Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
HmmerJSONProcessTest	18	28	5	0.00%	Show methods

Class HmmerJSONProcessTest

Class HmmerJSONProcessTest	Line # 18	Total Statements 28	Complexity 5	TOTAL Coverage 0.00%
getSearchResultFragmentAlignment() : AlignmentI   getSearchResultFragmentAlignment() : AlignmentI	2222	2.02	1.01	0.0 0.00%
getSearchResultAlignment() : AlignmentI   getSearchResultAlignment() : AlignmentI	3434	2.02	1.01	0.0 0.00%
parseHitTest() : void   parseHitTest() : void	4747	8.08	1.01	0.0 0.00%
parseJsonResultTest() : void   parseJsonResultTest() : void	7171	16.016	2.02	0.0 0.00%

 

Contributing tests

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1		package jalview.ws.ebi;
2
3		import jalview.datamodel.AlignmentAnnotation;
4		import jalview.datamodel.AlignmentI;
5		import jalview.datamodel.SequenceI;
6		import jalview.io.DataSourceType;
7		import jalview.io.FileFormat;
8		import jalview.io.FileParse;
9		import jalview.io.FormatAdapter;
10
11		import java.io.File;
12
13		import org.json.simple.JSONObject;
14		import org.json.simple.parser.JSONParser;
15		import org.testng.Assert;
16		import org.testng.annotations.Test;
17
		0% Uncovered Elements: 34 (34) Complexity: 5 Complexity Density: 0.18
18		public class HmmerJSONProcessTest {
19		public static File alignmentFragFile = new File(
20		"examples/testdata/hmmer3/alignment_frag.fa.gz");
21
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
22	0	private AlignmentI getSearchResultFragmentAlignment() throws Exception...
23		{
24	0	AlignmentI alf = new FormatAdapter().readFile(
25		alignmentFragFile.getAbsolutePath(), DataSourceType.FILE,
26		FileFormat.Fasta);
27
28	0	return alf;
29		}
30
31		public static File alignmentResultFile = new File(
32		"examples/testdata/hmmer3/alignment_res.fa.gz");
33
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
34	0	private AlignmentI getSearchResultAlignment() throws Exception...
35		{
36	0	AlignmentI alf = new FormatAdapter().readFile(
37		alignmentResultFile.getAbsolutePath(), DataSourceType.FILE,
38		FileFormat.Fasta);
39
40	0	return alf;
41		}
42
43		public static String hitTestFile = "examples/testdata/hmmer3/hit_fragment.json.gz",
44		hmmerResultFile = "examples/testdata/hmmer3/hmmeresult.json.gz";
45
46
		0% Uncovered Elements: 8 (8) Complexity: 1 Complexity Density: 0.12 4-
47	0	@Test(groups = { "Functional" })...
48		public void parseHitTest() throws Exception
49		{
50
51	0	Assert.assertTrue(new File(hitTestFile).exists(),
52		"Can't find test data.\n"
53		+ hitTestFile);
54	0	JSONParser jp = new JSONParser();
55		// read JSON in same way - via fileparse
56	0	Object hitfragment = jp.parse(new FileParse(hitTestFile,
57		DataSourceType.FILE).getReader());
58	0	Assert.assertTrue((hitfragment instanceof JSONObject),
59		"Didn't find a JSON object map in " + hitTestFile);
60	0	AlignmentI searchResult = getSearchResultFragmentAlignment();
61
62	0	Assert.assertTrue(searchResult != null && searchResult.getHeight() > 0,
63		"Didn't read search result alignment from " + alignmentFragFile);
64
65	0	HmmerJSONProcessor hjsp = new HmmerJSONProcessor(searchResult);
66	0	hjsp.addHit((JSONObject) hitfragment, 1);
67		// check that
68		// scores, posterior probabilities and stuff exist.
69		}
70
		0% Uncovered Elements: 18 (18) Complexity: 2 Complexity Density: 0.12 4-
71	0	@Test(groups = { "Functional" })...
72		public void parseJsonResultTest() throws Exception
73		{
74
75	0	Assert.assertTrue(new File(hmmerResultFile).exists(),
76		"Can't find test data.\n" + hmmerResultFile);
77
78	0	AlignmentI searchResult = getSearchResultAlignment();
79
80	0	Assert.assertTrue(searchResult != null && searchResult.getHeight() > 0,
81		"Didn't read search result alignment from " + alignmentFragFile);
82
83	0	HmmerJSONProcessor hjsp = new HmmerJSONProcessor(searchResult);
84	0	hjsp.parseFrom(new FileParse(hmmerResultFile, DataSourceType.FILE));
85	0	AlignmentAnnotation[] aa = searchResult.getSequenceAt(5)
86		.getAnnotation();
87	0	Assert.assertNotNull(aa);
88	0	Assert.assertEquals(aa.length, 3,
89		"didn't get expected set of annotation.\n");
90		// DPTSERWFHGHLSGKEAEKLLTeKGKHGSFLVRESQSHPGDFVLSVRTgddkgesndgKSKVTHVMIR-CQELKYDVGGGERFDSLTDLVEHYKKNPmvet
91		// LGTVLQLKQP
92		// 5789*****************9799***********************999998888888********.99**************************9999
93		// 899999*999
94		// AlignmentAnnotation
95		// 101 == 8
96	0	String seq = "tLGT";
97	0	SequenceI s5 = searchResult.getSequenceAt(5);
98	0	Assert.assertEquals(
99		s5.getSubSequence(s5.findIndex(225), s5.findIndex(229))
100		.getSequenceAsString(),
101		seq);
102	0	int pos = s5.findIndex(226);
103	0	for (AlignmentAnnotation an : aa)
104		{
105	0	if (an.label.startsWith("Posterior"))
106		{
107	0	Assert.assertEquals(an.annotations[pos].value, 8f);
108
109		}
110		}
111	0	;
112		// check that
113		// scores, posterior probabilities and stuff exist.
114		}
115		// Groovy test
116		// def al = Jalview.getAlignFrames()[0].getViewport().getAlignment()
117		// def jproc = new jalview.ws.ebi.HmmerJSONProcessor(al)
118		// jproc.parseFrom(new
119		// jalview.io.FileParse("examples/testdata/hmmer3/hmmeresult.json.gz","File"))
120		// jproc.updateView(Jalview.getAlignFrames()[0].getViewport())
121
122		}