X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=6c8e0e4e9573b1350249f2bf806649766bd7e4f4;hb=e5b366e9af81b30196c3c31727fd6b0091502527;hp=be7f8f4a9d67471d645f527146718ac03d8a25f1;hpb=0452450533728e478ef8c893ea2cb3483c740fb3;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index be7f8f4..6c8e0e4 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -61,6 +61,7 @@ public class AlignViewport
     boolean validCharWidth;
     int wrappedWidth;
     Font font;
+    boolean seqNameItalics;
     AlignmentI alignment;
     ColumnSelection colSel = new ColumnSelection();
     int threshold;
@@ -170,6 +171,8 @@ public class AlignViewport
        String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "") ;
        String fontSize = Cache.getDefault("FONT_SIZE", "10");
 
+       seqNameItalics = Cache.getDefault("ID_ITALICS", true);
+
        int style = 0;
 
        if (fontStyle.equals("bold"))
@@ -199,6 +202,7 @@ public class AlignViewport
                 11f,
                 AlignmentAnnotation.BAR_GRAPH);
             conservation.hasText = true;
+            conservation.autoCalculated = true;
 
 
             if (Cache.getDefault("SHOW_CONSERVATION", true))
@@ -215,6 +219,7 @@ public class AlignViewport
                                                 11f,
                                                 AlignmentAnnotation.BAR_GRAPH);
               quality.hasText = true;
+              quality.autoCalculated = true;
 
               alignment.addAnnotation(quality);
             }
@@ -224,6 +229,7 @@ public class AlignViewport
                                                new Annotation[1], 0f, 100f,
                                                AlignmentAnnotation.BAR_GRAPH);
           consensus.hasText = true;
+          consensus.autoCalculated = true;
 
            if (Cache.getDefault("SHOW_IDENTITY", true))
            {
@@ -1599,7 +1605,7 @@ public class AlignViewport
 
         resetAllColourSchemes();
 
-        alignment.adjustSequenceAnnotations();
+       // alignment.adjustSequenceAnnotations();
     }