made some window files add extension

src/main/java/scriptmanager/scripts/Coordinate_Manipulation/BED_Manipulation/SortBED.java

@@ -1,15 +1,12 @@
 package scriptmanager.scripts.Coordinate_Manipulation.BED_Manipulation;
 
-import java.io.BufferedOutputStream;
 import java.io.BufferedReader;
 import java.io.File;
-import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.PrintStream;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.HashMap;
-import java.util.zip.GZIPOutputStream;
 
 import scriptmanager.objects.CoordinateObjects.BEDCoord;
 import scriptmanager.util.GZipUtilities;
@@ -61,11 +58,8 @@ public static void sortBEDbyCDT(String outbase, File bed, File cdt, int START_IN
 
 		PrintStream OUT;
 		// Initialize output writer
-		if (gzOutput) {
-			OUT = new PrintStream(new BufferedOutputStream(new GZIPOutputStream(new FileOutputStream(outbase + ".cdt.gz"))));
-		} else {
-			OUT = new PrintStream(new BufferedOutputStream(new FileOutputStream(outbase + ".cdt")));
-		}
+		String suffix = ".cdt" + (gzOutput? ".gz": "");
+		OUT = GZipUtilities.makePrintStream(new File(outbase + suffix), gzOutput);
 		// Output sorted CDT File
 		OUT.println(CDTHeader);
 		for (int x = 0; x < SORT.size(); x++) {
@@ -91,11 +85,8 @@ public static void sortBEDbyCDT(String outbase, File bed, File cdt, int START_IN
 		br.close();
 
 		// Initialize output writer
-		if (gzOutput) {
-			OUT = new PrintStream(new BufferedOutputStream(new GZIPOutputStream(new FileOutputStream(outbase + ".bed.gz"))));
-		} else {
-			OUT = new PrintStream(new BufferedOutputStream(new FileOutputStream(outbase + ".bed")));
-		}
+		suffix = ".bed" + (gzOutput? ".gz": "");
+		OUT = GZipUtilities.makePrintStream(new File(outbase + suffix), gzOutput);
 		// Output sorted BED File
 		for (int x = 0; x < SORT.size(); x++) {
 			OUT.println(BEDFile.get(SORT.get(x).getName()));

src/main/java/scriptmanager/scripts/Peak_Analysis/FilterBEDbyProximity.java

@@ -34,8 +34,8 @@ public FilterBEDbyProximity(File input, int cutoff, String outputBase, PrintStre
 			if(outputBase == null) {
 				outputBase = ExtensionFileFilter.stripExtensionIgnoreGZ(input) + "_" + Integer.toString(CUTOFF) + "bp";
 			}
-			OUT_Filter = GZipUtilities.makePrintStream(new File(outputBase + "-FILTER" + ".bed"), gzOutput); 
-			OUT_Cluster = GZipUtilities.makePrintStream(new File(outputBase + "-CLUSTER" + ".bed"), gzOutput);
+			OUT_Filter = GZipUtilities.makePrintStream(new File(outputBase + "-FILTER.bed" + (gzOutput? ".gz": "")), gzOutput); 
+			OUT_Cluster = GZipUtilities.makePrintStream(new File(outputBase + "-CLUSTER.bed" + (gzOutput? ".gz": "")), gzOutput);
 		}catch (FileNotFoundException e) { e.printStackTrace(); }
 	}
 

src/main/java/scriptmanager/scripts/Read_Analysis/AggregateData.java

@@ -98,11 +98,11 @@ public void run() throws IOException {
 
 			String name = "ALL_SCORES.out";
 			if (OUT_PATH == null) {
-				OUT = GZipUtilities.makePrintStream(new File(name), OUTPUT_GZIP);
+				OUT = GZipUtilities.makePrintStream(new File(name + (OUTPUT_GZIP? ".gz": "")), OUTPUT_GZIP);
 			} else if (!OUT_PATH.isDirectory()) {
 				OUT = GZipUtilities.makePrintStream(OUT_PATH, OUTPUT_GZIP);
 			} else {
-				OUT = GZipUtilities.makePrintStream(new File(OUT_PATH.getCanonicalPath() + File.separator + name), OUTPUT_GZIP);
+				OUT = GZipUtilities.makePrintStream(new File(OUT_PATH.getCanonicalPath() + File.separator + name + (OUTPUT_GZIP? ".gz": "")), OUTPUT_GZIP);
 			}
 
