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