Project file reorganization and upgrade

William Lai · William Lai · commit 74ac84dba1bc · 2018-02-15T11:34:04.000-05:00
Upgrade to Java 8 and warning fixes from residual Java 6 syntax.
Re-organized location of JAR dependency files and renaming of master
folder
diff --git a/.DS_Store b/.DS_Store
diff --git a/PughPipeline/.classpath b/PughPipeline/.classpath
@@ -1,12 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
 	<classpathentry kind="src" path="src"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.7"/>
-	<classpathentry kind="lib" path="jcommon-1.0.21.jar"/>
-	<classpathentry kind="lib" path="jfreechart-1.0.17.jar"/>
 	<classpathentry kind="lib" path="picard-tools-1.140/htsjdk-1.140.jar"/>
 	<classpathentry kind="lib" path="picard-tools-1.140/picard-lib.jar"/>
 	<classpathentry kind="lib" path="picard-tools-1.140/picard.jar"/>
-	<classpathentry kind="lib" path="jfreesvg-3.0.jar"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+	<classpathentry kind="lib" path="dependecy/jcommon-1.0.21.jar"/>
+	<classpathentry kind="lib" path="dependecy/jfreechart-1.0.17.jar"/>
+	<classpathentry kind="lib" path="dependecy/jfreesvg-3.0.jar"/>
 	<classpathentry kind="output" path="bin"/>
 </classpath>
diff --git a/PughPipeline/.project b/PughPipeline/.project
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <projectDescription>
-	<name>PughPipeline</name>
+	<name>scriptmanager</name>
 	<comment></comment>
 	<projects>
 	</projects>
diff --git a/PughPipeline/dependecy/jcommon-1.0.21.jar b/PughPipeline/dependecy/jcommon-1.0.21.jar
diff --git a/PughPipeline/dependecy/jfreechart-1.0.17.jar b/PughPipeline/dependecy/jfreechart-1.0.17.jar
diff --git a/PughPipeline/dependecy/jfreesvg-3.0.jar b/PughPipeline/dependecy/jfreesvg-3.0.jar
diff --git a/PughPipeline/src/scripts/Tag_Analysis/PeakPair.java b/PughPipeline/src/scripts/Tag_Analysis/PeakPair.java
@@ -100,7 +100,7 @@ public void run() throws IOException {
 		String DETAIL = NAME + File.separator + "D_" + INPUT.getName().split("\\.")[0] + ".txt";
 		String SUMMARY = NAME + File.separator + "S_" + INPUT.getName().split("\\.")[0] + ".gff";
 		String ORPHAN = NAME + File.separator + "O_" + INPUT.getName().split("\\.")[0] + ".txt";
-		String PDF = NAME + File.separator + "P_" + INPUT.getName().split("\\.")[0] + ".pdf";
+		//String PDF = NAME + File.separator + "P_" + INPUT.getName().split("\\.")[0] + ".pdf";
 
 		try { DOUT = new PrintStream(new File(DETAIL)); }
 		catch (FileNotFoundException e) { e.printStackTrace(); }
diff --git a/PughPipeline/src/window_interface/BAM_Format_Converter/BAMtoBEDWindow.java b/PughPipeline/src/window_interface/BAM_Format_Converter/BAMtoBEDWindow.java
@@ -47,7 +47,7 @@ public class BAMtoBEDWindow extends JFrame implements ActionListener, PropertyCh
 	private JPanel contentPane;
 	protected JFileChooser fc = new JFileChooser(new File(System.getProperty("user.dir")));	
 	
-	final DefaultListModel expList;
+	final DefaultListModel<String> expList;
 	Vector<File> BAMFiles = new Vector<File>();
 	private File OUTPUT = null;
 	private int STRAND = 0;
@@ -151,8 +151,8 @@ public void actionPerformed(ActionEvent e) {
 		});
 		contentPane.add(btnLoad);
 		
