runner/compbio/runner/msa/ClustalO.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 \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.CommandBuilder;\r
  30 import compbio.engine.client.Executable;\r
  31 import compbio.engine.client.SkeletalExecutable;\r
  32 import compbio.engine.client.Executable.ExecProvider;\r
  33 import compbio.metadata.ResultNotAvailableException;\r
  34 import compbio.runner.Util;\r
  35 \r
  36 public class ClustalO extends SkeletalExecutable<ClustalO> {\r
  37 \r
  38         private static Logger log = Logger.getLogger(ClustalO.class);\r
  39 \r
  40         private static final String EXEC_STAT_FILE = "stat.log";\r
  41 \r
  42         public static final String KEY_VALUE_SEPARATOR = "=";\r
  43         \r
  44         /**\r
  45          * Number of cores parameter name\r
  46          */\r
  47         private final static String ncorePrm = "--threads";\r
  48 \r
  49         /**\r
  50          * Number of cores to use, defaults to 1 for local execution or the value of\r
  51          * "tcoffee.cluster.cpunum" property for cluster execution\r
  52          */\r
  53         private int ncoreNumber = 0;\r
  54 \r
  55         /**\r
  56          * --threads=<n> Number of processors to use\r
  57          * \r
  58          * -l, --log=<file> Log all non-essential output to this file\r
  59          */\r
  60         public ClustalO() {\r
  61                 super(KEY_VALUE_SEPARATOR);\r
  62                 addParameters(Arrays.asList("--outfmt=clustal", "-v", "--log=" + EXEC_STAT_FILE));\r
  63                 // set default in, outs and err files\r
  64                 this.setInput(super.inputFile);\r
  65                 this.setOutput(super.outputFile);\r
  66                 this.setError(super.errorFile);\r
  67         }\r
  68 \r
  69         @Override\r
  70         public ClustalO setOutput(String outFile) {\r
  71                 super.setOutput(outFile);\r
  72                 cbuilder.setParam("--outfile=" + outFile);\r
  73                 return this;\r
  74         }\r
  75 \r
  76         @Override\r
  77         public ClustalO setInput(String inFile) {\r
  78                 super.setInput(inFile);\r
  79                 cbuilder.setParam("--infile=" + inFile);\r
  80                 return this;\r
  81         }\r
  82 \r
  83         @SuppressWarnings("unchecked")\r
  84         public Alignment getResults(String workDirectory)\r
  85                         throws ResultNotAvailableException {\r
  86                 try {\r
  87                         return Util.readClustalFile(workDirectory, getOutput());\r
  88                 } catch (FileNotFoundException e) {\r
  89                         log.error(e.getMessage(), e.getCause());\r
  90                         throw new ResultNotAvailableException(e);\r
  91                 } catch (IOException e) {\r
  92                         log.error(e.getMessage(), e.getCause());\r
  93                         throw new ResultNotAvailableException(e);\r
  94                 } catch (UnknownFileFormatException e) {\r
  95                         log.error(e.getMessage(), e.getCause());\r
  96                         throw new ResultNotAvailableException(e);\r
  97                 } catch (NullPointerException e) {\r
  98                         log.error(e.getMessage(), e.getCause());\r
  99                         throw new ResultNotAvailableException(e);\r
 100                 }\r
 101         }\r
 102 \r
 103         public static String getStatFile() {\r
 104                 return EXEC_STAT_FILE;\r
 105         }\r
 106 \r
 107         @SuppressWarnings("unchecked")\r
 108         @Override\r
 109         public Class<ClustalO> getType() {\r
 110                 return (Class<ClustalO>) this.getClass();\r
 111         }\r
 112         \r
 113         @Override\r
 114         public CommandBuilder<ClustalO> getParameters(ExecProvider provider) {\r
 115                 // Limit number of cores to 1 for ANY execution which does not set\r
 116                 // Ncores explicitly using setNCore method\r
 117                 if (ncoreNumber == 0) {\r
 118                         setNCore(1);\r
 119                 }\r
 120                 if (provider == Executable.ExecProvider.Cluster) {\r
 121                         int cpunum = SkeletalExecutable.getClusterCpuNum(getType());\r
 122                         if (cpunum != 0) {\r
 123                                 setNCore(cpunum);\r
 124                         } \r
 125                 }\r
 126                 return super.getParameters(provider);\r
 127         }\r
 128         \r
 129         public void setNCore(int ncoreNumber) {\r
 130                 if (ncoreNumber < 1 || ncoreNumber > 100) {\r
 131                         throw new IndexOutOfBoundsException("Number of cores must be within 1 and 100 ");\r
 132                 }\r
 133                 this.ncoreNumber = ncoreNumber;\r
 134                 cbuilder.setParam(ncorePrm, Integer.toString(getNCore()));\r
 135         }\r
 136 \r
 137         int getNCore() {\r
 138                 return ncoreNumber;\r
 139         }\r
 140 \r
 141 }\r