JAL-98 JAL-1854 encapsulate 'magic number' threshold 3 in Conservation

[jalview.git] / src / jalview / io / AnnotationFile.java

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 34fdabe..61a30f8 100755 (executable)
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -1637,9 +1637,8 @@ public class AnnotationFile
         else if (key.equalsIgnoreCase("consThreshold"))
         {
           sg.cs.setConservationInc(Integer.parseInt(value));
-          Conservation c = new Conservation("Group", 3,
-                  sg.getSequences(null), sg.getStartRes(),
-                  sg.getEndRes() + 1);
+          Conservation c = new Conservation("Group", sg.getSequences(null),
+                  sg.getStartRes(), sg.getEndRes() + 1);
 
           c.calculate();
           c.verdict(false, 25); // TODO: refer to conservation percent threshold