-      	expList = new DefaultListModel();
-		final JList listExp = new JList(expList);
+      	expList = new DefaultListModel<String>();
+		final JList<String> listExp = new JList<String>(expList);
 		listExp.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
 		scrollPane.setViewportView(listExp);
 		
diff --git a/PughPipeline/src/window_interface/BAM_Format_Converter/BAMtoGFFWindow.java b/PughPipeline/src/window_interface/BAM_Format_Converter/BAMtoGFFWindow.java
@@ -45,7 +45,7 @@ public class BAMtoGFFWindow extends JFrame implements ActionListener, PropertyCh
 	private JPanel contentPane;
 	protected JFileChooser fc = new JFileChooser(new File(System.getProperty("user.dir")));	
 	
-	final DefaultListModel expList;
+	final DefaultListModel<String> expList;
 	Vector<File> BAMFiles = new Vector<File>();
 	private File OUTPUT = null;
 	private int STRAND = 0;
@@ -149,8 +149,8 @@ public void actionPerformed(ActionEvent e) {
 		});
 		contentPane.add(btnLoad);
 		
-      	expList = new DefaultListModel();
-		final JList listExp = new JList(expList);
+      	expList = new DefaultListModel<String>();
+		final JList<String> listExp = new JList<String>(expList);
 		listExp.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
 		scrollPane.setViewportView(listExp);
 		
diff --git a/PughPipeline/src/window_interface/BAM_Format_Converter/BAMtoscIDXWindow.java b/PughPipeline/src/window_interface/BAM_Format_Converter/BAMtoscIDXWindow.java
@@ -45,7 +45,7 @@ public class BAMtoscIDXWindow extends JFrame implements ActionListener, Property
 	private JPanel contentPane;
 	protected JFileChooser fc = new JFileChooser(new File(System.getProperty("user.dir")));	
 	
-	final DefaultListModel expList;
+	final DefaultListModel<String> expList;
 	Vector<File> BAMFiles = new Vector<File>();
 	private File OUTPUT = null;
 	private int STRAND = 0;
@@ -147,8 +147,8 @@ public void actionPerformed(ActionEvent e) {
 		});
 		contentPane.add(btnLoad);
 		
-      	expList = new DefaultListModel();
-		final JList listExp = new JList(expList);
+      	expList = new DefaultListModel<String>();
+		final JList<String> listExp = new JList<String>(expList);
 		listExp.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
 		scrollPane.setViewportView(listExp);
 		
diff --git a/PughPipeline/src/window_interface/BAM_Format_Converter/FilterforPermanganateSeqWindow.java b/PughPipeline/src/window_interface/BAM_Format_Converter/FilterforPermanganateSeqWindow.java
@@ -42,7 +42,7 @@ public class FilterforPermanganateSeqWindow extends JFrame implements ActionList
 	private JPanel contentPane;
 	protected JFileChooser fc = new JFileChooser(new File(System.getProperty("user.dir")));
 	
-	final DefaultListModel expList;
+	final DefaultListModel<String> expList;
 	private File OUTPUT_PATH = null;
 	private File GENOME = null;
 	List<File> BAMFiles = new ArrayList<File>();
@@ -113,8 +113,8 @@ public FilterforPermanganateSeqWindow() {
 		sl_contentPane.putConstraint(SpringLayout.EAST, scrollPane, -5, SpringLayout.EAST, contentPane);
 		contentPane.add(scrollPane);
 		
-      	expList = new DefaultListModel();
-		final JList listExp = new JList(expList);
+      	expList = new DefaultListModel<String>();
+		final JList<String> listExp = new JList<String>(expList);
 		listExp.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
 		scrollPane.setViewportView(listExp);
 		
diff --git a/PughPipeline/src/window_interface/BAM_Manipulation/BAIIndexerWindow.java b/PughPipeline/src/window_interface/BAM_Manipulation/BAIIndexerWindow.java
@@ -35,7 +35,7 @@ public class BAIIndexerWindow extends JFrame implements ActionListener, Property
 	private JPanel contentPane;
 	protected JFileChooser fc = new JFileChooser(new File(System.getProperty("user.dir")));	
 	
