X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=2922f0910e5b23904b95946ab7f6d96cd4601067;hb=133e5d7be0ca295fd4ac4ccfa6c82165c795ea80;hp=24d50d446e8c8bbf2febcd17eccafa92cc08789c;hpb=98eb909d0a4fe04ff6ad93f71086f1127fe4a530;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 24d50d4..2922f09 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -61,8 +61,7 @@ public class AlignViewport
     SequenceGroup selectionGroup;
     int charHeight;
     int charWidth;
-    int chunkWidth;
-    int chunkHeight;
+    int wrappedWidth;
     Font font = new Font("SansSerif", Font.PLAIN, 10);
     AlignmentI alignment;
     ColumnSelection colSel = new ColumnSelection();
@@ -139,6 +138,7 @@ public class AlignViewport
         // We must set conservation and consensus before setting colour,
         // as Blosum and Clustal require this to be done
         updateConservation();
+
         updateConsensus();
 
         if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
@@ -176,6 +176,9 @@ public class AlignViewport
      */
     public void updateConservation()
     {
+      if(alignment.isNucleotide())
+          return;
+
       try{
         Conservation cons = new jalview.analysis.Conservation("All",
             jalview.schemes.ResidueProperties.propHash, 3,
@@ -278,10 +281,18 @@ public class AlignViewport
           quality.annotations = qannotations;
           quality.graphMax = cons.qualityRange[1].floatValue();
         }
-      }catch(OutOfMemoryError error)
+      }
+      catch (OutOfMemoryError error)
       {
-        System.out.println("Out of memory calculating conservation.");
+        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();
+
       }
     }
 
@@ -358,7 +369,13 @@ public class AlignViewport
 
       }catch(OutOfMemoryError error)
       {
-        System.out.println("Out of memory calculating consensus.");
+        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);
+        System.out.println("Consensus calculation: " + error);
         System.gc();
       }
 
@@ -616,9 +633,9 @@ public class AlignViewport
      *
      * @param w DOCUMENT ME!
      */
-    public void setChunkWidth(int w)
+    public void setWrappedWidth(int w)
     {
-        this.chunkWidth = w;
+        this.wrappedWidth = w;
     }
 
     /**
@@ -626,30 +643,11 @@ public class AlignViewport
      *
      * @return DOCUMENT ME!
      */
-    public int getChunkWidth()
-    {
-        return chunkWidth;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param h DOCUMENT ME!
-     */
-    public void setChunkHeight(int h)
+    public int getWrappedWidth()
     {
-        this.chunkHeight = h;
+        return wrappedWidth;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getChunkHeight()
-    {
-        return chunkHeight;
-    }
 
     /**
      * DOCUMENT ME!