Merge branch 'JABAWS_Release_2_5' into develop

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

diff --git a/runner/compbio/runner/disorder/IUPred.java b/runner/compbio/runner/disorder/IUPred.java
index 30e8776..5d20829 100644 (file)
--- a/runner/compbio/runner/disorder/IUPred.java
+++ b/runner/compbio/runner/disorder/IUPred.java
@@ -17,6 +17,8 @@ package compbio.runner.disorder;
 import java.io.File;\r
 import java.io.FileNotFoundException;\r
 import java.io.IOException;\r
+import java.util.Arrays;\r
+import java.util.List;\r
 import java.util.Map;\r
 import java.util.Set;\r
 import java.util.TreeMap;\r
@@ -30,6 +32,7 @@ import compbio.data.sequence.SequenceUtil;
 import compbio.data.sequence.UnknownFileFormatException;\r
 import compbio.engine.client.SkeletalExecutable;\r
 import compbio.metadata.ResultNotAvailableException;\r
+import compbio.runner.msa.Mafft;\r
 \r
 /**\r
  * iupred sequenceFile <short long glob >\r
@@ -41,10 +44,11 @@ import compbio.metadata.ResultNotAvailableException;
 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
+       private static final String GLOB_OUTPUT = "out.glob";\r
+       private static final String SHORT_OUTPUT = "out.short";\r
+       private static final String LONG_OUTPUT = "out.long";\r
 \r
+       \r
        @Override\r
        @SuppressWarnings("unchecked")\r
        public ScoreManager getResults(String workDirectory)\r
@@ -52,31 +56,27 @@ public class IUPred extends SkeletalExecutable<IUPred> {
 \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
+                       File shortf = new File(workDirectory, SHORT_OUTPUT);\r
+                       if(shortf.exists()) {\r
+                               combineScores(combined, SequenceUtil.readIUPred(shortf));\r
+                       }\r
+                       File longf = new File(workDirectory, LONG_OUTPUT);\r
+                       if(longf.exists()) {\r
+                               combineScores(combined, SequenceUtil.readIUPred(longf));\r
+                       } \r
+                       \r
+                       File glob = new File(workDirectory, GLOB_OUTPUT);\r
+                       if(glob.exists()) {\r
+                               combineScores(combined, SequenceUtil.readIUPred(glob));\r
+                       }\r
+                       if(combined.isEmpty()) {\r
+                               throw new ResultNotAvailableException("Could not find any result " +\r
+                                               "files for the job: " + workDirectory); \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
@@ -90,11 +90,52 @@ public class IUPred extends SkeletalExecutable<IUPred> {
                return results;\r
        }\r
 \r
+       void combineScores(Map<String, Set<Score>> combined, Map<String, Score> scores)  { \r
+               if(scores==null) { \r
+                       return; \r
+               }\r
+               if (combined.isEmpty()) {\r
+                       for (String key : scores.keySet()) {\r
+                               Set<Score> allScores = new TreeSet<Score>();\r
+                               combined.put(key, allScores);\r
+                       }\r
+               }\r
+               for (String key : scores.keySet()) {\r
+                       Set<Score>      allScores= combined.get(key);\r
+                       assert allScores!=null; \r
+                       Score score = scores.get(key);\r
+                       allScores.add(score);\r
+                       combined.put(key, allScores);\r
+               }\r
+       }\r
+\r
+       \r
+       \r
        @Override\r
        public IUPred setInput(String inFile) {\r
                super.setInput(inFile);\r
                cbuilder.setFirst(inFile);\r
                return this;\r
+       } \r
+\r
+               \r
+       @Override\r
+       public IUPred setOutput(String outFile) {\r
+               log.warn("IUpred output is predefined and cannot be set!"); \r
+               return this; \r
+       }\r
+\r
+       UnsupportedOperationException newUnsupportedOutputException() { \r
+               return new UnsupportedOperationException("The outputs from this executable " +\r
+                               "are always either of those 3 files (depending on the method called): " + GLOB_OUTPUT + ", " \r
+                               + SHORT_OUTPUT + ", "+ LONG_OUTPUT);\r
+       }\r
+       @Override\r
+       public String getOutput() {\r
+               log.warn("IUpred output is predefined and is one of the three files " +\r
+                               "(depending on the method called): " + GLOB_OUTPUT + ", " \r
+                               + SHORT_OUTPUT + ", "+ LONG_OUTPUT);\r
+               return LONG_OUTPUT;\r
        }\r
 \r
        @SuppressWarnings("unchecked")\r