Merge branch 'JABAWS_Release_2_0'

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

diff --git a/runner/compbio/runner/_impl/RPSBlast.java b/runner/compbio/runner/_impl/RPSBlast.java
deleted file mode 100644 (file)
index 837e4b3..0000000
--- a/runner/compbio/runner/_impl/RPSBlast.java
+++ /dev/null
@@ -1,80 +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 static compbio.runner._impl.BlastParameters.parAlView;\r
-import static compbio.runner._impl.BlastParameters.parDatabase;\r
-\r
-import java.util.Arrays;\r
-import java.util.List;\r
-\r
-import compbio.runner._SkeletalCommandBuilder;\r
-\r
-public class RPSBlast extends _SkeletalCommandBuilder {\r
-\r
-       enum DB {\r
-               Pfam, Cdd, Cog, Smart, Kog, Tirg\r
-       }\r
-\r
-       private static final String command = Environment.getBlastBinDir()\r
-                       + getCommandName();\r
-\r
-       private final String workDirectory;\r
-\r
-       public RPSBlast(String workDirectory) {\r
-               this.workDirectory = workDirectory;\r
-       }\r
-\r
-       // my $blast =\r
-       // "$blast_dir/rpsblast -i $input -d $dblocat/$dbnam -m 9 -a 1 -o $output_dir/$outfile.rpsblastout";\r
-       // Could be static, but interface declaration requires to be overriden\r
-       public String getCommand(ExecProvider provider) {\r
-               return command;\r
-       }\r
-\r
-       public static String getTestCommand() {\r
-               return command;\r
-       }\r
-\r
-       public static String getCommandName() {\r
-               return "rpsblast";\r
-       }\r
-\r
-       static List<String> getTestArgs() {\r
-               return Arrays.asList(new String[] {\r
-                               parDatabase + Environment.getRPSBlastDatabasesDir() + DB.Smart,\r
-                               parAlView });\r
-       }\r
-\r
-       String getDefaultEvalue() {\r
-               return "1e-6";\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