Merge branch 'develop' into features/JAL-518_justify_seqs_in_region

[jalview.git] / test / jalview / ws / dbsources / EBIAlphaFoldTest.java

diff --git a/test/jalview/ws/dbsources/EBIAlphaFoldTest.java b/test/jalview/ws/dbsources/EBIAlphaFoldTest.java
new file mode 100644 (file)
index 0000000..8cba8ab
--- /dev/null
+++ b/test/jalview/ws/dbsources/EBIAlphaFoldTest.java
@@ -0,0 +1,110 @@
+package jalview.ws.dbsources;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+
+import org.json.simple.parser.ParseException;
+import org.testng.Assert;
+import org.testng.FileAssert;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
+import jalview.structure.StructureMapping;
+import jalview.structure.StructureSelectionManager;
+import jalview.ws.datamodel.alphafold.PAEContactMatrix;
+
+public class EBIAlphaFoldTest
+{
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
+  @DataProvider(name = "getExamplePAEfiles")
+  public Object[][] getExamplePAEfiles()
+  {
+    return new String[][] {
+        //
+        { "examples/test_fab41.result/test_fab41_predicted_aligned_error_v1.json" },
+        { "examples/AlphaFold/AF-A0A1U8FD60-F1-predicted_aligned_error_v4.json" },
+        { "examples/AlphaFold/AF-Q5VSL9-F1-predicted_aligned_error_v4.json" },
+        //
+    };
+  }
+
+  @Test(groups = { "Functional" }, dataProvider = "getExamplePAEfiles")
+  public void checkPAEimport(String paeFile) throws Exception
+  {
+    PAEContactMatrix cm = new PAEContactMatrix(
+            new Sequence("Dummy/1-2000", "ASDASDA"),
+            EBIAlfaFold.parseJSONtoPAEContactMatrix(
+                    new FileInputStream(paeFile)));
+    Assert.assertNotEquals(cm.getMax(), 0.0f, "No data from " + paeFile);
+  }
+
+  @Test(groups = { "Functional" }, dataProvider = "getPDBandPAEfiles")
+  public void checkImportPAEToStructure(String pdbFile, String paeFile)
+  {
+    FileInputStream paeInput = null;
+    try
+    {
+      paeInput = new FileInputStream(paeFile);
+    } catch (FileNotFoundException e)
+    {
+      e.printStackTrace();
+      FileAssert.assertFile(new File(paeFile),
+              "Test file '" + paeFile + "' doesn't seem to exist");
+    }
+    SequenceI seq = new Sequence("Dummy/1-2000", "ASDASDA");
+    AlignmentI al = new Alignment(new SequenceI[] { seq });
+    StructureSelectionManager ssm = StructureSelectionManager
+            .getStructureSelectionManager(Desktop.instance);
+    StructureMapping sm = new StructureMapping(seq, pdbFile, null, null,
+            null, null);
+    ssm.addStructureMapping(sm);
+
+    StructureMapping[] smArray = ssm.getMapping(pdbFile);
+
+    try
+    {
+      boolean done = EBIAlfaFold.importPaeJSONAsContactMatrixToStructure(
+              smArray, paeInput, "label");
+      Assert.assertTrue(done,
+              "Import of '" + paeFile + "' didn't complete successfully");
+    } catch (IOException | ParseException e)
+    {
+      Assert.fail("Exception importing paefile '" + paeFile + "'", e);
+    }
+  }
+
+  @DataProvider(name = "getPDBandPAEfiles")
+  public Object[][] getPDBandPAEfiles()
+  {
+    return new String[][] {
+        //
+        /*
+         */
+        { "examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb",
+            "examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3_scores.json" },
+        { "examples/AlphaFold/AF-A0A1U8FD60-F1-model_v4.pdb",
+            "examples/AlphaFold/AF-A0A1U8FD60-F1-predicted_aligned_error_v4.json" },
+        { "examples/AlphaFold/AF-Q5VSL9-F1-model_v4.pdb",
+            "examples/AlphaFold/AF-Q5VSL9-F1-predicted_aligned_error_v4.json" },
+        /*
+         */
+    };
+  }
+
+}