rename tool to match publication nomenclature

Author: William Lai

scriptmanager/src/main/ScriptManager.java

@@ -16,7 +16,7 @@
 import window_interface.BAM_Format_Converter.BAMtoBEDWindow;
 import window_interface.BAM_Format_Converter.BAMtoGFFWindow;
 import window_interface.BAM_Format_Converter.BAMtoscIDXWindow;
-import window_interface.BAM_Format_Converter.FilterforPermanganateSeqWindow;
+import window_interface.BAM_Format_Converter.FilterforPIPseqWindow;
 import window_interface.BAM_Manipulation.BAIIndexerWindow;
 import window_interface.BAM_Manipulation.BAMRemoveDupWindow;
 import window_interface.BAM_Manipulation.MergeBAMWindow;
@@ -198,7 +198,7 @@ public void actionPerformed(ActionEvent e) {
 						EventQueue.invokeLater(new Runnable() {
 							public void run() {
 								try {
-									FilterforPermanganateSeqWindow frame = new FilterforPermanganateSeqWindow();
+									FilterforPIPseqWindow frame = new FilterforPIPseqWindow();
 									frame.setVisible(true);
 								} catch (Exception e) {
 									e.printStackTrace();

…t_Converter/FilterforPenanganateSeq.java …AM_Format_Converter/FilterforPIPseq.javascriptmanager/src/scripts/BAM_Format_Converter/FilterforPenanganateSeq.java renamed to scriptmanager/src/scripts/BAM_Format_Converter/FilterforPIPseq.java scriptmanager/src/scripts/BAM_Format_Converter/FilterforPenanganateSeq.java renamed to scriptmanager/src/scripts/BAM_Format_Converter/FilterforPIPseq.java

@@ -24,7 +24,7 @@
 import util.FASTAUtilities;
 
 @SuppressWarnings("serial")
-public class FilterforPenanganateSeq extends JFrame {
+public class FilterforPIPseq extends JFrame {
 	File bamFile = null;
 	File genome = null;
 	File output = null;
@@ -34,7 +34,7 @@ public class FilterforPenanganateSeq extends JFrame {
 
 	private JTextArea textArea;
 
-	public FilterforPenanganateSeq(File in, File gen, File out, String s) {
+	public FilterforPIPseq(File in, File gen, File out, String s) {
 		setTitle("Permanganate-Seq Filtering Progress");
 		setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
 		setBounds(150, 150, 600, 800);

…rter/FilterforPermanganateSeqWindow.java …mat_Converter/FilterforPIPseqWindow.javascriptmanager/src/window_interface/BAM_Format_Converter/FilterforPermanganateSeqWindow.java renamed to scriptmanager/src/window_interface/BAM_Format_Converter/FilterforPIPseqWindow.java scriptmanager/src/window_interface/BAM_Format_Converter/FilterforPermanganateSeqWindow.java renamed to scriptmanager/src/window_interface/BAM_Format_Converter/FilterforPIPseqWindow.java

@@ -28,7 +28,7 @@
 import javax.swing.border.EmptyBorder;
 import javax.swing.JLabel;
 
-import scripts.BAM_Format_Converter.FilterforPenanganateSeq;
+import scripts.BAM_Format_Converter.FilterforPIPseq;
 import scripts.BAM_Manipulation.BAIIndexer;
 import util.FileSelection;
 import util.FASTAUtilities;
@@ -38,7 +38,7 @@
 import javax.swing.SwingConstants;
 
 @SuppressWarnings("serial")
-public class FilterforPermanganateSeqWindow extends JFrame implements ActionListener, PropertyChangeListener {
+public class FilterforPIPseqWindow extends JFrame implements ActionListener, PropertyChangeListener {
 	private JPanel contentPane;
 	protected JFileChooser fc = new JFileChooser(new File(System.getProperty("user.dir")));
 
@@ -74,7 +74,7 @@ public Void doInBackground() throws Exception {
 	        	    File OUTPUT = null;
 	        	    if(OUTPUT_PATH != null) { OUTPUT = new File(OUTPUT_PATH.getCanonicalPath() + File.separator + NAME[0] + "_PSfilter.bam"); }
 	        	    else { OUTPUT = new File(NAME[0] + "_PSfilter.bam"); }
-	        	    FilterforPenanganateSeq filter = new FilterforPenanganateSeq(BAMFiles.get(x), GENOME, OUTPUT, txtSeq.getText());
+	        	    FilterforPIPseq filter = new FilterforPIPseq(BAMFiles.get(x), GENOME, OUTPUT, txtSeq.getText());
         			filter.setVisible(true);
         			filter.run();
 
@@ -95,7 +95,7 @@ public void done() {
         }
 	}
 
-	public FilterforPermanganateSeqWindow() {
+	public FilterforPIPseqWindow() {
 		setTitle("Filter Permanganate-Seq Reads");
 		setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);