X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=382fcb6e8b2809568156463ab847531f5ba954ca;hb=2732a03c243a8d57c559e8e33c0e36bcd5d57624;hp=40d3dd499a51bb149c8ce4c70616cc70c16bd648;hpb=8da7acff9214ddaf0e6d28e76219ab51bd38e62d;p=jalview.git

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 40d3dd4..382fcb6 100755
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -36,7 +36,8 @@ public class AlignViewport
   int startSeq;
   int endSeq;
 
-  boolean showFullId = true;
+  boolean showDBPrefix = true;
+  boolean showJVSuffix = true;
   boolean showText = true;
   boolean showColourText = false;
   boolean showBoxes = true;
@@ -57,8 +58,7 @@ public class AlignViewport
 
   int charHeight;
   int charWidth;
-  int chunkWidth;
-  int chunkHeight;
+  int wrappedWidth;
 
   Font font = new Font("SansSerif", Font.PLAIN, 10);
   AlignmentI alignment;
@@ -99,7 +99,7 @@ public class AlignViewport
       String param = applet.getParameter("showFullId");
       if (param != null)
       {
-        showFullId = Boolean.valueOf(param).booleanValue();
+        showJVSuffix = Boolean.valueOf(param).booleanValue();
       }
 
       param = applet.getParameter("showAnnotation");
@@ -150,6 +150,9 @@ public class AlignViewport
 
   public void updateConservation()
   {
+    if(alignment.isNucleotide())
+          return;
+
     Conservation cons = new jalview.analysis.Conservation("All",
         jalview.schemes.ResidueProperties.propHash, 3,
         alignment.getSequences(), 0,
@@ -440,24 +443,14 @@ public class AlignViewport
     return charHeight;
   }
 
-  public void setChunkWidth(int w)
-  {
-    this.chunkWidth = w;
-  }
-
-  public int getChunkWidth()
-  {
-    return chunkWidth;
-  }
-
-  public void setChunkHeight(int h)
+  public void setWrappedWidth(int w)
   {
-    this.chunkHeight = h;
+    this.wrappedWidth = w;
   }
 
-  public int getChunkHeight()
+  public int getwrappedWidth()
   {
-    return chunkHeight;
+    return wrappedWidth;
   }
 
   public AlignmentI getAlignment()
@@ -604,14 +597,24 @@ public class AlignViewport
     return colourAppliesToAllGroups;
   }
 
-  public boolean getShowFullId()
+  public boolean getShowJVSuffix()
+  {
+    return showJVSuffix;
+  }
+
+  public void setShowJVSuffix(boolean b)
+  {
+    showJVSuffix = b;
+  }
+
+  public boolean getShowDBPrefix()
   {
-    return showFullId;
+    return showDBPrefix;
   }
 
-  public void setShowFullId(boolean b)
+  public void setShowDBPrefix(boolean b)
   {
-    showFullId = b;
+    showDBPrefix = b;
   }
 
   public boolean getShowAnnotation()