X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=ceb30d713f4db2e20f2f890bf88688332fc740de;hb=f2287ae5b61b6bf36ee90bd6bbf38d44331bf273;hp=9512c5a2b0da9b0616c7cf334db095cabcc6f297;hpb=7f93804f766c054832f87406d9c72c87cb5f3050;p=jalview.git

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 9512c5a..ceb30d7 100755
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -184,6 +184,12 @@ public class AlignViewport
         showConsensus = Boolean.valueOf(param).booleanValue();
       }
 
+      param = applet.getParameter("showUnconserved");
+      if (param != null)
+      {
+        this.showUnconserved = Boolean.valueOf(param).booleanValue();
+      }
+
       param = applet.getParameter("upperCase");
       if (param != null)
       {
@@ -192,6 +198,11 @@ public class AlignViewport
           upperCasebold = true;
         }
       }
+      param = applet.getParameter("sortByTree");
+      if (param != null)
+      {
+        sortByTree=Boolean.valueOf(param).booleanValue();
+      }
 
     }
 
@@ -1502,4 +1513,29 @@ public class AlignViewport
   public boolean getFollowHighlight() {
     return followHighlight;
   }
+  /**
+   * show non-conserved residues only
+   */
+  public boolean showUnconserved=false;
+
+  /**
+   * when set, alignment should be reordered according to a newly opened tree
+   */
+  public boolean sortByTree=false;
+
+  /**
+   * @return the showUnconserved
+   */
+  public boolean getShowunconserved()
+  {
+    return showUnconserved;
+  }
+
+  /**
+   * @param showUnconserved the showUnconserved to set
+   */
+  public void setShowunconserved(boolean displayNonconserved)
+  {
+    this.showUnconserved = displayNonconserved;
+  }
 }