X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=a88aa4a4ee30b6e5ea5920c84140c92bd5af46dc;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=ca9b95f12e7856b8f7491fdebb1a2f20f5695f43;hpb=46c34fb5b641a5ec57b5eec0e7bf964a9e72219f;p=jalview.git

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index ca9b95f..a88aa4a 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.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.
  * 
@@ -1067,7 +1067,8 @@ public class AnnotationPanel extends JPanel implements MouseListener,
         }
         if (row.hasIcons)
         {
-          char ss = row.annotations[column].secondaryStructure;
+          char ss = validRes ? row.annotations[column].secondaryStructure
+                  : ' ';
           if (ss == 'S')
           {
             // distinguish between forward/backward base-pairing
@@ -1120,11 +1121,9 @@ public class AnnotationPanel extends JPanel implements MouseListener,
             }
           }
         }
-
         column++;
         x++;
       }
-
       if (column >= row.annotations.length)
       {
         column = row.annotations.length - 1;
@@ -1558,14 +1557,6 @@ public class AnnotationPanel extends JPanel implements MouseListener,
         if (profl != null)
         {
 
-          /*
-           * if (profl != null) {
-           * 
-           * for (int i = 0; i < profl.length; i++) { System.out.print(profl[i]
-           * + ","); }
-           * 
-           * }
-           */
           int ht = y1, htn = y2 - y1;// aa.graphHeight;
           float wdth;
           double ht2 = 0;
@@ -1678,7 +1669,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
           //TODO check what happens for group selections
           return StructureFrequency.extractProfile(
                   aa.groupRef.consensusData[column], aa.groupRef
-                          .getIgnoreGapsConsensus(),column);
+                          .getIgnoreGapsConsensus());
         }
         // TODO extend annotation row to enable dynamic and static profile data
         // to
@@ -1687,10 +1678,9 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                 && av.isShowSequenceLogo())
         {
           return StructureFrequency.extractProfile(av.hStrucConsensus[column],
-                  av.getIgnoreGapsConsensus(),column);
+                  av.getIgnoreGapsConsensus());
         }
       }
-
     }
     return null;
   }