X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=6eb6ac333302c721983ad16f0cd6677e9e3f5fd0;hb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;hp=eab3580ee021b85a0452888dc26fe6384f5f006d;hpb=1889827c44c51f6353fe8619e5d44b421158af23;p=jalview.git

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index eab3580..6eb6ac3 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -202,7 +202,11 @@ public class AppJmol extends GStructureViewer implements Runnable,
               public void itemStateChanged(ItemEvent e)
               {
                 alignStructs.setEnabled(_alignwith.size() > 0);
-                alignStructs.setToolTipText(MessageManager.formatMessage("label.align_structures_using_linked_alignment_views", new String[] {new Integer(_alignwith.size()).toString()}));
+                alignStructs.setToolTipText(MessageManager
+                        .formatMessage(
+                                "label.align_structures_using_linked_alignment_views",
+                                new String[]
+                                { new Integer(_alignwith.size()).toString() }));
               }
             });
     handler.itemStateChanged(null);
@@ -254,9 +258,11 @@ public class AppJmol extends GStructureViewer implements Runnable,
     if (alreadyMapped != null)
     {
       int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
-    		  MessageManager.formatMessage("label.pdb_entry_is_already_displayed",  new String[]{pdbentry.getId()}),
-              MessageManager.formatMessage("label.map_sequences_to_visible_window", new String[]{pdbentry.getId()}),
-              JOptionPane.YES_NO_OPTION);
+              MessageManager.formatMessage(
+                      "label.pdb_entry_is_already_displayed", new String[]
+                      { pdbentry.getId() }), MessageManager.formatMessage(
+                      "label.map_sequences_to_visible_window", new String[]
+                      { pdbentry.getId() }), JOptionPane.YES_NO_OPTION);
 
       if (option == JOptionPane.YES_OPTION)
       {
@@ -311,10 +317,15 @@ public class AppJmol extends GStructureViewer implements Runnable,
       {
         AppJmol topJmol = (AppJmol) jm.nextElement();
         // TODO: highlight topJmol in view somehow
-        int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
-        		MessageManager.formatMessage("label.add_pdbentry_to_view", new String[]{pdbentry.getId(),topJmol.getTitle()}),
-        		MessageManager.getString("label.align_to_existing_structure_view"),
-                JOptionPane.YES_NO_OPTION);
+        int option = JOptionPane
+                .showInternalConfirmDialog(
+                        Desktop.desktop,
+                        MessageManager.formatMessage(
+                                "label.add_pdbentry_to_view", new String[]
+                                { pdbentry.getId(), topJmol.getTitle() }),
+                        MessageManager
+                                .getString("label.align_to_existing_structure_view"),
+                        JOptionPane.YES_NO_OPTION);
         if (option == JOptionPane.YES_OPTION)
         {
           topJmol.useAlignmentPanelForSuperposition(ap);
@@ -619,7 +630,8 @@ public class AppJmol extends GStructureViewer implements Runnable,
     {
       return;
     }
-    JMenuItem menuItem = new JMenuItem(MessageManager.getString("label.all"));
+    JMenuItem menuItem = new JMenuItem(
+            MessageManager.getString("label.all"));
     menuItem.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent evt)
@@ -781,9 +793,12 @@ public class AppJmol extends GStructureViewer implements Runnable,
     if (errormsgs.length() > 0)
     {
 
-      JOptionPane.showInternalMessageDialog(Desktop.desktop,
-    		  MessageManager.formatMessage("label.pdb_entries_couldnt_be_retrieved", new String[]{errormsgs.toString()}),
-              MessageManager.getString("label.couldnt_load_file"), JOptionPane.ERROR_MESSAGE);
+      JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+              .formatMessage("label.pdb_entries_couldnt_be_retrieved",
+                      new String[]
+                      { errormsgs.toString() }), MessageManager
+              .getString("label.couldnt_load_file"),
+              JOptionPane.ERROR_MESSAGE);
 
     }
     long lastnotify = jmb.getLoadNotifiesHandled();
@@ -831,7 +846,8 @@ public class AppJmol extends GStructureViewer implements Runnable,
 
       // need to wait around until script has finished
       while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled()
-              : (jmb.isFinishedInit() && jmb.getPdbFile()!=null && jmb.getPdbFile().length != jmb.pdbentry.length))
+              : (jmb.isFinishedInit() && jmb.getPdbFile() != null && jmb
+                      .getPdbFile().length != jmb.pdbentry.length))
       {
         try
         {
@@ -921,8 +937,9 @@ public class AppJmol extends GStructureViewer implements Runnable,
       cap.dispose();
       return;
     }
-    jalview.gui.Desktop.addInternalFrame(cap, MessageManager.getString("label.pdb_sequence_mapping"),
-            550, 600);
+    jalview.gui.Desktop.addInternalFrame(cap,
+            MessageManager.getString("label.pdb_sequence_mapping"), 550,
+            600);
   }
 
   /**
@@ -1144,7 +1161,8 @@ public class AppJmol extends GStructureViewer implements Runnable,
         g.fillRect(0, 0, currentSize.width, currentSize.height);
         g.setColor(Color.white);
         g.setFont(new Font("Verdana", Font.BOLD, 14));
-        g.drawString(MessageManager.getString("label.error_loading_file") + "...", 20, currentSize.height / 2);
+        g.drawString(MessageManager.getString("label.error_loading_file")
+                + "...", 20, currentSize.height / 2);
         StringBuffer sb = new StringBuffer();
         int lines = 0;
         for (int e = 0; e < jmb.pdbentry.length; e++)
@@ -1169,7 +1187,8 @@ public class AppJmol extends GStructureViewer implements Runnable,
         g.fillRect(0, 0, currentSize.width, currentSize.height);
         g.setColor(Color.white);
         g.setFont(new Font("Verdana", Font.BOLD, 14));
-        g.drawString(MessageManager.getString("label.retrieving_pdb_data"), 20, currentSize.height / 2);
+        g.drawString(MessageManager.getString("label.retrieving_pdb_data"),
+                20, currentSize.height / 2);
       }
       else
       {