+++ /dev/null
-/* 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