X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=9b4e1fe375b4e9ece81dc96fa07185ee69b3ed2b;hb=dbdc8807d9059dacf65a087b7bcb8363be53fb8f;hp=a4b494af16570f819c581afaee06d44e4f2f9616;hpb=bd4ab013e64863bbbffa93c58953051e11cfb236;p=jalview.git

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index a4b494a..9b4e1fe 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -616,6 +616,8 @@ public abstract class AlignmentViewport
 
   protected boolean ignoreBelowBackGroundFrequencyCalculation = false;
 
+  protected boolean infoLetterHeight = false;
+
   protected ResidueShaderI residueShading = new ResidueShader();
 
   @Override
@@ -779,6 +781,10 @@ public abstract class AlignmentViewport
   @Override
   public void setSequenceInformationHash(ProfilesI info, int index)
   {
+    if (hinformation.size() < index + 1)
+    {
+      return;
+    }
     hinformation.set(index, info);
   }
 
@@ -1366,6 +1372,16 @@ public abstract class AlignmentViewport
 
   }
 
+  public void setInfoLetterHeight(boolean b, AlignmentViewPanel ap)
+  {
+    infoLetterHeight = b;
+    if (ap != null)
+    {
+      updateInformation(ap);
+    }
+
+  }
+
   private long sgrouphash = -1, colselhash = -1;
 
   /**
@@ -1426,6 +1442,12 @@ public abstract class AlignmentViewport
     return ignoreBelowBackGroundFrequencyCalculation;
   }
 
+  @Override
+  public boolean isInfoLetterHeight()
+  {
+    return infoLetterHeight;
+  }
+
   // property change stuff
   // JBPNote Prolly only need this in the applet version.
   private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
@@ -1997,6 +2019,7 @@ public abstract class AlignmentViewport
     {
       updateStrucConsensus(ap);
     }
+    initInformation();
     updateInformation(ap);
 
     List<SequenceI> hmmSequences;
@@ -3117,4 +3140,18 @@ public abstract class AlignmentViewport
             + ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
     return sq;
   }
+
+  public boolean hasReferenceAnnotation()
+  {
+    AlignmentAnnotation[] annots = this.alignment.getAlignmentAnnotation();
+    for (AlignmentAnnotation annot : annots)
+    {
+      if ("RF".equals(annot.label) || annot.label.contains("Reference"))
+      {
+        return true;
+      }
+    }
+    return false;
+  }
+
 }