(JAL-958) - normalised sequence logo for applet

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

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index a088aa3..3c78573 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -912,7 +912,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       pg.translate(-idWidth - 3, (endSeq - startSeq) * av.charHeight + 3);
       alabels.drawComponent((Graphics2D) pg, idWidth);
       pg.translate(idWidth + 3, 0);
-      annotationPanel.drawComponent((Graphics2D) pg, startRes, endRes + 1);
+      annotationPanel.renderer.drawComponent(annotationPanel, av, (Graphics2D) pg, -1, startRes, endRes + 1);
     }
 
     return Printable.PAGE_EXISTS;
@@ -1357,6 +1357,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     boolean cons = av.isShowGroupConsensus();
     boolean showprf = av.isShowSequenceLogo();
     boolean showConsHist = av.isShowConsensusHistogram();
+    boolean normLogo = av.isNormaliseSequenceLogo();
 
     boolean sortg = true;
 
@@ -1392,6 +1393,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
           // set defaults for this group's conservation/consensus
           sg.setshowSequenceLogo(showprf);
           sg.setShowConsensusHistogram(showConsHist);
+          sg.setNormaliseSequenceLogo(normLogo);
         }
         if (conv)
         {