JAL-4090 JAL-4334 position status when start, end or pos is unknown is stored in...

[jalview.git] / src / jalview / appletgui / APopupMenu.java

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 80db11d..300167f 100644 (file)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -393,14 +393,14 @@ public class APopupMenu extends java.awt.PopupMenu
         urlLink = new UrlLink(link);
       } catch (Exception foo)
       {
-        System.err.println("Exception for URLLink '" + link + "': "
-                + foo.getMessage());
+        jalview.bin.Console.errPrintln("Exception for URLLink '" + link
+                + "': " + foo.getMessage());
         continue;
       }
 
       if (!urlLink.isValid())
       {
-        System.err.println(urlLink.getInvalidMessage());
+        jalview.bin.Console.errPrintln(urlLink.getInvalidMessage());
         continue;
       }
 
@@ -835,8 +835,8 @@ public class APopupMenu extends java.awt.PopupMenu
         if (start <= end)
         {
           seqs.add(sg.getSequenceAt(i));
-          features.add(new SequenceFeature(null, null, start, end,
-                  "Jalview"));
+          features.add(
+                  new SequenceFeature(null, null, start, end, "Jalview"));
         }
       }
 
@@ -945,8 +945,8 @@ public class APopupMenu extends java.awt.PopupMenu
       }
       else
       {
-        new mc_view.AppletPDBViewer(entry, new SequenceI[] { seq }, null, ap,
-                DataSourceType.URL);
+        new mc_view.AppletPDBViewer(entry, new SequenceI[] { seq }, null,
+                ap, DataSourceType.URL);
       }
 
     }
@@ -1072,8 +1072,8 @@ public class APopupMenu extends java.awt.PopupMenu
     hydrophobicityColour
             .setName(JalviewColourScheme.Hydrophobic.toString());
     hydrophobicityColour.addItemListener(this);
-    helixColour.setLabel(MessageManager
-            .getString("label.colourScheme_helixpropensity"));
+    helixColour.setLabel(
+            MessageManager.getString("label.colourScheme_helixpropensity"));
     helixColour.setName(JalviewColourScheme.Helix.toString());
     helixColour.addItemListener(this);
     strandColour.setLabel(MessageManager