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