JAL-2296 unit test for reading Chimera attributes to Jalview features

[jalview.git] / test / jalview / ext / rbvi / chimera / JalviewChimeraView.java

diff --git a/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java b/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
index a31a065..449b219 100644 (file)
--- a/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
+++ b/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
@@ -334,4 +334,141 @@ public class JalviewChimeraView
     chimeraViewer.closeViewer(true);
     chimeraViewer = null;
   }
+
+  /**
+   * Test for creating Jalview features from attributes on mapped residues in
+   * Chimera. Note this uses local copies of PDB and SIFTS file, no network
+   * connection required.
+   * 
+   * @throws IOException
+   * @throws SiftsException
+   */
+  // External as this requires a local install of Chimera
+  @Test(groups = { "External" })
+  public void testGetAttributes() throws IOException, SiftsException
+  {
+    String inFile = "examples/uniref50.fa";
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
+            FormatAdapter.FILE);
+    assertNotNull(af, "Failed to create AlignFrame");
+    SequenceI fer2Arath = af.getViewport().getAlignment()
+            .findName("FER2_ARATH");
+    assertNotNull(fer2Arath, "Didn't find FER2_ARATH");
+  
+    /*
+     * need a Uniprot dbref for SIFTS mapping to work!!
+     */
+    fer2Arath.addDBRef(new DBRefEntry("UNIPROT", "0", "P16972", null));
+  
+    /*
+     * use local test PDB and SIFTS files
+     */
+    String pdbFilePath = new File(
+            "test/jalview/ext/rbvi/chimera/4zho.pdb").getPath();
+    PDBEntry pdbEntry = new PDBEntry("4ZHO", null, null, pdbFilePath);
+    String siftsFilePath = new File(
+            "test/jalview/ext/rbvi/chimera/4zho.xml.gz")
+            .getPath();
+    SiftsClient.setMockSiftsFile(new File(siftsFilePath));
+  
+    StructureViewer structureViewer = new StructureViewer(af.getViewport()
+            .getStructureSelectionManager());
+    chimeraViewer = structureViewer.viewStructures(pdbEntry,
+            new SequenceI[] { fer2Arath }, af.getCurrentView()
+                    .getAlignPanel());
+  
+    JalviewChimeraBinding binding = (JalviewChimeraBinding) chimeraViewer
+            .getBinding();
+    do
+    {
+      try
+      {
+        Thread.sleep(500);
+      } catch (InterruptedException e)
+      {
+      }
+    } while (!binding.isFinishedInit());
+  
+    assertTrue(binding.isChimeraRunning(), "Failed to launch Chimera");
+  
+    assertEquals(binding.getPdbCount(), 1);
+  
+    /*
+     * 'perform' menu action to copy visible features to
+     * attributes in Chimera
+     */
+    // TODO rename and pull up method to binding interface
+    // once functionality is added for Jmol as well
+    binding.copyStructureAttributesToFeatures("isHelix", af.getViewport()
+            .getAlignPanel());
+
+    /*
+     * verify 22 residues have isHelix feature
+     * (may merge into ranges in future)
+     */
+    af.setShowSeqFeatures(true);
+    FeatureRenderer fr = af.getFeatureRenderer();
+    fr.setVisible("isHelix");
+    for (int res = 75; res <= 83; res++)
+    {
+      checkFeaturesAtRes(fer2Arath, fr, res, "isHelix");
+    }
+    for (int res = 117; res <= 123; res++)
+    {
+      checkFeaturesAtRes(fer2Arath, fr, res, "isHelix");
+    }
+    for (int res = 129; res <= 131; res++)
+    {
+      checkFeaturesAtRes(fer2Arath, fr, res, "isHelix");
+    }
+    for (int res = 143; res <= 145; res++)
+    {
+      checkFeaturesAtRes(fer2Arath, fr, res, "isHelix");
+    }
+
+    /*
+     * fetch a numeric valued attribute
+     */
+    binding.copyStructureAttributesToFeatures("phi", af.getViewport()
+            .getAlignPanel());
+    fr.setVisible("phi");
+    List<SequenceFeature> fs = fr.findFeaturesAtRes(fer2Arath, 54);
+    assertEquals(fs.size(), 3);
+    assertEquals(fs.get(0).getType(), "RESNUM");
+    assertEquals(fs.get(1).getType(), "phi");
+    assertEquals(fs.get(2).getType(), "phi");
+    assertEquals(fs.get(1).getDescription(), "A"); // chain
+    assertEquals(fs.get(2).getDescription(), "B");
+    assertEquals(fs.get(1).getScore(), -131.0713f, 0.001f);
+    assertEquals(fs.get(2).getScore(), -127.39512, 0.001f);
+
+    /*
+     * tear down - also in AfterMethod
+     */
+    SiftsClient.setMockSiftsFile(null);
+    chimeraViewer.closeViewer(true);
+    chimeraViewer = null;
+  }
+
+  /**
+   * Helper method to verify new feature at a sequence position
+   * 
+   * @param seq
+   * @param fr
+   * @param res
+   * @param featureType
+   */
+  protected void checkFeaturesAtRes(SequenceI seq, FeatureRenderer fr,
+          int res, String featureType)
+  {
+    String where = "at position " + res;
+    List<SequenceFeature> fs = fr.findFeaturesAtRes(seq, res);
+    assertEquals(fs.size(), 2, where);
+    assertEquals(fs.get(0).getType(), "RESNUM", where);
+    SequenceFeature sf = fs.get(1);
+    assertEquals(sf.getType(), featureType, where);
+    assertEquals(sf.getFeatureGroup(), "Chimera", where);
+    assertEquals(sf.getDescription(), "True", where);
+    assertEquals(sf.getScore(), Float.NaN, where);
+  }
 }