Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AnnotationFileIOTest	43	56	8	0.920634992.1%	Show methods

Class AnnotationFileIOTest

Class AnnotationFileIOTest	Line # 43	Total Statements 56	Complexity 8	TOTAL Coverage 0.920634992.1%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4646	2.02	1.01	1.0 1.0100%
exampleAnnotationFileIO() : void   exampleAnnotationFileIO() : void	6666	2.02	1.01	1.0 1.0100%
readAlignmentFile(File) : AlignmentI   readAlignmentFile(File) : AlignmentI	7676	12.012	3.03	0.78571427 0.7857142778.6%
testAnnotationFileIO(String,File,File) : void   testAnnotationFileIO(String,File,File) : void	113113	18.018	2.02	0.8888889 0.888888988.9%
testAnnotateAlignmentView() : void   testAnnotateAlignmentView() : void	163163	22.022	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.50793654	jalview.io.AnnotationFileIOTest.exampleAnnotationFileIOjalview.io.AnnotationFileIOTest.exampleAnnotationFileIO	1PASS
	0.36507937	jalview.io.AnnotationFileIOTest.testAnnotateAlignmentViewjalview.io.AnnotationFileIOTest.testAnnotateAlignmentView	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.io;
22
23		import static org.testng.AssertJUnit.assertEquals;
24		import static org.testng.AssertJUnit.assertNotNull;
25		import static org.testng.AssertJUnit.assertTrue;
26
27		import java.awt.Color;
28		import java.io.File;
29		import java.util.Hashtable;
30		import java.util.List;
31
32		import org.testng.Assert;
33		import org.testng.annotations.BeforeClass;
34		import org.testng.annotations.Test;
35
36		import jalview.datamodel.AlignmentI;
37		import jalview.datamodel.HiddenColumns;
38		import jalview.datamodel.SequenceGroup;
39		import jalview.gui.AlignFrame;
40		import jalview.gui.JvOptionPane;
41		import jalview.io.AnnotationFile.ViewDef;
42
		92.1% Uncovered Elements: 5 (63) Complexity: 8 Complexity Density: 0.14
43		public class AnnotationFileIOTest
44		{
45
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
46	1	@BeforeClass(alwaysRun = true)...
47		public void setUpJvOptionPane()
48		{
49	1	JvOptionPane.setInteractiveMode(false);
50	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
51		}
52
53		static String TestFiles[][] = { { "Test example annotation import/export",
54		"examples/uniref50.fa", "examples/testdata/example_annot_file.jva" },
55		{ "Test multiple combine annotation statements import/export",
56		"examples/uniref50.fa",
57		"examples/testdata/test_combine_annot.jva" },
58		{ "Test multiple combine annotation statements with sequence_ref import/export",
59		"examples/uniref50.fa", "examples/testdata/uniref50_iupred.jva" },
60		{ "Test group only annotation file parsing results in parser indicating annotation was parsed",
61		"examples/uniref50.fa", "examples/testdata/test_grpannot.jva" },
62		{ "Test hiding/showing of insertions on sequence_ref",
63		"examples/uniref50.fa",
64		"examples/testdata/uniref50_seqref.jva" } };
65
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5 1PASS
66	1	@Test(groups = { "Functional" })...
67		public void exampleAnnotationFileIO() throws Exception
68		{
69	1	for (String[] testPair : TestFiles)
70		{
71	5	testAnnotationFileIO(testPair[0], new File(testPair[1]),
72		new File(testPair[2]));
73		}
74		}
75
		78.6% Uncovered Elements: 3 (14) Complexity: 3 Complexity Density: 0.25
76	10	protected AlignmentI readAlignmentFile(File f)...
77		{
78	10	System.out.println("Reading file: " + f);
79	10	String ff = f.getPath();
80	10	try
81		{
82	10	FormatAdapter rf = new FormatAdapter();
83
84	10	AlignmentI al = rf.readFile(ff, DataSourceType.FILE,
85		new IdentifyFile().identify(ff, DataSourceType.FILE));
86
87		// make sure dataset is initialised ? not sure about this
88	160	for (int i = 0; i < al.getSequencesArray().length; ++i)
89		{
90	150	al.getSequenceAt(i).createDatasetSequence();
91		}
92	10	assertNotNull("Couldn't read supplied alignment data.", al);
93	10	return al;
94		} catch (Exception e)
95		{
96	0	e.printStackTrace();
97		}
98	0	Assert.fail(
99		"Couln't read the alignment in file '" + f.toString() + "'");
100	0	return null;
101		}
102
103		/**
104		* test alignment data in given file can be imported, exported and reimported
105		* with no dataloss
106		*
107		* @param f
108		* - source datafile (IdentifyFile.identify() should work with it)
109		* @param ioformat
110		* - label for IO class used to write and read back in the data from
111		* f
112		*/
		88.9% Uncovered Elements: 2 (18) Complexity: 2 Complexity Density: 0.11
113	5	void testAnnotationFileIO(String testname, File f, File annotFile)...
