-/* 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
\r
import compbio.data.sequence.Alignment;\r
import compbio.data.sequence.UnknownFileFormatException;\r
+\r
import compbio.engine.client.PipedExecutable;\r
import compbio.engine.client.SkeletalExecutable;\r
import compbio.metadata.ResultNotAvailableException;\r
import compbio.runner.Util;\r
\r
+/**\r
+ * \r
+ * @author pvtroshin\r
+ *\r
+ */\r
public class Mafft extends SkeletalExecutable<Mafft>\r
implements\r
PipedExecutable<Mafft> {\r
-\r
+ /*\r
+ * TODO get rid of piping: Mafft now supports --out option for output file. \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
private static Logger log = Logger.getLogger(Mafft.class);\r
\r
private static String autoOption = "--auto";\r
return this;\r
}\r
\r
+\r
+ \r
@SuppressWarnings("unchecked")\r
@Override\r
public Class<Mafft> getType() {\r