Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AnnotationFileIOTest	47	172	17	0.818181881.8%	Show methods

Class AnnotationFileIOTest

Class AnnotationFileIOTest	Line # 47	Total Statements 172	Complexity 17	TOTAL Coverage 0.818181881.8%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	5050	2.02	1.01	1.0 1.0100%
exampleAnnotationFileIO() : void   exampleAnnotationFileIO() : void	7575	2.02	1.01	1.0 1.0100%
readAlignmentFile(File) : AlignmentI   readAlignmentFile(File) : AlignmentI	8585	12.012	3.03	0.78571427 0.7857142778.6%
testAnnotationFileIO(String,File,File) : void   testAnnotationFileIO(String,File,File) : void	122122	18.018	2.02	0.8888889 0.888888988.9%
testAnnotateAlignmentView() : void   testAnnotateAlignmentView() : void	172172	22.022	1.01	1.0 1.0100%
testCalcIdRestore() : void   testCalcIdRestore() : void	214214	66.066	6.06	0.8857143 0.885714388.6%
testProviderRestore() : void   testProviderRestore() : void	328328	31.031	1.01	1.0 1.0100%
testIsPropertyValueToken() : void   testIsPropertyValueToken() : void	385385	10.010	1.01	0.0 0.00%
testValidKeywords() : void   testValidKeywords() : void	403403	9.09	1.01	0.0 0.00%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.3368984	jalview.io.AnnotationFileIOTest.testCalcIdRestorejalview.io.AnnotationFileIOTest.testCalcIdRestore	1PASS
	0.171123	jalview.io.AnnotationFileIOTest.exampleAnnotationFileIOjalview.io.AnnotationFileIOTest.exampleAnnotationFileIO	1PASS
	0.171123	jalview.io.AnnotationFileIOTest.testProviderRestorejalview.io.AnnotationFileIOTest.testProviderRestore	1PASS
	0.122994654	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.Assert.assertFalse;
24		import static org.testng.Assert.assertNull;
25		import static org.testng.AssertJUnit.assertEquals;
26		import static org.testng.AssertJUnit.assertNotNull;
27		import static org.testng.AssertJUnit.assertTrue;
28
29		import java.awt.Color;
30		import java.io.File;
31		import java.util.Hashtable;
32		import java.util.Iterator;
33		import java.util.List;
34
35		import org.testng.Assert;
36		import org.testng.annotations.BeforeClass;
37		import org.testng.annotations.Test;
38
39		import jalview.datamodel.AlignmentAnnotation;
40		import jalview.datamodel.AlignmentI;
41		import jalview.datamodel.HiddenColumns;
42		import jalview.datamodel.SequenceGroup;
43		import jalview.gui.AlignFrame;
44		import jalview.gui.JvOptionPane;
45		import jalview.io.AnnotationFile.ViewDef;
46
		81.8% Uncovered Elements: 34 (187) Complexity: 17 Complexity Density: 0.1
47		public class AnnotationFileIOTest
48		{
49
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
50	1	@BeforeClass(alwaysRun = true)...
51		public void setUpJvOptionPane()
52		{
53	1	JvOptionPane.setInteractiveMode(false);
54	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
55		}
56
57		static String TestFiles[][] = { { "Test example annotation import/export",
58		"examples/uniref50.fa", "examples/testdata/example_annot_file.jva" },
59		{ "Test multiple combine annotation statements import/export",
60		"examples/uniref50.fa",
61		"examples/testdata/test_combine_annot.jva" },
62		{ "Test multiple combine annotation statements with sequence_ref import/export",
63		"examples/uniref50.fa", "examples/testdata/uniref50_iupred.jva" },
64		{ "Test group only annotation file parsing results in parser indicating annotation was parsed",
65		"examples/uniref50.fa", "examples/testdata/test_grpannot.jva" },
66		{ "Test hiding/showing of insertions on sequence_ref",
67		"examples/uniref50.fa",
68		"examples/testdata/uniref50_seqref.jva" },
69		{ "Test example annotation with calcid import/export",
70		"examples/uniref50.fa", "examples/testdata/example_annot_file_calcid.jva" },
71		{ "Test example annotation with annotation property import/export",
72		"examples/uniref50.fa", "examples/testdata/example_annot_file_property.jva" }
73		};
74
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5 1PASS
75	1	@Test(groups = { "Functional" })...
