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