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.AlignFrame;
  20 import jalview.gui.Desktop;
  21 import jalview.gui.JvOptionPane;
  22 import jalview.structure.StructureMapping;
  23 import jalview.structure.StructureSelectionManager;
  24 import jalview.ws.datamodel.alphafold.PAEContactMatrix;
  25
  26 public class EBIAlphaFoldTest
  27 {
  28
  29   @BeforeClass(alwaysRun = true)
  30   public void setUpJvOptionPane()
  31   {
  32     JvOptionPane.setInteractiveMode(false);
  33     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  34   }
  35
  36   @DataProvider(name = "getExamplePAEfiles")
  37   public Object[][] getExamplePAEfiles()
  38   {
  39     return new String[][] { {
  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         { "examples/AlphaFold/AF-Q5VSL9-F1-predicted_aligned_error_v4_2023.json" } };
  44   }
  45
  46   @Test(groups = { "Functional" }, dataProvider = "getExamplePAEfiles")
  47   public void checkPAEimport(String paeFile) throws Exception
  48   {
  49     PAEContactMatrix cm = new PAEContactMatrix(
  50             new Sequence("Dummy/1-2000", "ASDASDA"),
  51             EBIAlfaFold.parseJSONtoPAEContactMatrix(
  52                     new FileInputStream(paeFile)));
  53     Assert.assertNotEquals(cm.getMax(), 0.0f, "No data from " + paeFile);
  54   }
  55
  56   @Test(groups = { "Functional" }, dataProvider = "getPDBandPAEfiles")
  57   public void checkImportPAEToStructure(String pdbFile, String paeFile)
  58   {
  59     FileInputStream paeInput = null;
  60     try
  61     {
  62       paeInput = new FileInputStream(paeFile);
  63     } catch (FileNotFoundException e)
  64     {
  65       e.printStackTrace();
  66       FileAssert.assertFile(new File(paeFile),
  67               "Test file '" + paeFile + "' doesn't seem to exist");
  68     }
  69     SequenceI seq = new Sequence("Dummy/1-2000",
  70             "ASDASDAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA");
  71     AlignmentI al = new Alignment(new SequenceI[] { seq });
  72     AlignFrame af = new AlignFrame(al, seq.getLength(), 1);
  73     StructureSelectionManager ssm = StructureSelectionManager
  74             .getStructureSelectionManager(Desktop.instance);
  75     StructureMapping sm = new StructureMapping(seq, pdbFile, null, null,
  76             null, null);
  77     ssm.addStructureMapping(sm);
  78
  79     StructureMapping[] smArray = ssm.getMapping(pdbFile);
  80
  81     try
  82     {
  83       boolean done = EBIAlfaFold.importPaeJSONAsContactMatrixToStructure(
  84               smArray, paeInput, "label");
  85       Assert.assertTrue(done,
  86               "Import of '" + paeFile + "' didn't complete successfully");
  87     } catch (IOException | ParseException e)
  88     {
  89       e.printStackTrace();
  90     }
  91   }
  92
  93   @DataProvider(name = "getPDBandPAEfiles")
  94   public Object[][] getPDBandPAEfiles()
  95   {
  96     return new String[][] {
  97         //
  98         /*
  99          */
 100         { "examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb",
 101             "examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3_scores.json" },
 102         /*
 103         { "examples/AlphaFold/AF-A0A1U8FD60-F1-model_v4.pdb",
 104             "examples/AlphaFold/AF-A0A1U8FD60-F1-predicted_aligned_error_v4.json" },
 105         { "examples/AlphaFold/AF-Q5VSL9-F1-model_v4.pdb",
 106             "examples/AlphaFold/AF-Q5VSL9-F1-predicted_aligned_error_v4.json" },
 107         { "examples/AlphaFold/AF-Q5VSL9-F1-model_v4.pdb",
 108             "examples/AlphaFold/AF-Q5VSL9-F1-predicted_aligned_error_v4_2023.json" },
 109          */
 110     };
 111   }
 112
 113 }