redirect output to stderr in order to prevent it getting redirected to files (e.g. citations in TreeAnnotator) #98

Author: rbouckaert

src/beastfx/app/tools/AppLauncher.java

@@ -312,11 +312,11 @@ public void runAppFromCMD(PackageApp packageApp, String[] additionalArgs) {
 
             Class<?> mainClass = BEASTClassLoader.forName(packageApp.className, "has.main.method");
             Method mainMethod = mainClass.getMethod("main", String[].class);
-            Log.info("About to invoke " + packageApp.className + " " + mainMethod);
+            Log.warning("About to invoke " + packageApp.className + " " + mainMethod);
             if (additionalArgs == null) {
                 additionalArgs = new String[]{};
             }
-            Log.info("Args:" + Arrays.toString(additionalArgs));
+            Log.warning("Args:" + Arrays.toString(additionalArgs));
 
             try {
                 mainMethod.invoke(null, (Object) additionalArgs);
@@ -330,7 +330,7 @@ public void runAppFromCMD(PackageApp packageApp, String[] additionalArgs) {
                 }
             }
 
-            Log.info("Done invoking " + packageApp.className);
+            Log.warning("Done invoking " + packageApp.className);
 
         } catch (Throwable e) {
             e.printStackTrace();

src/beastfx/app/treeannotator/TreeAnnotator.java

@@ -562,19 +562,19 @@ public void run(final int burninPercentage,
         String topoCitation = topologySettingService.getCitations();
 
         if (!nodeCitation.isBlank() || !topoCitation.isBlank()) {
-            System.out.println("======================================================");
-            System.out.println("Please cite the following when using the summary tree:\n");
+            Log.warning("======================================================");
+            Log.warning("Please cite the following when using the summary tree:\n");
             if (!nodeCitation.isBlank()) {
-                System.out.println(nodeCitation);
+            	Log.warning(nodeCitation);
             }
             // If both citations are present, print a separator line
             if (!nodeCitation.isBlank() && !topoCitation.isBlank()) {
-                System.out.println("\n-----------------------------------------------------\n");
+            	Log.warning("\n-----------------------------------------------------\n");
             }
             if (!topoCitation.isBlank()) {
-                System.out.println(topoCitation);
+            	Log.warning(topoCitation);
             }
-            System.out.println("======================================================");
+            Log.warning("======================================================");
 
         }  // Finished printing citations