Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AnnotationColumnChooserTest	50	67	4	1.0100%	Show methods

Class AnnotationColumnChooserTest

Class AnnotationColumnChooserTest	Line # 50	Total Statements 67	Complexity 4	TOTAL Coverage 1.0100%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	5252	2.02	1.01	1.0 1.0100%
setUp() : void   setUp() : void	7474	11.011	1.01	1.0 1.0100%
addAnnotations() : void   addAnnotations() : void	103103	17.017	1.01	1.0 1.0100%
testReset() : void   testReset() : void	127127	37.037	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.53521127	jalview.gui.AnnotationColumnChooserTest.testResetjalview.gui.AnnotationColumnChooserTest.testReset	1PASS

 

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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.gui;
22
23		import static org.testng.Assert.assertFalse;
24		import static org.testng.AssertJUnit.assertEquals;
25
26		import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
27		import jalview.bin.Cache;
28		import jalview.datamodel.AlignmentAnnotation;
29		import jalview.datamodel.AlignmentI;
30		import jalview.datamodel.Annotation;
31		import jalview.datamodel.HiddenColumns;
32		import jalview.datamodel.SequenceI;
33		import jalview.io.DataSourceType;
34		import jalview.io.FileFormat;
35		import jalview.io.FormatAdapter;
36
37		import java.io.IOException;
38		import java.util.Iterator;
39
40		import org.testng.annotations.BeforeClass;
41		import org.testng.annotations.BeforeMethod;
42		import org.testng.annotations.Test;
43
44		/**
45		* Unit tests for AnnotationChooser
46		*
47		* @author kmourao
48		*
49		*/
		100% Uncovered Elements: 0 (71) Complexity: 4 Complexity Density: 0.06
50		public class AnnotationColumnChooserTest
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
59		// 4 sequences x 13 positions
60		final static String TEST_DATA = ">FER_CAPAA Ferredoxin\n"
61		+ "TIETHKEAELVG-\n"
62		+ ">FER_CAPAN Ferredoxin, chloroplast precursor\n"
63		+ "TIETHKEAELVG-\n"
64		+ ">FER1_SOLLC Ferredoxin-1, chloroplast precursor\n"
65		+ "TIETHKEEELTA-\n" + ">Q93XJ9_SOLTU Ferredoxin I precursor\n"
66		+ "TIETHKEEELTA-\n";
67
68		AnnotationChooser testee;
69
70		AlignmentPanel parentPanel;
71
72		AlignFrame af;
73
		100% Uncovered Elements: 0 (11) Complexity: 1 Complexity Density: 0.09
74	1	@BeforeMethod(alwaysRun = true)...
75		public void setUp() throws IOException
76		{
77	1	Cache.loadProperties("test/jalview/io/testProps.jvprops");
78		// pin down annotation sort order for test
79	1	Cache.applicationProperties.setProperty(Preferences.SORT_ANNOTATIONS,
80		SequenceAnnotationOrder.NONE.name());
81	1	final String TRUE = Boolean.TRUE.toString();
82	1	Cache.applicationProperties.setProperty(Preferences.SHOW_AUTOCALC_ABOVE,
83		TRUE);
84	1	Cache.applicationProperties.setProperty("SHOW_QUALITY", TRUE);
85	1	Cache.applicationProperties.setProperty("SHOW_CONSERVATION", TRUE);
86	1	Cache.applicationProperties.setProperty("SHOW_IDENTITY", TRUE);
87
88	1	AlignmentI al = new FormatAdapter().readFile(TEST_DATA,
89		DataSourceType.PASTE, FileFormat.Fasta);
90	1	af = new AlignFrame(al, 700, 500);
91	1	parentPanel = new AlignmentPanel(af, af.getViewport());
92	1	addAnnotations();
93		}
94
95		/**
96		* Add 4 annotations, 3 of them sequence-specific.
97		*
98		* <PRE>
