JAL-2629 HMMER alignment background colour scheme is functional

[jalview.git] / src / jalview / util / ProbabilityAnalyserKickstarter.java

diff --git a/src/jalview/util/ProbabilityAnalyserKickstarter.java b/src/jalview/util/ProbabilityAnalyserKickstarter.java
index ffc1dec..ade09b1 100644 (file)
--- a/src/jalview/util/ProbabilityAnalyserKickstarter.java
+++ b/src/jalview/util/ProbabilityAnalyserKickstarter.java
@@ -125,7 +125,8 @@ public class ProbabilityAnalyserKickstarter
 
           inputScanner.next();
           boolean keepRaw = inputScanner.nextBoolean();
-          analyser.runToEnd(keepRaw);
+          boolean forClans = inputScanner.nextBoolean();
+          analyser.runToEnd(keepRaw, forClans);
           System.out.println("Task completed");
         } catch (Exception e)
         {