X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=9b4e1fe375b4e9ece81dc96fa07185ee69b3ed2b;hb=dbdc8807d9059dacf65a087b7bcb8363be53fb8f;hp=eeea831fc78a4c020285aab53b434ccbdc30c693;hpb=6fd5f99f753ae1ce8c09b22fff11de2b6cdb3954;p=jalview.git

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index eeea831..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
@@ -1370,6 +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;
 
   /**
@@ -1430,6 +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(
@@ -3122,4 +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;
+  }
+
 }