Merge branch 'features/JAL-1588saveChimeraSession' into develop

[jalview.git] / src / jalview / gui / AppJmolBinding.java

diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index 42a2f74..b7617ce 100644 (file)
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -20,28 +20,27 @@
  */
 package jalview.gui;
 
-import java.awt.Container;
-import java.util.BitSet;
-
 import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.ext.jmol.JalviewJmolBinding;
 import jalview.structure.StructureSelectionManager;
 
+import java.awt.Container;
+import java.util.BitSet;
+
 import org.jmol.api.JmolAppConsoleInterface;
 import org.jmol.api.JmolViewer;
 import org.jmol.popup.JmolPopup;
 import org.openscience.jmol.app.jmolpanel.AppConsole;
 
-public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
+public class AppJmolBinding extends JalviewJmolBinding
 {
-
-  /**
-   * 
-   */
   private AppJmol appJmolWindow;
 
+  private FeatureRenderer fr = null;
+
   public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm,
           PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
           String protocol)
@@ -50,13 +49,11 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
     appJmolWindow = appJmol;
   }
 
-  FeatureRenderer fr = null;
-
   @Override
-  public jalview.api.FeatureRenderer getFeatureRenderer(
+  public FeatureRenderer getFeatureRenderer(
           AlignmentViewPanel alignment)
   {
-    AlignmentPanel ap = (alignment == null) ? appJmolWindow.ap
+    AlignmentPanel ap = (alignment == null) ? appJmolWindow.getAlignmentPanel()
             : (AlignmentPanel) alignment;
     if (ap.av.isShowSequenceFeatures())
     {
@@ -74,7 +71,7 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
   }
 
   @Override
-  public jalview.api.SequenceRenderer getSequenceRenderer(
+  public SequenceRenderer getSequenceRenderer(
           AlignmentViewPanel alignment)
   {
     return new SequenceRenderer(((AlignmentPanel) alignment).av);
@@ -130,7 +127,9 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
     AlignmentPanel ap = (AlignmentPanel) source, topap;
     // ignore events from panels not used to colour this view
     if (!appJmolWindow.isUsedforcolourby(ap))
+    {
       return;
+    }
     if (!isLoadingFromArchive())
     {
       colourBySequence(ap.av.isShowSequenceFeatures(), ap);
@@ -153,7 +152,6 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
   public void newJmolPopup(boolean translateLocale, String menuName,
           boolean asPopup)
   {
-
     jmolpopup = new JmolPopup();
     jmolpopup.initialize(viewer, translateLocale, menuName, asPopup);
   }
@@ -175,25 +173,6 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
     appJmolWindow.showConsole(b);
   }
 
-  /**
-   * add the given sequences to the mapping scope for the given pdb file handle
-   * 
-   * @param pdbFile
-   *          - pdbFile identifier
-   * @param seq
-   *          - set of sequences it can be mapped to
-   */
-  public void addSequenceForStructFile(String pdbFile, SequenceI[] seq)
-  {
-    for (int pe = 0; pe < pdbentry.length; pe++)
-    {
-      if (pdbentry[pe].getFile().equals(pdbFile))
-      {
-        addSequence(pe, seq);
-      }
-    }
-  }
-
   @Override
   protected JmolAppConsoleInterface createJmolConsole(JmolViewer viewer2,
           Container consolePanel, String buttonsToShow)
@@ -205,20 +184,7 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
   protected void releaseUIResources()
   {
     appJmolWindow = null;
-    if (console != null)
-    {
-      try
-      {
-        console.setVisible(false);
-      } catch (Error e)
-      {
-      } catch (Exception x)
-      {
-      }
-      ;
-      console = null;
-    }
-
+    closeConsole();
   }
 
   @Override
@@ -227,8 +193,6 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
     if (svl instanceof SeqPanel)
     {
       appJmolWindow.removeAlignmentPanel(((SeqPanel) svl).ap);
-
     }
-    ;
   }
 }