runner/compbio/runner/msa/Probcons.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 \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 import java.util.List;\r
  25 \r
  26 import org.apache.log4j.Logger;\r
  27 \r
  28 import compbio.data.sequence.Alignment;\r
  29 import compbio.data.sequence.UnknownFileFormatException;\r
  30 import compbio.engine.client.PipedExecutable;\r
  31 import compbio.engine.client.SkeletalExecutable;\r
  32 import compbio.metadata.ResultNotAvailableException;\r
  33 import compbio.runner.Util;\r
  34 \r
  35 public class Probcons extends SkeletalExecutable<Probcons>\r
  36                 implements\r
  37                         PipedExecutable<Probcons> {\r
  38 \r
  39         private static Logger log = Logger.getLogger(Probcons.class);\r
  40 \r
  41         private final static String ANNOTATION = "annotation.txt";\r
  42 \r
  43         public static final String KEY_VALUE_SEPARATOR = Util.SPACE;\r
  44 \r
  45         /**\r
  46          * \r
  47          * @param workDirectory\r
  48          */\r
  49         public Probcons() {\r
  50                 addParameters(Arrays.asList("-v", "-clustalw", "-annot", ANNOTATION));\r
  51                 /*\r
  52                  * Could either have probabilities or the alignment, but not both "-t",\r
  53                  * "probabilities"\r
  54                  */\r
  55         }\r
  56 \r
  57         @SuppressWarnings("unchecked")\r
  58         @Override\r
  59         public Alignment getResults(String workDirectory)\r
  60                         throws ResultNotAvailableException {\r
  61                 try {\r
  62                         return Util.readClustalFile(workDirectory, getOutput());\r
  63                 } catch (FileNotFoundException e) {\r
  64                         log.error(e.getMessage(), e.getCause());\r
  65                         throw new ResultNotAvailableException(e);\r
  66                 } catch (IOException e) {\r
  67                         log.error(e.getMessage(), e.getCause());\r
  68                         throw new ResultNotAvailableException(e);\r
  69                 } catch (UnknownFileFormatException e) {\r
  70                         log.error(e.getMessage(), e.getCause());\r
  71                         throw new ResultNotAvailableException(e);\r
  72                 } catch (NullPointerException e) {\r
  73                         log.error(e.getMessage(), e.getCause());\r
  74                         throw new ResultNotAvailableException(e);\r
  75                 }\r
  76         }\r
  77 \r
  78         @Override\r
  79         public List<String> getCreatedFiles() {\r
  80                 return Arrays.asList(getOutput(), ANNOTATION, getError());\r
  81         }\r
  82 \r
  83         @Override\r
  84         public Probcons setInput(String inFile) {\r
  85                 String input = getInput();\r
  86                 super.setInput(inFile);\r
  87                 // TODO replace with setLast\r
  88                 cbuilder.setParam(inFile);\r
  89                 return this;\r
  90         }\r
  91 \r
  92         @SuppressWarnings("unchecked")\r
  93         @Override\r
  94         public Class<Probcons> getType() {\r
  95                 return (Class<Probcons>) this.getClass();\r
  96         }\r
  97 }\r