Refactored FIJI plugin organization and added Javadocs

src/beanshell/ConsoleFrame.java

@@ -51,6 +51,10 @@ public ConsoleFrame() {
         interpreter.setShowResults(true);
     }
 
+    /**
+     * 
+     * @return BeanShell interpreter associated with this ConsoleFrame
+     */
     public Interpreter getInterpreter() {
         return interpreter;
     }
@@ -109,23 +113,6 @@ private void console_panelComponentResized(java.awt.event.ComponentEvent evt) {/
         this.console.setSize(this.console_panel.getWidth(), this.console_panel.getHeight());
     }//GEN-LAST:event_console_panelComponentResized
 
-    /**
-     * Accessed from FIJI. Initializes console and prints welcome text.
-     * @param args the command line arguments
-     */
-    public static void main(String args[]) {
-        final ConsoleFrame console = new ConsoleFrame();
-        java.awt.EventQueue.invokeLater(new Runnable() {
-            public void run() {
-
-                console.setVisible(true);
-            }
-        });
-        CommandLineInterface.printWelcomeText(console.getInterpreter().getOut());
-        new Thread(console.getInterpreter()).start();
-        }
-
-
     // Variables declaration - do not modify//GEN-BEGIN:variables
     private javax.swing.JPanel console_panel;
     // End of variables declaration//GEN-END:variables

src/commandline/CommandLineInterface.java

@@ -40,23 +40,32 @@
 import org.apache.commons.cli.ParseException;
 
 /**
- *
- * @author stefko
+ * Main class of the project, launches the BeanShell script interface.
+ * @author Marcel Stefko
  */
 public final class CommandLineInterface {
 
     private static final Options options = constructOptions();
     private static final URL urlToWelcomeText = CommandLineInterface.class.getResource("/beanshell/welcome_text.txt");
 
+    /**
+     *
+     * @return all understood options for ALICA execution
+     */
     public static Options constructOptions() {
         final Options options = new Options();
         options.addOption("i", "interpreter", false, "run BeanShell interpreter inside current terminal window");
-        options.addOption("s", "script", true, "execute BeanShell script");
+        options.addOption("s", "script", true, "execute BeanShell script (can be combined with -i)");
         options.addOption("h", "help", false, "show this help");
         return options;
     }
 
+    /**
+     * Shows help, launches the interpreter and executes scripts according to input args.
+     * @param args input arguments
+     */
     public static void main(String args[]) {
+        // parse input arguments
         CommandLineParser parser = new DefaultParser();
         CommandLine line = null;
         try {
@@ -66,14 +75,20 @@ public static void main(String args[]) {
             System.err.println("Use -help for usage.");
             System.exit(1);
         }            
+
+        // decide how do we make the interpreter available based on options
         Interpreter interpreter = null;
+        // show help and exit
         if (line.hasOption("help")) {
             HelpFormatter helpFormatter = new HelpFormatter();
             helpFormatter.printHelp("java -jar <jar-name>", options, true);
             System.exit(0);
+        // launch interpreter inside current terminal
         } else if (line.hasOption("interpreter")) {
+            // assign in, out and err streams to the interpreter
             interpreter = new Interpreter(new InputStreamReader(System.in), System.out, System.err, true);
             interpreter.setShowResults(true);
+            // if a script was given, execute it before giving access to user
             if (line.hasOption("script")) {
                 try {
                     interpreter.source(line.getOptionValue("script"));
@@ -83,7 +98,9 @@ public static void main(String args[]) {
                     Logger.getLogger(ConsoleFrame.class.getName()).log(Level.SEVERE, "EvalError while executing shell script.", ex);
                 }
             }
+            // give access to user
             new Thread( interpreter ).start(); 
+        // only execute script and exit
         } else if (line.hasOption("script")) {
             interpreter = new Interpreter();
             try {
@@ -96,22 +113,30 @@ public static void main(String args[]) {
                 Logger.getLogger(ConsoleFrame.class.getName()).log(Level.SEVERE, "EvalError while executing shell script.", ex);
                 System.exit(1);
             }
+        // if System.console() returns null, it means we were launched by
+        // double-clicking the .jar, so launch own ConsoleFrame
         } else if (System.console() == null) {
             ConsoleFrame cframe = new ConsoleFrame();
             cframe.setVisible(true);
             System.setOut(cframe.getInterpreter().getOut());
             System.setErr(cframe.getInterpreter().getErr());
             new Thread(cframe.getInterpreter()).start();
+        // otherwise, show help
         } else {
             HelpFormatter helpFormatter = new HelpFormatter();
             helpFormatter.printHelp("java -jar <jar-name>", options, true);
             System.exit(0);
         }
+
         if (interpreter != null) {
             printWelcomeText(interpreter.getOut());
         }
     }
 
+    /**
+     * Reads the welcome_text file and prints it to a PrintStream.
+     * @param out stream to print to
+     */
     public static void printWelcomeText(PrintStream out) {
         try {
             InputStream inputStream = urlToWelcomeText.openStream();
@@ -121,7 +146,6 @@ public static void printWelcomeText(PrintStream out) {
             while ((length = inputStream.read(buffer)) != -1) {
                 result.write(buffer, 0, length);
             }
-            // StandardCharsets.UTF_8.name() > JDK 7
             String message = result.toString("UTF-8");
             out.print(message+"\n");
         } catch (IOException ex) {