-	final DefaultListModel expList;
+	final DefaultListModel<String> expList;
 	Vector<File> BAMFiles = new Vector<File>();
 	
 	private JButton btnLoad;
@@ -81,8 +81,8 @@ public BAIIndexerWindow() {
 		sl_contentPane.putConstraint(SpringLayout.EAST, scrollPane, -5, SpringLayout.EAST, contentPane);
 		contentPane.add(scrollPane);
 		
-      	expList = new DefaultListModel();
-		final JList listExp = new JList(expList);
+      	expList = new DefaultListModel<String>();
+		final JList<String> listExp = new JList<String>(expList);
 		listExp.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
 		scrollPane.setViewportView(listExp);
 		
diff --git a/PughPipeline/src/window_interface/BAM_Manipulation/BAMRemoveDupWindow.java b/PughPipeline/src/window_interface/BAM_Manipulation/BAMRemoveDupWindow.java
@@ -39,7 +39,7 @@ public class BAMRemoveDupWindow extends JFrame implements ActionListener, Proper
 	private JPanel contentPane;
 	protected JFileChooser fc = new JFileChooser(new File(System.getProperty("user.dir")));
 	
-	final DefaultListModel expList;
+	final DefaultListModel<String> expList;
 	private File OUTPUT_PATH = null;
 	List<File> BAMFiles = new ArrayList<File>();
 
@@ -98,8 +98,8 @@ public BAMRemoveDupWindow() {
 		sl_contentPane.putConstraint(SpringLayout.EAST, scrollPane, -5, SpringLayout.EAST, contentPane);
 		contentPane.add(scrollPane);
 		
-      	expList = new DefaultListModel();
-		final JList listExp = new JList(expList);
+      	expList = new DefaultListModel<String>();
+		final JList<String> listExp = new JList<String>(expList);
 		listExp.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
 		scrollPane.setViewportView(listExp);
 		
diff --git a/PughPipeline/src/window_interface/BAM_Manipulation/MergeBAMWindow.java b/PughPipeline/src/window_interface/BAM_Manipulation/MergeBAMWindow.java
@@ -38,7 +38,7 @@ public class MergeBAMWindow extends JFrame implements ActionListener, PropertyCh
 	private JPanel contentPane;
 	protected JFileChooser fc = new JFileChooser(new File(System.getProperty("user.dir")));
 	
-	final DefaultListModel expList;
+	final DefaultListModel<String> expList;
 	List<File> BAMFiles = new ArrayList<File>();
     private File OUTPUT = null;
 	private File OUTPUT_PATH = null;
@@ -95,8 +95,8 @@ public MergeBAMWindow() {
 		sl_contentPane.putConstraint(SpringLayout.EAST, scrollPane, -5, SpringLayout.EAST, contentPane);
 		contentPane.add(scrollPane);
 		
-      	expList = new DefaultListModel();
-		final JList listExp = new JList(expList);
+      	expList = new DefaultListModel<String>();
+		final JList<String> listExp = new JList<String>(expList);
 		listExp.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
 		scrollPane.setViewportView(listExp);
 		
diff --git a/PughPipeline/src/window_interface/BAM_Manipulation/SortBAMWindow.java b/PughPipeline/src/window_interface/BAM_Manipulation/SortBAMWindow.java
@@ -36,7 +36,7 @@ public class SortBAMWindow extends JFrame implements ActionListener, PropertyCha
 	private JPanel contentPane;
 	protected JFileChooser fc = new JFileChooser(new File(System.getProperty("user.dir")));
 	
-	final DefaultListModel expList;
+	final DefaultListModel<String> expList;
 	private File OUTPUT_PATH = null;
 	List<File> BAMFiles = new ArrayList<File>();
 
@@ -91,8 +91,8 @@ public SortBAMWindow() {
 		sl_contentPane.putConstraint(SpringLayout.EAST, scrollPane, -5, SpringLayout.EAST, contentPane);
 		contentPane.add(scrollPane);
 		