 			// Check all arrays are the same size
@@ -142,11 +142,11 @@ public String getMessage() {
 	}
 
 	public void outputFileScore(File IN) throws FileNotFoundException, IOException {
-		String NEWNAME = ExtensionFileFilter.stripExtension(IN);
+		String NEWNAME = ExtensionFileFilter.stripExtension(IN) + "_SCORES.out";
 		if (OUT_PATH != null) {
-			OUT = GZipUtilities.makePrintStream(new File(OUT_PATH.getAbsolutePath() + File.separator + NEWNAME + "_SCORES.out"), OUTPUT_GZIP);
+			OUT = GZipUtilities.makePrintStream(new File(OUT_PATH.getAbsolutePath() + File.separator + NEWNAME + (OUTPUT_GZIP? ".gz": "")), OUTPUT_GZIP);
 		} else {
-			OUT = GZipUtilities.makePrintStream(new File(NEWNAME + "_SCORES.out"), OUTPUT_GZIP);
+			OUT = GZipUtilities.makePrintStream(new File(NEWNAME + (OUTPUT_GZIP? ".gz": "")), OUTPUT_GZIP);
 		}
 		outputFileScore(IN, OUT);
 	}

src/main/java/scriptmanager/window_interface/BAM_Format_Converter/BAMtoBEDOutput.java

@@ -61,6 +61,7 @@ public BAMtoBEDOutput(File b, File out_dir, int s, int pair_status, int min_size
 	public void run() throws IOException, InterruptedException {
 		// Open Output File
 		String OUTPUT = BAM.getName().split("\\.")[0] + "_" + READ + ".bed";
+		OUTPUT = OUTPUT + (OUTPUT_GZIP? ".gz": "");
 		if (OUT_DIR != null) {
 			OUTPUT = OUT_DIR.getCanonicalPath() + File.separator + OUTPUT;
 		}

src/main/java/scriptmanager/window_interface/BAM_Format_Converter/BAMtoGFFOutput.java

@@ -64,6 +64,7 @@ public void run() throws IOException, InterruptedException {
 		if (OUT_DIR != null) {
 			OUTPUT = OUT_DIR.getCanonicalPath() + File.separator + OUTPUT;
 		}
+		OUTPUT = OUTPUT + (OUTPUT_GZIP? ".gz": "");
 
 		// Call script here, pass in ps and OUT
 		PrintStream PS = new PrintStream(new CustomOutputStream(textArea));

src/main/java/scriptmanager/window_interface/BAM_Format_Converter/BAMtoscIDXOutput.java

@@ -62,6 +62,7 @@ public void run() throws IOException, InterruptedException {
 		if (OUT_DIR != null) {
 			OUTPUT = OUT_DIR.getCanonicalPath() + File.separator + OUTPUT;
 		}
+		OUTPUT = OUTPUT + (OUTPUT_GZIP? ".gz": "");
 
 		// Call script here, pass in ps and OUT
 		PrintStream PS = new PrintStream(new CustomOutputStream(textArea));

src/main/java/scriptmanager/window_interface/Coordinate_Manipulation/BED_Manipulation/BEDtoGFFWindow.java

