test HMM annotaTION

[jalview.git] / src / jalview / viewmodel / AlignmentViewport.java

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index f86282f..dfd120b 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -610,6 +610,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   protected boolean ignoreGapsInConsensusCalculation = false;
 
+  protected boolean ignoreBelowBackGroundFrequencyCalculation = false;
+
   protected ResidueShaderI residueShading = new ResidueShader();
 
   @Override
@@ -1233,6 +1235,21 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   }
 
+  public void setIgnoreBelowBackground(boolean b, AlignmentViewPanel ap)
+  {
+    ignoreBelowBackGroundFrequencyCalculation = b;
+    if (ap != null)
+    {
+      // updateConsensus(ap);
+      if (residueShading != null)
+      {
+        residueShading.setThreshold(residueShading.getThreshold(),
+                ignoreBelowBackGroundFrequencyCalculation);
+      }
+    }
+
+  }
+
   private long sgrouphash = -1, colselhash = -1;
 
   /**
@@ -1287,6 +1304,11 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return ignoreGapsInConsensusCalculation;
   }
 
+  public boolean isIgnoreBelowBackground()
+  {
+    return ignoreBelowBackGroundFrequencyCalculation;
+  }
+
   // property change stuff
   // JBPNote Prolly only need this in the applet version.
   private PropertyChangeSupport changeSupport = new PropertyChangeSupport(