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.Map;\r
  21 import java.util.Set;\r
  22 import java.util.TreeMap;\r
  23 import java.util.TreeSet;\r
  24 \r
  25 import org.apache.log4j.Logger;\r
  26 \r
  27 import compbio.data.sequence.Score;\r
  28 import compbio.data.sequence.ScoreManager;\r
  29 import compbio.data.sequence.SequenceUtil;\r
  30 import compbio.data.sequence.UnknownFileFormatException;\r
  31 import compbio.engine.client.SkeletalExecutable;\r
  32 import compbio.metadata.ResultNotAvailableException;\r
  33 \r
  34 /**\r
  35  * iupred sequenceFile <short long glob >\r
  36  * \r
  37  * Maximum sequence length is 40000 chars. Single string length max is a 1000\r
  38  * chars!\r
  39  * \r
  40  */\r
  41 public class IUPred extends SkeletalExecutable<IUPred> {\r
  42 \r
  43         private static Logger log = Logger.getLogger(IUPred.class);\r
  44         private static final String GLOB_SUFFIX = ".glob";\r
  45         private static final String SHORT_SUFFIX = ".short";\r
  46         private static final String LONG_SUFFIX = ".long";\r
  47 \r
  48         @Override\r
  49         @SuppressWarnings("unchecked")\r
  50         public ScoreManager getResults(String workDirectory)\r
  51                         throws ResultNotAvailableException {\r
  52 \r
  53                 ScoreManager results = null;\r
  54                 try {\r
  55 \r
  56                         Map<String, Score> globScores = SequenceUtil.readIUPred(new File(\r
  57                                         workDirectory, getOutput() + GLOB_SUFFIX));\r
  58                         Map<String, Score> shortScores = SequenceUtil.readIUPred(new File(\r
  59                                         workDirectory, getOutput() + SHORT_SUFFIX));\r
  60                         Map<String, Score> longScores = SequenceUtil.readIUPred(new File(\r
  61                                         workDirectory, getOutput() + LONG_SUFFIX));\r
  62                         Map<String, Set<Score>> combined = new TreeMap<String, Set<Score>>();\r
  63                         for (String key : globScores.keySet()) {\r
  64                                 Set<Score> all = new TreeSet<Score>();\r
  65                                 Score globsc = globScores.get(key);\r
  66                                 assert globsc != null;\r
  67                                 Score shortsc = shortScores.get(key);\r
  68                                 assert shortsc != null;\r
  69                                 all.add(shortsc);\r
  70                                 Score longsc = longScores.get(key);\r
  71                                 assert longsc != null;\r
  72                                 all.add(longsc);\r
  73                                 combined.put(key, all);\r
  74                         }\r
  75                         results = ScoreManager.newInstance(combined);\r
  76 \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 (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         @Override\r
  94         public IUPred setInput(String inFile) {\r
  95                 super.setInput(inFile);\r
  96                 cbuilder.setFirst(inFile);\r
  97                 return this;\r
  98         }\r
  99 \r
 100         @SuppressWarnings("unchecked")\r
 101         @Override\r
 102         public Class<IUPred> getType() {\r
 103                 return (Class<IUPred>) this.getClass();\r
 104         }\r
 105 \r
 106 }\r