@@ -70,21 +70,22 @@ public class BEDtoGFFWindow extends JFrame implements ActionListener, PropertyCh
 	class Task extends SwingWorker<Void, Void> {
 		@Override
 		public Void doInBackground() throws IOException {
+			boolean GZIP = chckbxGzipOutput.isSelected();
 			setProgress(0);
 			LogItem old_li = new LogItem("");
 			for (int x = 0; x < BEDFiles.size(); x++) {
 				File XBED = BEDFiles.get(x);
 				// Set outfilepath
-				String OUTPUT = ExtensionFileFilter.stripExtensionIgnoreGZ(XBED) + ".gff";
+				String OUTPUT = ExtensionFileFilter.stripExtensionIgnoreGZ(XBED) + ".gff" + (GZIP? ".gz": "");
 				if (OUT_DIR != null) {
 					OUTPUT = OUT_DIR + File.separator + OUTPUT;
 				}
 				// Initialize LogItem
-				String command = BEDtoGFFCLI.getCLIcommand(new File(OUTPUT), XBED, chckbxGzipOutput.isSelected());
+				String command = BEDtoGFFCLI.getCLIcommand(new File(OUTPUT), XBED, GZIP);
 				LogItem new_li = new LogItem(command);
 				firePropertyChange("log", old_li, new_li);
 				// Execute conversion and update progress
-				BEDtoGFF.convertBEDtoGFF(new File(OUTPUT), XBED, chckbxGzipOutput.isSelected());
+				BEDtoGFF.convertBEDtoGFF(new File(OUTPUT), XBED, GZIP);
 				// Update log item
 				new_li.setStopTime(new Timestamp(new Date().getTime()));
 				new_li.setStatus(0);

src/main/java/scriptmanager/window_interface/Coordinate_Manipulation/BED_Manipulation/ExpandBEDWindow.java

@@ -79,6 +79,7 @@ public Void doInBackground() throws IOException {
 				if (SIZE < 1) {
 					JOptionPane.showMessageDialog(null, "Invalid Expansion Size!!! Must be larger than 0 bp");
 				} else {
+					boolean GZIP = chckbxGzipOutput.isSelected();
 					setProgress(0);
 					for (int x = 0; x < BEDFiles.size(); x++) {
 						// Save current BED to temp variable
@@ -90,10 +91,10 @@ public Void doInBackground() throws IOException {
 							OUTPUT = OUT_DIR + File.separator + OUTPUT;
 						}
 						// Add suffix
-						OUTPUT += "_" + Integer.toString(SIZE) + "bp.bed";
+						OUTPUT += "_" + Integer.toString(SIZE) + "bp.bed" + (GZIP? ".gz": "");
 
 						// Execute expansion and update progress
-						ExpandBED.expandBEDBorders(new File(OUTPUT), XBED, SIZE, rdbtnExpandFromCenter.isSelected(), chckbxGzipOutput.isSelected());
+						ExpandBED.expandBEDBorders(new File(OUTPUT), XBED, SIZE, rdbtnExpandFromCenter.isSelected(), GZIP);
 						int percentComplete = (int) (((double) (x + 1) / BEDFiles.size()) * 100);
 						setProgress(percentComplete);
 					}

src/main/java/scriptmanager/window_interface/Coordinate_Manipulation/GFF_Manipulation/GFFtoBEDWindow.java

@@ -56,17 +56,18 @@ public class GFFtoBEDWindow extends JFrame implements ActionListener, PropertyCh
 	class Task extends SwingWorker<Void, Void> {
 		@Override
 		public Void doInBackground() throws IOException {
+			boolean GZIP = chckbxGzipOutput.isSelected();
 			setProgress(0);
 			for (int x = 0; x < BEDFiles.size(); x++) {
 				File XGFF = BEDFiles.get(x);
 				// Set outfilepath
-				String OUTPUT = ExtensionFileFilter.stripExtensionIgnoreGZ(XGFF) + ".bed";
+				String OUTPUT = ExtensionFileFilter.stripExtensionIgnoreGZ(XGFF) + ".bed" + (GZIP? ".gz": "");
 				if (OUT_DIR != null) {
 					OUTPUT = OUT_DIR + File.separator + OUTPUT;
 				}
 
