X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Frbvi%2Fchimera%2FJalviewChimeraView.java;fp=test%2Fjalview%2Fext%2Frbvi%2Fchimera%2FJalviewChimeraView.java;h=7f9aa9bd3cc97ff6e202224192aceb8f4ef54bea;hb=3459a8a691cb22508d7067f240b7254e588e77d3;hp=e8b5bea8cf47ccbe9dd362cded257546455838be;hpb=5b27f1062b2203c4c31702e205f4c78e1992063e;p=jalview.git

diff --git a/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java b/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
index e8b5bea..7f9aa9b 100644
--- a/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
+++ b/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
@@ -79,8 +79,10 @@ public class JalviewChimeraView
   @BeforeClass(alwaysRun = true)
   public static void setUpBeforeClass() throws Exception
   {
-    Jalview.main(new String[] { "-noquestionnaire", "-nonews", "-props",
-        "test/jalview/ext/rbvi/chimera/testProps.jvprops" });
+    Jalview.main(
+            new String[]
+            { "-noquestionnaire", "-nonews", "-props",
+                "test/jalview/ext/rbvi/chimera/testProps.jvprops" });
     Cache.setProperty(Preferences.STRUCTURE_DISPLAY,
             ViewerType.CHIMERA.name());
     Cache.setProperty("SHOW_ANNOTATIONS", "false");
@@ -132,10 +134,11 @@ public class JalviewChimeraView
     assertEquals(pdbIds.size(), 1);
     PDBEntry pdbEntry = pdbIds.get(0);
     assertEquals(pdbEntry.getId(), "1GAQ");
-    StructureViewer structureViewer = new StructureViewer(af.getViewport()
-            .getStructureSelectionManager());
+    StructureViewer structureViewer = new StructureViewer(
+            af.getViewport().getStructureSelectionManager());
     chimeraViewer = structureViewer.viewStructures(pdbEntry,
-            new SequenceI[] { sq }, af.getCurrentView().getAlignPanel());
+            new SequenceI[]
+            { sq }, af.getCurrentView().getAlignPanel());
     JalviewChimeraBinding binding = (JalviewChimeraBinding) chimeraViewer
             .getBinding();
 
@@ -150,7 +153,7 @@ public class JalviewChimeraView
       } catch (InterruptedException e)
       {
       }
-    } while (!binding.isFinishedInit()  ||  !chimeraViewer.isVisible());
+    } while (!binding.isFinishedInit() || !chimeraViewer.isVisible());
 
     assertTrue(binding.isViewerRunning(), "Failed to start Chimera");
 
@@ -158,23 +161,30 @@ public class JalviewChimeraView
     assertTrue(chimeraViewer.hasViewerActionsMenu());
 
     // now add another sequence and bind to view
-    // 
+    //
     AlignmentI al = af.getViewport().getAlignment();
     PDBEntry xpdb = al.getSequenceAt(0).getPDBEntry("1GAQ");
-    sq = new Sequence("1GAQ", al.getSequenceAt(0).getSequence(25, 95).toString());
+    sq = new Sequence("1GAQ",
+            al.getSequenceAt(0).getSequence(25, 95).toString());
     al.addSequence(sq);
-    structureViewer.viewStructures(new PDBEntry[] { xpdb }, new SequenceI[] { sq }, af.getCurrentView().getAlignPanel());
+    structureViewer.viewStructures(new PDBEntry[] { xpdb },
+            new SequenceI[]
+            { sq }, af.getCurrentView().getAlignPanel());
 
     /*
      * Wait for viewer load thread to complete
      */
-    do 
+    do
     {
-      try {
+      try
+      {
         Thread.sleep(1500);
-      } catch (InterruptedException q) {};
+      } catch (InterruptedException q)
+      {
+      }
+      ;
     } while (!binding.isLoadingFinished());
-    
+
     // still just one PDB structure shown
     assertEquals(chimeraViewer.getBinding().getPdbCount(), 1);
     // and the viewer action menu should still be visible
@@ -212,18 +222,18 @@ public class JalviewChimeraView
     /*
      * use local test PDB and SIFTS files
      */
-    String pdbFilePath = new File(
-            "test/jalview/ext/rbvi/chimera/4zho.pdb").getPath();
+    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();
+            "test/jalview/ext/rbvi/chimera/4zho.xml.gz").getPath();
     SiftsClient.setMockSiftsFile(new File(siftsFilePath));
 
-    StructureViewer structureViewer = new StructureViewer(af.getViewport()
-            .getStructureSelectionManager());
+    StructureViewer structureViewer = new StructureViewer(
+            af.getViewport().getStructureSelectionManager());
     chimeraViewer = structureViewer.viewStructures(pdbEntry,
-            new SequenceI[] { sq }, af.getCurrentView().getAlignPanel());
+            new SequenceI[]
+            { sq }, af.getCurrentView().getAlignPanel());
 
