add support for setting TagExtend to GUI

TagExtend support already accounted for in TagPileup script. This commit allows the user to set a value from the GUI. The selection box was put where CPU setting used to be and CPU setting was moved over in the window interface. "Output Parameters" section label was removed.
#73

Author: owlang

src/window_interface/Read_Analysis/TagPileupWindow.java

@@ -83,6 +83,7 @@ public class TagPileupWindow extends JFrame implements ActionListener, PropertyC
 	private JLabel lblTagShift;
 	private JLabel lblStdDevSize;
 	private JLabel lblNumStd;
+	private JLabel lblTagExtend;
 	private JLabel lblDefaultToLocal;
 	private JLabel lblCurrentOutput;
 	private JLabel lblOutputMatrixFormat;
@@ -94,6 +95,7 @@ public class TagPileupWindow extends JFrame implements ActionListener, PropertyC
 	private JTextField txtSmooth;
 	private JTextField txtStdSize;
 	private JTextField txtNumStd;
+	private JTextField txtTagExtend;
 	private JTextField txtCPU;
 	private JTextField txtCompositeName;
 	private JCheckBox chckbxOutputData;
@@ -201,6 +203,7 @@ public Void doInBackground() throws IOException, InterruptedException {
 					param.setSmooth(Integer.parseInt(txtSmooth.getText()));
 					param.setStdSize(Integer.parseInt(txtStdSize.getText()));
 					param.setStdNum(Integer.parseInt(txtNumStd.getText()));
+					param.setTagExtend(Integer.parseInt(txtTagExtend.getText()));
 					param.setCPU(Integer.parseInt(txtCPU.getText()));
 
 					TagPileupOutput pile = new TagPileupOutput(BEDFiles, BAMFiles, param, colors);
@@ -579,27 +582,25 @@ public void actionPerformed(ActionEvent e) {
 		txtBin.setColumns(10);
 		contentPane.add(txtBin);
 
-		lblCpusToUse = new JLabel("CPU's to Use:");
-		sl_contentPane.putConstraint(SpringLayout.NORTH, lblCpusToUse, 0, SpringLayout.NORTH, lblTagShift);
-		sl_contentPane.putConstraint(SpringLayout.WEST, lblCpusToUse, 10, SpringLayout.EAST, txtBin);
-		lblCpusToUse.setFont(new Font("Lucida Grande", Font.BOLD, 13));
-		contentPane.add(lblCpusToUse);
-
-		txtCPU = new JTextField();
-		sl_contentPane.putConstraint(SpringLayout.NORTH, txtCPU, -1, SpringLayout.NORTH, lblTagShift);
-		sl_contentPane.putConstraint(SpringLayout.WEST, txtCPU, 10, SpringLayout.EAST, lblCpusToUse);
-		sl_contentPane.putConstraint(SpringLayout.EAST, txtCPU, 70, SpringLayout.EAST, lblCpusToUse);
-		txtCPU.setHorizontalAlignment(SwingConstants.CENTER);
-		txtCPU.setText("1");
-		contentPane.add(txtCPU);
-		txtCPU.setColumns(10);
-
 		chckbxTagStandard = new JCheckBox("Set Tags to Be Equal");
-		sl_contentPane.putConstraint(SpringLayout.NORTH, chckbxTagStandard, 40, SpringLayout.SOUTH,
-				lblReadManipulation);
+		sl_contentPane.putConstraint(SpringLayout.NORTH, chckbxTagStandard, 40, SpringLayout.SOUTH, lblReadManipulation);
 		sl_contentPane.putConstraint(SpringLayout.WEST, chckbxTagStandard, 10, SpringLayout.EAST, scrollPane_BAM);
 		contentPane.add(chckbxTagStandard);
 
+		lblTagExtend = new JLabel("Tag Extend (bp):");
+		sl_contentPane.putConstraint(SpringLayout.NORTH, lblTagExtend, 0, SpringLayout.NORTH, lblTagShift);
+		sl_contentPane.putConstraint(SpringLayout.WEST, lblTagExtend, 10, SpringLayout.EAST, txtBin);
+		contentPane.add(lblTagExtend);
+
+		txtTagExtend = new JTextField();
+		sl_contentPane.putConstraint(SpringLayout.NORTH, txtTagExtend, -1, SpringLayout.NORTH, lblTagExtend);
+		sl_contentPane.putConstraint(SpringLayout.WEST, txtTagExtend, 10, SpringLayout.EAST, lblTagExtend);
+		sl_contentPane.putConstraint(SpringLayout.EAST, txtTagExtend, 70, SpringLayout.EAST, lblTagExtend);
+		txtTagExtend.setHorizontalAlignment(SwingConstants.CENTER);
+		txtTagExtend.setText("0");
+		contentPane.add(txtTagExtend);
+		txtTagExtend.setColumns(10);
+
 		btnLoadBlacklistFilter = new JButton("Load Blacklist Filter");
 		btnLoadBlacklistFilter.setEnabled(false);
 		sl_contentPane.putConstraint(SpringLayout.NORTH, btnLoadBlacklistFilter, -1, SpringLayout.NORTH,
@@ -726,13 +727,23 @@ public void actionPerformed(ActionEvent e) {
 		sepOutput.setForeground(Color.BLACK);
 		contentPane.add(sepOutput);
 
-		JLabel lblOutputParameters = new JLabel("Output Parameters:");
-		sl_contentPane.putConstraint(SpringLayout.NORTH, lblOutputParameters, 8, SpringLayout.SOUTH, sepOutput);
-		sl_contentPane.putConstraint(SpringLayout.WEST, lblOutputParameters, 10, SpringLayout.WEST, contentPane);
-		contentPane.add(lblOutputParameters);
+		lblCpusToUse = new JLabel("CPU's to Use:");
+		sl_contentPane.putConstraint(SpringLayout.NORTH, lblCpusToUse, 15, SpringLayout.SOUTH, scrollPane_BAM);
+		sl_contentPane.putConstraint(SpringLayout.WEST, lblCpusToUse, 0, SpringLayout.WEST, scrollPane_BAM);
+		lblCpusToUse.setFont(new Font("Lucida Grande", Font.BOLD, 13));
+		contentPane.add(lblCpusToUse);
+
+		txtCPU = new JTextField();
+		sl_contentPane.putConstraint(SpringLayout.NORTH, txtCPU, -1, SpringLayout.NORTH, lblCpusToUse);
+		sl_contentPane.putConstraint(SpringLayout.WEST, txtCPU, 10, SpringLayout.EAST, lblCpusToUse);
+		sl_contentPane.putConstraint(SpringLayout.WEST, txtCPU, 70, SpringLayout.EAST, lblCpusToUse);
+		txtCPU.setHorizontalAlignment(SwingConstants.CENTER);
+		txtCPU.setText("1");
+		contentPane.add(txtCPU);
+		txtCPU.setColumns(10);
 
 		chckbxOutputData = new JCheckBox("Output Heatmap Matrix");
-		sl_contentPane.putConstraint(SpringLayout.NORTH, chckbxOutputData, 8, SpringLayout.SOUTH, lblOutputParameters);
+		sl_contentPane.putConstraint(SpringLayout.NORTH, chckbxOutputData, 8, SpringLayout.SOUTH, lblCpusToUse);
 		sl_contentPane.putConstraint(SpringLayout.WEST, chckbxOutputData, 0, SpringLayout.WEST, scrollPane_BAM);
 		chckbxOutputData.setSelected(true);
 		contentPane.add(chckbxOutputData);