 				// Execute conversion and update progress
-				GFFtoBED.convertGFFtoBED(new File(OUTPUT), XGFF, chckbxGzipOutput.isSelected());
+				GFFtoBED.convertGFFtoBED(new File(OUTPUT), XGFF, GZIP);
 				int percentComplete = (int) (((double) (x + 1) / BEDFiles.size()) * 100);
 				setProgress(percentComplete);
 			}

src/main/java/scriptmanager/window_interface/File_Utilities/ConvertBEDChrNamesWindow.java

@@ -62,12 +62,13 @@ public class ConvertBEDChrNamesWindow extends JFrame implements ActionListener,
 	class Task extends SwingWorker<Void, Void> {
 		@Override
 		public Void doInBackground() throws IOException {
+			boolean GZIP = chckbxGzipOutput.isSelected();
 			setProgress(0);
 			// apply to each fil in vector
 			for (int x = 0; x < BEDFiles.size(); x++) {
 				File XBED = BEDFiles.get(x);
 				// Set suffix format
-				String SUFFIX = rdbtnA2R.isSelected() ? "_toRoman.bed" : "_toArabic.bed";
+				String SUFFIX = (rdbtnA2R.isSelected() ? "_toRoman.bed" : "_toArabic.bed") + (GZIP? ".gz": "");
 				// Set output filepath with name and output directory
 				String OUTPUT = ExtensionFileFilter.stripExtensionIgnoreGZ(XBED);
 				// Add user-selected directory
@@ -76,9 +77,9 @@ public Void doInBackground() throws IOException {
 				}
 				// Execute conversion and update progress
 				if (rdbtnA2R.isSelected()) {
-					ConvertChrNames.convert_ArabictoRoman(XBED, new File(OUTPUT + SUFFIX), chckbxChrmt.isSelected(), chckbxGzipOutput.isSelected());
+					ConvertChrNames.convert_ArabictoRoman(XBED, new File(OUTPUT + SUFFIX), chckbxChrmt.isSelected(), GZIP);
 				} else {
-					ConvertChrNames.convert_RomantoArabic(XBED, new File(OUTPUT + SUFFIX), chckbxChrmt.isSelected(), chckbxGzipOutput.isSelected());
+					ConvertChrNames.convert_RomantoArabic(XBED, new File(OUTPUT + SUFFIX), chckbxChrmt.isSelected(), GZIP);
 				}
 				// Update progress bar
 				int percentComplete = (int) (((double) (x + 1) / BEDFiles.size()) * 100);

src/main/java/scriptmanager/window_interface/File_Utilities/ConvertGFFChrNamesWindow.java

@@ -62,12 +62,13 @@ public class ConvertGFFChrNamesWindow extends JFrame implements ActionListener,
 	class Task extends SwingWorker<Void, Void> {
 		@Override
 		public Void doInBackground() throws IOException {
+			boolean GZIP = chckbxGzipOutput.isSelected();
 			setProgress(0);
 			// apply to each fil in vector
 			for (int x = 0; x < GFFFiles.size(); x++) {
 				File XGFF = GFFFiles.get(x);
 				// Set suffix format
-				String SUFFIX = rdbtnA2R.isSelected() ? "_toRoman.gff" : "_toArabic.gff";
+				String SUFFIX = (rdbtnA2R.isSelected() ? "_toRoman.gff" : "_toArabic.gff") + (GZIP? ".gz": "");
 				// Set output filepath with name and output directory
 				String OUTPUT = ExtensionFileFilter.stripExtensionIgnoreGZ(XGFF);
 				// Add user-selected directory
@@ -76,9 +77,9 @@ public Void doInBackground() throws IOException {
 				}
 				// Execute conversion and update progress
 				if (rdbtnA2R.isSelected()) {
-					ConvertChrNames.convert_ArabictoRoman(XGFF, new File(OUTPUT + SUFFIX), chckbxChrmt.isSelected(), chckbxGzipOutput.isSelected());
+					ConvertChrNames.convert_ArabictoRoman(XGFF, new File(OUTPUT + SUFFIX), chckbxChrmt.isSelected(), GZIP);
 				} else {
-					ConvertChrNames.convert_RomantoArabic(XGFF, new File(OUTPUT + SUFFIX), chckbxChrmt.isSelected(), chckbxGzipOutput.isSelected());
+					ConvertChrNames.convert_RomantoArabic(XGFF, new File(OUTPUT + SUFFIX), chckbxChrmt.isSelected(), GZIP);
 				}
 				// Update progress bar
 				int percentComplete = (int) (((double) (x + 1) / GFFFiles.size()) * 100);

