JAL-1683 replace year/version strings with tokens in source

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

diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index 6734200..3a376b8 100644 (file)
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -1,44 +1,46 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 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)
@@ -47,19 +49,17 @@ 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.showSequenceFeatures)
+    if (ap.av.isShowSequenceFeatures())
     {
       if (fr == null)
       {
-        fr = ap.cloneFeatureRenderer();
+        fr = (jalview.gui.FeatureRenderer) ap.cloneFeatureRenderer();
       }
       else
       {
@@ -71,7 +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);
@@ -127,10 +127,12 @@ 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.getShowSequenceFeatures(), ap);
+      colourBySequence(ap.av.isShowSequenceFeatures(), ap);
     }
   }
 
@@ -150,7 +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);
   }
@@ -172,25 +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)
@@ -202,20 +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
@@ -224,8 +193,6 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
     if (svl instanceof SeqPanel)
     {
       appJmolWindow.removeAlignmentPanel(((SeqPanel) svl).ap);
-
     }
-    ;
   }
 }