basic implementation of profile display and todos

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

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index b39aaeb..ceb30d7 100755 (executable)
--- 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();
+      }
 
     }
 
@@ -1476,6 +1487,7 @@ public class AlignViewport
 
   boolean centreColumnLabels;
 
+  
   public boolean getCentreColumnLabels()
   {
     return centreColumnLabels;
@@ -1497,5 +1509,33 @@ public class AlignViewport
       }
     }
   }
+  public boolean followHighlight=false;
+  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;
+  }
 }