always output citations file

src/dr/app/beast/BeastMain.java

@@ -96,7 +96,7 @@ public BeastMain(File inputFile, BeastConsoleApp consoleApp, int maxErrorCount,
 
         String fileName = inputFile.getName();
 
-        final Logger infoLogger = Logger.getLogger("dr.app.beast");
+        final Logger infoLogger = Logger.getLogger("dr.apps.beast");
         try {
 
             FileReader fileReader = new FileReader(inputFile);
@@ -133,11 +133,14 @@ public boolean isLoggable(LogRecord record) {
             });
             infoLogger.addHandler(errorHandler);
 
-            if (System.getProperty("citations.filename") != null) {
+            /*if (System.getProperty("citations.filename") != null) {
                 FileOutputStream citationStream = new FileOutputStream(System.getProperty("citations.filename"));
                 Handler citationHandler = new MessageLogHandler(citationStream);
                 Logger.getLogger("dr.apps.beast").addHandler(citationHandler);
-            }
+            }*/
+            FileOutputStream citationStream = new FileOutputStream("citations.txt");
+            Handler citationHandler = new MessageLogHandler(citationStream);
+            Logger.getLogger("dr.app.beast").addHandler(citationHandler);
 
             logger.setUseParentHandlers(false);
 

src/dr/app/beast/BeastParser.java

@@ -205,7 +205,7 @@ private void loadProperties(Class c, String parsersFile, boolean verbose, boolea
 
     @Override
     protected void executingRunnable() {
-        Logger.getLogger("dr.apps.beast").info("\nCitations for this analysis: ");
+        Logger.getLogger("dr.app.beast").info("\nCitations for this analysis: ");
 
         Map<String, Set<Pair<String, String>>> categoryMap = new LinkedHashMap<String, Set<Pair<String, String>>>();
 
@@ -222,22 +222,22 @@ protected void executingRunnable() {
         }
 
         for (String category : categoryMap.keySet()) {
-            Logger.getLogger("dr.apps.beast").info("\n"+category.toUpperCase());
+            Logger.getLogger("dr.app.beast").info("\n"+category.toUpperCase());
             Set<Pair<String, String>> pairSet = categoryMap.get(category);
 
             for (Pair<String, String>keyPair : pairSet) {
-                Logger.getLogger("dr.apps.beast").info(keyPair.second + ":");
+                Logger.getLogger("dr.app.beast").info(keyPair.second + ":");
 
                 for (Citation citation : getCitationStore().get(keyPair)) {
-                    Logger.getLogger("dr.apps.beast").info("\t" + citation.toString());
+                    Logger.getLogger("dr.app.beast").info("\t" + citation.toString());
                 }
             }
         }
 
         // clear the citation store so all the same citations don't get cited again
         getCitationStore().clear();
 
-        Logger.getLogger("dr.apps.beast").info("\n");
+        Logger.getLogger("dr.app.beast").info("\n");
 
     }