IUPred wrapper, tester and new binary for X64 linux systems

[jabaws.git] / runner / compbio / runner / disorder / IUPred.java

diff --git a/runner/compbio/runner/disorder/IUPred.java b/runner/compbio/runner/disorder/IUPred.java
new file mode 100644 (file)
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+++ b/runner/compbio/runner/disorder/IUPred.java
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+/*\r
+ * Copyright (c) 2011 Peter Troshin JAva Bioinformatics Analysis Web Services\r
+ * (JABAWS) @version: 2.0 This library is free software; you can redistribute it\r
+ * and/or modify it under the terms of the Apache License version 2 as published\r
+ * by the Apache Software Foundation This library is distributed in the hope\r
+ * that it will be useful, but WITHOUT ANY WARRANTY; without even the implied\r
+ * warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * Apache License for more details. A copy of the license is in\r
+ * apache_license.txt. It is also available here:\r
+ * @see: http://www.apache.org/licenses/LICENSE-2.0.txt Any republication or\r
+ * derived work distributed in source code form must include this copyright and\r
+ * license notice.\r
+ */\r
+\r
+package compbio.runner.disorder;\r
+\r
+import java.io.File;\r
+import java.io.FileNotFoundException;\r
+import java.io.IOException;\r
+import java.util.Map;\r
+import java.util.Set;\r
+import java.util.TreeMap;\r
+import java.util.TreeSet;\r
+\r
+import org.apache.log4j.Logger;\r
+\r
+import compbio.data.sequence.Score;\r
+import compbio.data.sequence.ScoreManager;\r
+import compbio.data.sequence.SequenceUtil;\r
+import compbio.data.sequence.UnknownFileFormatException;\r
+import compbio.engine.client.SkeletalExecutable;\r
+import compbio.metadata.ResultNotAvailableException;\r
+\r
+/**\r
+ * iupred sequenceFile <short long glob >\r
+ * \r
+ * Maximum sequence length is 40000 chars. Single string length max is a 1000\r
+ * chars!\r
+ * \r
+ */\r
+public class IUPred extends SkeletalExecutable<IUPred> {\r
+\r
+       private static Logger log = Logger.getLogger(IUPred.class);\r
+       private static final String GLOB_SUFFIX = ".glob";\r
+       private static final String SHORT_SUFFIX = ".short";\r
+       private static final String LONG_SUFFIX = ".long";\r
+\r
+       @Override\r
+       @SuppressWarnings("unchecked")\r
+       public ScoreManager getResults(String workDirectory)\r
+                       throws ResultNotAvailableException {\r
+\r
+               ScoreManager results = null;\r
+               try {\r
+\r
+                       Map<String, Score> globScores = SequenceUtil.readIUPred(new File(\r
+                                       workDirectory, getOutput() + GLOB_SUFFIX));\r
+                       Map<String, Score> shortScores = SequenceUtil.readIUPred(new File(\r
+                                       workDirectory, getOutput() + SHORT_SUFFIX));\r
+                       Map<String, Score> longScores = SequenceUtil.readIUPred(new File(\r
+                                       workDirectory, getOutput() + LONG_SUFFIX));\r
+                       Map<String, Set<Score>> combined = new TreeMap<String, Set<Score>>();\r
+                       for (String key : globScores.keySet()) {\r
+                               Set<Score> all = new TreeSet<Score>();\r
+                               Score globsc = globScores.get(key);\r
+                               assert globsc != null;\r
+                               Score shortsc = shortScores.get(key);\r
+                               assert shortsc != null;\r
+                               all.add(shortsc);\r
+                               Score longsc = longScores.get(key);\r
+                               assert longsc != null;\r
+                               all.add(longsc);\r
+                               combined.put(key, all);\r
+                       }\r
+                       results = ScoreManager.newInstance(combined);\r
+\r
+               } catch (FileNotFoundException e) {\r
+                       log.error(e.getMessage(), e.getCause());\r
+                       throw new ResultNotAvailableException(e);\r
+               } catch (IOException e) {\r
+                       log.error(e.getMessage(), e.getCause());\r
+                       throw new ResultNotAvailableException(e);\r
+               } catch (UnknownFileFormatException e) {\r
+                       log.error(e.getMessage(), e.getCause());\r
+                       throw new ResultNotAvailableException(e);\r
+               } catch (NullPointerException e) {\r
+                       log.error(e.getMessage(), e.getCause());\r
+                       throw new ResultNotAvailableException(e);\r
+               }\r
+               return results;\r
+       }\r
+\r
+       @Override\r
+       public IUPred setInput(String inFile) {\r
+               super.setInput(inFile);\r
+               cbuilder.setFirst(inFile);\r
+               return this;\r
+       }\r
+\r
+       @SuppressWarnings("unchecked")\r
+       @Override\r
+       public Class<IUPred> getType() {\r
+               return (Class<IUPred>) this.getClass();\r
+       }\r
+\r
+}\r