runner/compbio/runner/msa/Tcoffee.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.security.InvalidParameterException;\r
  24 import java.util.Arrays;\r
  25 import java.util.List;\r
  26 \r
  27 import org.apache.log4j.Logger;\r
  28 \r
  29 import compbio.data.sequence.Alignment;\r
  30 import compbio.data.sequence.UnknownFileFormatException;\r
  31 import compbio.engine.client.ClusterNativeSpecExecutable;\r
  32 import compbio.engine.client.CommandBuilder;\r
  33 import compbio.engine.client.Executable;\r
  34 import compbio.engine.client.PipedExecutable;\r
  35 import compbio.engine.client.SkeletalExecutable;\r
  36 import compbio.engine.conf.PropertyHelperManager;\r
  37 import compbio.metadata.Limit;\r
  38 import compbio.metadata.LimitsManager;\r
  39 import compbio.metadata.ResultNotAvailableException;\r
  40 import compbio.runner.Util;\r
  41 import compbio.util.PropertyHelper;\r
  42 \r
  43 public class Tcoffee extends SkeletalExecutable<Tcoffee> implements\r
  44 PipedExecutable<Tcoffee>, ClusterNativeSpecExecutable<Tcoffee> {\r
  45 \r
  46         private static Logger log = Logger.getLogger(Tcoffee.class);\r
  47 \r
  48         private static PropertyHelper ph = PropertyHelperManager\r
  49         .getPropertyHelper();\r
  50 \r
  51         // Cache for Limits information\r
  52         private static LimitsManager<Tcoffee> limits;\r
  53 \r
  54         public static final String KEY_VALUE_SEPARATOR = "=";\r
  55 \r
  56         /**\r
  57          * Number of cores to use, defaults to 1 for local execution or the value of\r
  58          * "tcoffee.cluster.cpunum" property for cluster execution\r
  59          */\r
  60         private int ncoreNumber = 0;\r
  61 \r
  62         /*\r
  63          * Number of cores parameter name\r
  64          */\r
  65         private final static String ncorePrm = "-n_core";\r
  66 \r
  67         /**\r
  68          * \r
  69          * @param workDirectory\r
  70          */\r
  71         public Tcoffee() {\r
  72                 super(KEY_VALUE_SEPARATOR);\r
  73                 /*\r
  74                  * Use "-quiet" to disable sdtout and progress to stderr inorder=input -\r
  75                  * prevent t-coffee from sorting sequences\r
  76                  */\r
  77                 addParameters(Arrays.asList("-output=clustalw"));\r
  78                 setInput(super.inputFile);\r
  79         }\r
  80 \r
  81         @Override\r
  82         public Tcoffee setInput(String inFile) {\r
  83                 super.setInput(inFile);\r
  84                 cbuilder.setParam("-seq", inFile);\r
  85                 return this;\r
  86         }\r
  87 \r
  88         @SuppressWarnings("unchecked")\r
  89         @Override\r
  90         public Alignment getResults(String workDirectory)\r
  91         throws ResultNotAvailableException {\r
  92                 try {\r
  93                         return Util.readClustalFile(workDirectory, getOutput());\r
  94                 } catch (FileNotFoundException e) {\r
  95                         log.error(e.getMessage(), e.getCause());\r
  96                         throw new ResultNotAvailableException(e);\r
  97                 } catch (IOException e) {\r
  98                         log.error(e.getMessage(), e.getCause());\r
  99                         throw new ResultNotAvailableException(e);\r
 100                 } catch (UnknownFileFormatException e) {\r
 101                         log.error(e.getMessage(), e.getCause());\r
 102                         throw new ResultNotAvailableException(e);\r
 103                 } catch (NullPointerException e) {\r
 104                         log.error(e.getMessage(), e.getCause());\r
 105                         throw new ResultNotAvailableException(e);\r
 106                 }\r
 107         }\r
 108 \r
 109         @Override\r
 110         public List<String> getCreatedFiles() {\r
 111                 return Arrays.asList(getOutput());\r
 112         }\r
 113 \r
 114         public void setNCore(int ncoreNumber) {\r
 115                 if (ncoreNumber < 1 || ncoreNumber > 100) {\r
 116                         throw new IndexOutOfBoundsException(\r
 117                                         "Number of cores must be within 1 and 100 ");\r
 118                 }\r
 119                 this.ncoreNumber = ncoreNumber;\r
 120                 cbuilder.setParam(ncorePrm, Integer.toString(getNCore()));\r
 121         }\r
 122 \r
 123         int getNCore() {\r
 124                 return ncoreNumber;\r
 125         }\r
 126 \r
 127         @Override\r
 128         public CommandBuilder<Tcoffee> getParameters(ExecProvider provider) {\r
 129                 // Limit number of cores to 1 for ANY execution which does not set\r
 130                 // Ncores explicitly using setNCore method\r
 131                 if (ncoreNumber == 0) {\r
 132                         setNCore(1);\r
 133                 }\r
 134                 if (provider == Executable.ExecProvider.Cluster) {\r
 135                         int cpunum = SkeletalExecutable.getClusterCpuNum(getType());\r
 136                         if (cpunum != 0) {\r
 137                                 setNCore(cpunum);\r
 138                         }\r
 139                 }\r
 140                 return super.getParameters(provider);\r
 141         }\r
 142 \r
 143         @Override\r
 144         public Limit<Tcoffee> getLimit(String presetName) {\r
 145                 if (limits == null) {\r
 146                         limits = getLimits();\r
 147                 }\r
 148 \r
 149                 Limit<Tcoffee> limit = null;\r
 150                 if (limits != null) {\r
 151                         // this returns default limit if preset is undefined!\r
 152                         limit = limits.getLimitByName(presetName);\r
 153                 }\r
 154                 // If limit is not defined for a particular preset, then return default\r
 155                 // limit\r
 156                 if (limit == null) {\r
 157                         log.debug("Limit for the preset " + presetName\r
 158                                         + " is not found. Using default");\r
 159                         limit = limits.getDefaultLimit();\r
 160                 }\r
 161                 return limit;\r
 162         }\r
 163 \r
 164         @Override\r
 165         public LimitsManager<Tcoffee> getLimits() {\r
 166                 // synchronise on static field\r
 167                 synchronized (log) {\r
 168                         if (limits == null) {\r
 169                                 limits = Util.getLimits(this.getClass());\r
 170                         }\r
 171                 }\r
 172                 return limits;\r
 173         }\r
 174 \r
 175         @Override\r
 176         public String getNativeSpecs() {\r
 177                 return getClusterSettings();\r
 178         }\r
 179 \r
 180 \r
 181         @Override\r
 182         public Class<? extends Executable<?>> getType() {\r
 183                 return this.getClass();\r
 184         }\r
 185 }\r