-      	expList = new DefaultListModel();
-		final JList listExp = new JList(expList);
+      	expList = new DefaultListModel<String>();
+		final JList<String> listExp = new JList<String>(expList);
 		listExp.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
 		scrollPane.setViewportView(listExp);
 		
diff --git a/PughPipeline/src/window_interface/BAM_Statistics/PEStatWindow.java b/PughPipeline/src/window_interface/BAM_Statistics/PEStatWindow.java
@@ -48,7 +48,7 @@ public class PEStatWindow extends JFrame implements ActionListener, PropertyChan
 	JButton btnRemoveBam;
 	JButton btnRun;
 	
-	final DefaultListModel expList;
+	final DefaultListModel<String> expList;
 	Vector<File> BAMFiles = new Vector<File>();
 	private JTextField txtMin;
 	private JTextField txtMax;
@@ -109,8 +109,8 @@ public PEStatWindow() {
 		sl_contentPane.putConstraint(SpringLayout.EAST, scrollPane, -5, SpringLayout.EAST, contentPane);
 		contentPane.add(scrollPane);
 		
-      	expList = new DefaultListModel();
-		final JList listExp = new JList(expList);
+      	expList = new DefaultListModel<String>();
+		final JList<String> listExp = new JList<String>(expList);
 		listExp.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
 		scrollPane.setViewportView(listExp);
 		
diff --git a/PughPipeline/src/window_interface/BAM_Statistics/SEStatWindow.java b/PughPipeline/src/window_interface/BAM_Statistics/SEStatWindow.java
@@ -35,7 +35,7 @@ public class SEStatWindow extends JFrame {
 	private JLabel lblOutputName;
 	private JCheckBox chckbxOutputStatistics;
 	
-	final DefaultListModel expList;
+	final DefaultListModel<String> expList;
 	Vector<File> BAMFiles = new Vector<File>();
 
 	public SEStatWindow() {
@@ -54,8 +54,8 @@ public SEStatWindow() {
 		sl_contentPane.putConstraint(SpringLayout.EAST, scrollPane, -5, SpringLayout.EAST, contentPane);
 		contentPane.add(scrollPane);
 		
-      	expList = new DefaultListModel();
-		final JList listExp = new JList(expList);
+      	expList = new DefaultListModel<String>();
+		final JList<String> listExp = new JList<String>(expList);
 		listExp.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
 		scrollPane.setViewportView(listExp);
 		
diff --git a/PughPipeline/src/window_interface/BAM_Statistics/SignalDuplicationWindow.java b/PughPipeline/src/window_interface/BAM_Statistics/SignalDuplicationWindow.java
@@ -38,7 +38,7 @@ public class SignalDuplicationWindow extends JFrame implements ActionListener, P
 	private JPanel contentPane;
 	protected JFileChooser fc = new JFileChooser(new File(System.getProperty("user.dir")));	
 	
-	final DefaultListModel expList;
+	final DefaultListModel<String> expList;
 	Vector<File> BAMFiles = new Vector<File>();
 	private File INPUT = null;
 	
@@ -104,8 +104,8 @@ public SignalDuplicationWindow() {
 		sl_contentPane.putConstraint(SpringLayout.EAST, scrollPane, -10, SpringLayout.EAST, contentPane);
 		contentPane.add(scrollPane);
 		
-      	expList = new DefaultListModel();
-		final JList listExp = new JList(expList);
+      	expList = new DefaultListModel<String>();
+		final JList<String> listExp = new JList<String>(expList);
 		listExp.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
 		scrollPane.setViewportView(listExp);
 		
diff --git a/PughPipeline/src/window_interface/Coordinate_Manipulation/BED_Manipulation/BEDtoGFFWindow.java b/PughPipeline/src/window_interface/Coordinate_Manipulation/BED_Manipulation/BEDtoGFFWindow.java
@@ -38,7 +38,7 @@ public class BEDtoGFFWindow extends JFrame implements ActionListener, PropertyCh
 	protected JFileChooser fc = new JFileChooser(new File(System.getProperty("user.dir")));	
 	
 	private File OUTPUT_PATH = null;
-	final DefaultListModel expList;
+	final DefaultListModel<String> expList;
 	Vector<File> BEDFiles = new Vector<File>();
 	
 	private JButton btnLoad;
@@ -87,8 +87,8 @@ public BEDtoGFFWindow() {
 		sl_contentPane.putConstraint(SpringLayout.EAST, scrollPane, -5, SpringLayout.EAST, contentPane);
 		contentPane.add(scrollPane);
 		
