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Coverage Report

  1. Project Clover database Fri Jul 3 2026 14:09:54 BST
  2. Package jalview.ws.dbsources

File EBIAlphaFoldTest.java

 
checkImportPAEToStructure: Exception importing paefile 'examples/AlphaFold/AF-Q5VSL9...
testImportPAEAndStructureForMultiChainSeqs: Couln't create a mapping for this matrix.
 

Code metrics

2
60
9
1
211
173
14
0.23
6.67
9
1.56

Classes

Class Line # Actions
EBIAlphaFoldTest 31 60 14
0.6478873564.8%
 

Contributing tests

This file is covered by 16 tests. .

Source view

1    package jalview.ws.dbsources;
2   
3    import static org.junit.Assert.assertNotEquals;
4   
5    import java.io.File;
6    import java.io.FileInputStream;
7    import java.io.FileNotFoundException;
8    import java.io.IOException;
9   
10    import org.json.simple.parser.ParseException;
11    import org.testng.Assert;
12    import org.testng.FileAssert;
13    import org.testng.annotations.BeforeClass;
14    import org.testng.annotations.DataProvider;
15    import org.testng.annotations.Test;
16   
17    import jalview.analysis.AlignmentUtils;
18    import jalview.bin.Console;
19    import jalview.datamodel.Alignment;
20    import jalview.datamodel.AlignmentI;
21    import jalview.datamodel.Sequence;
22    import jalview.datamodel.SequenceI;
23    import jalview.gui.Desktop;
24    import jalview.gui.JvOptionPane;
25    import jalview.io.DataSourceType;
26    import jalview.io.FileLoader;
27    import jalview.structure.StructureMapping;
28    import jalview.structure.StructureSelectionManager;
29    import jalview.ws.datamodel.alphafold.PAEContactMatrix;
30   
 
31    public class EBIAlphaFoldTest
32    {
33   
 
34  1 toggle @BeforeClass(alwaysRun = true)
35    public void setUpJvOptionPane()
36    {
37  1 JvOptionPane.setInteractiveMode(false);
38  1 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
39    }
40   
 
41  1 toggle @DataProvider(name = "getExamplePAEfiles")
42    public Object[][] getExamplePAEfiles()
43    {
44  1 return new String[][] {
45    //
46    { "examples/test_fab41.result/test_fab41_predicted_aligned_error_v1.json" },
47    { "examples/AlphaFold/AF-A0A1U8FD60-F1-predicted_aligned_error_v4.json" },
48    { "examples/AlphaFold/AF-Q5VSL9-F1-predicted_aligned_error_v4.json" },
49    {"examples/AlphaFold/AF-Q5VSL9-F1-predicted_aligned_error_v4_cmp.json" },
50    {"examples/AlphaFold/AF-0000000203848083-predicted_aligned_error_v1.json" },
51    //
52    };
53    }
54   
 
55  5 toggle @Test(groups = { "Functional" }, dataProvider = "getExamplePAEfiles")
56    public void checkPAEimport(String paeFile) throws Exception
57    {
58  5 PAEContactMatrix cm = new PAEContactMatrix(
59    new Sequence("Dummy/1-2000", "ASDASDA"),
60    EBIAlfaFold.parseJSONtoPAEContactMatrix(
61    new FileInputStream(paeFile)));
62  5 Assert.assertNotEquals(cm.getMax(), 0.0f, "No data from " + paeFile);
63    }
64   
 
65  5 toggle @Test(groups = { "Functional" }, dataProvider = "getPDBandPAEfiles")
66    public void checkImportPAEToStructure(String pdbFile, String paeFile)
67    {
68  5 FileInputStream paeInput = null;
69  5 try
70    {
71  5 paeInput = new FileInputStream(paeFile);
72    } catch (FileNotFoundException e)
73    {
74  0 e.printStackTrace();
75  0 FileAssert.assertFile(new File(paeFile),
76    "Test file '" + paeFile + "' doesn't seem to exist");
77    }
78  5 SequenceI seq = new Sequence("Dummy/1-2000", "ASDASDA");
79  5 AlignmentI al = new Alignment(new SequenceI[] { seq });
80  5 StructureSelectionManager ssm = StructureSelectionManager
81    .getStructureSelectionManager(Desktop.instance);
82  5 StructureMapping sm = new StructureMapping(seq, pdbFile, null, null,
83    null, null);
84  5 ssm.addStructureMapping(sm);
85   
86  5 StructureMapping[] smArray = ssm.getMapping(pdbFile);
87   
88  5 try
89    {
90  5 Test failure here boolean done = EBIAlfaFold.importPaeJSONAsContactMatrixToStructure(
91    smArray, paeInput, "label");
92  4 Assert.assertTrue(done,
93    "Import of '" + paeFile + "' didn't complete successfully");
94    } catch (IOException | ParseException e)
95    {
96  0 Test failure here Assert.fail("Exception importing paefile '" + paeFile + "'", e);
97    }
98    }
99   
 
