JAL-4220 if a threshold is defined, use it to show - for symbols present below assign...

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index b1505d6..aa0deed 100755 (executable)
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -252,6 +252,11 @@ public class AAFrequency
       return;
     }
 
       return;
     }
 

+    float threshhold = 100;
+    if (consensus.getThreshold()!=null)
+    {
+      threshhold =  consensus.getThreshold().value;
+    }

     for (int i = startCol; i < endCol; i++)
     {
       ProfileI profile = profiles.get(i);
     for (int i = startCol; i < endCol; i++)
     {
       ProfileI profile = profiles.get(i);

@@ -273,7 +278,7 @@ public class AAFrequency
               ignoreGaps, dp);
 
       String modalResidue = profile.getModalResidue();
               ignoreGaps, dp);
 
       String modalResidue = profile.getModalResidue();

-      if ("".equals(modalResidue))
+      if ("".equals(modalResidue) || threshhold>value)

       {
         modalResidue = "-";
       }
       {
         modalResidue = "-";
       }