Merge branch 'develop' into features/JAL-2446NCList

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

diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index eadc2ad..ba360af 100644 (file)
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -91,8 +91,8 @@ public class ChimeraViewFrame extends StructureViewerBase
 
     viewerActionMenu.setText(MessageManager.getString("label.chimera"));
 
-    viewerColour.setText(MessageManager
-            .getString("label.colour_with_chimera"));
+    viewerColour
+            .setText(MessageManager.getString("label.colour_with_chimera"));
     viewerColour.setToolTipText(MessageManager
             .getString("label.let_chimera_manage_structure_colours"));
 
@@ -197,8 +197,8 @@ public class ChimeraViewFrame extends StructureViewerBase
   protected void sendFeaturesToChimera()
   {
     int count = jmb.sendFeaturesToViewer(getAlignmentPanel());
-    statusBar.setText(MessageManager.formatMessage("label.attributes_set",
-            count));
+    statusBar.setText(
+            MessageManager.formatMessage("label.attributes_set", count));
   }
 
   /**
@@ -238,7 +238,8 @@ public class ChimeraViewFrame extends StructureViewerBase
      * a new viewer
      */
     openNewChimera(ap, new PDBEntry[] { pdbentry },
-            new SequenceI[][] { seq });
+            new SequenceI[][]
+            { seq });
   }
 
   /**
@@ -277,7 +278,8 @@ public class ChimeraViewFrame extends StructureViewerBase
     this.addInternalFrameListener(new InternalFrameAdapter()
     {
       @Override
-      public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
+      public void internalFrameClosing(
+              InternalFrameEvent internalFrameEvent)
       {
         closeViewer(false);
       }
@@ -398,9 +400,8 @@ public class ChimeraViewFrame extends StructureViewerBase
       boolean opened = jmb.openSession(chimeraSessionFile);
       if (!opened)
       {
-        System.err
-                .println("An error occurred opening Chimera session file "
-                        + chimeraSessionFile);
+        System.err.println("An error occurred opening Chimera session file "
+                + chimeraSessionFile);
       }
     }
 
@@ -443,10 +444,9 @@ public class ChimeraViewFrame extends StructureViewerBase
     {
       if (!closeChimera)
       {
-        String prompt = MessageManager.formatMessage(
-                "label.confirm_close_chimera",
-                        new Object[] { jmb.getViewerTitle(getViewerName(),
-                                false) });
+        String prompt = MessageManager
+                .formatMessage("label.confirm_close_chimera", new Object[]
+                { jmb.getViewerTitle(getViewerName(), false) });
         prompt = JvSwingUtils.wrapTooltip(true, prompt);
         int confirm = JvOptionPane.showConfirmDialog(this, prompt,
                 MessageManager.getString("label.close_viewer"),
@@ -542,15 +542,16 @@ public class ChimeraViewFrame extends StructureViewerBase
     } catch (Exception ex)
     {
       ex.printStackTrace();
-      errormsgs.append("When retrieving pdbfiles for '"
-              + thePdbEntry.getId() + "'");
+      errormsgs.append(
+              "When retrieving pdbfiles for '" + thePdbEntry.getId() + "'");
     }
     if (errormsgs.length() > 0)
     {
 
-      JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
-              .formatMessage("label.pdb_entries_couldnt_be_retrieved",
-                      new Object[] { errormsgs.toString() }),
+      JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+              MessageManager.formatMessage(
+                      "label.pdb_entries_couldnt_be_retrieved", new Object[]
+                      { errormsgs.toString() }),
               MessageManager.getString("label.couldnt_load_file"),
               JvOptionPane.ERROR_MESSAGE);
     }
@@ -607,8 +608,9 @@ public class ChimeraViewFrame extends StructureViewerBase
                     oomerror);
           } catch (Exception ex)
           {
-            Cache.log.error("Couldn't open " + pe.getFile()
-                    + " in Chimera viewer!", ex);
+            Cache.log.error(
+                    "Couldn't open " + pe.getFile() + " in Chimera viewer!",
+                    ex);
           } finally
           {
             Cache.log.debug("File locations are " + files);
@@ -667,12 +669,13 @@ public class ChimeraViewFrame extends StructureViewerBase
   {
     for (int i = 0; i < pdb.getChains().size(); i++)
     {
-      String chid = new String(pdb.getId() + ":"
-              + pdb.getChains().elementAt(i).id);
+      String chid = new String(
+              pdb.getId() + ":" + pdb.getChains().elementAt(i).id);
       jmb.getChainNames().add(chid);
       jmb.getChainFile().put(chid, file);
     }
   }
+
   private String fetchPdbFile(PDBEntry processingEntry) throws Exception
   {
     // FIXME: this is duplicated code with Jmol frame ?
@@ -687,7 +690,8 @@ public class ChimeraViewFrame extends StructureViewerBase
      * Write 'fetching PDB' progress on AlignFrame as we are not yet visible
      */
     String msg = MessageManager.formatMessage("status.fetching_pdb",
-            new Object[] { pdbid });
+            new Object[]
+            { pdbid });
     getAlignmentPanel().alignFrame.setProgressBar(msg, handle);
     // long hdl = startProgressBar(MessageManager.formatMessage(
     // "status.fetching_pdb", new Object[]
@@ -755,17 +759,15 @@ public class ChimeraViewFrame extends StructureViewerBase
   @Override
   public void eps_actionPerformed(ActionEvent e)
   {
-    throw new Error(
-            MessageManager
-                    .getString("error.eps_generation_not_implemented"));
+    throw new Error(MessageManager
+            .getString("error.eps_generation_not_implemented"));
   }
 
   @Override
   public void png_actionPerformed(ActionEvent e)
   {
-    throw new Error(
-            MessageManager
-                    .getString("error.png_generation_not_implemented"));
+    throw new Error(MessageManager
+            .getString("error.png_generation_not_implemented"));
   }
 
   @Override