X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=runner%2Fcompbio%2Frunner%2Fmsa%2FMafft.java;h=86c759900ca584df038d5c73619739458b615ce6;hb=c97b1954611988b2b1d2e9aeec6e4b0696a0ab66;hp=508d5f787edce5ad0dcfd46a4b8ca0dacf4b3539;hpb=b6814b6b8761dba56f9e5fe34164f783af1aca4f;p=jabaws.git

diff --git a/runner/compbio/runner/msa/Mafft.java b/runner/compbio/runner/msa/Mafft.java
index 508d5f7..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
@@ -27,15 +27,27 @@ import org.apache.log4j.Logger;
 
 import compbio.data.sequence.Alignment;
 import compbio.data.sequence.UnknownFileFormatException;
+
 import compbio.engine.client.PipedExecutable;
 import compbio.engine.client.SkeletalExecutable;
 import compbio.metadata.ResultNotAvailableException;
 import compbio.runner.Util;
 
+/**
+ * 
+ * @author pvtroshin
+ *
+ */
 public class Mafft extends SkeletalExecutable<Mafft>
 		implements
 			PipedExecutable<Mafft> {
-
+	/*
+	 * TODO get rid of piping: Mafft now supports --out option for output file. 
+     * 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  
+	 */
+	
+	
 	private static Logger log = Logger.getLogger(Mafft.class);
 
 	private static String autoOption = "--auto";
@@ -88,6 +100,8 @@ public class Mafft extends SkeletalExecutable<Mafft>
 		return this;
 	}
 
+
+	
 	@SuppressWarnings("unchecked")
 	@Override
 	public Class<Mafft> getType() {