test HMM annotaTION

[jalview.git] / src / jalview / datamodel / SequenceGroup.java

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 520bfaf..688c7ae 100755 (executable)
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -102,6 +102,8 @@ public class SequenceGroup implements AnnotatedCollectionI
    */
   private boolean ignoreGapsInConsensus = true;
 
+  private boolean ignoreBelowBackground = true;
+
   /**
    * consensus calculation property
    */
@@ -209,6 +211,7 @@ public class SequenceGroup implements AnnotatedCollectionI
       thresholdTextColour = seqsel.thresholdTextColour;
       width = seqsel.width;
       ignoreGapsInConsensus = seqsel.ignoreGapsInConsensus;
+      ignoreBelowBackground = seqsel.ignoreBelowBackground;
       if (seqsel.conserve != null)
       {
         recalcConservation(); // safer than
@@ -1189,6 +1192,20 @@ public class SequenceGroup implements AnnotatedCollectionI
     return ignoreGapsInConsensus;
   }
 
+  public void setIgnoreBelowBackground(boolean state)
+  {
+    if (this.ignoreBelowBackground != state)
+    {
+      ignoreBelowBackground = state;
+    }
+    ignoreBelowBackground = state;
+  }
+
+  public boolean getIgnoreBelowBackground()
+  {
+    return true;
+  }
+
   /**
    * @param showSequenceLogo
    *          indicates if a sequence logo is shown for consensus annotation