GUI fixes.

src/edu/uconn/tripoint/pathwayimport/GraphiteImport.java

@@ -57,9 +57,10 @@ public GraphiteImport(String pathwaylibrary, String gid){
 				String pathwayname = c.parseAndEval("names(cpathwaylist)["+rindex+"]").asString();
 				c.parseAndEval("curpath = cpathwaylist[["+rindex+"]]");
 				c.parseAndEval("ed <- edges(curpath)");
-				String[] sources = c.parseAndEval("ed[,2]").asStrings();
-				String[] destinations = c.parseAndEval("ed[,4]").asStrings();
-				String[] edgetype = c.parseAndEval("ed[,6]").asStrings();
+
+				String[] sources = c.parseAndEval("ed$src").asStrings();
+				String[] destinations = c.parseAndEval("ed$dest").asStrings();
+				String[] edgetype = c.parseAndEval("ed$type").asStrings();
 
 				System.out.println("Loading "+pathwayname);
 				Pathway p = new Pathway(pathwaylibrary+":"+pathwayname);

src/edu/uconn/tripoint/ui/CommandOutputPanel.java

@@ -0,0 +1,41 @@
+package edu.uconn.tripoint.ui;
+
+import java.awt.BorderLayout;
+import java.awt.Font;
+
+import javax.swing.BoxLayout;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTextArea;
+
+@SuppressWarnings("serial")
+public class CommandOutputPanel extends JPanel {
+
+	private JTextArea _ota;
+
+	public CommandOutputPanel(Font font){
+		setLayout(new BoxLayout(this, BoxLayout.Y_AXIS));
+
+		JLabel sol = new JLabel("Command Line Output:");
+		sol.setHorizontalAlignment(JLabel.LEFT);
+		sol.setFont(font);
+		_ota = new JTextArea(15, 35);
+		_ota.setEditable(false);
+		JScrollPane osp = new JScrollPane(_ota);
+		osp.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS);
+		osp.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_ALWAYS);
+		JPanel opanel = new JPanel(new BorderLayout());
+		opanel.add(sol, BorderLayout.NORTH);
+		opanel.add(osp, BorderLayout.CENTER);
+
+		add(opanel);
+	}
+
+	public void addLine(String s){
+		_ota.append(s+"\n");
+		revalidate();
+		repaint();
+	}
+
+}

src/edu/uconn/tripoint/ui/CommandRunner.java

@@ -0,0 +1,131 @@
+package edu.uconn.tripoint.ui;
+
+
+import java.awt.BorderLayout;
+import java.awt.Font;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.PipedInputStream;
+import java.io.PipedOutputStream;
+import java.io.PrintStream;
+
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JFrame;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JProgressBar;
+import javax.swing.SwingWorker;
+
+public class CommandRunner {
+
+	private JFrame _frame;
+	private Font _labelfont;
+	private Process _p;
+	private String _title;
+
+	public CommandRunner(JFrame frame, String title){
+		_frame = frame;
+		_title = title;
+	}
+
+
+
+	public void run() {
+		final JOptionPane pane = new JOptionPane();
+
+		final CommandOutputPanel op = new CommandOutputPanel(_labelfont);
+
+		final JProgressBar jpb = new JProgressBar();
+		jpb.setSize(500, 10);
+		jpb.setIndeterminate(true);
+
+		final JButton cancel = new JButton("Cancel");
+		final JButton finish = new JButton("Finish");
+
+
+		final JPanel cp = new JPanel(new BorderLayout());
+		cp.add(jpb, BorderLayout.CENTER);
+		cp.add(cancel, BorderLayout.EAST);
+
+		final JPanel combinedpanel = new JPanel(new BorderLayout());
+		combinedpanel.add(op, BorderLayout.NORTH);
+		combinedpanel.add(cp, BorderLayout.SOUTH);
+
+
+		pane.setMessage(combinedpanel);
+		pane.setOptions(new Object[]{});
+
+		final JDialog dialog = pane.createDialog(_frame, _title);
+
+		finish.addActionListener(new ActionListener(){
+			@Override
+			public void actionPerformed(ActionEvent e) {
+				dialog.dispose();
+			}
+
+		});
+
+		cancel.addActionListener(new ActionListener(){
+			@Override
+			public void actionPerformed(ActionEvent e) {
+				if(_p != null){
+					_p.destroy();
+				}
+				dialog.dispose();
+			}
+		});
+
+
+		SwingWorker<Void, Void> sw = new SwingWorker<Void, Void>(){
+
+			@Override
+			protected Void doInBackground() throws Exception {
+
+				try {
+					PipedOutputStream pout = new PipedOutputStream();   
+					System.setOut(new PrintStream(pout));   
+					PipedInputStream pin = new PipedInputStream();  
+
+					BufferedReader stdin = new BufferedReader(new InputStreamReader(pin));
+					System.out.println("Test");
+					String s = null;
+					while((s = stdin.readLine()) != null){
+						op.addLine(s);
+						op.revalidate();
+						op.repaint();
+					}
+
+					stdin.close();
+
+				} catch (IOException e1) {
+					e1.printStackTrace();
+				}
+				return null;
+			}
+
+			@Override 
+			protected void done(){
+				cp.remove(jpb);
+				cp.remove(cancel);
+				cp.add(finish, BorderLayout.EAST);
+				dialog.setDefaultCloseOperation(JDialog.DISPOSE_ON_CLOSE);
+				dialog.revalidate();
+				dialog.repaint();
+			}
+
+		};
+
+		sw.execute();
+
+
+		dialog.setDefaultCloseOperation(JDialog.DO_NOTHING_ON_CLOSE);
+	    dialog.setVisible(true);
+
+	}
+
+}

src/edu/uconn/tripoint/ui/TriPOINT.java

@@ -138,7 +138,9 @@ public void actionPerformed(ActionEvent e) {
 
 				}
 				else{
-
+					final CommandRunner ppcr = new CommandRunner(_frame, "Run TriPOINT");
+					//JOptionPane.showMessageDialog(_frame, iv.getErrorMessages().toString(),"Run TriPOINT");
+
 				}
 			}