Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AlignViewControllerTest	50	98	3	0.00%	Show methods

Class AlignViewControllerTest

Class AlignViewControllerTest	Line # 50	Total Statements 98	Complexity 3	TOTAL Coverage 0.00%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	5353	2.02	1.01	0.0 0.00%
testFindColumnsWithFeature() : void   testFindColumnsWithFeature() : void	6060	79.079	1.01	0.0 0.00%
testSelectColumnsWithHighlight() : void   testSelectColumnsWithHighlight() : void	202202	17.017	1.01	0.0 0.00%

 

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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
		0% Uncovered Elements: 101 (101) Complexity: 3 Complexity Density: 0.03
50		public class AlignViewControllerTest
51		{
52
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
53	0	@BeforeClass(alwaysRun = true)...
54		public void setUpJvOptionPane()
55		{
56	0	JvOptionPane.setInteractiveMode(false);
57	0	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
58		}
59
		0% Uncovered Elements: 79 (79) Complexity: 1 Complexity Density: 0.01 4-
60	0	@Test(groups = "Functional")...
61		public void testFindColumnsWithFeature()
62		{
63	0	SequenceI seq1 = new Sequence("seq1", "-a-MMMaaaaaaaaaaaaaaaa");
64	0	SequenceI seq2 = new Sequence("seq2", "aa--aMM-MMMMMaaaaaaaaaa");
65	0	SequenceI seq3 = new Sequence("seq3", "abcab-caD-aaMMMMMaaaaa");
66	0	SequenceI seq4 = new Sequence("seq4", "abc--abcaaaaaaaaaaaaaa");
67
68		/*
69		* features start/end are base 1
70		*/
71	0	seq1.addSequenceFeature(
72		new SequenceFeature("Metal", "desc", 2, 4, 0f, null));
73	0	seq1.addSequenceFeature(
74		new SequenceFeature("Helix", "desc", 1, 15, 0f, null));
75	0	seq2.addSequenceFeature(
76		new SequenceFeature("Metal", "desc", 4, 10, 10f, null));
77	0	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	0	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	0	SequenceGroup sg = new SequenceGroup();
87	0	sg.setStartRes(0); // base 0
88	0	sg.setEndRes(4);
89	0	sg.addSequence(seq1, false);
90	0	sg.addSequence(seq2, false);
91	0	sg.addSequence(seq3, false);
92	0	sg.addSequence(seq4, false);
93
94		/*
95		* set features visible on a viewport as only visible features are selected
96		*/
97	0	AlignFrame af = new AlignFrame(
98		new Alignment(new SequenceI[]
99		{ seq1, seq2, seq3, seq4 }), 100, 100);
100	0	af.getFeatureRenderer().findAllFeatures(true);
101
102	0	AlignViewController avc = new AlignViewController(af, af.getViewport(),
103		af.alignPanel);
104
105	0	BitSet bs = new BitSet();
106	0	int seqCount = avc.findColumnsWithFeature("Metal", sg, bs);
107	0	assertEquals(1, seqCount);
108	0	assertEquals(2, bs.cardinality());
109	0	assertTrue(bs.get(3)); // base 0
110	0	assertTrue(bs.get(4));
111
112		/*
113		* select the first seven columns: Metal in seq1 cols 4-6, seq2 cols 6-7
114		*/
115	0	sg.setEndRes(6);
116	0	bs.clear();
117	0	seqCount = avc.findColumnsWithFeature("Metal", sg, bs);
118	0	assertEquals(2, seqCount);
119	0	assertEquals(4, bs.cardinality());
120	0	assertTrue(bs.get(3));
121	0	assertTrue(bs.get(4));
122	0	assertTrue(bs.get(5));
123	0	assertTrue(bs.get(6));
124
125		/*
126		* select column 14: Metal in seq3 only
127		*/