76		public void exampleAnnotationFileIO() throws Exception
77		{
78	1	for (String[] testPair : TestFiles)
79		{
80	7	testAnnotationFileIO(testPair[0], new File(testPair[1]),
81		new File(testPair[2]));
82		}
83		}
84
		78.6% Uncovered Elements: 3 (14) Complexity: 3 Complexity Density: 0.25
85	14	protected AlignmentI readAlignmentFile(File f)...
86		{
87	14	System.out.println("Reading file: " + f);
88	14	String ff = f.getPath();
89	14	try
90		{
91	14	FormatAdapter rf = new FormatAdapter();
92
93	14	AlignmentI al = rf.readFile(ff, DataSourceType.FILE,
94		new IdentifyFile().identify(ff, DataSourceType.FILE));
95
96		// make sure dataset is initialised ? not sure about this
97	224	for (int i = 0; i < al.getSequencesArray().length; ++i)
98		{
99	210	al.getSequenceAt(i).createDatasetSequence();
100		}
101	14	assertNotNull("Couldn't read supplied alignment data.", al);
102	14	return al;
103		} catch (Exception e)
104		{
105	0	e.printStackTrace();
106		}
107	0	Assert.fail(
108		"Couln't read the alignment in file '" + f.toString() + "'");
109	0	return null;
110		}
111
112		/**
113		* test alignment data in given file can be imported, exported and reimported
114		* with no dataloss
115		*
116		* @param f
117		* - source datafile (IdentifyFile.identify() should work with it)
118		* @param ioformat
119		* - label for IO class used to write and read back in the data from
120		* f
121		*/
		88.9% Uncovered Elements: 2 (18) Complexity: 2 Complexity Density: 0.11
122	7	void testAnnotationFileIO(String testname, File f, File annotFile)...
123		{
124	7	System.out.println("Test: " + testname + "\nReading annotation file '"
125		+ annotFile + "' onto : " + f);
126	7	String af = annotFile.getPath();
127	7	try
128		{
129	7	AlignmentI al = readAlignmentFile(f);
130	7	HiddenColumns cs = new HiddenColumns();
131	7	assertTrue("Test " + testname
132		+ "\nAlignment was not annotated - annotation file not imported.",
133		new AnnotationFile().readAnnotationFile(al, cs, af,
134		DataSourceType.FILE));
135
136	7	AnnotationFile aff = new AnnotationFile();
137		// ViewDef is not used by Jalview
138	7	ViewDef v = aff.new ViewDef(null, al.getHiddenSequences(), cs,
139		new Hashtable());
140	7	String anfileout = new AnnotationFile().printAnnotations(
141		al.getAlignmentAnnotation(), al.getGroups(),
142		al.getProperties(), null, al, v);
143	7	assertTrue("Test " + testname
144		+ "\nAlignment annotation file was not regenerated. Null string",
145		anfileout != null);
146	7	assertTrue("Test " + testname
147		+ "\nAlignment annotation file was not regenerated. Empty string",
148		anfileout.length() > "JALVIEW_ANNOTATION".length());
149
150	7	System.out.println(
151		"Output annotation file:\n" + anfileout + "\n<<EOF\n");
152
153	7	AlignmentI al_new = readAlignmentFile(f);
154	7	assertTrue("Test " + testname
155		+ "\nregenerated annotation file did not annotate alignment.",
156		new AnnotationFile().readAnnotationFile(al_new, anfileout,
157		DataSourceType.PASTE));
158
159		// test for consistency in io
160	7	StockholmFileTest.testAlignmentEquivalence(al, al_new, false, false,
161		false);
162	7	return;
163		} catch (Exception e)
164		{
165	0	e.printStackTrace();
166		}
167	0	Assert.fail("Test " + testname
168		+ "\nCouldn't complete Annotation file roundtrip input/output/input test for '"
169		+ annotFile + "'.");
170		}
171
		100% Uncovered Elements: 0 (22) Complexity: 1 Complexity Density: 0.05 1PASS
172	1	@Test(groups = "Functional")...