src/main/java/scriptmanager/window_interface/Peak_Analysis/BEDPeakAligntoRefOutput.java

@@ -36,12 +36,14 @@ public BEDPeakAligntoRefOutput(File ref, File peak, File outpath, boolean gzOutp
 		REF = ref;
 		PEAK = peak;
 		OUTPUT_GZIP = gzOutput;
-
 		if(outpath != null) {
 			OUTFILE = new File(outpath.getCanonicalPath() + File.separator + PEAK.getName().split("\\.")[0] + "_" + REF.getName().split("\\.")[0] + "_Output.cdt");
 		} else {
 			OUTFILE = new File(PEAK.getName().split("\\.")[0] + "_" + REF.getName().split("\\.")[0] + "_Output.cdt");
 		}
+		if (OUTPUT_GZIP){
+			OUTFILE = new File(OUTFILE.getAbsolutePath() + ".gz");
+		}
 	}
 
 	public void run() throws IOException, InterruptedException {

src/main/java/scriptmanager/window_interface/Peak_Analysis/BEDPeakAligntoRefWindow.java

@@ -237,7 +237,7 @@ public void actionPerformed(ActionEvent e) {
 
 		chckbxGzipOutput = new JCheckBox("Output GZip");
 		sl_contentPane.putConstraint(SpringLayout.NORTH, chckbxGzipOutput, 0, SpringLayout.NORTH, btnCalculate);
-		sl_contentPane.putConstraint(SpringLayout.WEST, chckbxGzipOutput, 10, SpringLayout.WEST, contentPane);
+		sl_contentPane.putConstraint(SpringLayout.WEST, chckbxGzipOutput, 31, SpringLayout.WEST, contentPane);
 		contentPane.add(chckbxGzipOutput);
 	}
 

src/main/java/scriptmanager/window_interface/Peak_Analysis/FilterBEDbyProximityWindow.java

@@ -184,7 +184,7 @@ public void actionPerformed(ActionEvent e) {
 
 		chckbxGzipOutput = new JCheckBox("Output GZip");
 		sl_contentPane.putConstraint(SpringLayout.NORTH, chckbxGzipOutput, 0, SpringLayout.NORTH, btnFilter);
-		sl_contentPane.putConstraint(SpringLayout.WEST, chckbxGzipOutput, 10, SpringLayout.WEST, contentPane);
+		sl_contentPane.putConstraint(SpringLayout.WEST, chckbxGzipOutput, 25, SpringLayout.WEST, contentPane);
 		contentPane.add(chckbxGzipOutput);
 
 		progressBar = new JProgressBar();

src/main/java/scriptmanager/window_interface/Peak_Analysis/RandomCoordinateWindow.java

