Merge branch 'JABAWS_Release_2_0'

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

diff --git a/runner/compbio/runner/_impl/NetNglyc.java b/runner/compbio/runner/_impl/NetNglyc.java
deleted file mode 100644 (file)
index cb3729d..0000000
--- a/runner/compbio/runner/_impl/NetNglyc.java
+++ /dev/null
@@ -1,117 +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.Arrays;\r
-import java.util.List;\r
-\r
-import compbio.engine.client.CommandBuilder;\r
-import compbio.engine.client.Executable;\r
-import compbio.engine.client.RunConfiguration;\r
-import compbio.metadata.Limit;\r
-import compbio.metadata.LimitsManager;\r
-\r
-/*\r
- @see http://www.cbs.dtu.dk/cgi-bin/nph-runsafe?man=netNglyc\r
- */\r
-public class NetNglyc implements Executable<NetNglyc> {\r
-\r
-       private static final String command = "/homes/www-refine/bin/Brunak/NOBACK/netNglyc-1.0a/netNglyc";\r
-\r
-       List<String> params;\r
-\r
-       public NetNglyc() {\r
-       }\r
-\r
-       @Override\r
-       public CommandBuilder<NetNglyc> getParameters(ExecProvider provider) {\r
-               return null; // Arrays.asList(new String[] { "-a", "-f" }); // "-g"\r
-               // potentially\r
-       }\r
-\r
-       public static List<String> getTestArgs() {\r
-               return Arrays.asList(new String[] { "-a", "-f" });\r
-       }\r
-\r
-       @Override\r
-       public NetNglyc addParameters(List<String> parameters) {\r
-               this.params = parameters;\r
-               return this;\r
-       }\r
-\r
-       public static String getTestCommand() {\r
-               return command;\r
-       }\r
-\r
-       public String getCommandName() {\r
-               return "netNglyc";\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
-       @Override\r
-       public <V> V getResults(String directory) {\r
-               // TODO Auto-generated method stub\r
-               return null;\r
-       }\r
-\r
-       @Override\r
-       public Executable<?> loadRunConfiguration(RunConfiguration rconfig) {\r
-               // TODO Auto-generated method stub\r
-               return null;\r
-       }\r
-\r
-       @Override\r
-       public String getOutput() {\r
-               // TODO Auto-generated method stub\r
-               return null;\r
-       }\r
-\r
-       @Override\r
-       public String getError() {\r
-               // TODO Auto-generated method stub\r
-               return null;\r
-       }\r
-\r
-       @Override\r
-       public Limit<NetNglyc> getLimit(String presetName) {\r
-               // TODO Auto-generated method stub\r
-               return null;\r
-       }\r
-\r
-       @Override\r
-       public LimitsManager<NetNglyc> getLimits() {\r
-               // TODO Auto-generated method stub\r
-               return null;\r
-       }\r
-       @Override\r
-       public String getClusterJobSettings() {\r
-               // TODO Auto-generated method stub\r
-               return null; \r
-       }\r
-}\r