From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 18 Apr 2018 11:13:23 +0000 (+0100)
Subject: JAL-2629 corrected cutoff parameter passing to hmmsearch
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=064b38c667ab15290bc73ffe369eeb4c55c3304e;p=jalview.git

JAL-2629 corrected cutoff parameter passing to hmmsearch
---

diff --git a/src/jalview/hmmer/HMMSearch.java b/src/jalview/hmmer/HMMSearch.java
index 7413d14..d4c9656 100644
--- a/src/jalview/hmmer/HMMSearch.java
+++ b/src/jalview/hmmer/HMMSearch.java
@@ -160,7 +160,7 @@ public class HMMSearch extends HmmerCommand
         }
         else if (MessageManager.getString("label.seq_e_value").equals(name))
         {
-          args.add("--incE");
+          args.add("-E");
           args.add(arg.getValue());
         }
         else if (MessageManager.getString("label.seq_score").equals(name))
@@ -168,10 +168,10 @@ public class HMMSearch extends HmmerCommand
           args.add("-incT");
           args.add(arg.getValue());
         }
-        else if (MessageManager.getString("label.dom_e_value_desc")
+        else if (MessageManager.getString("label.dom_e_value")
                 .equals(name))
         {
-          args.add("--incdomE");
+          args.add("--domE");
           args.add(arg.getValue());
         }
         else if (MessageManager.getString("label.dom_score").equals(name))