+++ /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.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