+++ /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 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
-/*\r
- * TODO look at how a command can be build with an argument list\r
- */\r
-public class PSIBlast extends _SkeletalCommandBuilder {\r
-\r
- private static final String command = "blastpgp";\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 PSIBlast(String workDirectory) {\r
- this.workDirectory = workDirectory;\r
- }\r
-\r
- // Resulting command:\r
- // TODO lease note that the location seem to be different for 64 bit nodes\r
- // fc_gpfs/gjb_lab/www-refine/bin/blast_32bit/blast-2.2.17/bin/blastpgp -i\r
- // $input -d $dbnam -o $output_dir/$outfile.psiblastout.$clus -j $iterations\r
- // -Q $output_dir/$outfile.PSImatrix.$clus -m $mo\r
-\r
- // BlastAll\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