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