100  2 toggle @DataProvider(name = "getPDBandPAEfiles")
101    public Object[][] getPDBandPAEfiles()
102    {
103  2 return new String[][] {
104    //
105    /*
106    */
107    { "examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb",
108    "examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3_scores.json" },
109    { "examples/AlphaFold/AF-A0A1U8FD60-F1-model_v4.pdb",
110    "examples/AlphaFold/AF-A0A1U8FD60-F1-predicted_aligned_error_v4.json" },
111    { "examples/AlphaFold/AF-Q5VSL9-F1-model_v4.pdb",
112    "examples/AlphaFold/AF-Q5VSL9-F1-predicted_aligned_error_v4.json" },
113    { "examples/AlphaFold/AF-Q5VSL9-F1-model_v4.pdb",
114    "examples/AlphaFold/AF-Q5VSL9-F1-predicted_aligned_error_v4_cmp.json" },
115    { "examples/AlphaFold/AF-0000000203848083-model_v1.cif","examples/AlphaFold/AF-0000000203848083-predicted_aligned_error_v1.json" },
116    /*
117    */
118    };
119    }
120   
121    /**
122    * import PAE and structure as a fresh alignment
123    * @param pdbFile
124    * @param paeFile
125    */
 
126  5 toggle @Test(groups = { "Functional" }, dataProvider = "getPDBandPAEfiles")
127    public void checkImportPAEForStructure(String pdbFile, String paeFile) throws Exception
128    {
129  5 doTestImportMsaPaeForStructure(pdbFile, pdbFile, paeFile);
130    }
 
131  5 toggle protected void doTestImportMsaPaeForStructure(String alFile, String pdbFile, String paeFile) throws Exception
132    {
133  5 FileInputStream paeInput = null;
134  5 try
135    {
136  5 paeInput = new FileInputStream(paeFile);
137    } catch (FileNotFoundException e)
138    {
139  0 e.printStackTrace();
140  0 FileAssert.assertFile(new File(paeFile),
141    "Test file '" + paeFile + "' doesn't seem to exist");
142    }
143  5 String mp=new File(alFile).getAbsolutePath();
144  5 AlignmentI al = new FileLoader().LoadFileWaitTillLoaded(mp, DataSourceType.FILE).getViewport().getAlignment();
145   
146  5 StructureSelectionManager ssm = StructureSelectionManager
147    .getStructureSelectionManager(Desktop.instance);
148  5 String[] chainIds = new String[al.getHeight()];
149  5 int s=0;
150  5 for (SequenceI sq:al.getSequences())
151    {
152  6 chainIds[s++]=sq.getDatasetSequence().getAllPDBEntries().get(0).getChainCode();
153    }
154   
155  5 if (chainIds.length>1)
156    {
157  1 Console.info("Checking for multimer PAE import");
158    }
159    // lower level call - should do everything
160   
161  5 ssm.computeMapping(false, al.getSequencesArray(), chainIds, mp, DataSourceType.FILE, null, null, paeFile, true);
162  5 AlignmentUtils.addAllReferenceAnnotations(al);
163   
164  5 for (SequenceI sq:al.getSequences()) {
165  6 String failed=" no contact map found for "+sq.getName();
166  6 Assert.assertTrue(sq.getContactMaps()!=null,failed);
167  6 Assert.assertEquals(sq.getContactMaps().size(),1,failed);
168    }
169    }
170   
 
171  0 toggle @Test(groups= {"Functional"})
172    public void testImportPAEAndStructureForMultiChainSeqs() throws Exception
173    {
174  0 String pdbFile="examples/AlphaFold/AF-0000000203848083-model_v1.cif",paeFile="examples/AlphaFold/AF-0000000203848083-predicted_aligned_error_v1.json",faFile="examples/AlphaFold/AF-0000000203848083-uniprot.fa";
175  0 FileInputStream paeInput = null;
176  0 try
177    {
178  0 paeInput = new FileInputStream(paeFile);
179    } catch (FileNotFoundException e)
180    {
181  0 e.printStackTrace();
182  0 FileAssert.assertFile(new File(paeFile),
183    "Test file '" + paeFile + "' doesn't seem to exist");
184    }
185  0 AlignmentI al = new FileLoader().LoadFileWaitTillLoaded(new File(faFile).getAbsolutePath(), DataSourceType.FILE).getViewport().getAlignment();
186   
187  0 StructureSelectionManager ssm = StructureSelectionManager
188    .getStructureSelectionManager(Desktop.instance);
189  0 String[] chainIds = new String[] { "A","B"};
190   
191  0 String mp=new File(pdbFile).getAbsolutePath();
192   
193    // lower level call - should do everything
194  0 Test failure here ssm.computeMapping(false, al.getSequencesArray(), chainIds, mp, DataSourceType.FILE, null, null, paeFile, true);
195  0 AlignmentUtils.addAllReferenceAnnotations(al);
196   
197  0 for (SequenceI sq:al.getSequences()) {
198  0 String failed=" no contact map found for "+sq.getName();
199  0 Assert.assertTrue(sq.getContactMaps()!=null,failed);
200  0 Assert.assertEquals(sq.getContactMaps().size(),1,failed);
201    }
202   
203    }
204   
 
205  0 toggle @Test(groups = { "Network" })
206    public void testPing() throws Exception
207    {
208  0 String version = EBIAlfaFold.pingAPIVersion();
209  0 assertNotEquals("", version);
210    }
211    }
  • Report generated by OpenClover v 4.4.1 on Fri Jul 3 2026 14:18:07 BST using coverage data from Fri Jul 3 2026 14:17:56 BST.
  • OpenClover is free and open-source software.