runner/compbio/runner/msa/ClustalO.java

   1 /* Copyright (c) 2009 Peter Troshin\r
   2  *  \r
   3  *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0\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 \r
  19 package compbio.runner.msa;\r
  20 \r
  21 import java.io.FileNotFoundException;\r
  22 import java.io.IOException;\r
  23 import java.util.Arrays;\r
  24 \r
  25 import org.apache.log4j.Logger;\r
  26 \r
  27 import compbio.data.sequence.Alignment;\r
  28 import compbio.data.sequence.UnknownFileFormatException;\r
  29 import compbio.engine.client.SkeletalExecutable;\r
  30 import compbio.metadata.ResultNotAvailableException;\r
  31 import compbio.runner.Util;\r
  32 \r
  33 public class ClustalO extends SkeletalExecutable<ClustalO> {\r
  34 \r
  35         private static Logger log = Logger.getLogger(ClustalO.class);\r
  36         private static final String EXEC_STAT_FILE = "stat.log";\r
  37         private static final String TREE_FILE_EXT = ".dnd";\r
  38 \r
  39         public static final String KEY_VALUE_SEPARATOR = "=";\r
  40 \r
  41         /**\r
  42          * \r
  43          * --auto Set options automatically (might overwrite some of your options)\r
  44          * \r
  45          * --threads=<n> Number of processors to use\r
  46          * \r
  47          * -l, --log=<file> Log all non-essential output to this file\r
  48          */\r
  49         public ClustalO() {\r
  50                 super(KEY_VALUE_SEPARATOR);\r
  51                 addParameters(Arrays.asList("--outfmt=clustal", "-v", "--log="\r
  52                                 + EXEC_STAT_FILE));\r
  53                 // set default in, outs and err files\r
  54                 this.setInput(super.inputFile);\r
  55                 this.setOutput(super.outputFile);\r
  56                 this.setError(super.errorFile);\r
  57         }\r
  58 \r
  59         @Override\r
  60         public ClustalO setOutput(String outFile) {\r
  61                 super.setOutput(outFile);\r
  62                 cbuilder.setParam("--outfile=" + outFile);\r
  63                 return this;\r
  64         }\r
  65 \r
  66         @Override\r
  67         public ClustalO setInput(String inFile) {\r
  68                 super.setInput(inFile);\r
  69                 cbuilder.setParam("--infile=" + inFile);\r
  70                 return this;\r
  71         }\r
  72 \r
  73         @SuppressWarnings("unchecked")\r
  74         public Alignment getResults(String workDirectory)\r
  75                         throws ResultNotAvailableException {\r
  76                 try {\r
  77                         return Util.readClustalFile(workDirectory, getOutput());\r
  78                 } catch (FileNotFoundException e) {\r
  79                         log.error(e.getMessage(), e.getCause());\r
  80                         throw new ResultNotAvailableException(e);\r
  81                 } catch (IOException e) {\r
  82                         log.error(e.getMessage(), e.getCause());\r
  83                         throw new ResultNotAvailableException(e);\r
  84                 } catch (UnknownFileFormatException e) {\r
  85                         log.error(e.getMessage(), e.getCause());\r
  86                         throw new ResultNotAvailableException(e);\r
  87                 } catch (NullPointerException e) {\r
  88                         log.error(e.getMessage(), e.getCause());\r
  89                         throw new ResultNotAvailableException(e);\r
  90                 }\r
  91         }\r
  92 \r
  93         public static String getStatFile() {\r
  94                 return EXEC_STAT_FILE;\r
  95         }\r
  96 \r
  97         @SuppressWarnings("unchecked")\r
  98         @Override\r
  99         public Class<ClustalO> getType() {\r
 100                 return (Class<ClustalO>) this.getClass();\r
 101         }\r
 102 \r
 103 }\r