Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
EBIAlphaFoldTest	25	21	7	0.8846153688.5%	Show methods

Class EBIAlphaFoldTest

Class EBIAlphaFoldTest	Line # 25	Total Statements 21	Complexity 7	TOTAL Coverage 0.8846153688.5%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	2828	2.02	1.01	1.0 1.0100%
getExamplePAEfiles() : Object[][]   getExamplePAEfiles() : Object[][]	3535	1.01	1.01	1.0 1.0100%
checkPAEimport(String) : void   checkPAEimport(String) : void	4747	2.02	1.01	1.0 1.0100%
checkImportPAEToStructure(String,String) : void   checkImportPAEToStructure(String,String) : void	5757	15.015	3.03	0.8 0.880%
getPDBandPAEfiles() : Object[][]   getPDBandPAEfiles() : Object[][]	9292	1.01	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.5	jalview.ws.dbsources.EBIAlphaFoldTest.checkImportPAEToStructurejalview.ws.dbsources.EBIAlphaFoldTest.checkImportPAEToStructure	1PASS
	0.5	jalview.ws.dbsources.EBIAlphaFoldTest.checkImportPAEToStructurejalview.ws.dbsources.EBIAlphaFoldTest.checkImportPAEToStructure	1PASS
	0.5	jalview.ws.dbsources.EBIAlphaFoldTest.checkImportPAEToStructurejalview.ws.dbsources.EBIAlphaFoldTest.checkImportPAEToStructure	1PASS
	0.115384616	jalview.ws.dbsources.EBIAlphaFoldTest.checkPAEimportjalview.ws.dbsources.EBIAlphaFoldTest.checkPAEimport	1PASS
	0.115384616	jalview.ws.dbsources.EBIAlphaFoldTest.checkPAEimportjalview.ws.dbsources.EBIAlphaFoldTest.checkPAEimport	1PASS
	0.115384616	jalview.ws.dbsources.EBIAlphaFoldTest.checkPAEimportjalview.ws.dbsources.EBIAlphaFoldTest.checkPAEimport	1PASS

 

Source view

1		package jalview.ws.dbsources;
2
3		import java.io.File;
4		import java.io.FileInputStream;
5		import java.io.FileNotFoundException;
6		import java.io.IOException;
7
8		import org.json.simple.parser.ParseException;
9		import org.testng.Assert;
10		import org.testng.FileAssert;
11		import org.testng.annotations.BeforeClass;
12		import org.testng.annotations.DataProvider;
13		import org.testng.annotations.Test;
14
15		import jalview.datamodel.Alignment;
16		import jalview.datamodel.AlignmentI;
17		import jalview.datamodel.Sequence;
18		import jalview.datamodel.SequenceI;
19		import jalview.gui.Desktop;
20		import jalview.gui.JvOptionPane;
21		import jalview.structure.StructureMapping;
22		import jalview.structure.StructureSelectionManager;
23		import jalview.ws.datamodel.alphafold.PAEContactMatrix;
24
		88.5% Uncovered Elements: 3 (26) Complexity: 7 Complexity Density: 0.33
25		public class EBIAlphaFoldTest
26		{
27
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
28	1	@BeforeClass(alwaysRun = true)...
29		public void setUpJvOptionPane()
30		{
31	1	JvOptionPane.setInteractiveMode(false);
32	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
33		}
34
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
35	1	@DataProvider(name = "getExamplePAEfiles")...
36		public Object[][] getExamplePAEfiles()
37		{
38	1	return new String[][] {
39		//
40		{ "examples/test_fab41.result/test_fab41_predicted_aligned_error_v1.json" },
41		{ "examples/AlphaFold/AF-A0A1U8FD60-F1-predicted_aligned_error_v4.json" },
42		{ "examples/AlphaFold/AF-Q5VSL9-F1-predicted_aligned_error_v4.json" },
43		//
44		};
45		}
46
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5 1PASS
47	3	@Test(groups = { "Functional" }, dataProvider = "getExamplePAEfiles")...
48		public void checkPAEimport(String paeFile) throws Exception
49		{
50	3	PAEContactMatrix cm = new PAEContactMatrix(
51		new Sequence("Dummy/1-2000", "ASDASDA"),
52		EBIAlfaFold.parseJSONtoPAEContactMatrix(
53		new FileInputStream(paeFile)));
54	3	Assert.assertNotEquals(cm.getMax(), 0.0f, "No data from " + paeFile);
55		}
56
		80% Uncovered Elements: 3 (15) Complexity: 3 Complexity Density: 0.2 1PASS
57	3	@Test(groups = { "Functional" }, dataProvider = "getPDBandPAEfiles")...
58		public void checkImportPAEToStructure(String pdbFile, String paeFile)
59		{
60	3	FileInputStream paeInput = null;
61	3	try
62		{
63	3	paeInput = new FileInputStream(paeFile);
64		} catch (FileNotFoundException e)
65		{
66	0	e.printStackTrace();
67	0	FileAssert.assertFile(new File(paeFile),
68		"Test file '" + paeFile + "' doesn't seem to exist");
69		}
70	3	SequenceI seq = new Sequence("Dummy/1-2000", "ASDASDA");
71	3	AlignmentI al = new Alignment(new SequenceI[] { seq });
72	3	StructureSelectionManager ssm = StructureSelectionManager
73		.getStructureSelectionManager(Desktop.instance);
74	3	StructureMapping sm = new StructureMapping(seq, pdbFile, null, null,
75		null, null);
76	3	ssm.addStructureMapping(sm);
77
78	3	StructureMapping[] smArray = ssm.getMapping(pdbFile);
79
80	3	try
81		{
82	3	boolean done = EBIAlfaFold.importPaeJSONAsContactMatrixToStructure(
83		smArray, paeInput, "label");
84	3	Assert.assertTrue(done,
85		"Import of '" + paeFile + "' didn't complete successfully");
86		} catch (IOException | ParseException e)
87		{
88	0	Assert.fail("Exception importing paefile '" + paeFile + "'", e);
89		}
90		}
91
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
92	1	@DataProvider(name = "getPDBandPAEfiles")...
93		public Object[][] getPDBandPAEfiles()
94		{
95	1	return new String[][] {
96		//
97		/*
98		*/
99		{ "examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb",
100		"examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3_scores.json" },
101		{ "examples/AlphaFold/AF-A0A1U8FD60-F1-model_v4.pdb",
102		"examples/AlphaFold/AF-A0A1U8FD60-F1-predicted_aligned_error_v4.json" },
103		{ "examples/AlphaFold/AF-Q5VSL9-F1-model_v4.pdb",
104		"examples/AlphaFold/AF-Q5VSL9-F1-predicted_aligned_error_v4.json" },
105		/*
106		*/
107		};
108		}
109
110		}