runner/compbio/runner/disorder/IUPred.java

   1 /*\r
   2  * Copyright (c) 2011 Peter Troshin JAva Bioinformatics Analysis Web Services\r
   3  * (JABAWS) @version: 2.0 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.disorder;\r
  16 \r
  17 import java.io.File;\r
  18 import java.io.IOException;\r
  19 import java.util.Map;\r
  20 import java.util.Set;\r
  21 import java.util.TreeMap;\r
  22 import java.util.TreeSet;\r
  23 \r
  24 import org.apache.log4j.Logger;\r
  25 \r
  26 import compbio.data.sequence.Score;\r
  27 import compbio.data.sequence.ScoreManager;\r
  28 import compbio.data.sequence.SequenceUtil;\r
  29 import compbio.data.sequence.UnknownFileFormatException;\r
  30 import compbio.engine.client.SkeletalExecutable;\r
  31 import compbio.metadata.ResultNotAvailableException;\r
  32 \r
  33 /**\r
  34  * iupred sequenceFile <short long glob >\r
  35  * \r
  36  * Maximum sequence length is 40000 chars. Single string length max is a 1000\r
  37  * chars!\r
  38  * \r
  39  */\r
  40 public class IUPred extends SkeletalExecutable<IUPred> {\r
  41 \r
  42         private static Logger log = Logger.getLogger(IUPred.class);\r
  43         private static final String GLOB_OUTPUT = "out.glob";\r
  44         private static final String SHORT_OUTPUT = "out.short";\r
  45         private static final String LONG_OUTPUT = "out.long";\r
  46 \r
  47         @Override\r
  48         @SuppressWarnings("unchecked")\r
  49         public ScoreManager getResults(String workDirectory)\r
  50                         throws ResultNotAvailableException {\r
  51 \r
  52                 ScoreManager results = null;\r
  53                 try {\r
  54                         Map<String, Set<Score>> combined = new TreeMap<String, Set<Score>>();\r
  55                         \r
  56                         File shortf = new File(workDirectory, SHORT_OUTPUT);\r
  57                         if(shortf.exists()) {\r
  58                                 combineScores(combined, SequenceUtil.readIUPred(shortf));\r
  59                         }\r
  60                         File longf = new File(workDirectory, LONG_OUTPUT);\r
  61                         if(longf.exists()) {\r
  62                                 combineScores(combined, SequenceUtil.readIUPred(longf));\r
  63                         } \r
  64                         \r
  65                         File glob = new File(workDirectory, GLOB_OUTPUT);\r
  66                         if(glob.exists()) {\r
  67                                 combineScores(combined, SequenceUtil.readIUPred(glob));\r
  68                         }\r
  69                         if(combined.isEmpty()) {\r
  70                                 throw new ResultNotAvailableException("Could not find any result " +\r
  71                                                 "files for the job: " + workDirectory); \r
  72                         }\r
  73                         results = ScoreManager.newInstance(combined);\r
  74 \r
  75                 } catch (IOException e) {\r
  76                         log.error(e.getMessage(), e.getCause());\r
  77                         throw new ResultNotAvailableException(e);\r
  78                 } catch (UnknownFileFormatException e) {\r
  79                         log.error(e.getMessage(), e.getCause());\r
  80                         throw new ResultNotAvailableException(e);\r
  81                 } catch (NullPointerException e) {\r
  82                         log.error(e.getMessage(), e.getCause());\r
  83                         throw new ResultNotAvailableException(e);\r
  84                 }\r
  85                 return results;\r
  86         }\r
  87 \r
  88         void combineScores(Map<String, Set<Score>> combined, Map<String, Score> scores)  { \r
  89                 if(scores==null) { \r
  90                         return; \r
  91                 }\r
  92                 if (combined.isEmpty()) {\r
  93                         for (String key : scores.keySet()) {\r
  94                                 Set<Score> allScores = new TreeSet<Score>();\r
  95                                 combined.put(key, allScores);\r
  96                         }\r
  97                 }\r
  98                 for (String key : scores.keySet()) {\r
  99                         Set<Score>      allScores= combined.get(key);\r
 100                         assert allScores!=null; \r
 101                         Score score = scores.get(key);\r
 102                         allScores.add(score);\r
 103                         combined.put(key, allScores);\r
 104                 }\r
 105         }\r
 106 \r
 107         @Override\r
 108         public IUPred setInput(String inFile) {\r
 109                 super.setInput(inFile);\r
 110                 cbuilder.setFirst(inFile);\r
 111                 return this;\r
 112         } \r
 113 \r
 114         @Override\r
 115         public IUPred setOutput(String outFile) {\r
 116                 log.warn("IUpred output is predefined and cannot be set!"); \r
 117                 return this; \r
 118         }\r
 119 \r
 120         UnsupportedOperationException newUnsupportedOutputException() { \r
 121                 return new UnsupportedOperationException("The outputs from this executable " +\r
 122                                 "are always either of those 3 files (depending on the method called): " + GLOB_OUTPUT + ", " \r
 123                                 + SHORT_OUTPUT + ", "+ LONG_OUTPUT);\r
 124         }\r
 125 \r
 126         @Override\r
 127         public String getOutput() {\r
 128                 log.warn("IUpred output is predefined and is one of the three files " +\r
 129                                 "(depending on the method called): " + GLOB_OUTPUT + ", " \r
 130                                 + SHORT_OUTPUT + ", "+ LONG_OUTPUT);\r
 131                 return LONG_OUTPUT;\r
 132         }\r
 133 \r
 134         @SuppressWarnings("unchecked")\r
 135         @Override\r
 136         public Class<IUPred> getType() {\r
 137                 return (Class<IUPred>) this.getClass();\r
 138         }\r
 139 \r
 140 }\r