Simplified code

(accidentally was on sort-by-ref branch when making documentation, so I rewrote some tools which turned out to be better than the code on this branch)

src/main/java/scriptmanager/cli/Coordinate_Manipulation/BED_Manipulation/BEDtoGFFCLI.java

@@ -64,7 +64,7 @@ private String validateInput() throws IOException {
 		}
 		//set default output filename
 		if(output==null && !stdout){
-			String NAME = ExtensionFileFilter.stripExtension(bedFile) + ".gff";
+			String NAME = ExtensionFileFilter.stripExtensionIgnoreGZ(bedFile) + ".gff";
 			NAME += gzOutput ? ".gz" : "";
 			output = new File(NAME);
 		//check stdout and output not both selected

src/main/java/scriptmanager/cli/Coordinate_Manipulation/BED_Manipulation/SortBEDCLI.java

@@ -36,10 +36,10 @@ public class SortBEDCLI implements Callable<Integer> {
 
 	@Option(names = {"-o", "--output"}, description = "specify output file basename with no .cdt/.bed/.jtv extension (default=<bedFile>_SORT")
 	private String outputBasename = null;
-	@Option(names = {"-c", "--center"}, description = "sort by center on the input size of expansion in bins (default=100)")
-	private int center = -999;
 	@Option(names = {"-z", "--gzip"}, description = "gzip output (default=false)")
 	private boolean gzOutput = false;
+	@Option(names = {"-c", "--center"}, description = "sort by center on the input size of expansion in bins (default=100)")
+	private int center = -999;
 	@Option(names = {"-x", "--index"}, description = "sort by index from the specified start to the specified stop (0-indexed and half-open interval)",
 		arity = "2")
 	private int[] index = {-999, -999};

src/main/java/scriptmanager/cli/Coordinate_Manipulation/GFF_Manipulation/ExpandGFFCLI.java

@@ -30,7 +30,7 @@ public class ExpandGFFCLI implements Callable<Integer> {
 
 	@Option(names = {"-o", "--output"}, description = "specify output filename (name will be same as original with coordinate info appended)")
 	private File output = null;
-	@Option(names = {"-s", "--stdout"}, description = "output bed to STDOUT")
+	@Option(names = {"-s", "--stdout"}, description = "output gff to STDOUT")
 	private boolean stdout = false;
 	@Option(names = {"-z", "--gzip"}, description = "gzip output (default=false)")
 	private boolean gzOutput = false;
@@ -72,7 +72,7 @@ private String validateInput() throws IOException {
 			return(r);
 		}
 		//check input extensions
-		if(!"gff".equals(ExtensionFileFilter.getExtension(gffFile))){
+		if(!"gff".equals(ExtensionFileFilter.getExtensionIgnoreGZ(gffFile))){
 			r += "(!)Is this a GFF file? Check extension: " + gffFile.getName() + "\n";
 		}
 

src/main/java/scriptmanager/cli/Coordinate_Manipulation/GFF_Manipulation/GFFtoBEDCLI.java

@@ -60,7 +60,7 @@ private String validateInput() throws IOException {
 		}
 		//set default output filename
 		if(output==null && !stdout){
-			output = new File(ExtensionFileFilter.stripExtension(gffFile) + ".bed");
+			output = new File(ExtensionFileFilter.stripExtensionIgnoreGZ(gffFile) + ".bed");
 		//check stdout and output not both selected
 		}else if(stdout){
 			if(output!=null){ r += "(!)Cannot use -s flag with -o.\n"; }

src/main/java/scriptmanager/cli/Coordinate_Manipulation/GFF_Manipulation/SortGFFCLI.java

@@ -33,7 +33,7 @@ public class SortGFFCLI implements Callable<Integer> {
 
 	@Option(names = {"-o", "--output"}, description = "specify output file basename with no .cdt/.gff/.jtv extension (default=<gffFile>_SORT")
 	private String outputBasename = null;
-	@Option(names = {"-z", "--compression"}, description = "Output compressed GFF file" )
+	@Option(names = {"-z", "--gzip"}, description = "gzip output (default=false)")
 	private boolean gzOutput = false;
 	@Option(names = {"-c", "--center"}, description = "sort by center on the input size of expansion in bins (default=100)")
 	private int center = -999;
@@ -93,7 +93,7 @@ private String validateInput() throws IOException {
 
