Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
AlignViewControllerTest	49	100	3	0	1.0100%	Show methods

Class AlignViewControllerTest

Class AlignViewControllerTest	Line # 49	Total Statements 100	Complexity 3	Uncovered Elements 0	TOTAL Coverage 1.0100%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	5252	2.02	1.01	0.00	1.0 1.0100%
testFindColumnsWithFeature() : void   testFindColumnsWithFeature() : void	5959	79.079	1.01	0.00	1.0 1.0100%
testSelectColumnsWithHighlight() : void   testSelectColumnsWithHighlight() : void	200200	19.019	1.01	0.00	1.0 1.0100%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.776699	jalview.controller.AlignViewControllerTest.testFindColumnsWithFeaturejalview.controller.AlignViewControllerTest.testFindColumnsWithFeature	1PASS
	0.19417475	jalview.controller.AlignViewControllerTest.testSelectColumnsWithHighlightjalview.controller.AlignViewControllerTest.testSelectColumnsWithHighlight	1PASS

 

Source view

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 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;
41
42		import java.awt.Color;
43		import java.util.Arrays;
44		import java.util.BitSet;
45
46		import org.testng.annotations.BeforeClass;
47		import org.testng.annotations.Test;
48
		100% Uncovered Elements: 0 (103) Complexity: 3 Complexity Density: 0.03
49		public class AlignViewControllerTest
50		{
51
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
52	1	@BeforeClass(alwaysRun = true)...
53		public void setUpJvOptionPane()
54		{
55	1	JvOptionPane.setInteractiveMode(false);
56	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
57		}
58
		100% Uncovered Elements: 0 (79) Complexity: 1 Complexity Density: 0.01 1PASS
59	1	@Test(groups = "Functional")...
60		public void testFindColumnsWithFeature()
61		{
62	1	SequenceI seq1 = new Sequence("seq1", "-a-MMMaaaaaaaaaaaaaaaa");
63	1	SequenceI seq2 = new Sequence("seq2", "aa--aMM-MMMMMaaaaaaaaaa");
64	1	SequenceI seq3 = new Sequence("seq3", "abcab-caD-aaMMMMMaaaaa");
65	1	SequenceI seq4 = new Sequence("seq4", "abc--abcaaaaaaaaaaaaaa");
66
67		/*
68		* features start/end are base 1
69		*/
70	1	seq1.addSequenceFeature(new SequenceFeature("Metal", "desc", 2, 4, 0f,
71		null));
72	1	seq1.addSequenceFeature(new SequenceFeature("Helix", "desc", 1, 15, 0f,
73		null));
74	1	seq2.addSequenceFeature(new SequenceFeature("Metal", "desc", 4, 10,
75		10f,
76		null));
77	1	seq3.addSequenceFeature(new SequenceFeature("Metal", "desc", 11, 15,
78		10f, null));
79		// disulfide bond is a 'contact feature' - only select its 'start' and 'end'
80	1	seq3.addSequenceFeature(new SequenceFeature("disulfide bond", "desc",
81		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(new Alignment(new SequenceI[] { seq1,
98		seq2, seq3, seq4 }), 100, 100);
99	1	af.getFeatureRenderer().findAllFeatures(true);
100
101	1	AlignViewController avc = new AlignViewController(af, af.getViewport(),
102		af.alignPanel);
103
104	1	BitSet bs = new BitSet();
105	1	int seqCount = avc.findColumnsWithFeature("Metal", sg, bs);
106	1	assertEquals(1, seqCount);
107	1	assertEquals(2, bs.cardinality());
108	1	assertTrue(bs.get(3)); // base 0
109	1	assertTrue(bs.get(4));
110
111		/*
112		* select the first seven columns: Metal in seq1 cols 4-6, seq2 cols 6-7
113		*/
114	1	sg.setEndRes(6);
115	1	bs.clear();
116	1	seqCount = avc.findColumnsWithFeature("Metal", sg, bs);
117	1	assertEquals(2, seqCount);
118	1	assertEquals(4, bs.cardinality());
119	1	assertTrue(bs.get(3));
120	1	assertTrue(bs.get(4));
121	1	assertTrue(bs.get(5));
122	1	assertTrue(bs.get(6));
123
124		/*
125		* select column 14: Metal in seq3 only
126		*/
