runner/compbio/runner/conservation/AACon.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.conservation;\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.ScoreManager;\r
  32 import compbio.data.sequence.SequenceUtil;\r
  33 import compbio.engine.client.CommandBuilder;\r
  34 import compbio.engine.client.Executable;\r
  35 import compbio.engine.client.SkeletalExecutable;\r
  36 import compbio.metadata.ResultNotAvailableException;\r
  37 \r
  38 /**\r
  39  * Command line\r
  40  * \r
  41  * java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out\r
  42  * \r
  43  * @author pvtroshin\r
  44  * \r
  45  */\r
  46 public class AACon extends SkeletalExecutable<AACon> {\r
  47 \r
  48         private static Logger log = Logger.getLogger(AACon.class);\r
  49 \r
  50         /**\r
  51          * Number of cores to use, defaults to 1 for local execution or the value of\r
  52          * "jronn.cluster.cpunum" property for cluster execution\r
  53          */\r
  54         private int ncoreNumber = 0;\r
  55 \r
  56         private final String ncorePrm = "-t=";\r
  57 \r
  58         public static final String KEY_VALUE_SEPARATOR = "=";\r
  59         public static final String STAT_FILE = "stat.txt";\r
  60 \r
  61         public AACon() {\r
  62                 addParameters(Arrays.asList("-jar", getLibPath(), "-d=" + STAT_FILE,\r
  63                                 "-f=RESULT_NO_ALIGNMENT"));\r
  64         }\r
  65         // HashMap<Method, float[]>\r
  66         @Override\r
  67         public ScoreManager getResults(String workDirectory)\r
  68                         throws ResultNotAvailableException {\r
  69                 ScoreManager annotations = null;\r
  70                 try {\r
  71                         InputStream inStream = new FileInputStream(new File(workDirectory,\r
  72                                         getOutput()));\r
  73                         annotations = ScoreManager.newInstanceSingleSequence(SequenceUtil\r
  74                                         .readAAConResults(inStream));\r
  75                         inStream.close();\r
  76                 } catch (FileNotFoundException e) {\r
  77                         log.error(e.getMessage(), e.getCause());\r
  78                         throw new ResultNotAvailableException(e);\r
  79                 } catch (IOException e) {\r
  80                         log.error(e.getMessage(), e.getCause());\r
  81                         throw new ResultNotAvailableException(e);\r
  82                 } catch (NullPointerException e) {\r
  83                         log.error(e.getMessage(), e.getCause());\r
  84                         throw new ResultNotAvailableException(e);\r
  85                 }\r
  86                 return annotations;\r
  87         }\r
  88 \r
  89         private static String getLibPath() {\r
  90 \r
  91                 String settings = ph.getProperty("aacon.jar.file");\r
  92                 if (compbio.util.Util.isEmpty(settings)) {\r
  93                         throw new NullPointerException(\r
  94                                         "Please define aacon.jar.file property in Executable.properties file"\r
  95                                                         + "and initialize it with the location of jronn jar file");\r
  96                 }\r
  97                 if (new File(settings).isAbsolute()) {\r
  98                         // the jar can be found so no actions necessary\r
  99                         // no further actions is necessary\r
 100                         return settings;\r
 101                 }\r
 102                 return compbio.engine.client.Util.convertToAbsolute(settings);\r
 103         }\r
 104 \r
 105         @Override\r
 106         public List<String> getCreatedFiles() {\r
 107                 return Arrays.asList(getOutput(), getError());\r
 108         }\r
 109 \r
 110         @Override\r
 111         public AACon setInput(String inFile) {\r
 112                 super.setInput(inFile);\r
 113                 cbuilder.setParam("-i=" + inFile);\r
 114                 return this;\r
 115         }\r
 116 \r
 117         @Override\r
 118         public AACon setOutput(String outFile) {\r
 119                 super.setOutput(outFile);\r
 120                 cbuilder.setParam("-o=" + outFile);\r
 121                 return this;\r
 122         }\r
 123 \r
 124         @SuppressWarnings("unchecked")\r
 125         @Override\r
 126         public Class<AACon> getType() {\r
 127                 return (Class<AACon>) this.getClass();\r
 128         }\r
 129 \r
 130         public static String getStatFile() {\r
 131                 return STAT_FILE;\r
 132         }\r
 133 \r
 134         public void setNCore(int ncoreNumber) {\r
 135                 if (ncoreNumber < 1 || ncoreNumber > 100) {\r
 136                         throw new IndexOutOfBoundsException(\r
 137                                         "Number of cores must be within 1 and 100 ");\r
 138                 }\r
 139                 this.ncoreNumber = ncoreNumber;\r
 140                 cbuilder.setParam(ncorePrm + Integer.toString(getNCore()));\r
 141         }\r
 142 \r
 143         int getNCore() {\r
 144                 return ncoreNumber;\r
 145         }\r
 146 \r
 147         @Override\r
 148         public CommandBuilder<AACon> getParameters(ExecProvider provider) {\r
 149                 // If number of cores is provided, set it for the cluster execution\r
 150                 // only!\r
 151                 if (provider == Executable.ExecProvider.Cluster) {\r
 152                         int cpunum = SkeletalExecutable.getClusterCpuNum(getType());\r
 153                         cpunum = (cpunum == 0) ? 1 : cpunum;\r
 154                         setNCore(cpunum);\r
 155                 } else {\r
 156                         // Limit number of cores to 1 for ANY execution which does not set\r
 157                         // Ncores explicitly using setNCore method or is run on local VM\r
 158                         if (ncoreNumber == 0) {\r
 159                                 setNCore(1);\r
 160                         }\r
 161                 }\r
 162                 return super.getParameters(provider);\r
 163         }\r
 164 \r
 165 }\r