173		public void testAnnotateAlignmentView()
174		{
175	1	long t1 = System.currentTimeMillis();
176		/*
177		* JAL-3779 test multiple groups of the same name get annotated
178		*/
179	1	AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
180		">Seq1\nQRSIL\n>Seq2\nFTHND\n>Seq3\nRPVSL\n",
181		DataSourceType.PASTE);
182	1	long t2 = System.currentTimeMillis();
183	1	System.err.println("t0: " + (t2 - t1));
184		// seq1 and seq3 are in distinct groups both named Group1
185	1	String annotationFile = "JALVIEW_ANNOTATION\nSEQUENCE_GROUP\tGroup1\t*\t*\t1\n"
186		+ "SEQUENCE_GROUP\tGroup2\t*\t*\t2\n"
187		+ "SEQUENCE_GROUP\tGroup1\t*\t*\t3\n"
188		+ "PROPERTIES\tGroup1\toutlineColour=blue\tidColour=red\n";
189	1	new AnnotationFile().annotateAlignmentView(af.getViewport(),
190		annotationFile, DataSourceType.PASTE);
191
192	1	AlignmentI al = af.getViewport().getAlignment();
193	1	List<SequenceGroup> groups = al.getGroups();
194	1	assertEquals(3, groups.size());
195	1	SequenceGroup sg = groups.get(0);
196	1	assertEquals("Group1", sg.getName());
197	1	assertTrue(sg.contains(al.getSequenceAt(0)));
198	1	assertEquals(Color.BLUE, sg.getOutlineColour());
199	1	assertEquals(Color.RED, sg.getIdColour());
200	1	sg = groups.get(1);
201	1	assertEquals("Group2", sg.getName());
202	1	assertTrue(sg.contains(al.getSequenceAt(1)));
203
204		/*
205		* the bug fix: a second group of the same name is also given properties
206		*/
207	1	sg = groups.get(2);
208	1	assertEquals("Group1", sg.getName());
209	1	assertTrue(sg.contains(al.getSequenceAt(2)));
210	1	assertEquals(Color.BLUE, sg.getOutlineColour());
211	1	assertEquals(Color.RED, sg.getIdColour());
212		}
213
		88.6% Uncovered Elements: 8 (70) Complexity: 6 Complexity Density: 0.09 1PASS
214	1	@Test(groups = "Functional")...