127	1	sg.setStartRes(13);
128	1	sg.setEndRes(13);
129	1	bs.clear();
130	1	seqCount = avc.findColumnsWithFeature("Metal", sg, bs);
131	1	assertEquals(1, seqCount);
132	1	assertEquals(1, bs.cardinality());
133	1	assertTrue(bs.get(13));
134
135		/*
136		* select columns 18-20: no Metal feature
137		*/
138	1	sg.setStartRes(17);
139	1	sg.setEndRes(19);
140	1	bs.clear();
141	1	seqCount = avc.findColumnsWithFeature("Metal", sg, bs);
142	1	assertEquals(0, seqCount);
143	1	assertEquals(0, bs.cardinality());
144
145		/*
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
149		*/
150	1	FeatureColourI fc = new FeatureColour(Color.red, Color.blue, 0f, 10f);
151	1	fc.setAboveThreshold(true);
152	1	fc.setThreshold(5f);
153	1	af.getFeatureRenderer().setColour("Metal", fc);
154	1	sg.setStartRes(0);
155	1	sg.setEndRes(6);
156	1	bs.clear();
157	1	seqCount = avc.findColumnsWithFeature("Metal", sg, bs);
158	1	assertEquals(1, seqCount);
159	1	assertEquals(2, bs.cardinality());
160	1	assertTrue(bs.get(5));
161	1	assertTrue(bs.get(6));
162
163		/*
164		* columns 11-13 should not match disulfide bond at 8/12
165		*/
166	1	sg.setStartRes(10);
167	1	sg.setEndRes(12);
168	1	bs.clear();
169	1	seqCount = avc.findColumnsWithFeature("disulfide bond", sg, bs);
170	1	assertEquals(0, seqCount);
171	1	assertEquals(0, bs.cardinality());
172
173		/*
174		* columns 6-18 should match disulfide bond at columns 9, 14
175		*/
176	1	sg.setStartRes(5);
177	1	sg.setEndRes(17);
178	1	bs.clear();
179	1	seqCount = avc.findColumnsWithFeature("disulfide bond", sg, bs);
180	1	assertEquals(1, seqCount);
181	1	assertEquals(2, bs.cardinality());
182	1	assertTrue(bs.get(8));
183	1	assertTrue(bs.get(13));
184
185		/*
186		* look for a feature that isn't there
187		*/
188	1	sg.setStartRes(0);
189	1	sg.setEndRes(19);
190	1	bs.clear();
191	1	seqCount = avc.findColumnsWithFeature("Pfam", sg, bs);
192	1	assertEquals(0, seqCount);
193	1	assertEquals(0, bs.cardinality());
194		}
195
196		/**
197		* shameless copy of test data from findFeature for testing mark columns from
198		* highlight
199		*/
		100% Uncovered Elements: 0 (19) Complexity: 1 Complexity Density: 0.05 1PASS
200	1	@Test(groups = "Functional")...
201		public void testSelectColumnsWithHighlight()
202		{
203	1	AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
204		"seq1 aMMMaaaaaaaaaaaaaaaa\n" + "seq2 aaaMMMMMMMaaaaaaaaaa\n"
205		+ "seq3 aaaaaaaaaaMMMMMaaaaa\n"
206		+ "seq4 aaaaaaaaaaaaaaaaaaaa\n", DataSourceType.PASTE);
207
208	1	SearchResultsI sr = new SearchResults();
209	1	SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray();
210	1	SequenceI seq1 = sqs[0];
211	1	SequenceI seq2 = sqs[1];
212	1	SequenceI seq3 = sqs[2];
213	1	SequenceI seq4 = sqs[3];
214
215		/*
216		* features start/end are base 1
217		*/
218	1	sr.addResult(seq1, 2, 4);
219	1	sr.addResult(seq2, 4, 10);
220	1	sr.addResult(seq3, 11, 15);
221
222		/*
223		* test Match/Find works first
224		*/
225	1	Finder f = new Finder(af.getViewport().getAlignment(), null);
226	1	f.setFindAll(true);
227	1	f.setCaseSensitive(true);
228	1	f.find("M+");
229	1	assertEquals(
230		"Finder found different set of results to manually created SearchResults",
231		sr, f.getSearchResults());
232
233		/*
234		* now check simple mark columns from find operation
235		*/
236	1	af.getViewport().setSearchResults(sr);
237	1	AlignViewControllerI avc = af.avc;
238
239	1	avc.markHighlightedColumns(false, false, false);
240	1	assertTrue("Didn't select highlighted columns", Arrays.deepEquals(af
241		.getViewport().getColumnSelection().getSelectedRanges()
242		.toArray(), new int[][] { { 1, 14 } }));
243		}
244		}