     JalviewChimeraBinding binding = (JalviewChimeraBinding) chimeraViewer
             .getBinding();
@@ -273,11 +283,11 @@ public class JalviewChimeraView
     sq.addSequenceFeature(new SequenceFeature("metal ion-binding site",
             "Iron-Sulfur (2Fe-2S)", 96, 96, Float.NaN, null));
     // on a sequence region that is partially mapped to structure:
-    sq.addSequenceFeature(new SequenceFeature("helix", null, 50, 60,
-            Float.NaN, null));
+    sq.addSequenceFeature(
+            new SequenceFeature("helix", null, 50, 60, Float.NaN, null));
     // and again:
-    sq.addSequenceFeature(new SequenceFeature("chain", null, 50, 70,
-            Float.NaN, null));
+    sq.addSequenceFeature(
+            new SequenceFeature("chain", null, 50, 70, Float.NaN, null));
     // add numeric valued features - score is set as attribute value
     sq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 62,
             62, -2.1f, null));
@@ -340,14 +350,14 @@ public class JalviewChimeraView
             new StructureCommand("list resi att jv_metal_ion_binding_site"),
             true);
     assertEquals(reply.size(), 4);
-    assertTrue(reply
-            .contains("residue id #0:40.A jv_metal_ion_binding_site \"Iron-Sulfur (2Fe-2S)\" index 40"));
-    assertTrue(reply
-            .contains("residue id #0:45.A jv_metal_ion_binding_site \"Iron-Sulfur (2Fe-2S)\" index 45"));
-    assertTrue(reply
-            .contains("residue id #0:40.B jv_metal_ion_binding_site \"Iron-Sulfur (2Fe-2S)\" index 40"));
-    assertTrue(reply
-            .contains("residue id #0:45.B jv_metal_ion_binding_site \"Iron-Sulfur (2Fe-2S)\" index 45"));
+    assertTrue(reply.contains(
+            "residue id #0:40.A jv_metal_ion_binding_site \"Iron-Sulfur (2Fe-2S)\" index 40"));
+    assertTrue(reply.contains(
+            "residue id #0:45.A jv_metal_ion_binding_site \"Iron-Sulfur (2Fe-2S)\" index 45"));
+    assertTrue(reply.contains(
+            "residue id #0:40.B jv_metal_ion_binding_site \"Iron-Sulfur (2Fe-2S)\" index 40"));
+    assertTrue(reply.contains(
+            "residue id #0:45.B jv_metal_ion_binding_site \"Iron-Sulfur (2Fe-2S)\" index 45"));
 
     /*
      * check attributes with score values
@@ -395,29 +405,28 @@ public class JalviewChimeraView
     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();
+    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();
+            "test/jalview/ext/rbvi/chimera/4zho.xml.gz").getPath();
     SiftsClient.setMockSiftsFile(new File(siftsFilePath));
-  
-    StructureViewer structureViewer = new StructureViewer(af.getViewport()
-            .getStructureSelectionManager());
+
+    StructureViewer structureViewer = new StructureViewer(
+            af.getViewport().getStructureSelectionManager());
     chimeraViewer = structureViewer.viewStructures(pdbEntry,
-            new SequenceI[] { fer2Arath }, af.getCurrentView()
-                    .getAlignPanel());
-  
+            new SequenceI[]
+            { fer2Arath }, af.getCurrentView().getAlignPanel());
+
     JalviewChimeraBinding binding = (JalviewChimeraBinding) chimeraViewer
             .getBinding();
     do
@@ -429,19 +438,19 @@ public class JalviewChimeraView
       {
       }
     } while (!binding.isFinishedInit());
-  
+
     assertTrue(binding.isViewerRunning(), "Failed to launch Chimera");
-  
+
     assertEquals(binding.getPdbCount(), 1);
-  
+
     /*
      * 'perform' menu action to copy Chimera attributes
      * to features in Jalview
      */
     // TODO rename and pull up method to binding interface
     // once functionality is added for Jmol as well
-    binding.copyStructureAttributesToFeatures("isHelix", af.getViewport()
-            .getAlignPanel());
+    binding.copyStructureAttributesToFeatures("isHelix",
+            af.getViewport().getAlignPanel());
 
     /*
      * verify 22 residues have isHelix feature
@@ -470,8 +479,8 @@ public class JalviewChimeraView
     /*
      * fetch a numeric valued attribute
      */
-    binding.copyStructureAttributesToFeatures("phi", af.getViewport()
-            .getAlignPanel());
+    binding.copyStructureAttributesToFeatures("phi",
+            af.getViewport().getAlignPanel());
     fr.setVisible("phi");
     List<SequenceFeature> fs = fer2Arath.getFeatures().findFeatures(54, 54,
             "phi");