215		public void testCalcIdRestore()
216		{
217	1	long t1 = System.currentTimeMillis();
218		/*
219		* JAL-3779 test multiple groups of the same name get annotated
220		*/
221	1	AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
222		">Seq1\nQRSIL\n>Seq2\nFTHND\n>Seq3\nRPVSL\n",
223		DataSourceType.PASTE);
224	1	long t2 = System.currentTimeMillis();
225	1	System.err.println("t0: " + (t2 - t1));
226		// seq1 and seq3 are in distinct groups both named Group1
227	1	String annotationFile = "JALVIEW_ANNOTATION\nCALCID\tmyCalcId\tNO_GRAPH\tA Label\tfoolabel\tt|t|t|t\n"
228		+ "CALCID\tmyCalcId\tROWPROPERTIES\tA Label\tspecial=property\n"
229		+ "NO_GRAPH\tWithout CALCID 1\tfoolabel\tt|t|t|t\n"
230		+ "ROWPROPERTIES\tWithout CALCID 1\tspecial=property\n"
231		+ "CALCID\tNO_GRAPH\tWithout CALCID 2\tfoolabel\tt|t|t|t\n"
232		+ "CALCID\tROWPROPERTIES\tWithout CALCID 2\tspecial=property\n"
233		+ "CALCID\tmyCalcId2\tNO_GRAPH\tA Label\tfoolabel\tt|t|t|t\n"
234		+ "CALCID\tmyCalcId2\tROWPROPERTIES\tA Label\tspecial=property\n"
235		+ "SEQUENCE_REF\tSeq3\n"
236		+ "CALCID\tmyCalcId\tNO_GRAPH\tA Label\tfoolabel\tt|t|t|t\n"
237		+ "CALCID\tmyCalcId\tROWPROPERTIES\tA Label\tspecial=seqproperty\n"
238		+ "SEQUENCE_REF\t\n"
239		+ "BAR_GRAPH\tSeqTrack\tseqs 4\tt|t|t|t\tNO_OF_SEQUENCES=4\tNO_OF_TRACKS=1\n"
240		;
241
242
243	1	assertTrue(new AnnotationFile().annotateAlignmentView(af.getViewport(),
244		annotationFile, DataSourceType.PASTE));
245	1	AlignmentI al = af.getViewport().getAlignment();
246	1	int length = al.getAlignmentAnnotation().length;
247	1	AlignmentAnnotation[] alignAnnot = al.getAlignmentAnnotation();
248	1	Iterable<AlignmentAnnotation> myCalcIdRows = al
249		.findAnnotation("myCalcId");
250	1	assertNotNull(myCalcIdRows);
251		// Expect 2 - one for the alignment and one for the sequence
252	1	Iterator<AlignmentAnnotation> rows = myCalcIdRows.iterator();
253	1	assertTrue(rows.hasNext());
254	1	AlignmentAnnotation nextan = rows.next();
255	1	assertEquals(nextan.label, "A Label");
256	1	assertEquals("property", nextan.getProperty("special"));
257	1	assertTrue(nextan.sequenceRef == null);
258
259
260		// second expected to be sequence associated
261	1	assertTrue(rows.hasNext());
262	1	nextan = rows.next();
263	1	assertEquals("seqproperty", nextan.getProperty("special"));
264	1	assertTrue(nextan.sequenceRef != null);
265		// Now check that the track is transferred to the dataset
266	1	AlignmentAnnotation dsseqan = nextan.sequenceRef.getDatasetSequence()
267		.getAlignmentAnnotations(nextan.getCalcId(), nextan.label)
268		.get(0);
269	1	assertEquals("seqproperty", dsseqan.getProperty("special"));
270	1	assertFalse(rows.hasNext());
271
272	1	Iterable<AlignmentAnnotation> myCalcId2Rows = al
273		.findAnnotation("myCalcId2");
274	1	assertNotNull(myCalcId2Rows);
275	1	rows = myCalcId2Rows.iterator();
276	1	assertTrue(rows.hasNext());
277	1	nextan = rows.next();
278	1	assertEquals(nextan.label, "A Label");
279	1	assertEquals("property", nextan.getProperty("special"));
280	1	assertTrue(nextan.sequenceRef == null);
281
282	1	Iterable<AlignmentAnnotation> withoutCalcIdRows = al
283		.findAnnotation("");
284	1	assertNotNull(withoutCalcIdRows);
285	1	rows = withoutCalcIdRows.iterator();
286	1	assertTrue(rows.hasNext());
287	1	nextan = rows.next();
288	1	assertEquals(nextan.label, "Without CALCID 1");
289	1	assertTrue(rows.hasNext());
290	1	nextan = rows.next();
291	1	assertEquals(nextan.label, "Without CALCID 2");
292	1	assertEquals(-1,nextan.getNoOfSequencesIncluded());
293	1	assertEquals(-1,nextan.getNoOfTracksIncluded());
294
295		// Check sequence and annotation track counts are imported
296	1	nextan = rows.next();
297	1	assertEquals("SeqTrack",nextan.label);
298	1	assertEquals(4,nextan.getNoOfSequencesIncluded());
299	1	assertEquals(1,nextan.getNoOfTracksIncluded());
300	1	assertFalse(nextan.getProperties().contains(jalview.io.AnnotationFile.NO_OF_SEQUENCES));
301	1	assertFalse(nextan.getProperties().contains(jalview.io.AnnotationFile.NO_OF_TRACKS));
302	1	AlignmentAnnotation consAnn=null;
303	1	long tries=100;
304	?	while (tries-->0 && (consAnn = af.getViewport().getAlignmentConsensusAnnotation())==null
305		|| consAnn.getNoOfSequencesIncluded()==-1) {
306	0	try {
307	0	Thread.sleep(30);
308	0	} catch (Exception x) { Assert.fail("Interrupted wating for calculation...");};
309		}
310	1	if (tries==0)
311		{
312	0	Assert.fail("Gave up waiting for consensus calculation.");
313		}
314		// Now check we have expected metadata - ideally we'd do a round trip here..
