Merge branch 'JABAWS_Release_2_0'

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

diff --git a/runner/compbio/runner/_impl/BlastAll.java b/runner/compbio/runner/_impl/BlastAll.java
deleted file mode 100644 (file)
index 36a306f..0000000
--- a/runner/compbio/runner/_impl/BlastAll.java
+++ /dev/null
@@ -1,118 +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
-import static compbio.runner._impl.BlastParameters.parDel;\r
-import static compbio.runner._impl.BlastParameters.parEvalue;\r
-import static compbio.runner._impl.BlastParameters.parInput;\r
-import static compbio.runner._impl.BlastParameters.parOutput;\r
-\r
-import java.io.File;\r
-import java.util.Arrays;\r
-import java.util.List;\r
-\r
-import compbio.runner._SkeletalCommandBuilder;\r
-\r
-public class BlastAll extends _SkeletalCommandBuilder {\r
-\r
-       static final String command = "blastall";\r
-\r
-       enum blastType {\r
-               blastp, tbastn, blastn\r
-       }\r
-\r
-       enum dataBase {\r
-               pdb\r
-       }\r
-\r
-       static double default_evalue = 0.001d;\r
-       static final String parBlastType = "-p";\r
-\r
-       private final String workDirectory;\r
-\r
-       public BlastAll(String workDirectory) {\r
-               this.workDirectory = workDirectory;\r
-       }\r
-\r
-       // Resulting command:\r
-       // /fc_gpfs/gjb_lab/www-refine/bin/blast_32bit/blast-2.2.17/bin/blastall -p\r
-       // blastp -i $input -d $dbnam -e $evalue -m 9 -o $outfile\r
-\r
-       String getCommand(blastType btype, dataBase database, String input,\r
-                       String output) {\r
-               return Environment.getBlastBinDir() + command + parDel + parBlastType\r
-                               + blastType.blastp + parDel + parInput + input + parDel\r
-                               + parDatabase + Environment.getBlastDatabasesDir() + database\r
-                               + parDel + parEvalue + default_evalue + parAlView + parOutput\r
-                               + output;\r
-       }\r
-\r
-       String getFullTestCommand(String test_input, String test_outfile) {\r
-               return Environment.getBlastBinDir() + command + parDel + parBlastType\r
-                               + blastType.blastp + parDel + parInput + test_input + parDel\r
-                               + parDatabase + Environment.getBlastDatabasesDir()\r
-                               + dataBase.pdb + parDel + parEvalue + default_evalue\r
-                               + parAlView + parOutput + test_outfile;\r
-       }\r
-\r
-       static String getTestCommand() {\r
-               return Environment.getBlastBinDir() + command;\r
-       }\r
-\r
-       static List<String> getTestArgs() {\r
-               return Arrays\r
-                               .asList(new String[]{\r
-                                               parBlastType + blastType.blastp,\r
-                                               parDatabase + Environment.getBlastDatabasesDir()\r
-                                                               + dataBase.pdb, parEvalue + default_evalue,\r
-                                               parAlView});\r
-       }\r
-\r
-       public boolean removeOutput(String outfile) {\r
-               File out = new File(outfile);\r
-               if (out.exists()) {\r
-                       if (out.canWrite()) {\r
-                               return out.delete();\r
-                       }\r
-               }\r
-               return false;\r
-       }\r
-\r
-       public String getCommand(ExecProvider provider) {\r
-               return Environment.getBlastBinDir() + command;\r
-       }\r
-\r
-       public String getCommandName() {\r
-               return command;\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