Take into account scroll value

[jalview.git] / src / jalview / gui / AlignViewport.java

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