315	1	String annFile = new jalview.io.AnnotationFile().printAnnotationsForView(af.getViewport());
316	1	assertTrue(annFile.contains("NO_OF_SEQUENCES=4"));
317	1	assertTrue(annFile.contains("NO_OF_TRACKS=1"));
318		// expect at least one NO_OF_SEQUENCES=3 that occurs after 'Consensus'
319	1	assertTrue(annFile.contains("Consensus"));
320	1	int consensusLineEnds = annFile.indexOf("\n",annFile.indexOf("Consensus"));
321	1	int no_of_seq_pos=annFile.indexOf("NO_OF_SEQUENCES=3",annFile.indexOf("Consensus"));
322	1	assertTrue("Couldn't find NO_OF_SEQUENCES after start of Consensus annotation row",no_of_seq_pos>-1);
323	1	assertTrue("Couldn't find NO_OF_SEQUENCES before end of Consensus annotation row",no_of_seq_pos<consensusLineEnds);
324
325		}
326
327
		100% Uncovered Elements: 0 (31) Complexity: 1 Complexity Density: 0.03 1PASS
328	1	@Test(groups = "Functional")...
329		public void testProviderRestore()
330		{
331	1	long t1 = System.currentTimeMillis();
332		/*
333		* JAL-3779 test multiple groups of the same name get annotated
334		*/
335	1	AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
336		">Seq1\nQRSIL\n>Seq2\nFTHND\n>Seq3\nRPVSL\n",
337		DataSourceType.PASTE);
338	1	long t2 = System.currentTimeMillis();
339	1	System.err.println("t0: " + (t2 - t1));
340		// seq1 and seq3 are in distinct groups both named Group1
341	1	String annotationFile = "JALVIEW_ANNOTATION\n"
342		+ "CALCID\tmyCalcId\tNO_GRAPH\tA Label\tfoolabel\tt|t|t|t\tSS_PROVIDER=PDB\tproperty2=abc\t4property=xyz\n"
343		+ "CALCID\tmyCalcId\tROWPROPERTIES\tA Label\tspecial=property\n"
344		+ "CALCID\tmyCalcId\tNO_GRAPH\tA Label\tfoolabel\tt|t|t|t\t\n"
345		+ "CALCID\tmyCalcId\tROWPROPERTIES\tA Label\tspecial=property\n"
346		+ "SEQUENCE_REF\tSeq3\n"
347		+ "\nCALCID\tmyCalcId\tNO_GRAPH\tA Label\tfoolabel\tt|t|t|t\t1.0\t2.0\t3.0\tSS_PROVIDER=JPred\tproperty3=value1\n"
348		+ "\nCALCID\tmyCalcId\tROWPROPERTIES\tA Label\tspecial=seqproperty\n";
349	1	new AnnotationFile().annotateAlignmentView(af.getViewport(),
350		annotationFile, DataSourceType.PASTE);
351	1	AlignmentI al = af.getViewport().getAlignment();
352	1	Iterable<AlignmentAnnotation> myCalcIdRows = al
353		.findAnnotation("myCalcId");
354	1	assertNotNull(myCalcIdRows);
355		// Expect 3 - 2 for the alignment and one for the sequence
356	1	Iterator<AlignmentAnnotation> rows = myCalcIdRows.iterator();
357	1	assertTrue(rows.hasNext());
358	1	AlignmentAnnotation nextan = rows.next();
359	1	assertEquals(nextan.label, "A Label");
360	1	assertEquals("property", nextan.getProperty("special"));
361	1	assertEquals("PDB", nextan.getProperty("SS_PROVIDER"));
362	1	assertEquals("abc", nextan.getProperty("property2"));