 		//set default output filename
 		if(outputBasename==null){
-			outputBasename = ExtensionFileFilter.stripExtension(gffFile) + "_SORT";
+			outputBasename = ExtensionFileFilter.stripExtensionIgnoreGZ(gffFile) + "_SORT";
 		//check output filename is valid
 		}else{
 			//no extension check

src/main/java/scriptmanager/cli/Sequence_Analysis/SearchMotifCLI.java

@@ -77,7 +77,6 @@ private String validateInput() throws IOException {
 		if (output == null) {
 			String NAME = motif + "_" + Integer.toString(ALLOWED_MISMATCH) + "Mismatch_"
 					+ ExtensionFileFilter.stripExtension(fastaFile) + ".bed";
-			NAME += gzOutput ? ".gz" : "";
 			output = new File(NAME);
 			// check output filename is valid
 		} else {

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

@@ -1,16 +1,10 @@
 package scriptmanager.scripts.Coordinate_Manipulation.BED_Manipulation;
 
-import java.io.BufferedOutputStream;
 import java.io.BufferedReader;
 import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileOutputStream;
 import java.io.IOException;
-import java.io.InputStreamReader;
 import java.io.PrintStream;
 import java.util.Arrays;
-import java.util.zip.GZIPInputStream;
-import java.util.zip.GZIPOutputStream;
 
 import scriptmanager.util.GZipUtilities;
 
@@ -35,19 +29,10 @@ public static void convertBEDtoGFF(File outpath, File input, boolean gzOutput) t
 		// Initialize output writer
 		PrintStream OUT = System.out;
 		if (outpath != null) {
-			if (gzOutput) {
-				OUT = new PrintStream(new BufferedOutputStream(new GZIPOutputStream(new FileOutputStream(outpath))));
-			} else {
-				OUT = new PrintStream(new BufferedOutputStream(new FileOutputStream(outpath)));
-			}
+			OUT = GZipUtilities.makePrintStream(outpath, gzOutput);
 		}
 		// Check if file is gzipped and instantiate appropriate BufferedReader
-		BufferedReader br;
-		if(GZipUtilities.isGZipped(input)) {
-			br = new BufferedReader(new InputStreamReader(new GZIPInputStream(new FileInputStream(input)), "UTF-8"));
-		} else {
-			br = new BufferedReader(new InputStreamReader(new FileInputStream(input), "UTF-8"));
-		}
+		BufferedReader br = GZipUtilities.makeReader(input);
 		// Initialize line variable to loop through
 		String line = br.readLine();
 		while (line != null) {

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

@@ -78,6 +78,7 @@ public static void sortBEDbyCDT(String outbase, File bed, File cdt, int START_IN
 			if (!ID.contains("YORF") && !ID.contains("NAME")) {
 				BEDFile.put(ID, line);
 			}
+			line = br.readLine();
 		}
 		br.close();
 

src/main/java/scriptmanager/scripts/Coordinate_Manipulation/GFF_Manipulation/GFFtoBED.java

@@ -5,22 +5,22 @@
 import java.io.IOException;
 import java.io.PrintStream;
 import java.util.Arrays;
-import scriptmanager.util.GZipUtilities;
 
+import scriptmanager.util.GZipUtilities;
 
 public class GFFtoBED {
-	public static void convertGFFtoBED(File out_filepath, File input, boolean outputGzip) throws IOException {
+	public static void convertGFFtoBED(File out_filepath, File input, boolean gzOutput) throws IOException {
 		// GFF: chr22 TeleGene enhancer 10000000 10001000 500 + . touch1
 		// BED: chr12 605113 605120 region_0 0 +
 
 		PrintStream OUT = System.out;
 		if (out_filepath != null)
-			OUT = GZipUtilities.makePrintStream(out_filepath, outputGzip);
+			OUT = GZipUtilities.makePrintStream(out_filepath, gzOutput);
 
