Change header template for a new version

[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 508d5f7..86c7599 100644 (file)
--- a/runner/compbio/runner/msa/Mafft.java
+++ b/runner/compbio/runner/msa/Mafft.java
@@ -1,6 +1,6 @@
-/* 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
@@ -27,15 +27,27 @@ import org.apache.log4j.Logger;
 \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
@@ -88,6 +100,8 @@ public class Mafft extends SkeletalExecutable<Mafft>
                return this;\r
        }\r
 \r
+\r
+       \r
        @SuppressWarnings("unchecked")\r
        @Override\r
        public Class<Mafft> getType() {\r