X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=runner%2Fcompbio%2Frunner%2Fmsa%2FMafft.java;h=86c759900ca584df038d5c73619739458b615ce6;hb=0ec796d8e2a97d2c006a88522010cd2fff5a0d96;hp=dbe49fee34abc4dc5c4dccd992c3c9aaab5ad69d;hpb=87413bfedfbbb0dfb2a1110c37c9279bd1614ba5;p=jabaws.git

diff --git a/runner/compbio/runner/msa/Mafft.java b/runner/compbio/runner/msa/Mafft.java
index dbe49fe..86c7599 100644
--- a/runner/compbio/runner/msa/Mafft.java
+++ b/runner/compbio/runner/msa/Mafft.java
@@ -1,6 +1,6 @@
-/* Copyright (c) 2009 Peter Troshin
+/* Copyright (c) 2011 Peter Troshin
  *  
- *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 
+ *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0     
  * 
  *  This library is free software; you can redistribute it and/or modify it under the terms of the
  *  Apache License version 2 as published by the Apache Software Foundation
@@ -43,19 +43,10 @@ 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
+     * Multi-threading supported with e.g. "thread 4" only for Linux, so JABAWS 
+     * will not support it for now, it also need editing of mafft makefile  
 	 */
 	
-	/**
-	 * 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 +101,6 @@ 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