@@ -66,18 +66,20 @@ public Void doInBackground() throws IOException, InterruptedException {
 	        		} else if(Integer.parseInt(txtSize.getText()) < 1) {
 	    				JOptionPane.showMessageDialog(null, "Invalid Window Size Entered!!!");
 	        		} else {
+						boolean GZIP = chckbxGzipOutput.isSelected();
 						boolean bedStatus = rdbtnBed.isSelected();
 						String randomName = (String)cmbGenome.getSelectedItem() + "_" + Integer.parseInt(txtSites.getText()) + "SITES_" + Integer.parseInt(txtSize.getText()) + "bp";
 						if(bedStatus){ randomName += ".bed"; }
 						else{ randomName += ".gff"; }
+						if(GZIP){ randomName += ".gz"; }
 						File OUTFILE;
 						if(OUTPUT_PATH != null){
 							OUTFILE = new File(OUTPUT_PATH + File.separator + randomName);
 						}else{
 							OUTFILE = new File(randomName);
 						}
 						RandomCoordinate.execute((String)cmbGenome.getSelectedItem(), Integer.parseInt(txtSites.getText()), Integer.parseInt(txtSize.getText()), 
-													bedStatus, OUTFILE, chckbxGzipOutput.isSelected());
+													bedStatus, OUTFILE, GZIP);
 	        			JOptionPane.showMessageDialog(null, "Random Coordinate Generation Complete");
 	        		}
 	        	} catch(NumberFormatException nfe){
@@ -149,8 +151,13 @@ public void actionPerformed(ActionEvent e) {
         });
 		contentPane.add(btnOutputDirectory);
 
+		chckbxGzipOutput = new JCheckBox("Output GZip");
+		sl_contentPane.putConstraint(SpringLayout.NORTH, chckbxGzipOutput, 10, SpringLayout.SOUTH, btnOutputDirectory);
+		sl_contentPane.putConstraint(SpringLayout.WEST, chckbxGzipOutput, 105, SpringLayout.WEST, contentPane);
+		contentPane.add(chckbxGzipOutput);
+
 		JLabel lblCurrentOutputDirectory = new JLabel("Current Output:");
-		sl_contentPane.putConstraint(SpringLayout.NORTH, lblCurrentOutputDirectory, 10, SpringLayout.SOUTH, btnOutputDirectory);
+		sl_contentPane.putConstraint(SpringLayout.NORTH, lblCurrentOutputDirectory, 10, SpringLayout.SOUTH, chckbxGzipOutput);
 		sl_contentPane.putConstraint(SpringLayout.WEST, lblCurrentOutputDirectory, 5, SpringLayout.WEST, contentPane);
 		sl_contentPane.putConstraint(SpringLayout.NORTH, lblDefaultToLocal, 6, SpringLayout.SOUTH, lblCurrentOutputDirectory);
 		lblCurrentOutputDirectory.setFont(new Font("Lucida Grande", Font.BOLD, 13));
@@ -199,11 +206,6 @@ public void actionPerformed(ActionEvent e) {
 		OutputFormat.add(rdbtnBed);
 		OutputFormat.add(rdbtnGff);
 		rdbtnBed.setSelected(true);
-
-		chckbxGzipOutput = new JCheckBox("Output GZip");
-		sl_contentPane.putConstraint(SpringLayout.NORTH, chckbxGzipOutput, 10, SpringLayout.SOUTH, btnOutputDirectory);
-		sl_contentPane.putConstraint(SpringLayout.WEST, chckbxGzipOutput, 105, SpringLayout.WEST, contentPane);
-		contentPane.add(chckbxGzipOutput);
 	}
 
 	@Override

src/main/java/scriptmanager/window_interface/Peak_Analysis/TileGenomeWindow.java

@@ -61,17 +61,19 @@ public Void doInBackground() throws IOException, InterruptedException {
 	        		} else if(Integer.parseInt(txtSize.getText()) < 1) {
 	    				JOptionPane.showMessageDialog(null, "Invalid Window Size Entered!!!");
 	        		} else {
+						boolean GZIP = chckbxGzipOutput.isSelected();
 	        			boolean bedStatus = rdbtnBed.isSelected();
 						String randomName = (String)cmbGenome.getSelectedItem() + "_" + Integer.parseInt(txtSize.getText()) + "bp";
 						if(bedStatus){ randomName += ".bed"; }
 						else{ randomName += ".gff"; }
+						if(GZIP){ randomName += ".gz"; }
 						File OUTFILE;
 						if(OUTPUT_PATH != null){
 							OUTFILE = new File(OUTPUT_PATH + File.separator + randomName);
 						}else{
 							OUTFILE = new File(randomName);
 						}
-						TileGenome.execute((String)cmbGenome.getSelectedItem(), Integer.parseInt(txtSize.getText()), bedStatus, OUTFILE, chckbxGzipOutput.isSelected());
+						TileGenome.execute((String)cmbGenome.getSelectedItem(), Integer.parseInt(txtSize.getText()), bedStatus, OUTFILE, GZIP);
 	    				JOptionPane.showMessageDialog(null, "Genomic Tiling Complete");
 	        		}
 	        	} catch(NumberFormatException nfe){

