWithFeature("Pfam", sg, bs); |
194 | 1 | assertEquals(0, seqCount); |
195 | 1 | assertEquals(0, bs.cardinality()); |
196 | } | |
197 | ||
198 | /** | |
199 | * shameless copy of test data from findFeature for testing mark columns from | |
200 | * highlight | |
201 | */ | |
202 | 1 | @Test(groups = "Functional") |
203 | public void testSelectColumnsWithHighlight() | |
204 | { | |
205 | 1 | AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( |
206 | "seq1 aMMMaaaaaaaaaaaaaaaa\n" + "seq2 aaaMMMMMMMaaaaaaaaaa\n" | |
207 | + "seq3 aaaaaaaaaaMMMMMaaaaa\n" | |
208 | + "seq4 aaaaaaaaaaaaaaaaaaaa\n", | |
209 | DataSourceType.PASTE); | |
210 | ||
211 | 1 | SearchResultsI sr = new SearchResults(); |
212 | 1 | SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray(); |
213 | 1 | SequenceI seq1 = sqs[0]; |
214 | 1 | SequenceI seq2 = sqs[1]; |
215 | 1 | SequenceI seq3 = sqs[2]; |
216 | 1 | SequenceI seq4 = sqs[3]; |
217 | ||
218 | /* | |
219 | * features start/end are base 1 | |
220 | */ | |
221 | 1 | sr.addResult(seq1, 2, 4); |
222 | 1 | sr.addResult(seq2, 4, 10); |
223 | 1 | sr.addResult(seq3, 11, 15); |
224 | ||
225 | /* | |
226 | * test Match/Find works first | |
227 | */ | |
228 | 1 | FinderI f = new Finder(af.getViewport()); |
229 | 1 | f.findAll("M+", true, false, false, false); |
230 | 1 | assertEquals( |
231 | "Finder found different set of results to manually created SearchResults", | |
232 | sr, f.getSearchResults()); | |
233 | ||
234 | /* | |
235 | * now check simple mark columns from find operation | |
236 | */ | |
237 | 1 | af.getViewport().setSearchResults(sr); |
238 | 1 | AlignViewControllerI avc = af.avc; |
239 | ||
240 | 1 | avc.markHighlightedColumns(false, false, false); |
241 | 1 | assertTrue("Didn't select highlighted columns", |
242 | Arrays.deepEquals(af.getViewport().getColumnSelection() | |
243 | .getSelectedRanges().toArray(), new int[][] | |
244 | { { 1, 14 } })); | |
245 | } | |
246 | } |