-      	expList = new DefaultListModel();
-		final JList listExp = new JList(expList);
+      	expList = new DefaultListModel<String>();
+		final JList<String> listExp = new JList<String>(expList);
 		listExp.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
 		scrollPane.setViewportView(listExp);
 		
diff --git a/PughPipeline/src/window_interface/Coordinate_Manipulation/BED_Manipulation/ExpandBEDWindow.java b/PughPipeline/src/window_interface/Coordinate_Manipulation/BED_Manipulation/ExpandBEDWindow.java
@@ -44,7 +44,7 @@ public class ExpandBEDWindow extends JFrame implements ActionListener, PropertyC
 	
 	private File OUTPUT_PATH = null;
 	private static int SIZE = -999;
-	final DefaultListModel expList;
+	final DefaultListModel<String> expList;
 	Vector<File> BEDFiles = new Vector<File>();
 	
 	private JButton btnLoad;
@@ -106,8 +106,8 @@ public ExpandBEDWindow() {
 		sl_contentPane.putConstraint(SpringLayout.EAST, scrollPane, -10, SpringLayout.EAST, contentPane);
 		contentPane.add(scrollPane);
 		
-      	expList = new DefaultListModel();
-		final JList listExp = new JList(expList);
+      	expList = new DefaultListModel<String>();
+		final JList<String> listExp = new JList<String>(expList);
 		listExp.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
 		scrollPane.setViewportView(listExp);
 		
diff --git a/PughPipeline/src/window_interface/Coordinate_Manipulation/GFF_Manipulation/ExpandGFFWindow.java b/PughPipeline/src/window_interface/Coordinate_Manipulation/GFF_Manipulation/ExpandGFFWindow.java
@@ -43,7 +43,7 @@ public class ExpandGFFWindow extends JFrame implements ActionListener, PropertyC
 	
 	private File OUTPUT_PATH = null;
 	private static int SIZE = -999;
-	final DefaultListModel expList;
+	final DefaultListModel<String> expList;
 	Vector<File> GFFFiles = new Vector<File>();
 	
 	private JButton btnLoad;
@@ -106,8 +106,8 @@ public ExpandGFFWindow() {
 		sl_contentPane.putConstraint(SpringLayout.EAST, scrollPane, -10, SpringLayout.EAST, contentPane);
 		contentPane.add(scrollPane);
 		
-      	expList = new DefaultListModel();
-		final JList listExp = new JList(expList);
+      	expList = new DefaultListModel<String>();
+		final JList<String> listExp = new JList<String>(expList);
 		listExp.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
 		scrollPane.setViewportView(listExp);
 		
diff --git a/PughPipeline/src/window_interface/Coordinate_Manipulation/GFF_Manipulation/GFFtoBEDWindow.java b/PughPipeline/src/window_interface/Coordinate_Manipulation/GFF_Manipulation/GFFtoBEDWindow.java
@@ -38,7 +38,7 @@ public class GFFtoBEDWindow extends JFrame implements ActionListener, PropertyCh
 	protected JFileChooser fc = new JFileChooser(new File(System.getProperty("user.dir")));	
 	
 	private File OUTPUT_PATH = null;
-	final DefaultListModel expList;
+	final DefaultListModel<String> expList;
 	Vector<File> BEDFiles = new Vector<File>();
 	
 	private JButton btnLoad;
@@ -87,8 +87,8 @@ public GFFtoBEDWindow() {
 		sl_contentPane.putConstraint(SpringLayout.EAST, scrollPane, -5, SpringLayout.EAST, contentPane);
 		contentPane.add(scrollPane);
 		
