X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=5b5b1f3b5524c62eea16538b9ba79d4fa58a8dc2;hb=f0ea7e292e26e7cec19720be39b143d261f53821;hp=15c10e764b5d928cb4ba3b4344ff9f3db83faadf;hpb=92f2bdf5a7a89ceefe2bff76ca75414cf0fb633c;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 15c10e7..5b5b1f3 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -62,7 +62,7 @@ public class AlignViewport
     int charHeight;
     int charWidth;
     int wrappedWidth;
-    Font font = new Font("SansSerif", Font.PLAIN, 10);
+    Font font;
     AlignmentI alignment;
     ColumnSelection colSel = new ColumnSelection();
     int threshold;
@@ -138,6 +138,8 @@ public class AlignViewport
 
       autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
 
+      padGaps = Cache.getDefault("PAD_GAPS", false);
+
        String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
        String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "") ;
        String fontSize = Cache.getDefault("FONT_SIZE", "10");
@@ -315,12 +317,19 @@ public class AlignViewport
       }
       catch (OutOfMemoryError error)
       {
-        javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
-            "Out of memory calculating conservation!!"
-            +
-            "\nSee help files for increasing Java Virtual Machine memory."
-            , "Out of memory",
-            javax.swing.JOptionPane.WARNING_MESSAGE);
+        javax.swing.SwingUtilities.invokeLater(new Runnable()
+        {
+          public void run()
+          {
+            javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                "Out of memory calculating conservation!!"
+                +
+                "\nSee help files for increasing Java Virtual Machine memory."
+                , "Out of memory",
+                javax.swing.JOptionPane.WARNING_MESSAGE);
+          }
+        });
+
         System.out.println("Conservation calculation: " + error);
         System.gc();
 
@@ -400,12 +409,20 @@ public class AlignViewport
 
       }catch(OutOfMemoryError error)
       {
-        javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
-            "Out of memory calculating consensus!!"
-            +
-            "\nSee help files for increasing Java Virtual Machine memory."
-            , "Out of memory",
-            javax.swing.JOptionPane.WARNING_MESSAGE);
+        javax.swing.SwingUtilities.invokeLater(new Runnable()
+        {
+          public void run()
+          {
+            javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                "Out of memory calc45ulating consensus!!"
+                +
+                "\nSee help files for increasing Java Virtual Machine memory."
+                , "Out of memory",
+                javax.swing.JOptionPane.WARNING_MESSAGE);
+          }
+        });
+
+
         System.out.println("Consensus calculation: " + error);
         System.gc();
       }