1 files changed, 43 insertions, 21 deletions

diff --git a/src/uk/ac/ox/cs/pagoda/Pagoda.java b/src/uk/ac/ox/cs/pagoda/Pagoda.java
index 3263c03..4ad7678 100644
--- a/src/uk/ac/ox/cs/pagoda/Pagoda.java
+++ b/src/uk/ac/ox/cs/pagoda/Pagoda.java
@@ -9,7 +9,7 @@ import uk.ac.ox.cs.pagoda.util.Utility;
 import java.nio.file.Path;
 
 /**
- * The main class
+ * Executable command line user interface.
  */
 public class Pagoda implements Runnable {
 
@@ -19,31 +19,62 @@ public class Pagoda implements Runnable {
     private static final String OPTION_ANSWER = "a";
     private static final String OPTION_CLASSIFY = "c";
     private static final String OPTION_HERMIT = "f";
+    private final Properties properties;
+
+    /**
+     * Do not use it
+     * */
+    private Pagoda() {
+        properties = new Properties();
+    }
 
     public static void main(String... args) {
 
         Options options = new Options();
-        options.addOption(Option.builder(OPTION_ONTOLOGY).argName(OPTION_ONTOLOGY).required().hasArg().desc("The ontology path").build());
+        options.addOption(Option.builder(OPTION_ONTOLOGY)
+                                .argName(OPTION_ONTOLOGY)
+                                .required()
+                                .hasArg()
+                                .desc("The ontology path")
+                                .build());
         options.addOption(Option.builder(OPTION_DATA).argName(OPTION_DATA).hasArg().desc("The data path").build());
-        options.addOption(Option.builder(OPTION_QUERY).argName(OPTION_QUERY).required().hasArg().desc("The query path").build());
-        options.addOption(Option.builder(OPTION_ANSWER).argName(OPTION_ANSWER).hasArg().desc("The answer path").build());
-        options.addOption(Option.builder(OPTION_CLASSIFY).argName(OPTION_CLASSIFY).desc("Tell whether to classify").type(Boolean.class).build());
-        options.addOption(Option.builder(OPTION_HERMIT).argName(OPTION_HERMIT).desc("Tell whether to call Hermit").type(Boolean.class).build());
+        options.addOption(Option.builder(OPTION_QUERY)
+                                .argName(OPTION_QUERY)
+                                .required()
+                                .hasArg()
+                                .desc("The query path")
+                                .build());
+        options.addOption(Option.builder(OPTION_ANSWER)
+                                .argName(OPTION_ANSWER)
+                                .hasArg()
+                                .desc("The answer path")
+                                .build());
+        options.addOption(Option.builder(OPTION_CLASSIFY)
+                                .argName(OPTION_CLASSIFY)
+                                .desc("Tell whether to classify")
+                                .type(Boolean.class)
+                                .build());
+        options.addOption(Option.builder(OPTION_HERMIT)
+                                .argName(OPTION_HERMIT)
+                                .desc("Tell whether to call Hermit")
+                                .type(Boolean.class)
+                                .build());
 
         CommandLineParser parser = new DefaultParser();
         try {
-            CommandLine cmd = parser.parse( options, args );
+            CommandLine cmd = parser.parse(options, args);
             PagodaBuilder pagodaBuilder = Pagoda.builder()
                                                 .ontology(cmd.getOptionValue(OPTION_ONTOLOGY))
                                                 .query(cmd.getOptionValue(OPTION_QUERY));
             if(cmd.hasOption(OPTION_DATA)) pagodaBuilder.data(cmd.getOptionValue(OPTION_DATA));
-            if(cmd.hasOption(OPTION_ANSWER))  pagodaBuilder.answer(cmd.getOptionValue(OPTION_ANSWER));
-            if(cmd.hasOption(OPTION_CLASSIFY)) pagodaBuilder.classify(Boolean.parseBoolean(cmd.getOptionValue(OPTION_CLASSIFY)));
-            if(cmd.hasOption(OPTION_HERMIT)) pagodaBuilder.hermit(Boolean.parseBoolean(cmd.getOptionValue(OPTION_HERMIT)));
+            if(cmd.hasOption(OPTION_ANSWER)) pagodaBuilder.answer(cmd.getOptionValue(OPTION_ANSWER));
+            if(cmd.hasOption(OPTION_CLASSIFY))
+                pagodaBuilder.classify(Boolean.parseBoolean(cmd.getOptionValue(OPTION_CLASSIFY)));
+            if(cmd.hasOption(OPTION_HERMIT))
+                pagodaBuilder.hermit(Boolean.parseBoolean(cmd.getOptionValue(OPTION_HERMIT)));
 
             pagodaBuilder.build().run();
-        }
-        catch( ParseException exp ) {
+        } catch(ParseException exp) {
             HelpFormatter formatter = new HelpFormatter();
             formatter.printHelp("PAGOdA", options);
             Utility.logError("Parsing failed.  Reason: " + exp.getMessage());
@@ -52,15 +83,6 @@ public class Pagoda implements Runnable {
     }
 
     /**
-     * Do not use it
-     * */
-    private Pagoda() {
-        properties = new Properties();
-    }
-
-    private final Properties properties;
-
-    /**
      * Get a builder.
      * */
     public static PagodaBuilder builder() {