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

diff --git a/runner/compbio/runner/msa/Mafft.java b/runner/compbio/runner/msa/Mafft.java
index dbe49fe..86c7599 100644 (file)
--- a/runner/compbio/runner/msa/Mafft.java
+++ b/runner/compbio/runner/msa/Mafft.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
@@ -43,19 +43,10 @@ public class Mafft extends SkeletalExecutable<Mafft>
                        PipedExecutable<Mafft> {\r
        /*\r
         * TODO get rid of piping: Mafft now supports --out option for output file. \r
-     * TODO enable multithreading support\r
+     * Multi-threading supported with e.g. "thread 4" only for Linux, so JABAWS \r
+     * will not support it for now, it also need editing of mafft makefile  \r
         */\r
        \r
-       /**\r
-        * Number of cores to use, not used if "mafft.cluster.cpunum" property \r
-        * is not defined and in case of local execution \r
-        */\r
-       private int ncoreNumber = 0;\r
-       \r
-       /*\r
-        * Number of cores parameter name\r
-        */\r
-       private final static String ncorePrm = "--thread";\r
        \r
        private static Logger log = Logger.getLogger(Mafft.class);\r
 \r
@@ -110,19 +101,6 @@ public class Mafft extends SkeletalExecutable<Mafft>
        }\r
 \r
 \r
-       public void setNCore(int ncoreNumber) {\r
-               if (ncoreNumber < 1 || ncoreNumber > 100) {\r
-                       throw new IndexOutOfBoundsException(\r
-                                       "Number of cores must be within 1 and 100 ");\r
-               }\r
-               this.ncoreNumber = ncoreNumber;\r
-               cbuilder.setParam(ncorePrm, Integer.toString(getNCore()));\r
-       }\r
-\r
-       int getNCore() {\r
-               return ncoreNumber;\r
-       }\r
-       \r
        \r
        @SuppressWarnings("unchecked")\r
        @Override\r