-      	expList = new DefaultListModel();
-		final JList listExp = new JList(expList);
+      	expList = new DefaultListModel<String>();
+		final JList<String> listExp = new JList<String>(expList);
 		listExp.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
 		scrollPane.setViewportView(listExp);
 		
diff --git a/PughPipeline/src/window_interface/Sequence_Analysis/DNAShapefromFASTAWindow.java b/PughPipeline/src/window_interface/Sequence_Analysis/DNAShapefromFASTAWindow.java
@@ -40,7 +40,7 @@ public class DNAShapefromFASTAWindow extends JFrame implements ActionListener, P
 	private JPanel contentPane;
 	protected JFileChooser fc = new JFileChooser(new File(System.getProperty("user.dir")));	
 	
-	final DefaultListModel expList;
+	final DefaultListModel<String> expList;
 	ArrayList<File> FASTAFiles = new ArrayList<File>();
 	private File OUTPUT_PATH = null;
 	
@@ -118,8 +118,8 @@ public DNAShapefromFASTAWindow() {
 		sl_contentPane.putConstraint(SpringLayout.EAST, scrollPane, -10, SpringLayout.EAST, contentPane);
 		contentPane.add(scrollPane);
 		
-      	expList = new DefaultListModel();
-		final JList listExp = new JList(expList);
+      	expList = new DefaultListModel<String>();
+		final JList<String> listExp = new JList<String>(expList);
 		listExp.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
 		scrollPane.setViewportView(listExp);
 		
diff --git a/PughPipeline/src/window_interface/Sequence_Analysis/FASTAExtractWindow.java b/PughPipeline/src/window_interface/Sequence_Analysis/FASTAExtractWindow.java
@@ -40,7 +40,7 @@ public class FASTAExtractWindow extends JFrame implements ActionListener, Proper
 	private JPanel contentPane;
 	protected JFileChooser fc = new JFileChooser(new File(System.getProperty("user.dir")));	
 	
-	final DefaultListModel expList;
+	final DefaultListModel<String> expList;
 	ArrayList<File> BEDFiles = new ArrayList<File>();
 	private File INPUT = null;
 	private File OUTPUT_PATH = null;
@@ -115,8 +115,8 @@ public FASTAExtractWindow() {
 		sl_contentPane.putConstraint(SpringLayout.EAST, scrollPane, -10, SpringLayout.EAST, contentPane);
 		contentPane.add(scrollPane);
 		
-      	expList = new DefaultListModel();
-		final JList listExp = new JList(expList);
+      	expList = new DefaultListModel<String>();
+		final JList<String> listExp = new JList<String>(expList);
 		listExp.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
 		scrollPane.setViewportView(listExp);
 		
diff --git a/PughPipeline/src/window_interface/Sequence_Analysis/FourColorSequenceWindow.java b/PughPipeline/src/window_interface/Sequence_Analysis/FourColorSequenceWindow.java
@@ -41,7 +41,7 @@ public class FourColorSequenceWindow extends JFrame implements ActionListener, P
 	private JPanel contentPane;
 	protected JFileChooser fc = new JFileChooser(new File(System.getProperty("user.dir")));	
 	
-	final DefaultListModel expList;
+	final DefaultListModel<String> expList;
 	Vector<File> fastaFiles = new Vector<File>();
 	private File OUTPUTPATH = null;
 	
@@ -123,8 +123,8 @@ public FourColorSequenceWindow() {
 		sl_contentPane.putConstraint(SpringLayout.EAST, scrollPane, -5, SpringLayout.EAST, contentPane);
 		contentPane.add(scrollPane);
 		
-      	expList = new DefaultListModel();
-		final JList listExp = new JList(expList);
+      	expList = new DefaultListModel<String>();
+		final JList<String> listExp = new JList<String>(expList);
 		listExp.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
 		scrollPane.setViewportView(listExp);
 		
diff --git a/PughPipeline/src/window_interface/Tag_Analysis/HeatMapWindow.java b/PughPipeline/src/window_interface/Tag_Analysis/HeatMapWindow.java
diff --git a/PughPipeline/src/window_interface/Tag_Analysis/MergeHeatMapWindow.java b/PughPipeline/src/window_interface/Tag_Analysis/MergeHeatMapWindow.java
diff --git a/PughPipeline/src/window_interface/Tag_Analysis/PeakPairWindow.java b/PughPipeline/src/window_interface/Tag_Analysis/PeakPairWindow.java
