X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=5ac946ad23d4dcbb69c2c01bc4e42542095a57e8;hb=bbfdb203ce3a889600caa52478478b75ab03809f;hp=1dbcf5647dd15d35923d42e79e3f62b0a3a38500;hpb=227daebd9bdf92c83712e077d958a690cdee0f7a;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 1dbcf56..5ac946a 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.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.
  * 
@@ -404,6 +404,7 @@ public class AlignViewport implements SelectionSource, VamsasSource
       showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM",
               true);
       showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false);
+      normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO", false);
       showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
       // TODO: add menu option action that nulls or creates consensus object
       // depending on if the user wants to see the annotation or not in a
@@ -413,17 +414,22 @@ public class AlignViewport implements SelectionSource, VamsasSource
       consensus.hasText = true;
       consensus.autoCalculated = true;
 
-      // TODO check if this can done accordingly
-      strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID",
-              new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
-      strucConsensus.hasText = true;
-      strucConsensus.autoCalculated = true;
-
+      if (alignment.isNucleotide() && alignment.hasRNAStructure())
+      {
+        strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID",
+                new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
+        strucConsensus.hasText = true;
+        strucConsensus.autoCalculated = true;
+      }
+      
       if (Cache.getDefault("SHOW_IDENTITY", true))
       {
         alignment.addAnnotation(consensus);
         // TODO: Make own if for structure
-        alignment.addAnnotation(strucConsensus);
+        if (alignment.isNucleotide() && alignment.hasRNAStructure())
+        {
+          alignment.addAnnotation(strucConsensus);
+        }
       }
 
     }
@@ -2297,7 +2303,10 @@ public class AlignViewport implements SelectionSource, VamsasSource
    * should consensus profile be rendered by default
    */
   public boolean showSequenceLogo = false;
-
+  /**
+   * should consensus profile be rendered normalised to row height
+   */
+  public  boolean normaliseSequenceLogo = false;
   /**
    * should consensus histograms be rendered by default
    */
@@ -2461,4 +2470,15 @@ public class AlignViewport implements SelectionSource, VamsasSource
     }
     return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
   }
+
+  
+  public boolean isNormaliseSequenceLogo()
+  {
+    return normaliseSequenceLogo;
+  }
+
+  public void setNormaliseSequenceLogo(boolean state)
+  {
+    normaliseSequenceLogo = state;
+  }
 }