runner/compbio/runner/_impl/BlastAll.java

   1 /* Copyright (c) 2011 Peter Troshin\r
   2  *  \r
   3  *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0     \r
   4  * \r
   5  *  This library is free software; you can redistribute it and/or modify it under the terms of the\r
   6  *  Apache License version 2 as published by the Apache Software Foundation\r
   7  * \r
   8  *  This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
   9  *  even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
  10  *  License for more details.\r
  11  * \r
  12  *  A copy of the license is in apache_license.txt. It is also available here:\r
  13  * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
  14  * \r
  15  * Any republication or derived work distributed in source code form\r
  16  * must include this copyright and license notice.\r
  17  */\r
  18 package compbio.runner._impl;\r
  19 \r
  20 import static compbio.runner._impl.BlastParameters.parAlView;\r
  21 import static compbio.runner._impl.BlastParameters.parDatabase;\r
  22 import static compbio.runner._impl.BlastParameters.parDel;\r
  23 import static compbio.runner._impl.BlastParameters.parEvalue;\r
  24 import static compbio.runner._impl.BlastParameters.parInput;\r
  25 import static compbio.runner._impl.BlastParameters.parOutput;\r
  26 \r
  27 import java.io.File;\r
  28 import java.util.Arrays;\r
  29 import java.util.List;\r
  30 \r
  31 import compbio.runner._SkeletalCommandBuilder;\r
  32 \r
  33 public class BlastAll extends _SkeletalCommandBuilder {\r
  34 \r
  35         static final String command = "blastall";\r
  36 \r
  37         enum blastType {\r
  38                 blastp, tbastn, blastn\r
  39         }\r
  40 \r
  41         enum dataBase {\r
  42                 pdb\r
  43         }\r
  44 \r
  45         static double default_evalue = 0.001d;\r
  46         static final String parBlastType = "-p";\r
  47 \r
  48         private final String workDirectory;\r
  49 \r
  50         public BlastAll(String workDirectory) {\r
  51                 this.workDirectory = workDirectory;\r
  52         }\r
  53 \r
  54         // Resulting command:\r
  55         // /fc_gpfs/gjb_lab/www-refine/bin/blast_32bit/blast-2.2.17/bin/blastall -p\r
  56         // blastp -i $input -d $dbnam -e $evalue -m 9 -o $outfile\r
  57 \r
  58         String getCommand(blastType btype, dataBase database, String input,\r
  59                         String output) {\r
  60                 return Environment.getBlastBinDir() + command + parDel + parBlastType\r
  61                                 + blastType.blastp + parDel + parInput + input + parDel\r
  62                                 + parDatabase + Environment.getBlastDatabasesDir() + database\r
  63                                 + parDel + parEvalue + default_evalue + parAlView + parOutput\r
  64                                 + output;\r
  65         }\r
  66 \r
  67         String getFullTestCommand(String test_input, String test_outfile) {\r
  68                 return Environment.getBlastBinDir() + command + parDel + parBlastType\r
  69                                 + blastType.blastp + parDel + parInput + test_input + parDel\r
  70                                 + parDatabase + Environment.getBlastDatabasesDir()\r
  71                                 + dataBase.pdb + parDel + parEvalue + default_evalue\r
  72                                 + parAlView + parOutput + test_outfile;\r
  73         }\r
  74 \r
  75         static String getTestCommand() {\r
  76                 return Environment.getBlastBinDir() + command;\r
  77         }\r
  78 \r
  79         static List<String> getTestArgs() {\r
  80                 return Arrays\r
  81                                 .asList(new String[]{\r
  82                                                 parBlastType + blastType.blastp,\r
  83                                                 parDatabase + Environment.getBlastDatabasesDir()\r
  84                                                                 + dataBase.pdb, parEvalue + default_evalue,\r
  85                                                 parAlView});\r
  86         }\r
  87 \r
  88         public boolean removeOutput(String outfile) {\r
  89                 File out = new File(outfile);\r
  90                 if (out.exists()) {\r
  91                         if (out.canWrite()) {\r
  92                                 return out.delete();\r
  93                         }\r
  94                 }\r
  95                 return false;\r
  96         }\r
  97 \r
  98         public String getCommand(ExecProvider provider) {\r
  99                 return Environment.getBlastBinDir() + command;\r
 100         }\r
 101 \r
 102         public String getCommandName() {\r
 103                 return command;\r
 104         }\r
 105 \r
 106         @Override\r
 107         public List<String> getCreatedFiles() {\r
 108                 // TODO Auto-generated method stub\r
 109                 return null;\r
 110         }\r
 111 \r
 112         @Override\r
 113         public String getInput() {\r
 114                 // TODO Auto-generated method stub\r
 115                 return null;\r
 116         }\r
 117 \r
 118 }\r