runner/compbio/runner/msa/ClustalW.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.SkeletalExecutable;\r
  31 import compbio.metadata.ResultNotAvailableException;\r
  32 import compbio.runner.Util;\r
  33 \r
  34 public class ClustalW extends SkeletalExecutable<ClustalW> {\r
  35 \r
  36         private static Logger log = Logger.getLogger(ClustalW.class);\r
  37         private static final String EXEC_STAT_FILE = "stat.log";\r
  38         private static final String TREE_FILE_EXT = ".dnd";\r
  39 \r
  40         public static final String KEY_VALUE_SEPARATOR = "=";\r
  41 \r
  42         public ClustalW() {\r
  43                 super(KEY_VALUE_SEPARATOR);\r
  44                 addParameters(Arrays.asList("-OUTORDER=ALIGNED", "-QUIET", "-STATS="\r
  45                                 + EXEC_STAT_FILE));\r
  46                 // set default in, outs and err files\r
  47                 this.setInput(super.inputFile);\r
  48                 this.setOutput(super.outputFile);\r
  49                 this.setError(super.errorFile);\r
  50         }\r
  51 \r
  52         @Override\r
  53         public ClustalW setOutput(String outFile) {\r
  54                 super.setOutput(outFile);\r
  55                 cbuilder.setParam("-OUTFILE=" + outFile);\r
  56                 return this;\r
  57         }\r
  58 \r
  59         @Override\r
  60         public ClustalW setInput(String inFile) {\r
  61                 super.setInput(inFile);\r
  62                 cbuilder.setParam("-INFILE=" + inFile);\r
  63                 return this;\r
  64         }\r
  65 \r
  66         @SuppressWarnings("unchecked")\r
  67         public Alignment getResults(String workDirectory)\r
  68                         throws ResultNotAvailableException {\r
  69                 try {\r
  70                         return Util.readClustalFile(workDirectory, getOutput());\r
  71                 } catch (FileNotFoundException e) {\r
  72                         log.error(e.getMessage(), e.getCause());\r
  73                         throw new ResultNotAvailableException(e);\r
  74                 } catch (IOException e) {\r
  75                         log.error(e.getMessage(), e.getCause());\r
  76                         throw new ResultNotAvailableException(e);\r
  77                 } catch (UnknownFileFormatException e) {\r
  78                         log.error(e.getMessage(), e.getCause());\r
  79                         throw new ResultNotAvailableException(e);\r
  80                 } catch (NullPointerException e) {\r
  81                         log.error(e.getMessage(), e.getCause());\r
  82                         throw new ResultNotAvailableException(e);\r
  83                 }\r
  84         }\r
  85 \r
  86         @Override\r
  87         public List<String> getCreatedFiles() {\r
  88                 return Arrays.asList(getOutput(), EXEC_STAT_FILE,\r
  89                                 convertInputNameToTreeName());\r
  90         }\r
  91 \r
  92         /*\r
  93          * Clustal output tree with same name as input file but .dnd extension e.g.\r
  94          * this methods do similar conversion TO122.fasta -> TO122.dnd or\r
  95          * TO122.fasta.in -> TO122.fasta.dnd It does not seems that there is any\r
  96          * limits on the name length\r
  97          * \r
  98          * @return\r
  99          */\r
 100         private String convertInputNameToTreeName() {\r
 101                 assert super.getInput() != null;\r
 102                 int dotIdx = getInput().lastIndexOf(".");\r
 103                 String treeFileName = "";\r
 104                 if (dotIdx > 0) {\r
 105                         treeFileName = getInput().substring(0, dotIdx);\r
 106                 }\r
 107                 return treeFileName + TREE_FILE_EXT;\r
 108         }\r
 109 \r
 110         public static String getStatFile() {\r
 111                 return EXEC_STAT_FILE;\r
 112         }\r
 113 \r
 114         @SuppressWarnings("unchecked")\r
 115         @Override\r
 116         public Class<ClustalW> getType() {\r
 117                 return (Class<ClustalW>) this.getClass();\r
 118         }\r
 119 \r
 120 }\r