Merge branch 'JABAWS_Release_2_0'

[jabaws.git] / runner / compbio / runner / _impl / Tmhmm2.java

diff --git a/runner/compbio/runner/_impl/Tmhmm2.java b/runner/compbio/runner/_impl/Tmhmm2.java
deleted file mode 100644 (file)
index 2fce62f..0000000
--- a/runner/compbio/runner/_impl/Tmhmm2.java
+++ /dev/null
@@ -1,67 +0,0 @@
-/* Copyright (c) 2011 Peter Troshin\r
- *  \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
- *  This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
- *  even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
- *  License for more details.\r
- * \r
- *  A copy of the license is in apache_license.txt. It is also available here:\r
- * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
- * \r
- * Any republication or derived work distributed in source code form\r
- * must include this copyright and license notice.\r
- */\r
-package compbio.runner._impl;\r
-\r
-import java.util.List;\r
-\r
-import compbio.runner._SkeletalCommandBuilder;\r
-\r
-/*\r
- @see file:///(/homes/www-refine/SSPF_01/) Z:/bin/Brunak/TMHMM2/TMHMM2.0c/TMHMM2.0.html\r
- could have used decodeanhmm directly \r
- for more options @see ./decodeanhmm -h\r
- e.g. decodeanhmm -f <path>/TMHMM2.0.options -modelfile <path>/TMHMM2.0.model\r
- */\r
-class Tmhmm2 extends _SkeletalCommandBuilder {\r
-\r
-       /*\r
-        * This is a standard tmhmm binary, but slightly modified the only\r
-        * difference is that it will always write results in $workDirectory/TMHMM\r
-        */\r
-       private static final String command = "/homes/www-refine/bin/Brunak/TMHMM2/TMHMM2.0c/bin/tmhmm_samedir";\r
-       String input;\r
-       String output;\r
-       List<String> params;\r
-\r
-       private final String workDirectory;\r
-\r
-       public Tmhmm2(String workDirectory) {\r
-               this.workDirectory = workDirectory;\r
-       }\r
-\r
-       public static String getTestCommand() {\r
-               return command;\r
-       }\r
-\r
-       public String getCommandName() {\r
-               return "tmhmm";\r
-       }\r
-\r
-       @Override\r
-       public List<String> getCreatedFiles() {\r
-               // TODO Auto-generated method stub\r
-               return null;\r
-       }\r
-\r
-       @Override\r
-       public String getInput() {\r
-               // TODO Auto-generated method stub\r
-               return null;\r
-       }\r
-\r
-}\r