-		// Checks if file is gzipped and instantiate appropriate BufferedReader
-		String line;
 		BufferedReader br = GZipUtilities.makeReader(input);
-		while ((line = br.readLine()) != null) {
+		// Initialize line variable to loop through
+		String line = br.readLine();
+		while (line != null) {
 			String[] temp = line.split("\t");
 			if (temp[0].toLowerCase().contains("track") || temp[0].startsWith("#")) {
 				OUT.println(String.join("\t", temp));
@@ -42,6 +42,7 @@ public static void convertGFFtoBED(File out_filepath, File input, boolean output
 					System.out.println("Invalid Coordinate in File!!!\n" + Arrays.toString(temp));
 				}
 			}
+			line = br.readLine();
 		}
 		br.close();
 		OUT.close();

src/main/java/scriptmanager/scripts/Coordinate_Manipulation/GFF_Manipulation/SortGFF.java

@@ -17,10 +17,11 @@ public static void sortGFFbyCDT(String outname, File gff, File cdt, int START_IN
 		ArrayList<GFFCoord> SORT = new ArrayList<GFFCoord>();
 		HashMap<String, String> CDTFile = new HashMap<String, String>();
 		String CDTHeader = "";
-		// Parse CDT File first
-		String line;
+		// Check if file is gzipped and instantiate appropriate BufferedReader
 		BufferedReader br = GZipUtilities.makeReader(cdt);
-		while ((line = br.readLine()) != null) {
+		// Parse CDT File first
+		String line = br.readLine();
+		while (line != null) {
 			String[] ID = line.split("\t");
 			if (!ID[0].contains("YORF") && !ID[0].contains("NAME")) {
 				double count = 0;
@@ -32,14 +33,14 @@ public static void sortGFFbyCDT(String outname, File gff, File cdt, int START_IN
 			} else {
 				CDTHeader = line;
 			}
+			line = br.readLine();
 		}
 		br.close();
 		// Sort by score
 		Collections.sort(SORT, GFFCoord.ScoreComparator);
 
 		// Output sorted CDT File
-		String newCDT = outname + ".cdt";
-		PrintStream OUT = GZipUtilities.makePrintStream(new File(newCDT), gzOutput);
+		PrintStream OUT = GZipUtilities.makePrintStream(new File(outname + ".cdt"), gzOutput);
 		OUT.println(CDTHeader);
 		for (int x = 0; x < SORT.size(); x++) {
 			OUT.println(CDTFile.get(SORT.get(x).getName()));
@@ -49,18 +50,21 @@ public static void sortGFFbyCDT(String outname, File gff, File cdt, int START_IN
 
 		// Match to gff file after
 		HashMap<String, String> GFFFile = new HashMap<String, String>();
-		line = null;
+		// Check if file is gzipped and instantiate appropriate BufferedReader
 		br = GZipUtilities.makeReader(gff);
-		while ((line = br.readLine()) != null) {
-			String ID = line.split("\t")[8].split(";")[0];
+		// Initialize line variable to loop through
+		line = br.readLine();
+		while (line != null) {
+			String ID = line.split("\t")[3];
 			if (!ID.contains("YORF") && !ID.contains("NAME")) {
 				GFFFile.put(ID, line);
 			}
+			line = br.readLine();
 		}
 		br.close();
+
 		// Output sorted GFF File
-		String newGFF = outname + ".gff";
-		OUT = GZipUtilities.makePrintStream(new File(newGFF), gzOutput);
+		OUT = GZipUtilities.makePrintStream(new File(outname + ".gff"), gzOutput);
 		for (int x = 0; x < SORT.size(); x++) {
 			OUT.println(GFFFile.get(SORT.get(x).getName()));
 		}

src/main/java/scriptmanager/scripts/Sequence_Analysis/SearchMotif.java

@@ -1,9 +1,7 @@
 package scriptmanager.scripts.Sequence_Analysis;
 
-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.sql.Timestamp;
@@ -12,7 +10,6 @@
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
-import java.util.zip.GZIPOutputStream;
 
 import scriptmanager.util.GZipUtilities;
 
@@ -126,12 +123,7 @@ public void run() throws IOException, InterruptedException {
 		// Initialize output writer
 		PrintStream OUT = System.out;
 		if (out_filepath != null) {
-			if (gzOutput) {
-				OUT = new PrintStream(
-						new BufferedOutputStream(new GZIPOutputStream(new FileOutputStream(out_filepath))));
-			} else {
-				OUT = new PrintStream(new BufferedOutputStream(new FileOutputStream(out_filepath)));
-			}
+			OUT = GZipUtilities.makePrintStream(out_filepath, gzOutput);
 		}
 