114		{
115	5	System.out.println("Test: " + testname + "\nReading annotation file '"
116		+ annotFile + "' onto : " + f);
117	5	String af = annotFile.getPath();
118	5	try
119		{
120	5	AlignmentI al = readAlignmentFile(f);
121	5	HiddenColumns cs = new HiddenColumns();
122	5	assertTrue("Test " + testname
123		+ "\nAlignment was not annotated - annotation file not imported.",
124		new AnnotationFile().readAnnotationFile(al, cs, af,
125		DataSourceType.FILE));
126
127	5	AnnotationFile aff = new AnnotationFile();
128		// ViewDef is not used by Jalview
129	5	ViewDef v = aff.new ViewDef(null, al.getHiddenSequences(), cs,
130		new Hashtable());
131	5	String anfileout = new AnnotationFile().printAnnotations(
132		al.getAlignmentAnnotation(), al.getGroups(),
133		al.getProperties(), null, al, v);
134	5	assertTrue("Test " + testname
135		+ "\nAlignment annotation file was not regenerated. Null string",
136		anfileout != null);
137	5	assertTrue("Test " + testname
138		+ "\nAlignment annotation file was not regenerated. Empty string",
139		anfileout.length() > "JALVIEW_ANNOTATION".length());
140
141	5	System.out.println(
142		"Output annotation file:\n" + anfileout + "\n<<EOF\n");
143
144	5	AlignmentI al_new = readAlignmentFile(f);
145	5	assertTrue("Test " + testname
146		+ "\nregenerated annotation file did not annotate alignment.",
147		new AnnotationFile().readAnnotationFile(al_new, anfileout,
148		DataSourceType.PASTE));
149
150		// test for consistency in io
151	5	StockholmFileTest.testAlignmentEquivalence(al, al_new, false, false,
152		false);
153	5	return;
154		} catch (Exception e)
155		{
156	0	e.printStackTrace();
157		}
158	0	Assert.fail("Test " + testname
159		+ "\nCouldn't complete Annotation file roundtrip input/output/input test for '"
160		+ annotFile + "'.");
161		}
162
		100% Uncovered Elements: 0 (22) Complexity: 1 Complexity Density: 0.05 1PASS
163	1	@Test(groups = "Functional")...
164		public void testAnnotateAlignmentView()
165		{
166	1	long t1 = System.currentTimeMillis();
167		/*
168		* JAL-3779 test multiple groups of the same name get annotated
169		*/
170	1	AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
171		">Seq1\nQRSIL\n>Seq2\nFTHND\n>Seq3\nRPVSL\n",
172		DataSourceType.PASTE);
173	1	long t2 = System.currentTimeMillis();
174	1	System.err.println("t0: " + (t2 - t1));
175		// seq1 and seq3 are in distinct groups both named Group1
176	1	String annotationFile = "JALVIEW_ANNOTATION\nSEQUENCE_GROUP\tGroup1\t*\t*\t1\n"
177		+ "SEQUENCE_GROUP\tGroup2\t*\t*\t2\n"
178		+ "SEQUENCE_GROUP\tGroup1\t*\t*\t3\n"
179		+ "PROPERTIES\tGroup1\toutlineColour=blue\tidColour=red\n";
180	1	new AnnotationFile().annotateAlignmentView(af.getViewport(),
181		annotationFile, DataSourceType.PASTE);
182
183	1	AlignmentI al = af.getViewport().getAlignment();
184	1	List<SequenceGroup> groups = al.getGroups();
185	1	assertEquals(3, groups.size());
186	1	SequenceGroup sg = groups.get(0);
187	1	assertEquals("Group1", sg.getName());
188	1	assertTrue(sg.contains(al.getSequenceAt(0)));
189	1	assertEquals(Color.BLUE, sg.getOutlineColour());
190	1	assertEquals(Color.RED, sg.getIdColour());
191	1	sg = groups.get(1);
192	1	assertEquals("Group2", sg.getName());
193	1	assertTrue(sg.contains(al.getSequenceAt(1)));
194
195		/*
196		* the bug fix: a second group of the same name is also given properties
197		*/
198	1	sg = groups.get(2);
199	1	assertEquals("Group1", sg.getName());
200	1	assertTrue(sg.contains(al.getSequenceAt(2)));
201	1	assertEquals(Color.BLUE, sg.getOutlineColour());
202	1	assertEquals(Color.RED, sg.getIdColour());
203		}
204		}