build GUI for PlotComposite tool

Build the actual GUI for the composite plot image generating tool (#96). Include JavaDocs linking to other classes.

GUI, unlike CLI, does not yet offer color customization options or title customization.

Author: owlang

src/main/ScriptManagerGUI.java

@@ -56,6 +56,7 @@
 import window_interface.Figure_Generation.TwoColorHeatMapWindow;
 import window_interface.Figure_Generation.ThreeColorHeatMapWindow;
 import window_interface.Figure_Generation.MergeHeatMapWindow;
+import window_interface.Figure_Generation.PlotCompositeWindow;
 import window_interface.Figure_Generation.LabelHeatMapWindow;
 
 public class ScriptManagerGUI {
@@ -1347,12 +1348,40 @@ public void run() {
 				});
 			}
 		});
-		sl_pnlFigure.putConstraint(SpringLayout.NORTH, btncolorSequencePlot, 0, SpringLayout.NORTH,
-				txtcolorSequencePlot);
+		sl_pnlFigure.putConstraint(SpringLayout.NORTH, btncolorSequencePlot, 0, SpringLayout.NORTH, txtcolorSequencePlot);
 		sl_pnlFigure.putConstraint(SpringLayout.WEST, btncolorSequencePlot, 10, SpringLayout.WEST, pnlFigure);
-		sl_pnlFigure.putConstraint(SpringLayout.WEST, txtcolorSequencePlot, 10, SpringLayout.EAST,
-				btncolorSequencePlot);
+		sl_pnlFigure.putConstraint(SpringLayout.WEST, txtcolorSequencePlot, 10, SpringLayout.EAST, btncolorSequencePlot);
 		pnlFigure.add(btncolorSequencePlot);
+		
+
+		// >FourColorPlot
+		JTextArea txtMakeCompositePlot = new JTextArea();
+		initializeTextArea(txtMakeCompositePlot);
+		txtMakeCompositePlot.setText(ToolDescriptions.composite_description);
+		sl_pnlFigure.putConstraint(SpringLayout.NORTH, txtMakeCompositePlot, 10, SpringLayout.SOUTH, txtcolorSequencePlot);
+		sl_pnlFigure.putConstraint(SpringLayout.NORTH, txtMakeCompositePlot, 10, SpringLayout.SOUTH, btncolorSequencePlot);
+		sl_pnlFigure.putConstraint(SpringLayout.EAST, txtMakeCompositePlot, -10, SpringLayout.EAST, pnlFigure);
+		pnlFigure.add(txtMakeCompositePlot);
+
+		JButton btnMakeCompositePlot = new JButton("Composite Plot");
+		btnMakeCompositePlot.addActionListener(new ActionListener() {
+			public void actionPerformed(ActionEvent e) {
+				EventQueue.invokeLater(new Runnable() {
+					public void run() {
+						try {
+							PlotCompositeWindow frame = new PlotCompositeWindow();
+							frame.setVisible(true);
+						} catch (Exception e) {
+							e.printStackTrace();
+						}
+					}
+				});
+			}
+		});
+		sl_pnlFigure.putConstraint(SpringLayout.NORTH, btnMakeCompositePlot, 0, SpringLayout.NORTH, txtMakeCompositePlot);
+		sl_pnlFigure.putConstraint(SpringLayout.WEST, btnMakeCompositePlot, 10, SpringLayout.WEST, pnlFigure);
+		sl_pnlFigure.putConstraint(SpringLayout.WEST, txtMakeCompositePlot, 10, SpringLayout.EAST, btnMakeCompositePlot);
+		pnlFigure.add(btnMakeCompositePlot);
 
 		// Set default tab to open to...
 		// 0=BAM_Statistics 5=Peak_Analysis

src/scripts/Figure_Generation/PlotComposite.java

@@ -111,6 +111,9 @@ public static JFreeChart plotCompositeFile(File input, File OUT_PATH, boolean ou
 			// set default output filename
 			if (OUT_PATH == null) {
 				OUT_PATH = new File(ExtensionFileFilter.stripExtension(input) + "_plot.png");
+			} else if (OUT_PATH.isDirectory()) {
+				OUT_PATH = new File(OUT_PATH.getCanonicalFile() + File.separator + ExtensionFileFilter.stripExtension(input) + "_plot.png");
+
 			}
 			ChartUtils.writeChartAsPNG(new FileOutputStream(OUT_PATH), chart, pxWidth, pxHeight);
 		}

src/window_interface/Figure_Generation/PlotCompositeOutput.java

@@ -0,0 +1,78 @@
+package window_interface.Figure_Generation;
+
+import java.io.File;
+import java.io.IOException;
+import java.sql.Timestamp;
+import java.util.ArrayList;
+import java.util.Date;
+
+import javax.swing.JFrame;
+import javax.swing.JOptionPane;
+import javax.swing.JTabbedPane;
+
+import org.jfree.chart.ChartPanel;
+
+import scripts.Figure_Generation.PlotComposite;
+
+/**
+ * Initialize a tabbed window where all composite data images are displayed for each file input from a window_interface.Figure_Generation.PlotCompositeWindow instance.
+ * 
+ * The object will loop through and call the scripts.Figure_Generation.PlotComposite script on each input file to generate the line charts. Each chart's title will be the filename. Legend will be included if indicated by input. Default colors will be used for the chart (see scripts.Figure_Generation.PlotComposite for details). If specified by the input parameter values, a PNG image is saved to the indicated output directory with the passed pixel values for the saved file dimensions.
+ * @author Olivia Lang
+ * @see window_interface.Figure_Generation.PlotCompositeWindow
+ * @see scripts.Figure_Generation.PlotComposite
+ *
+ */
+@SuppressWarnings("serial")
+public class PlotCompositeOutput extends JFrame {
+
+	protected static ArrayList<File> SAMPLE = null;
+	protected static File OUT_DIR;
+	protected static boolean outputImg;
+	
+	protected static boolean includeLegend = true;
+	protected static int pxHeight;
+	protected static int pxWidth;
+
+	JTabbedPane newpane;
+
+	public PlotCompositeOutput(ArrayList<File> in, File o_dir, boolean o, boolean l, int ph, int pw) {
+		setTitle("Composite");
+		setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
+		setBounds(150, 150, 800, 600);
+
+		newpane = new JTabbedPane(JTabbedPane.TOP);
+		this.getContentPane().add(newpane);
+
+		SAMPLE = in;
+		OUT_DIR = o_dir;
+		outputImg = o;
+		includeLegend = l;
+		pxHeight = ph;
+		pxWidth = pw;
+	}
+
+	public void run() throws IOException {
+		for (int x = 0; x < SAMPLE.size(); x++) {
+			try {
+				// Execute script
+				ChartPanel chart = new ChartPanel(PlotComposite.plotCompositeFile(SAMPLE.get(x), OUT_DIR, outputImg, SAMPLE.get(x).getName(), null, includeLegend, pxHeight, pxWidth));
+				chart.setPreferredSize(new java.awt.Dimension(500, 270));
+				// Output image/error to GUI
+				newpane.addTab(SAMPLE.get(x).getName(), chart);
+			} catch (Exception e) {
+				JOptionPane.showMessageDialog(null, e.getMessage());
+			}
+			
+			firePropertyChange("composite", x, x + 1);
+		}
+		System.out.println("Program Complete");
+		System.out.println(getTimeStamp());
+	}
+
+	private static String getTimeStamp() {
+		Date date = new Date();
+		String time = new Timestamp(date.getTime()).toString();
+		return time;
+	}
+}