 		// Check if file is gzipped and instantiate appropriate BufferedReader

src/main/java/scriptmanager/util/BEDUtilities.java

@@ -6,6 +6,7 @@
 import java.io.UnsupportedEncodingException;
 import java.util.ArrayList;
 import java.util.Arrays;
+
 import scriptmanager.objects.CoordinateObjects.BEDCoord;
 
 /**

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

@@ -75,11 +75,10 @@ public Void doInBackground() throws IOException {
 			for (int x = 0; x < BEDFiles.size(); x++) {
 				File XBED = BEDFiles.get(x);
 				// Set outfilepath
-				String OUTPUT = ExtensionFileFilter.stripExtension(XBED) + ".gff";
+				String OUTPUT = ExtensionFileFilter.stripExtensionIgnoreGZ(XBED) + ".gff";
 				if (OUT_DIR != null) {
 					OUTPUT = OUT_DIR + File.separator + OUTPUT;
 				}
-				OUTPUT += chckbxGzipOutput.isSelected() ? ".gz" : "";
 				// Initialize LogItem
 				String command = BEDtoGFFCLI.getCLIcommand(new File(OUTPUT), XBED, chckbxGzipOutput.isSelected());
 				LogItem new_li = new LogItem(command);
@@ -203,8 +202,8 @@ public void actionPerformed(ActionEvent e) {
 		btnConvert.addActionListener(this);
 
 		chckbxGzipOutput = new JCheckBox("Output GZIP");
-		sl_contentPane.putConstraint(SpringLayout.NORTH, chckbxGzipOutput, 0, SpringLayout.NORTH, btnOutput);
-		sl_contentPane.putConstraint(SpringLayout.EAST, chckbxGzipOutput, -10, SpringLayout.EAST, contentPane);
+		sl_contentPane.putConstraint(SpringLayout.NORTH, chckbxGzipOutput, 0, SpringLayout.NORTH, btnConvert);
+		sl_contentPane.putConstraint(SpringLayout.WEST, chckbxGzipOutput, 36, SpringLayout.WEST, contentPane);
 		contentPane.add(chckbxGzipOutput);
 	}
 

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

@@ -106,8 +106,7 @@ public Void doInBackground() throws IOException {
 						STOP_INDEX = Integer.parseInt(txtStop.getText());
 					}
 
-					String OUTPUT = ExtensionFileFilter.stripExtension(txtOutput.getText());
-					OUTPUT = txtOutput.getText().endsWith(".gz") ? ExtensionFileFilter.stripExtension(OUTPUT) : OUTPUT;
+					String OUTPUT = ExtensionFileFilter.stripExtensionIgnoreGZ(BED_File);
 					if (OUT_DIR != null) {
 						OUTPUT = OUT_DIR.getCanonicalPath() + File.separator + OUTPUT;
 					}
@@ -328,11 +327,13 @@ public void actionPerformed(ActionEvent e) {
 					lblBEDFile.setText(BED_File.getName());
 					txtOutput.setEnabled(true);
 					// Set default output filename
-					String NAME = ExtensionFileFilter.stripExtension(BED_File.getName());
-					NAME = BED_File.getName().endsWith(".bed.gz") ? ExtensionFileFilter.stripExtension(NAME) : NAME;
-					NAME += "_SORT.bed";
-					NAME += chckbxGzipOutput.isSelected() ? ".gz" : "";
-					txtOutput.setText(NAME);
+					String sortName = "";
+					try {
+						sortName = ExtensionFileFilter.stripExtensionIgnoreGZ(BED_File) + "_SORT.bed";
+					} catch (IOException e1) {
+						JOptionPane.showMessageDialog(null, "Invalid BED");
+					};
+					txtOutput.setText(sortName);
 				}
 			}
 		});

