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package jalview.ws.dbsources; |
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import java.io.File; |
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import java.io.FileInputStream; |
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import java.io.FileNotFoundException; |
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import java.io.IOException; |
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import org.json.simple.parser.ParseException; |
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import org.testng.Assert; |
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import org.testng.FileAssert; |
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import org.testng.annotations.BeforeClass; |
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import org.testng.annotations.DataProvider; |
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import org.testng.annotations.Test; |
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import jalview.datamodel.Alignment; |
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import jalview.datamodel.AlignmentI; |
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import jalview.datamodel.Sequence; |
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import jalview.datamodel.SequenceI; |
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import jalview.gui.Desktop; |
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import jalview.gui.JvOptionPane; |
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import jalview.structure.StructureMapping; |
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import jalview.structure.StructureSelectionManager; |
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import jalview.ws.datamodel.alphafold.PAEContactMatrix; |
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| 88.5% |
Uncovered Elements: 3 (26) |
Complexity: 7 |
Complexity Density: 0.33 |
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public class EBIAlphaFoldTest |
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{ |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
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 @BeforeClass(alwaysRun = true)... |
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public void setUpJvOptionPane() |
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{ |
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JvOptionPane.setInteractiveMode(false); |
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JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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@DataProvider(name = "getExamplePAEfiles")... |
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public Object[][] getExamplePAEfiles() |
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{ |
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return new String[][] { |
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{ "examples/test_fab41.result/test_fab41_predicted_aligned_error_v1.json" }, |
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{ "examples/AlphaFold/AF-A0A1U8FD60-F1-predicted_aligned_error_v4.json" }, |
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{ "examples/AlphaFold/AF-Q5VSL9-F1-predicted_aligned_error_v4.json" }, |
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}; |
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} |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
1PASS
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3 |
@Test(groups = { "Functional" }, dataProvider = "getExamplePAEfiles")... |
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public void checkPAEimport(String paeFile) throws Exception |
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{ |
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PAEContactMatrix cm = new PAEContactMatrix( |
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new Sequence("Dummy/1-2000", "ASDASDA"), |
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EBIAlfaFold.parseJSONtoPAEContactMatrix( |
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new FileInputStream(paeFile))); |
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Assert.assertNotEquals(cm.getMax(), 0.0f, "No data from " + paeFile); |
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} |
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| 80% |
Uncovered Elements: 3 (15) |
Complexity: 3 |
Complexity Density: 0.2 |
1PASS
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@Test(groups = { "Functional" }, dataProvider = "getPDBandPAEfiles")... |
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public void checkImportPAEToStructure(String pdbFile, String paeFile) |
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{ |
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FileInputStream paeInput = null; |
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try |
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{ |
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paeInput = new FileInputStream(paeFile); |
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} catch (FileNotFoundException e) |
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{ |
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e.printStackTrace(); |
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FileAssert.assertFile(new File(paeFile), |
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"Test file '" + paeFile + "' doesn't seem to exist"); |
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} |
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SequenceI seq = new Sequence("Dummy/1-2000", "ASDASDA"); |
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AlignmentI al = new Alignment(new SequenceI[] { seq }); |
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StructureSelectionManager ssm = StructureSelectionManager |
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.getStructureSelectionManager(Desktop.instance); |
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StructureMapping sm = new StructureMapping(seq, pdbFile, null, null, |
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null, null); |
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ssm.addStructureMapping(sm); |
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StructureMapping[] smArray = ssm.getMapping(pdbFile); |
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try |
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{ |
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boolean done = EBIAlfaFold.importPaeJSONAsContactMatrixToStructure( |
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smArray, paeInput, "label"); |
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Assert.assertTrue(done, |
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"Import of '" + paeFile + "' didn't complete successfully"); |
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} catch (IOException | ParseException e) |
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{ |
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Assert.fail("Exception importing paefile '" + paeFile + "'", e); |
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} |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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1 |
@DataProvider(name = "getPDBandPAEfiles")... |
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public Object[][] getPDBandPAEfiles() |
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{ |
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return new String[][] { |
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{ "examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb", |
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"examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3_scores.json" }, |
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{ "examples/AlphaFold/AF-A0A1U8FD60-F1-model_v4.pdb", |
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"examples/AlphaFold/AF-A0A1U8FD60-F1-predicted_aligned_error_v4.json" }, |
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{ "examples/AlphaFold/AF-Q5VSL9-F1-model_v4.pdb", |
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"examples/AlphaFold/AF-Q5VSL9-F1-predicted_aligned_error_v4.json" }, |
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}; |
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} |
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} |
