From: pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>
Date: Tue, 21 Jun 2011 12:29:25 +0000 (+0000)
Subject: Revert multithreading support for mafft as it does not seem to work
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=2eb05b9319960f2346045e5e2119d112c5909490;p=jabaws.git

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

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4296 e3abac25-378b-4346-85de-24260fe3988d
---

diff --git a/runner/compbio/runner/msa/Mafft.java b/runner/compbio/runner/msa/Mafft.java
index dbe49fe..55d6e2b 100644
--- 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> {
 	/*
 	 * TODO get rid of piping: Mafft now supports --out option for output file. 
-     * TODO enable multithreading support
+     * Multithreading support does not seem to work reliably!  
 	 */
 	
-	/**
-	 * Number of cores to use, not used if "mafft.cluster.cpunum" property 
-	 * is not defined and in case of local execution 
-	 */
-	private int ncoreNumber = 0;
-	
-	/*
-	 * Number of cores parameter name
-	 */
-	private final static String ncorePrm = "--thread";
 	
 	private static Logger log = Logger.getLogger(Mafft.class);
 
@@ -110,19 +100,6 @@ public class Mafft extends SkeletalExecutable<Mafft>
 	}
 
 
-	public void setNCore(int ncoreNumber) {
-		if (ncoreNumber < 1 || ncoreNumber > 100) {
-			throw new IndexOutOfBoundsException(
-					"Number of cores must be within 1 and 100 ");
-		}
-		this.ncoreNumber = ncoreNumber;
-		cbuilder.setParam(ncorePrm, Integer.toString(getNCore()));
-	}
-
-	int getNCore() {
-		return ncoreNumber;
-	}
-	
 	
 	@SuppressWarnings("unchecked")
 	@Override