Added gzip output for DNA shape tools

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

@@ -36,6 +36,8 @@ public class DNAShapefromBEDCLI implements Callable<Integer> {
 	@Option(names = { "-o",
 			"--output" }, description = "Specify basename for output files, files for each shape indicated will share this name with a different suffix")
 	private String outputBasename = null;
+	@Option(names = {"-z", "--gzip"}, description = "output compressed output (default=false)")
+	private boolean zip = false;
 	@Option(names = { "--avg-composite" }, description = "Save average composite")
 	private boolean avgComposite = false;
 	@Option(names = { "-n", "--no-force" }, description = "don't force-strandedness (default is to force strandedness)")
@@ -74,7 +76,7 @@ public Integer call() throws Exception {
 		try {
 			// Generate Composite Plot
 			DNAShapefromBED script_obj = new DNAShapefromBED(genomeFASTA, bedFile, outputBasename, OUTPUT_TYPE,
-					forceStrand, new PrintStream[] { null, null, null, null });
+					forceStrand, new PrintStream[] { null, null, null, null }, zip);
 			script_obj.run();
 
 			if (avgComposite) {

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

@@ -36,6 +36,8 @@ public class DNAShapefromFASTACLI implements Callable<Integer> {
 	private String outputBasename = null;
 	@Option(names = { "--avg-composite" }, description = "Save average composite")
 	private boolean avgComposite = false;
+	@Option(names = {"-z", "--gzip"}, description = "output compressed output (default=false)")
+	private boolean zip = false;
 
 	@ArgGroup(validate = false, heading = "Shape Options%n")
 	ShapeType shape = new ShapeType();
@@ -68,7 +70,7 @@ public Integer call() throws Exception {
 
 		// Generate Composite Plot
 		DNAShapefromFASTA script_obj = new DNAShapefromFASTA(fastaFile, outputBasename, OUTPUT_TYPE,
-				new PrintStream[] { null, null, null, null });
+				new PrintStream[] { null, null, null, null }, zip);
 		script_obj.run();
 
 		// Print Composite Scores

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

@@ -33,6 +33,8 @@ public class RandomizeFASTACLI implements Callable<Integer> {
 	private File output;
 	@Option(names = {"-s", "--seed"}, description = "specify an integer seed for reproducible outputs")
 	private Integer seed = null;
+	@Option(names = {"-z", "--gzip"}, description = "output compressed output (default=false)")
+	private boolean zip = false;
 
 	@Override
 	public Integer call() throws Exception {
@@ -44,7 +46,7 @@ public Integer call() throws Exception {
 			System.exit(1);
 		}
 
-		RandomizeFASTA.randomizeFASTA(fastaFile, output, seed);
+		RandomizeFASTA.randomizeFASTA(fastaFile, output, seed, zip);
 
 		System.err.println("Randomization Complete.");
 		return (0);

src/main/java/scriptmanager/scripts/Figure_Generation/PlotComposite.java

@@ -1,12 +1,12 @@
 package scriptmanager.scripts.Figure_Generation;
 
 import java.awt.Color;
+import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.FileOutputStream;
 import java.io.IOException;
 import java.util.ArrayList;
-import java.util.Scanner;
 
 import org.jfree.chart.ChartUtils;
 import org.jfree.chart.JFreeChart;
@@ -16,6 +16,7 @@
 import scriptmanager.charts.CompositePlot;
 import scriptmanager.util.ColorSeries;
 import scriptmanager.util.ExtensionFileFilter;
+import scriptmanager.util.GZipUtilities;
 
 /**
  * The script class to create/display line plot images based on the output files
@@ -64,11 +65,13 @@ public class PlotComposite {
 	 * @throws FileNotFoundException
 	 */
 	public static JFreeChart plotCompositeFile(File input, File OUT_PATH, boolean outputImage, String title, ArrayList<Color> COLORS, boolean legend, int pxHeight, int pxWidth) throws IOException, IllegalArgumentException, FileNotFoundException {
-		Scanner scan = new Scanner(input);
+		BufferedReader br = GZipUtilities.makeReader(input);
 		// parse x values
-		String[] tokens = scan.nextLine().split("\t");
+		String line;
+		String[] tokens = {""};
+		if ((line = br.readLine()) != null){ tokens = line.split("\t"); }
 		if (!tokens[0].equals("")) {
-			scan.close();
+			br.close();
 			throw new IllegalArgumentException("(!) First row of input file must have an empty first column (as x-values)");
 		}
 		double[] x = new double[tokens.length - 1];
@@ -81,11 +84,11 @@ public static JFreeChart plotCompositeFile(File input, File OUT_PATH, boolean ou
 
