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.junit.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.Sequence;
  16 import jalview.gui.Desktop;
  17 import jalview.gui.JvOptionPane;
  18 import jalview.structure.StructureMapping;
  19 import jalview.structure.StructureSelectionManager;
  20 import jalview.ws.datamodel.alphafold.PAEContactMatrix;
  21
  22 public class EBIAlphaFoldTest
  23 {
  24
  25   @BeforeClass(alwaysRun = true)
  26   public void setUpJvOptionPane()
  27   {
  28     JvOptionPane.setInteractiveMode(false);
  29     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  30   }
  31
  32   @DataProvider(name = "getExamplePAEfiles")
  33   public Object[][] getExamplePAEfiles()
  34   {
  35     return new String[][] { {
  36         "examples/test_fab41.result/test_fab41_predicted_aligned_error_v1.json" },
  37         { "examples/AlphaFold/AF-A0A1U8FD60-F1-predicted_aligned_error_v4.json" },
  38         { "examples/AlphaFold/AF-Q5VSL9-F1-predicted_aligned_error_v4.json" },
  39         { "examples/AlphaFold/AF-Q5VSL9-F1-predicted_aligned_error_v4_2023.json" } };
  40   }
  41
  42   @Test(groups = { "Functional" }, dataProvider = "getExamplePAEfiles")
  43   public void checkPAEimport(String paeFile) throws Exception
  44   {
  45     PAEContactMatrix cm = new PAEContactMatrix(
  46             new Sequence("Dummy/1-2000", "ASDASDA"),
  47             EBIAlfaFold.parseJSONtoPAEContactMatrix(
  48                     new FileInputStream(paeFile)));
  49     Assert.assertNotEquals("No data from " + paeFile, cm.getMax(), 0);
  50   }
  51
  52   @Test(groups = { "Functional" }, dataProvider = "getPDBandPAEfiles")
  53   public void checkImportPAEToStructure(String pdbFile, String paeFile)
  54   {
  55     FileInputStream paeInput = null;
  56     try
  57     {
  58       paeInput = new FileInputStream(paeFile);
  59     } catch (FileNotFoundException e)
  60     {
  61       e.printStackTrace();
  62       FileAssert.assertFile(new File(paeFile),
  63               "Test file '" + paeFile + "' doesn't seem to exist");
  64     }
  65     StructureSelectionManager ssm = StructureSelectionManager
  66             .getStructureSelectionManager(Desktop.instance);
  67
  68     StructureMapping[] smArray = ssm.getMapping(pdbFile);
  69
  70     try
  71     {
  72       boolean done = EBIAlfaFold.importPaeJSONAsContactMatrixToStructure(
  73               smArray, paeInput, "label");
  74       Assert.assertTrue(
  75               "Import of '" + paeFile + "' didn't complete successfully",
  76               done);
  77     } catch (IOException | ParseException e)
  78     {
  79       e.printStackTrace();
  80     }
  81
  82   }
  83 }