128	0	sg.setStartRes(13);
129	0	sg.setEndRes(13);
130	0	bs.clear();
131	0	seqCount = avc.findColumnsWithFeature("Metal", sg, bs);
132	0	assertEquals(1, seqCount);
133	0	assertEquals(1, bs.cardinality());
134	0	assertTrue(bs.get(13));
135
136		/*
137		* select columns 18-20: no Metal feature
138		*/
139	0	sg.setStartRes(17);
140	0	sg.setEndRes(19);
141	0	bs.clear();
142	0	seqCount = avc.findColumnsWithFeature("Metal", sg, bs);
143	0	assertEquals(0, seqCount);
144	0	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	0	FeatureColourI fc = new FeatureColour(null, Color.red, Color.blue, null,
152		0f, 10f);
153	0	fc.setAboveThreshold(true);
154	0	fc.setThreshold(5f);
155	0	af.getFeatureRenderer().setColour("Metal", fc);
156	0	sg.setStartRes(0);
157	0	sg.setEndRes(6);
158	0	bs.clear();
159	0	seqCount = avc.findColumnsWithFeature("Metal", sg, bs);
160	0	assertEquals(1, seqCount);
161	0	assertEquals(2, bs.cardinality());
162	0	assertTrue(bs.get(5));
163	0	assertTrue(bs.get(6));
164
165		/*
166		* columns 11-13 should not match disulfide bond at 8/12
167		*/
168	0	sg.setStartRes(10);
169	0	sg.setEndRes(12);
170	0	bs.clear();
171	0	seqCount = avc.findColumnsWithFeature("disulfide bond", sg, bs);
172	0	assertEquals(0, seqCount);
173	0	assertEquals(0, bs.cardinality());
174
175		/*
176		* columns 6-18 should match disulfide bond at columns 9, 14
177		*/
178	0	sg.setStartRes(5);
179	0	sg.setEndRes(17);
180	0	bs.clear();
181	0	seqCount = avc.findColumnsWithFeature("disulfide bond", sg, bs);
182	0	assertEquals(1, seqCount);
183	0	assertEquals(2, bs.cardinality());
184	0	assertTrue(bs.get(8));
185	0	assertTrue(bs.get(13));
186
187		/*
188		* look for a feature that isn't there
189		*/
190	0	sg.setStartRes(0);
191	0	sg.setEndRes(19);
192	0	bs.clear();
193	0	seqCount = avc.findColumnsWithFeature("Pfam", sg, bs);
194	0	assertEquals(0, seqCount);
195	0	assertEquals(0, bs.cardinality());
196		}
197
198		/**
199		* shameless copy of test data from findFeature for testing mark columns from
200		* highlight
201		*/
		0% Uncovered Elements: 17 (17) Complexity: 1 Complexity Density: 0.06 4-
202	0	@Test(groups = "Functional")...
203		public void testSelectColumnsWithHighlight()
204		{
205	0	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	0	SearchResultsI sr = new SearchResults();
212	0	SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray();
213	0	SequenceI seq1 = sqs[0];
214	0	SequenceI seq2 = sqs[1];
215	0	SequenceI seq3 = sqs[2];
216	0	SequenceI seq4 = sqs[3];
217
218		/*
219		* features start/end are base 1
220		*/
221	0	sr.addResult(seq1, 2, 4);
222	0	sr.addResult(seq2, 4, 10);
223	0	sr.addResult(seq3, 11, 15);
224
225		/*
226		* test Match/Find works first
227		*/
228	0	FinderI f = new Finder(af.getViewport());
229	0	f.findAll("M+", true, false, false, false);
230	0	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	0	af.getViewport().setSearchResults(sr);
238	0	AlignViewControllerI avc = af.avc;
239
240	0	avc.markHighlightedColumns(false, false, false);
241	0	assertTrue("Didn't select highlighted columns",
242		Arrays.deepEquals(af.getViewport().getColumnSelection()
243		.getSelectedRanges().toArray(), new int[][]
244		{ { 1, 14 } }));
245		}
246		}