 		XYSeries s;
 		// line-by-line through file
-		while (scan.hasNextLine()) {
-			tokens = scan.nextLine().split("\t");
+		while ((line = br.readLine()) != null) {
+			tokens = line.split("\t");
 			// check for format consistency: number of x-values matches y-values
 			if (tokens.length - 1 != x.length) {
-				scan.close();
+				br.close();
 				throw new IllegalArgumentException("(!) Check number of x-values matches number of y-values");
 			}
 			// skip any rows with blank labels
@@ -94,7 +97,7 @@ public static JFreeChart plotCompositeFile(File input, File OUT_PATH, boolean ou
 					if (x[i - 1] != Double.parseDouble(tokens[i])) {
 						System.err.println(x[i - 1]);
 						System.err.println(tokens[i]);
-						scan.close();
+						br.close();
 						throw new IllegalArgumentException("(!) Check dataseries based on same x-scale file");
 					}
 				}
@@ -108,7 +111,7 @@ public static JFreeChart plotCompositeFile(File input, File OUT_PATH, boolean ou
 			}
 			dataset.addSeries(s);
 		}
-		scan.close();
+		br.close();
 
 		// Set-up colors
 		if (COLORS==null) {

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

@@ -38,6 +38,7 @@ public class DNAShapefromBED {
 	private String OUTBASENAME = null;
 	private boolean[] OUTPUT_TYPE = null;
 	private File BED = null;
+	private boolean GZIP_OUTPUT;
 
 	private boolean STRAND = true;
 	private boolean INDEX = true;
@@ -73,16 +74,18 @@ public class DNAShapefromBED {
 	 * @param str  force strandedness (true=forced, false=not forced)
 	 * @param ps   list of four PrintStream objects corresponding to each shape type
 	 *             (for GUI)
+	 * @param gzOutput Whether to output compressed file
 	 * @throws IOException
 	 */
-	public DNAShapefromBED(File gen, File b, String out, boolean[] type, boolean str, PrintStream[] ps)
+	public DNAShapefromBED(File gen, File b, String out, boolean[] type, boolean str, PrintStream[] ps, boolean gzOutput)
 			throws IOException {
 		GENOME = gen;
 		BED = b;
 		OUTBASENAME = out;
 		OUTPUT_TYPE = type;
 		STRAND = str;
 		PS = ps;
+		GZIP_OUTPUT = gzOutput;
 
 		File FAI = new File(GENOME + ".fai");
 		// Check if FAI index file exists
@@ -394,18 +397,18 @@ private void openOutputFiles() {
 		// Open Output File
 		try {
 			if (OUTPUT_TYPE[0]) {
-				OUT_M = new PrintStream(new File(OUTBASENAME + "_MGW.cdt"));
+				OUT_M = GZipUtilities.makePrintStream(new File(OUTBASENAME + "_MGW.cdt"), GZIP_OUTPUT);
 			}
 			if (OUTPUT_TYPE[1]) {
-				OUT_P = new PrintStream(new File(OUTBASENAME + "_PropT.cdt"));
+				OUT_P = GZipUtilities.makePrintStream(new File(OUTBASENAME + "_PropT.cdt"), GZIP_OUTPUT);
 			}
 			if (OUTPUT_TYPE[2]) {
-				OUT_H = new PrintStream(new File(OUTBASENAME + "_HelT.cdt"));
+				OUT_H = GZipUtilities.makePrintStream(new File(OUTBASENAME + "_HelT.cdt"), GZIP_OUTPUT);
 			}
 			if (OUTPUT_TYPE[3]) {
-				OUT_R = new PrintStream(new File(OUTBASENAME + "_Roll.cdt"));
+				OUT_R = GZipUtilities.makePrintStream(new File(OUTBASENAME + "_Roll.cdt"), GZIP_OUTPUT);
 			}
-		} catch (FileNotFoundException e) {
+		} catch (IOException e) {
 			e.printStackTrace();
 		}
 	}

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

@@ -3,14 +3,14 @@
 import java.awt.Component;
 import java.io.BufferedReader;
 import java.io.File;
-import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.PrintStream;
 import java.sql.Timestamp;
 import java.util.ArrayList;
 import java.util.Date;
 import java.util.List;
 import java.util.Map;
+
 import scriptmanager.charts.CompositePlot;
 import scriptmanager.util.DNAShapeReference;
 import scriptmanager.util.GZipUtilities;
@@ -29,6 +29,7 @@ public class DNAShapefromFASTA {
 	private String OUTBASENAME = null;
 	private boolean[] OUTPUT_TYPE = null;
 	private File FASTA = null;
+	private boolean GZIP_OUTPUT;
 
 	private PrintStream OUT_M = null;
 	private PrintStream OUT_P = null;
@@ -58,12 +59,14 @@ public class DNAShapefromFASTA {
 	 *             (no enforcement on size)
 	 * @param ps   list of four PrintStream objects corresponding to each shape type
 	 *             (for GUI)
+	 * @param gzOutput Whether to output compressed file
 	 */
-	public DNAShapefromFASTA(File fa, String out, boolean[] type, PrintStream[] ps) {
+	public DNAShapefromFASTA(File fa, String out, boolean[] type, PrintStream[] ps, boolean gzOutput) {
 		FASTA = fa;
 		OUTBASENAME = out;
 		OUTPUT_TYPE = type;
 		PS = ps;
+		GZIP_OUTPUT = gzOutput;
 
