Switch JpredWS from SequenceAnnotation to MsaWS

[jabaws.git] / runner / compbio / runner / msa / Muscle.java

diff --git a/runner/compbio/runner/msa/Muscle.java b/runner/compbio/runner/msa/Muscle.java
index f3ac1c7..54c7732 100644 (file)
--- a/runner/compbio/runner/msa/Muscle.java
+++ b/runner/compbio/runner/msa/Muscle.java
@@ -1,6 +1,6 @@
-/* Copyright (c) 2009 Peter Troshin\r
+/* Copyright (c) 2011 Peter Troshin\r
  *  \r
- *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0  \r
+ *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0     \r
  * \r
  *  This library is free software; you can redistribute it and/or modify it under the terms of the\r
  *  Apache License version 2 as published by the Apache Software Foundation\r
@@ -50,7 +50,6 @@ public class Muscle extends SkeletalExecutable<Muscle> {
         * \r
         * -clwstrict - write output in clustal format\r
         * \r
-        * @param workDirectory\r
         */\r
        public Muscle() {\r
                /*\r
@@ -60,7 +59,8 @@ public class Muscle extends SkeletalExecutable<Muscle> {
                 * completes. So –quiet and –verbose are not contradictory."-quiet",\r
                 * "-verbose"\r
                 */\r
-               addParameters(Arrays.asList("-clwstrict", "-quiet", "-verbose"));\r
+               addParameters(Arrays.asList("-clwstrict", "-quiet", "-verbose",\r
+                               "-nocore"));\r
                cbuilder.setParam("-log", EXEC_STAT_FILE);\r
        }\r
 \r