runner/compbio/runner/conservation/AACon.java

   1 /*\r
   2  * Copyright (c) 2009 Peter Troshin JAva Bioinformatics Analysis Web Services\r
   3  * (JABAWS) @version: 1.0 This library is free software; you can redistribute it\r
   4  * and/or modify it under the terms of the Apache License version 2 as published\r
   5  * by the Apache Software Foundation This library is distributed in the hope\r
   6  * that it will be useful, but WITHOUT ANY WARRANTY; without even the implied\r
   7  * warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
   8  * Apache License for more details. A copy of the license is in\r
   9  * apache_license.txt. It is also available here:\r
  10  * @see: http://www.apache.org/licenses/LICENSE-2.0.txt Any republication or\r
  11  * derived work distributed in source code form must include this copyright and\r
  12  * license notice.\r
  13  */\r
  14 \r
  15 package compbio.runner.conservation;\r
  16 \r
  17 import java.io.File;\r
  18 import java.io.FileInputStream;\r
  19 import java.io.FileNotFoundException;\r
  20 import java.io.IOException;\r
  21 import java.io.InputStream;\r
  22 import java.util.Arrays;\r
  23 import java.util.List;\r
  24 \r
  25 import org.apache.log4j.Logger;\r
  26 \r
  27 import compbio.data.sequence.SMERFSConstraints;\r
  28 import compbio.data.sequence.ScoreManager;\r
  29 import compbio.data.sequence.SequenceUtil;\r
  30 import compbio.engine.client.CommandBuilder;\r
  31 import compbio.engine.client.Executable;\r
  32 import compbio.engine.client.SkeletalExecutable;\r
  33 import compbio.metadata.ResultNotAvailableException;\r
  34 \r
  35 /**\r
  36  * Command line\r
  37  * \r
  38  * java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out\r
  39  * \r
  40  * @author pvtroshin\r
  41  * \r
  42  */\r
  43 public class AACon extends SkeletalExecutable<AACon> {\r
  44 \r
  45         private static Logger log = Logger.getLogger(AACon.class);\r
  46 \r
  47         /**\r
  48          * Number of cores to use, defaults to 1 for local execution or the value of\r
  49          * "jronn.cluster.cpunum" property for cluster execution\r
  50          */\r
  51         private int ncoreNumber = 0;\r
  52 \r
  53         private final String ncorePrm = "-t=";\r
  54 \r
  55         public static final String KEY_VALUE_SEPARATOR = "=";\r
  56         public static final String STAT_FILE = "stat.txt";\r
  57 \r
  58         private final int windowWidth = SMERFSConstraints.DEFAULT_WINDOW_SIZE;\r
  59         private final SMERFSConstraints colScoreMethod = SMERFSConstraints.MID_SCORE;\r
  60         private final double gapTreshold = SMERFSConstraints.DEFAULT_GAP_THRESHOLD;\r
  61 \r
  62         public AACon() {\r
  63                 addParameters(Arrays.asList("-jar", getLibPath(), "-d=" + STAT_FILE,\r
  64                                 "-f=RESULT_NO_ALIGNMENT"));\r
  65         }\r
  66         // HashMap<Method, float[]>\r
  67         @Override\r
  68         public ScoreManager getResults(String workDirectory)\r
  69                         throws ResultNotAvailableException {\r
  70                 ScoreManager annotations = null;\r
  71                 try {\r
  72                         InputStream inStream = new FileInputStream(new File(workDirectory,\r
  73                                         getOutput()));\r
  74                         annotations = ScoreManager.newInstanceSingleSequence(SequenceUtil\r
  75                                         .readAAConResults(inStream));\r
  76                         inStream.close();\r
  77                 } catch (FileNotFoundException e) {\r
  78                         log.error(e.getMessage(), e.getCause());\r
  79                         throw new ResultNotAvailableException(e);\r
  80                 } catch (IOException e) {\r
  81                         log.error(e.getMessage(), e.getCause());\r
  82                         throw new ResultNotAvailableException(e);\r
  83                 } catch (NullPointerException e) {\r
  84                         log.error(e.getMessage(), e.getCause());\r
  85                         throw new ResultNotAvailableException(e);\r
  86                 }\r
  87                 return annotations;\r
  88         }\r
  89 \r
  90         private static String getLibPath() {\r
  91 \r
  92                 String settings = ph.getProperty("aacon.jar.file");\r
  93                 if (compbio.util.Util.isEmpty(settings)) {\r
  94                         throw new NullPointerException(\r
  95                                         "Please define aacon.jar.file property in Executable.properties file"\r
  96                                                         + "and initialize it with the location of jronn jar file");\r
  97                 }\r
  98                 if (new File(settings).isAbsolute()) {\r
  99                         // the jar can be found so no actions necessary\r
 100                         // no further actions is necessary\r
 101                         return settings;\r
 102                 }\r
 103                 return compbio.engine.client.Util.convertToAbsolute(settings);\r
 104         }\r
 105 \r
 106         @Override\r
 107         public List<String> getCreatedFiles() {\r
 108                 return Arrays.asList(getOutput(), getError());\r
 109         }\r
 110 \r
 111         @Override\r
 112         public AACon setInput(String inFile) {\r
 113                 super.setInput(inFile);\r
 114                 cbuilder.setParam("-i=" + inFile);\r
 115                 return this;\r
 116         }\r
 117 \r
 118         @Override\r
 119         public AACon setOutput(String outFile) {\r
 120                 super.setOutput(outFile);\r
 121                 cbuilder.setParam("-o=" + outFile);\r
 122                 return this;\r
 123         }\r
 124 \r
 125         @SuppressWarnings("unchecked")\r
 126         @Override\r
 127         public Class<AACon> getType() {\r
 128                 return (Class<AACon>) this.getClass();\r
 129         }\r
 130 \r
 131         public static String getStatFile() {\r
 132                 return STAT_FILE;\r
 133         }\r
 134 \r
 135         public void setNCore(int ncoreNumber) {\r
 136                 if (ncoreNumber < 1 || ncoreNumber > 100) {\r
 137                         throw new IndexOutOfBoundsException(\r
 138                                         "Number of cores must be within 1 and 100 ");\r
 139                 }\r
 140                 this.ncoreNumber = ncoreNumber;\r
 141                 cbuilder.setParam(ncorePrm + Integer.toString(getNCore()));\r
 142         }\r
 143 \r
 144         int getNCore() {\r
 145                 return ncoreNumber;\r
 146         }\r
 147 \r
 148         @Override\r
 149         public CommandBuilder<AACon> getParameters(ExecProvider provider) {\r
 150                 // If number of cores is provided, set it for the cluster execution\r
 151                 // only!\r
 152                 if (provider == Executable.ExecProvider.Cluster) {\r
 153                         int cpunum = SkeletalExecutable.getClusterCpuNum(getType());\r
 154                         cpunum = (cpunum == 0) ? 1 : cpunum;\r
 155                         setNCore(cpunum);\r
 156                 } else {\r
 157                         // Limit number of cores to 1 for ANY execution which does not set\r
 158                         // Ncores explicitly using setNCore method or is run on local VM\r
 159                         if (ncoreNumber == 0) {\r
 160                                 setNCore(1);\r
 161                         }\r
 162                 }\r
 163                 return super.getParameters(provider);\r
 164         }\r
 165 \r
 166 }\r