runner/compbio/runner/predictors/Jpred.java

   1 /* Copyright (c) 2013 Alexander Sherstnev\r
   2  *  \r
   3  *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 3.0     \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.predictors;\r
  20 \r
  21 import java.io.File;\r
  22 import java.io.FileInputStream;\r
  23 import java.io.FileNotFoundException;\r
  24 import java.io.IOException;\r
  25 import java.io.InputStream;\r
  26 import java.util.Arrays;\r
  27 import java.util.List;\r
  28 \r
  29 import org.apache.log4j.Logger;\r
  30 \r
  31 import compbio.data.sequence.Alignment;\r
  32 import compbio.data.sequence.AlignmentMetadata;\r
  33 import compbio.data.sequence.Program;\r
  34 import compbio.data.sequence.ScoreManager;\r
  35 import compbio.data.sequence.SequenceUtil;\r
  36 import compbio.engine.client.CommandBuilder;\r
  37 import compbio.engine.client.Executable;\r
  38 import compbio.engine.client.SkeletalExecutable;\r
  39 import compbio.metadata.ResultNotAvailableException;\r
  40 import compbio.runner.Util;\r
  41 \r
  42 /**\r
  43  * Command line\r
  44  * \r
  45  * jpred.pl -in d16vpa_.fas -outfile res_d16vpa_ -dbname ported_db -dbpath /data/UNIREFdb -ncpu 4\r
  46  * \r
  47  * @author asherstnev\r
  48  * \r
  49  */\r
  50 public class Jpred extends SkeletalExecutable<Jpred> {\r
  51 \r
  52         private static Logger log = Logger.getLogger(Jpred.class);\r
  53 \r
  54         /**\r
  55          * Number of cores to use, defaults to 1 for local execution or the value of\r
  56          * "jpred.cluster.cpunum" property for cluster execution\r
  57          */\r
  58         private int ncoreNumber = 0;\r
  59 \r
  60         public static final String KEY_VALUE_SEPARATOR = " ";\r
  61         public static final String STAT_FILE = "stat.txt";\r
  62 \r
  63         public Jpred() {\r
  64                 addParameters(Arrays.asList("-logfile " + STAT_FILE));\r
  65         }\r
  66 \r
  67         // HashMap<Method, float[]>\r
  68         @Override\r
  69         public Alignment getResults(String workDirectory)\r
  70                         throws ResultNotAvailableException {\r
  71                 Alignment annotations = null;\r
  72                 try {\r
  73                         InputStream inStream = new FileInputStream(new File(workDirectory, getOutput()));\r
  74                         annotations = new Alignment(SequenceUtil.readJpredFile(inStream), new AlignmentMetadata(Program.Jpred, '-'));\r
  75                 } catch (FileNotFoundException e) {\r
  76                         log.error(e.getMessage(), e.getCause());\r
  77                         throw new ResultNotAvailableException(e);\r
  78                 } catch (IOException e) {\r
  79                         log.error(e.getMessage(), e.getCause());\r
  80                         throw new ResultNotAvailableException(e);\r
  81                 } catch (NullPointerException e) {\r
  82                         log.error(e.getMessage(), e.getCause());\r
  83                         throw new ResultNotAvailableException(e);\r
  84                 }\r
  85                 return annotations;\r
  86         }\r
  87 \r
  88         @Override\r
  89         public List<String> getCreatedFiles() {\r
  90                 return Arrays.asList(getOutput(), getError());\r
  91         }\r
  92 \r
  93         @Override\r
  94         public Jpred setInput(String inFile) {\r
  95                 super.setInput(inFile);\r
  96                 cbuilder.setParam("-in " + inFile);\r
  97                 return this;\r
  98         }\r
  99 \r
 100         @Override\r
 101         public Jpred setOutput(String outFile) {\r
 102                 super.setOutput(outFile);\r
 103                 cbuilder.setParam("-outfile " + outFile);\r
 104                 return this;\r
 105         }\r
 106 \r
 107         @SuppressWarnings("unchecked")\r
 108         @Override\r
 109         public Class<Jpred> getType() {\r
 110                 return (Class<Jpred>) this.getClass();\r
 111         }\r
 112 \r
 113         public static String getStatFile() {\r
 114                 return STAT_FILE;\r
 115         }\r
 116 \r
 117         public void setNCore(int ncoreNumber) {\r
 118                 if (0 < ncoreNumber && ncoreNumber < 9) {\r
 119                         this.ncoreNumber = ncoreNumber;\r
 120                         cbuilder.setParam("-ncpu " + Integer.toString(getNCore()));\r
 121                 } else {\r
 122                         throw new IndexOutOfBoundsException("Number of cores must be between 1 and 8 ");\r
 123                 }\r
 124         }\r
 125 \r
 126         int getNCore() {\r
 127                 return ncoreNumber;\r
 128         }\r
 129 \r
 130         @Override\r
 131         public CommandBuilder<Jpred> getParameters(ExecProvider provider) {\r
 132                 // If number of cores is provided, set it for the cluster execution only!\r
 133                 if (provider == Executable.ExecProvider.Cluster) {\r
 134                         int cpunum = SkeletalExecutable.getClusterCpuNum(getType());\r
 135                         cpunum = (cpunum == 0) ? 1 : cpunum;\r
 136                         setNCore(cpunum);\r
 137                 } else {\r
 138                         // Limit number of cores to 1 for ANY execution which does not set\r
 139                         // Ncores explicitly using setNCore method or is run on local VM\r
 140                         if (ncoreNumber == 0) {\r
 141                                 setNCore(1);\r
 142                         }\r
 143                 }\r
 144                 return super.getParameters(provider);\r
 145         }\r
 146 \r
 147 }\r