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