X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=5b5b1f3b5524c62eea16538b9ba79d4fa58a8dc2;hb=f0ea7e292e26e7cec19720be39b143d261f53821;hp=23d7612882a0e987cde599a647f6b45cbf2e237b;hpb=0125a426aecc7065538a13f48236dc1e8d268044;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 23d7612..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;
@@ -74,6 +74,8 @@ public class AlignViewport
     boolean hasHiddenColumns = false;
     boolean hasHiddenRows = false;
 
+    boolean cursorMode = false;
+
     // The following vector holds the features which are
     // currently visible, in the correct order or rendering
     Hashtable featuresDisplayed = null;
@@ -84,6 +86,7 @@ public class AlignViewport
     AlignmentAnnotation consensus;
     AlignmentAnnotation conservation;
     AlignmentAnnotation quality;
+    boolean autoCalculateConsensus = true;
 
     /** DOCUMENT ME!! */
     public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
@@ -97,6 +100,8 @@ public class AlignViewport
 
     boolean antiAlias = false;
 
+    boolean padGaps = false;
+
 
     public AlignViewport(AlignmentI al, boolean dataset)
     {
@@ -131,6 +136,10 @@ public class AlignViewport
       showQuality = Cache.getDefault("SHOW_QUALITY", true);
       showIdentity = Cache.getDefault("SHOW_IDENTITY", true);
 
+      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");
@@ -308,12 +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();
 
@@ -393,12 +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();
       }