Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
AnnotationFileIOTest	38	34	7	5	0.87587.5%	Show methods

Class AnnotationFileIOTest

Class AnnotationFileIOTest	Line # 38	Total Statements 34	Complexity 7	Uncovered Elements 5	TOTAL Coverage 0.87587.5%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4141	2.02	1.01	0.00	1.0 1.0100%
exampleAnnotationFileIO() : void   exampleAnnotationFileIO() : void	6363	2.02	1.01	0.00	1.0 1.0100%
readAlignmentFile(File) : AlignmentI   readAlignmentFile(File) : AlignmentI	7373	12.012	3.03	3.03	0.78571427 0.7857142778.6%
testAnnotationFileIO(String,File,File) : void   testAnnotationFileIO(String,File,File) : void	109109	18.018	2.02	2.02	0.8888889 0.888888988.9%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.8	jalview.io.AnnotationFileIOTest.exampleAnnotationFileIOjalview.io.AnnotationFileIOTest.exampleAnnotationFileIO	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.io;
22
23		import static org.testng.AssertJUnit.assertNotNull;
24		import static org.testng.AssertJUnit.assertTrue;
25
26		import jalview.datamodel.AlignmentI;
27		import jalview.datamodel.HiddenColumns;
28		import jalview.gui.JvOptionPane;
29		import jalview.io.AnnotationFile.ViewDef;
30
31		import java.io.File;
32		import java.util.Hashtable;
33
34		import org.testng.Assert;
35		import org.testng.annotations.BeforeClass;
36		import org.testng.annotations.Test;
37
		87.5% Uncovered Elements: 5 (40) Complexity: 7 Complexity Density: 0.21
38		public class AnnotationFileIOTest
39		{
40
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
41	1	@BeforeClass(alwaysRun = true)...
42		public void setUpJvOptionPane()
43		{
44	1	JvOptionPane.setInteractiveMode(false);
45	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
46		}
47
48		static String TestFiles[][] = {
49		{ "Test example annotation import/export", "examples/uniref50.fa",
50		"examples/testdata/example_annot_file.jva" },
51		{ "Test multiple combine annotation statements import/export",
52		"examples/uniref50.fa",
53		"examples/testdata/test_combine_annot.jva" },
54		{
55		"Test multiple combine annotation statements with sequence_ref import/export",
56		"examples/uniref50.fa", "examples/testdata/uniref50_iupred.jva" },
57		{
58		"Test group only annotation file parsing results in parser indicating annotation was parsed",
59		"examples/uniref50.fa", "examples/testdata/test_grpannot.jva" },
60		{ "Test hiding/showing of insertions on sequence_ref",
61		"examples/uniref50.fa", "examples/testdata/uniref50_seqref.jva" } };
62
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5 1PASS
63	1	@Test(groups = { "Functional" })...
64		public void exampleAnnotationFileIO() throws Exception
65		{
66	1	for (String[] testPair : TestFiles)
67		{
68	5	testAnnotationFileIO(testPair[0], new File(testPair[1]), new File(
69		testPair[2]));
70		}
71		}
72
		78.6% Uncovered Elements: 3 (14) Complexity: 3 Complexity Density: 0.25
73	10	AlignmentI readAlignmentFile(File f)...
74		{
75	10	System.out.println("Reading file: " + f);
76	10	String ff = f.getPath();
77	10	try
78		{
79	10	FormatAdapter rf = new FormatAdapter();
80
81	10	AlignmentI al = rf.readFile(ff, DataSourceType.FILE,
82		new IdentifyFile().identify(ff, DataSourceType.FILE));
83
84		// make sure dataset is initialised ? not sure about this
85	160	for (int i = 0; i < al.getSequencesArray().length; ++i)
86		{
87	150	al.getSequenceAt(i).createDatasetSequence();
88		}
89	10	assertNotNull("Couldn't read supplied alignment data.", al);
90	10	return al;
91		} catch (Exception e)
92		{
93	0	e.printStackTrace();
94		}
95	0	Assert.fail("Couln't read the alignment in file '" + f.toString() + "'");
96	0	return null;
97		}
98
99		/**
100		* test alignment data in given file can be imported, exported and reimported
101		* with no dataloss
102		*
103		* @param f
104		* - source datafile (IdentifyFile.identify() should work with it)
105		* @param ioformat
106		* - label for IO class used to write and read back in the data from
107		* f
108		*/
		88.9% Uncovered Elements: 2 (18) Complexity: 2 Complexity Density: 0.11
109	5	void testAnnotationFileIO(String testname, File f,...
110		File annotFile)
111		{
112	5	System.out.println("Test: " + testname + "\nReading annotation file '"
113		+ annotFile + "' onto : " + f);
114	5	String af = annotFile.getPath();
115	5	try
116		{
117	5	AlignmentI al = readAlignmentFile(f);
118	5	HiddenColumns cs = new HiddenColumns();
119	5	assertTrue(
120		"Test "
121		+ testname
122		+ "\nAlignment was not annotated - annotation file not imported.",
123		new AnnotationFile().readAnnotationFile(al, cs, af,
124		DataSourceType.FILE));
125
126	5	AnnotationFile aff = new AnnotationFile();
127		// ViewDef is not used by Jalview
128	5	ViewDef v = aff.new ViewDef(null, al.getHiddenSequences(), cs,
129		new Hashtable());
130	5	String anfileout = new AnnotationFile().printAnnotations(
131		al.getAlignmentAnnotation(), al.getGroups(),
132		al.getProperties(), null, al, v);
133	5	assertTrue(
134		"Test "
135		+ testname
136		+ "\nAlignment annotation file was not regenerated. Null string",
137		anfileout != null);
138	5	assertTrue(
139		"Test "
140		+ testname
141		+ "\nAlignment annotation file was not regenerated. Empty string",
142		anfileout.length() > "JALVIEW_ANNOTATION".length());
143
144	5	System.out.println("Output annotation file:\n" + anfileout
145		+ "\n<<EOF\n");
146
147	5	AlignmentI al_new = readAlignmentFile(f);
148	5	assertTrue(
149		"Test "
150		+ testname
151		+ "\nregenerated annotation file did not annotate alignment.",
152		new AnnotationFile().readAnnotationFile(al_new, anfileout,
153		DataSourceType.PASTE));
154
155		// test for consistency in io
156	5	StockholmFileTest.testAlignmentEquivalence(al, al_new, false, false,
157		false);
158	5	return;
159		} catch (Exception e)
160		{
161	0	e.printStackTrace();
162		}
163	0	Assert.fail("Test "
164		+ testname
165		+ "\nCouldn't complete Annotation file roundtrip input/output/input test for '"
166		+ annotFile + "'.");
167		}
168		}