99		* ann1 - for sequence 0 - label 'IUPRED' ann2 - not sequence related - label
100		* 'Beauty' ann3 - for sequence 3 - label 'JMol' ann4 - for sequence 2 - label
101		* 'IUPRED' ann5 - for sequence 1 - label 'JMol'
102		*/
		100% Uncovered Elements: 0 (17) Complexity: 1 Complexity Density: 0.06
103	1	private void addAnnotations()...
104		{
105	1	Annotation an = new Annotation(2f);
106	1	Annotation[] anns = new Annotation[] { an, an, an };
107	1	AlignmentAnnotation ann0 = new AlignmentAnnotation("IUPRED", "", anns);
108	1	AlignmentAnnotation ann1 = new AlignmentAnnotation("Beauty", "", anns);
109	1	AlignmentAnnotation ann2 = new AlignmentAnnotation("JMol", "", anns);
110	1	AlignmentAnnotation ann3 = new AlignmentAnnotation("IUPRED", "", anns);
111	1	AlignmentAnnotation ann4 = new AlignmentAnnotation("JMol", "", anns);
112	1	SequenceI[] seqs = parentPanel.getAlignment().getSequencesArray();
113	1	ann0.setSequenceRef(seqs[0]);
114	1	ann2.setSequenceRef(seqs[3]);
115	1	ann3.setSequenceRef(seqs[2]);
116	1	ann4.setSequenceRef(seqs[1]);
117	1	parentPanel.getAlignment().addAnnotation(ann0);
118	1	parentPanel.getAlignment().addAnnotation(ann1);
119	1	parentPanel.getAlignment().addAnnotation(ann2);
120	1	parentPanel.getAlignment().addAnnotation(ann3);
121	1	parentPanel.getAlignment().addAnnotation(ann4);
122		}
123
124		/**
125		* Test reset
126		*/
		100% Uncovered Elements: 0 (37) Complexity: 1 Complexity Density: 0.03 1PASS
127	1	@Test(groups = { "Functional" })...
128		public void testReset()
129		{
130	1	AnnotationColumnChooser acc = new AnnotationColumnChooser(
131		af.getViewport(), af.alignPanel);
132
133	1	HiddenColumns oldhidden = new HiddenColumns();
134	1	oldhidden.hideColumns(10, 20);
135	1	acc.setOldHiddenColumns(oldhidden);
136
137	1	HiddenColumns newHidden = new HiddenColumns();
138	1	newHidden.hideColumns(0, 3);
139	1	newHidden.hideColumns(22, 25);
140	1	af.getViewport().setHiddenColumns(newHidden);
141
142	1	HiddenColumns currentHidden = af.getViewport().getAlignment()
143		.getHiddenColumns();
144	1	Iterator<int[]> regions = currentHidden.iterator();
145	1	int[] next = regions.next();
146	1	assertEquals(0, next[0]);
147	1	assertEquals(3, next[1]);
148	1	next = regions.next();
149	1	assertEquals(22, next[0]);
150	1	assertEquals(25, next[1]);
151
152		// now reset hidden columns
153	1	acc.reset();
154	1	currentHidden = af.getViewport().getAlignment().getHiddenColumns();
155	1	regions = currentHidden.iterator();
156	1	next = regions.next();
157	1	assertEquals(10, next[0]);
158	1	assertEquals(20, next[1]);
159
160		// check works with empty hidden columns as old columns
161	1	oldhidden = new HiddenColumns();
162	1	acc.setOldHiddenColumns(oldhidden);
163	1	acc.reset();
164	1	currentHidden = af.getViewport().getAlignment().getHiddenColumns();
165	1	assertFalse(currentHidden.hasHiddenColumns());
166
167		// check works with empty hidden columns as new columns
168	1	oldhidden.hideColumns(10, 20);
169	1	acc.setOldHiddenColumns(oldhidden);
170	1	currentHidden = af.getViewport().getAlignment().getHiddenColumns();
171	1	assertFalse(currentHidden.hasHiddenColumns());
172
173	1	acc.reset();
174	1	currentHidden = af.getViewport().getAlignment().getHiddenColumns();
175	1	regions = currentHidden.iterator();
176	1	next = regions.next();
177	1	assertEquals(10, next[0]);
178	1	assertEquals(20, next[1]);
179		}
180		}