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