Revert multithreading support for mafft as it does not seem to work

[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..55d6e2b 100644 (file)
--- a/runner/compbio/runner/msa/Mafft.java
+++ b/runner/compbio/runner/msa/Mafft.java
@@ -43,19 +43,9 @@ 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
+     * Multithreading support does not seem to work reliably!  \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 +100,6 @@ 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