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

@@ -45,21 +45,21 @@ public class GFFtoBEDWindow extends JFrame implements ActionListener, PropertyCh
 	private JButton btnLoad;
 	private JButton btnRemoveGFF;
 	private JButton btnConvert;
-	private JCheckBox chckbxGzipOutput;
 
 	private JProgressBar progressBar;
 	public Task task;
 	private JLabel lblCurrent;
 	private JLabel lblDefaultToLocal;
 	private JButton btnOutput;
+	private static JCheckBox chckbxGzipOutput;
 
 	class Task extends SwingWorker<Void, Void> {
 		@Override
 		public Void doInBackground() throws IOException {
 			setProgress(0);
 			for (int x = 0; x < BEDFiles.size(); x++) {
 				File XGFF = BEDFiles.get(x);
-				// Check if file is gzipped and assigns appropriate file name
+				// Set outfilepath
 				String OUTPUT = ExtensionFileFilter.stripExtensionIgnoreGZ(XGFF) + ".bed";
 				if (OUT_DIR != null) {
 					OUTPUT = OUT_DIR + File.separator + OUTPUT;
@@ -172,13 +172,12 @@ public void actionPerformed(ActionEvent e) {
 		sl_contentPane.putConstraint(SpringLayout.WEST, btnOutput, 150, SpringLayout.WEST, contentPane);
 		sl_contentPane.putConstraint(SpringLayout.EAST, btnOutput, -150, SpringLayout.EAST, contentPane);
 		contentPane.add(btnOutput);
+		btnConvert.addActionListener(this);
 
 		chckbxGzipOutput = new JCheckBox("Output GZIP");
-		sl_contentPane.putConstraint(SpringLayout.NORTH, chckbxGzipOutput, 0, SpringLayout.NORTH, btnOutput);
-		sl_contentPane.putConstraint(SpringLayout.EAST, chckbxGzipOutput, -10, SpringLayout.EAST, contentPane);
+		sl_contentPane.putConstraint(SpringLayout.NORTH, chckbxGzipOutput, 0, SpringLayout.NORTH, btnConvert);
+		sl_contentPane.putConstraint(SpringLayout.WEST, chckbxGzipOutput, 36, SpringLayout.WEST, contentPane);
 		contentPane.add(chckbxGzipOutput);
-
-		btnConvert.addActionListener(this);	
 	}
 
 	@Override

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

@@ -95,7 +95,7 @@ public Void doInBackground() throws IOException {
 						STOP_INDEX = Integer.parseInt(txtStop.getText());
 					}
 
-					String OUTPUT = txtOutput.getText();
+					String OUTPUT = ExtensionFileFilter.stripExtensionIgnoreGZ(GFF_File);
 					if (OUT_DIR != null) {
 						OUTPUT = OUT_DIR.getCanonicalPath() + File.separator + OUTPUT;
 					}
@@ -172,6 +172,22 @@ public void actionPerformed(ActionEvent e) {
 		sl_contentPane.putConstraint(SpringLayout.EAST, chckbxGzipOutput, -10, SpringLayout.EAST, contentPane);
 		contentPane.add(chckbxGzipOutput);
 
+		chckbxGzipOutput.addItemListener(new ItemListener() {
+			public void itemStateChanged(ItemEvent e) {
+				String NAME = txtOutput.getText();
+				if (chckbxGzipOutput.isSelected()) {
+					if (!NAME.endsWith(".gz")) {
+						txtOutput.setText(NAME + ".gz");
+					}
+				} else {
+					if (NAME.endsWith(".gz")) {
+						NAME = ExtensionFileFilter.stripExtension(NAME);
+						txtOutput.setText(NAME);
+					}
+				}
+			}
+		});
+
 		rdbtnSortbyCenter = new JRadioButton("Sort by Center");
 		sl_contentPane.putConstraint(SpringLayout.NORTH, rdbtnSortbyCenter, 129, SpringLayout.NORTH, contentPane);
 		contentPane.add(rdbtnSortbyCenter);
@@ -293,11 +309,12 @@ public void actionPerformed(ActionEvent e) {
 					GFF_File = newGFFFile;
 					lblGFFFile.setText(GFF_File.getName());
 					txtOutput.setEnabled(true);
+					// Set default output filename
 					String sortName = "";
 					try {
-						sortName = ExtensionFileFilter.stripExtensionIgnoreGZ(GFF_File) + "_SORT";
+						sortName = ExtensionFileFilter.stripExtensionIgnoreGZ(GFF_File) + "_SORT.gff";
 					} catch (IOException e1) {
-						e1.printStackTrace();
+						JOptionPane.showMessageDialog(null, "Invalid GFF");
 					}
 					txtOutput.setText(sortName);
 				}