src/main/java/scriptmanager/window_interface/Read_Analysis/AggregateDataWindow.java

@@ -248,7 +248,7 @@ public void actionPerformed(ActionEvent e) {
 
 		chckbxGzipOutput = new JCheckBox("Output GZip");
 		sl_contentPane.putConstraint(SpringLayout.NORTH, chckbxGzipOutput, 0, SpringLayout.NORTH, btnConvert);
-		sl_contentPane.putConstraint(SpringLayout.WEST, chckbxGzipOutput, 0, SpringLayout.WEST, chckbxMergeToOne);
+		sl_contentPane.putConstraint(SpringLayout.WEST, chckbxGzipOutput, 25, SpringLayout.WEST, contentPane);
 		contentPane.add(chckbxGzipOutput);
 	}
 

src/main/java/scriptmanager/window_interface/Read_Analysis/ScaleMatrixWindow.java

@@ -108,6 +108,7 @@ public Void doInBackground() throws IOException {
 							SCALE = Double.parseDouble(txtUniform.getText());
 						}
 
+						boolean GZIP = chckbxGzipOutput.isSelected();
 						for (int x = 0; x < TABFiles.size(); x++) {
 							if (rdbtnFilespecifcScaling.isSelected()) {
 								SCALE = Double.parseDouble(expTable.getValueAt(x, 1).toString());
@@ -120,9 +121,12 @@ public Void doInBackground() throws IOException {
 							if (OUT_DIR != null) {
 								OUTPUT = OUT_DIR + File.separator + OUTPUT;
 							}
+							if (GZIP) {
+								OUTPUT += ".gz";
+							}
 
 							ScaleMatrix scale = new ScaleMatrix(XTAB, new File(OUTPUT), SCALE,
-									Integer.parseInt(txtRow.getText()), Integer.parseInt(txtCol.getText()), chckbxGzipOutput.isSelected());
+									Integer.parseInt(txtRow.getText()), Integer.parseInt(txtCol.getText()), GZIP);
 							scale.run();
 
 							int percentComplete = (int) (((double) (x + 1) / TABFiles.size()) * 100);
@@ -299,6 +303,13 @@ public void actionPerformed(ActionEvent e) {
 		txtUniform.setText("1");
 		contentPane.add(txtUniform);
 		txtUniform.setColumns(10);
+		txtUniform.addActionListener(new ActionListener() {
+			public void actionPerformed(ActionEvent e) {
+				for (int x = 0; x < expTable.getRowCount(); x++) {
+					expTable.setValueAt(txtUniform.getText(), x, 1);
+				}
+        	}
+		});
 
 		JLabel lblRow = new JLabel("Start at Row:");
 		sl_contentPane.putConstraint(SpringLayout.NORTH, lblRow, 10, SpringLayout.SOUTH, lblUniformScalingFactor);

src/main/java/scriptmanager/window_interface/Read_Analysis/ScalingFactorOutput.java

@@ -80,6 +80,7 @@ public void run() throws IOException {
 			if(OUT_DIR != null) {
 				OUTBASE = OUT_DIR.getAbsolutePath() + File.separator + OUTBASE;
 			}
+
 
 			ScalingFactor script_obj = new ScalingFactor(SAMPLE, BLACKLISTFile, CONTROL, OUTBASE, OUTPUTSTATUS,
 					scaleType, windowSize, minFraction);