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.datamodel.SearchResults;
29 import jalview.datamodel.SearchResultsI;
30 import jalview.datamodel.Sequence;
31 import jalview.datamodel.SequenceFeature;
32 import jalview.datamodel.SequenceGroup;
33 import jalview.datamodel.SequenceI;
34 import jalview.gui.AlignFrame;
35 import jalview.io.FileLoader;
36 import jalview.io.FormatAdapter;
38 import java.util.Arrays;
39 import java.util.BitSet;
41 import org.testng.annotations.Test;
43 public class AlignViewControllerTest
45 @Test(groups = "Functional")
46 public void testFindColumnsWithFeature()
48 SequenceI seq1 = new Sequence("seq1", "-a-MMMaaaaaaaaaaaaaaaa");
49 SequenceI seq2 = new Sequence("seq2", "aa--aMM-MMMMMaaaaaaaaaa");
50 SequenceI seq3 = new Sequence("seq3", "abcab-caD-aaMMMMMaaaaa");
51 SequenceI seq4 = new Sequence("seq4", "abc--abcaaaaaaaaaaaaaa");
54 * features start/end are base 1
56 seq1.addSequenceFeature(new SequenceFeature("Metal", "desc", 2, 4, 0f,
58 seq1.addSequenceFeature(new SequenceFeature("Helix", "desc", 1, 15, 0f,
60 seq2.addSequenceFeature(new SequenceFeature("Metal", "desc", 4, 10, 0f,
62 seq3.addSequenceFeature(new SequenceFeature("Metal", "desc", 11, 15,
64 // disulfide bond is a 'contact feature' - only select its 'start' and 'end'
65 seq3.addSequenceFeature(new SequenceFeature("disulfide bond", "desc", 8, 12,
69 * select the first five columns --> Metal in seq1 cols 4-5
71 SequenceGroup sg = new SequenceGroup();
72 sg.setStartRes(0); // base 0
74 sg.addSequence(seq1, false);
75 sg.addSequence(seq2, false);
76 sg.addSequence(seq3, false);
77 sg.addSequence(seq4, false);
79 BitSet bs = new BitSet();
80 int seqCount = AlignViewController.findColumnsWithFeature("Metal", sg,
82 assertEquals(1, seqCount);
83 assertEquals(2, bs.cardinality());
84 assertTrue(bs.get(3)); // base 0
85 assertTrue(bs.get(4));
88 * select the first seven columns: Metal in seq1 cols 4-6, seq2 cols 6-7
92 seqCount = AlignViewController.findColumnsWithFeature("Metal", sg, bs);
93 assertEquals(2, seqCount);
94 assertEquals(4, bs.cardinality());
95 assertTrue(bs.get(3));
96 assertTrue(bs.get(4));
97 assertTrue(bs.get(5));
98 assertTrue(bs.get(6));
101 * select column 14: Metal in seq3 only
106 seqCount = AlignViewController.findColumnsWithFeature("Metal", sg, bs);
107 assertEquals(1, seqCount);
108 assertEquals(1, bs.cardinality());
109 assertTrue(bs.get(13));
112 * select columns 18-20: no Metal feature
117 seqCount = AlignViewController.findColumnsWithFeature("Metal", sg, bs);
118 assertEquals(0, seqCount);
119 assertEquals(0, bs.cardinality());
122 * columns 11-13 should not match disulfide bond at 8/12
127 seqCount = AlignViewController.findColumnsWithFeature("disulfide bond",
129 assertEquals(0, seqCount);
130 assertEquals(0, bs.cardinality());
133 * columns 6-18 should match disulfide bond at columns 9, 14
138 seqCount = AlignViewController.findColumnsWithFeature("disulfide bond",
140 assertEquals(1, seqCount);
141 assertEquals(2, bs.cardinality());
142 assertTrue(bs.get(8));
143 assertTrue(bs.get(13));
146 * look for a feature that isn't there
151 seqCount = AlignViewController.findColumnsWithFeature("Pfam", sg, bs);
152 assertEquals(0, seqCount);
153 assertEquals(0, bs.cardinality());
157 * shameless copy of test data from findFeature for testing mark columns from
160 @Test(groups = "Functional")
161 public void testSelectColumnsWithHighlight()
163 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
164 "seq1 aMMMaaaaaaaaaaaaaaaa\n" + "seq2 aaaMMMMMMMaaaaaaaaaa\n"
165 + "seq3 aaaaaaaaaaMMMMMaaaaa\n"
166 + "seq4 aaaaaaaaaaaaaaaaaaaa\n", FormatAdapter.PASTE);
168 SearchResultsI sr = new SearchResults();
169 SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray();
170 SequenceI seq1 = sqs[0];
171 SequenceI seq2 = sqs[1];
172 SequenceI seq3 = sqs[2];
173 SequenceI seq4 = sqs[3];
176 * features start/end are base 1
178 sr.addResult(seq1, 2, 4);
179 sr.addResult(seq2, 4, 10);
180 sr.addResult(seq3, 11, 15);
183 * test Match/Find works first
185 Finder f = new Finder(af.getViewport().getAlignment(), null);
187 f.setCaseSensitive(true);
190 "Finder found different set of results to manually created SearchResults",
191 sr, f.getSearchResults());
194 * now check simple mark columns from find operation
196 af.getViewport().setSearchResults(sr);
197 AlignViewControllerI avc = af.avc;
199 avc.markHighlightedColumns(false, false, false);
200 assertTrue("Didn't select highlighted columns", Arrays.deepEquals(af
201 .getViewport().getColumnSelection().getSelectedRanges()
202 .toArray(), new int[][] { { 1, 14 } }));