363	1	assertEquals(null, nextan.getProperty("4property"));
364	1	assertTrue(nextan.sequenceRef == null);
365		// second row without data properties
366	1	assertTrue(rows.hasNext());
367	1	nextan = rows.next();
368	1	assertEquals(nextan.label, "A Label");
369		// third expected to be sequence associated
370	1	assertTrue(rows.hasNext());
371	1	nextan = rows.next();
372	1	assertEquals("seqproperty", nextan.getProperty("special"));
373	1	assertEquals("JPred", nextan.getProperty("SS_PROVIDER"));
374	1	assertEquals("value1", nextan.getProperty("property3"));
375	1	assertEquals(3.0, nextan.score);
376	1	assertTrue(nextan.sequenceRef != null);
377		// Now check that the track is transferred to the dataset
378	1	AlignmentAnnotation dsseqan = nextan.sequenceRef.getDatasetSequence()
379		.getAlignmentAnnotations(nextan.getCalcId(), nextan.label)
380		.get(0);
381	1	assertEquals("seqproperty", dsseqan.getProperty("special"));
382	1	assertEquals("JPred", dsseqan.getProperty("SS_PROVIDER"));
383		}
384
		0% Uncovered Elements: 10 (10) Complexity: 1 Complexity Density: 0.1 1PASS
385	0	@Test...
386		public void testIsPropertyValueToken() {
387	0	AnnotationFile annotationFile = new AnnotationFile();
388
389		// Valid cases
390	0	assertTrue(annotationFile.isPropertyValueToken("property=value"));
391	0	assertTrue(annotationFile.isPropertyValueToken("_myProperty123=myValue123"));
392	0	assertTrue(annotationFile.isPropertyValueToken("_myProperty123=123"));
393
394		// Invalid cases
395	0	assertFalse(annotationFile.isPropertyValueToken("=value")); // no key
396	0	assertFalse(annotationFile.isPropertyValueToken("key=")); // no value
397	0	assertFalse(annotationFile.isPropertyValueToken("123key=value")); // invalid key
398	0	assertFalse(annotationFile.isPropertyValueToken("@key=value")); // invalid key
399	0	assertFalse(annotationFile.isPropertyValueToken("property")); // no =
400	0	assertFalse(annotationFile.isPropertyValueToken("")); // empty string
401		}
402
		0% Uncovered Elements: 9 (9) Complexity: 1 Complexity Density: 0.11 1PASS
403	0	@Test...
404		public void testValidKeywords() {
405	0	AnnotationFile annotationFile = new AnnotationFile();
406	0	assertTrue(annotationFile.isAnnotationKeyword("BAR_GRAPH"));
407	0	assertTrue(annotationFile.isAnnotationKeyword("bar_graph"));
408	0	assertTrue(annotationFile.isAnnotationKeyword("BarGraph"));
409	0	assertTrue(annotationFile.isAnnotationKeyword("rowproperties"));
410	0	assertTrue(annotationFile.isAnnotationKeyword("VIEW_HIDECOLS"));
411	0	assertFalse(annotationFile.isAnnotationKeyword("INVALID"));
412	0	assertFalse(annotationFile.isAnnotationKeyword("ANNOTATION_ROW"));
413	0	assertFalse(annotationFile.isAnnotationKeyword(null));
414		}
415
416		}