X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FAppletJmol.java;h=cca9affe260e0a49fbdbc97fc4d2fe4a5734be29;hb=9c970ce520ca5480fcd289c8ef32ed78284cde29;hp=6e95633daaef72cc6c6c788730ad25df2643d35c;hpb=d85a2741994c169e1b81db8f9166f5214ff1f561;p=jalview.git

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index 6e95633..cca9aff 100644
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -104,16 +104,16 @@ public class AppletJmol extends EmbmenuFrame implements
           MessageManager.getString("label.colourScheme_hydrophobic"));
 
   MenuItem helix = new MenuItem(
-          MessageManager.getString("label.colourScheme_helix_propensity"));
+          MessageManager.getString("label.colourScheme_helixpropensity"));
 
   MenuItem strand = new MenuItem(
-          MessageManager.getString("label.colourScheme_strand_propensity"));
+          MessageManager.getString("label.colourScheme_strandpropensity"));
 
   MenuItem turn = new MenuItem(
-          MessageManager.getString("label.colourScheme_turn_propensity"));
+          MessageManager.getString("label.colourScheme_turnpropensity"));
 
   MenuItem buried = new MenuItem(
-          MessageManager.getString("label.colourScheme_buried_index"));
+          MessageManager.getString("label.colourScheme_buriedindex"));
 
   MenuItem purinepyrimidine = new MenuItem(
           MessageManager.getString("label.colourScheme_purine/pyrimidine"));
@@ -135,7 +135,7 @@ public class AppletJmol extends EmbmenuFrame implements
   AlignmentPanel ap;
 
   List<AlignmentPanel> _aps = new ArrayList<>(); // remove? never
-                                                               // added to
+                                                 // added to
 
   String fileLoadingError;
 
@@ -275,7 +275,7 @@ public class AppletJmol extends EmbmenuFrame implements
               "-applet", scriptWindow, null);
     } catch (Exception e)
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Couldn't create a jmol viewer. Args to allocate viewer were:\nDocumentBase="
                       + ap.av.applet.getDocumentBase() + "\nCodebase="
                       + ap.av.applet.getCodeBase());
@@ -320,7 +320,7 @@ public class AppletJmol extends EmbmenuFrame implements
           {
             if (jalview.bin.JalviewLite.debug)
             {
-              System.err.println(
+              jalview.bin.Console.errPrintln(
                       "AppletJmol:Trying to reuse existing PDBfile IO parser.");
             }
             // re-use the one we opened earlier
@@ -330,12 +330,12 @@ public class AppletJmol extends EmbmenuFrame implements
           {
             if (jalview.bin.JalviewLite.debug)
             {
-              System.err.println(
+              jalview.bin.Console.errPrintln(
                       "AppletJmol:Creating new PDBfile IO parser.");
             }
             FileParse fp = new FileParse(pdbentry.getFile(), protocol);
             fp.mark();
-            // reader = new MCview.PDBfile(fp);
+            // reader = new mc_view.PDBfile(fp);
             // could set ID, etc.
             // if (!reader.isValid())
             // {
@@ -355,7 +355,7 @@ public class AppletJmol extends EmbmenuFrame implements
         } catch (Exception e)
         {
           // give up!
-          System.err.println("Couldn't access pdbentry id="
+          jalview.bin.Console.errPrintln("Couldn't access pdbentry id="
                   + pdbentry.getId() + " and file=" + pdbentry.getFile()
                   + " using protocol=" + protocol);
           e.printStackTrace();
@@ -433,7 +433,7 @@ public class AppletJmol extends EmbmenuFrame implements
       } catch (OutOfMemoryError ex)
       {
         frame.dispose();
-        System.err.println(
+        jalview.bin.Console.errPrintln(
                 "Out of memory when trying to create dialog box with sequence-structure mapping.");
         return;
       }