test/jalview/ws/dbsources/EBIAlphaFoldTest.java

   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
  25 public class EBIAlphaFoldTest
  26 {
  27
  28   @BeforeClass(alwaysRun = true)
  29   public void setUpJvOptionPane()
  30   {
  31     JvOptionPane.setInteractiveMode(false);
  32     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  33   }
  34
  35   @DataProvider(name = "getExamplePAEfiles")
  36   public Object[][] getExamplePAEfiles()
  37   {
  38     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
  47   @Test(groups = { "Functional" }, dataProvider = "getExamplePAEfiles")
  48   public void checkPAEimport(String paeFile) throws Exception
  49   {
  50     PAEContactMatrix cm = new PAEContactMatrix(
  51             new Sequence("Dummy/1-2000", "ASDASDA"),
  52             EBIAlfaFold.parseJSONtoPAEContactMatrix(
  53                     new FileInputStream(paeFile)));
  54     Assert.assertNotEquals(cm.getMax(), 0.0f, "No data from " + paeFile);
  55   }
  56
  57   @Test(groups = { "Functional" }, dataProvider = "getPDBandPAEfiles")
  58   public void checkImportPAEToStructure(String pdbFile, String paeFile)
  59   {
  60     FileInputStream paeInput = null;
  61     try
  62     {
  63       paeInput = new FileInputStream(paeFile);
  64     } catch (FileNotFoundException e)
  65     {
  66       e.printStackTrace();
  67       FileAssert.assertFile(new File(paeFile),
  68               "Test file '" + paeFile + "' doesn't seem to exist");
  69     }
  70     SequenceI seq = new Sequence("Dummy/1-2000", "ASDASDA");
  71     AlignmentI al = new Alignment(new SequenceI[] { seq });
  72     StructureSelectionManager ssm = StructureSelectionManager
  73             .getStructureSelectionManager(Desktop.instance);
  74     StructureMapping sm = new StructureMapping(seq, pdbFile, null, null,
  75             null, null);
  76     ssm.addStructureMapping(sm);
  77
  78     StructureMapping[] smArray = ssm.getMapping(pdbFile);
  79
  80     try
  81     {
  82       boolean done = EBIAlfaFold.importPaeJSONAsContactMatrixToStructure(
  83               smArray, paeInput, "label");
  84       Assert.assertTrue(done,
  85               "Import of '" + paeFile + "' didn't complete successfully");
  86     } catch (IOException | ParseException e)
  87     {
  88       Assert.fail("Exception importing paefile '" + paeFile + "'", e);
  89     }
  90   }
  91
  92   @DataProvider(name = "getPDBandPAEfiles")
  93   public Object[][] getPDBandPAEfiles()
  94   {
  95     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 }