 		STRUCTURE = DNAShapeReference.InitializeStructure();
 	}
@@ -304,18 +307,18 @@ private void openOutputFiles() {
 		// Open Output File
 		try {
 			if (OUTPUT_TYPE[0]) {
-				OUT_M = new PrintStream(new File(OUTBASENAME + "_MGW.cdt"));
+				OUT_M = GZipUtilities.makePrintStream(new File(OUTBASENAME + "_MGW.cdt"), GZIP_OUTPUT);
 			}
 			if (OUTPUT_TYPE[1]) {
-				OUT_P = new PrintStream(new File(OUTBASENAME + "_PropT.cdt"));
+				OUT_P = GZipUtilities.makePrintStream(new File(OUTBASENAME + "_PropT.cdt"), GZIP_OUTPUT);
 			}
 			if (OUTPUT_TYPE[2]) {
-				OUT_H = new PrintStream(new File(OUTBASENAME + "_HelT.cdt"));
+				OUT_H = GZipUtilities.makePrintStream(new File(OUTBASENAME + "_HelT.cdt"), GZIP_OUTPUT);
 			}
 			if (OUTPUT_TYPE[3]) {
-				OUT_R = new PrintStream(new File(OUTBASENAME + "_Roll.cdt"));
+				OUT_R = GZipUtilities.makePrintStream(new File(OUTBASENAME + "_Roll.cdt"), GZIP_OUTPUT);
 			}
-		} catch (FileNotFoundException e) {
+		} catch (IOException e) {
 			e.printStackTrace();
 		}
 	}

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

@@ -2,14 +2,10 @@
 
 import java.io.BufferedReader;
 import java.io.File;
-import java.io.FileInputStream;
 import java.io.IOException;
-import java.io.InputStreamReader;
 import java.io.PrintStream;
 import java.util.ArrayList;
 import java.util.Random;
-import java.util.zip.GZIPInputStream;
-
 import scriptmanager.util.GZipUtilities;
 
 /**
@@ -28,16 +24,17 @@ public class RandomizeFASTA {
 	 * @param FASTA filepath to FASTA-formatted sequences to randomize
 	 * @param RANDOUT filepath to write randomized sequences to
 	 * @param seed set a random seed
+	 * @param gzOutput Whether to output a compressed file
 	 * @return name of output filename
 	 * @throws IOException
 	 */
-	public static File randomizeFASTA(File FASTA, File RANDOUT, Integer seed) throws IOException {
+	public static File randomizeFASTA(File FASTA, File RANDOUT, Integer seed, boolean gzOutput) throws IOException {
 		Random randnum = new Random();
 		if( seed != null) {
 			System.err.println("Set Seed=" + seed);
 			randnum.setSeed(seed);
 		}
-		PrintStream OUT = new PrintStream(RANDOUT);
+		PrintStream OUT = GZipUtilities.makePrintStream(RANDOUT, gzOutput);
 
 		// Check if file is gzipped and instantiate appropriate BufferedReader
 		BufferedReader br = GZipUtilities.makeReader(FASTA);

src/main/java/scriptmanager/window_interface/Sequence_Analysis/DNAShapefromBEDOutput.java

@@ -34,6 +34,7 @@ public class DNAShapefromBEDOutput extends JFrame {
 	private File OUT_DIR = null;
 	private boolean[] OUTPUT_TYPE = null;
 	private ArrayList<File> BED = null;
+	private boolean OUTPUT_GZIP;
 
 	private boolean STRAND = true;
 
@@ -51,8 +52,9 @@ public class DNAShapefromBEDOutput extends JFrame {
 	 * @param out_dir the output directory to save output files to
 	 * @param type    the information on the shape types to generate
 	 * @param str     the force-strandedness to pass to the script
+	 * @param gzOutput Whether to output compressed file
 	 */
-	public DNAShapefromBEDOutput(File gen, ArrayList<File> b, File out_dir, boolean[] type, boolean str) {
+	public DNAShapefromBEDOutput(File gen, ArrayList<File> b, File out_dir, boolean[] type, boolean str, boolean gzOutput) {
 		setTitle("DNA Shape Prediction Composite");
 		setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
 		setBounds(150, 150, 800, 600);
@@ -80,6 +82,7 @@ public DNAShapefromBEDOutput(File gen, ArrayList<File> b, File out_dir, boolean[
 		OUT_DIR = out_dir;
 		OUTPUT_TYPE = type;
 		STRAND = str;
+		OUTPUT_GZIP = gzOutput;
 	}
 
 	/**
@@ -134,7 +137,7 @@ public void run() throws IOException, InterruptedException {
 				}
 
 				// Initialize Script Object and execute calculations
-				DNAShapefromBED script_obj = new DNAShapefromBED(GENOME, BED.get(x), BASENAME, OUTPUT_TYPE, STRAND, PS);
+				DNAShapefromBED script_obj = new DNAShapefromBED(GENOME, BED.get(x), BASENAME, OUTPUT_TYPE, STRAND, PS, OUTPUT_GZIP);
 				script_obj.run();
 
 				// Exit if FAI failed checks

src/main/java/scriptmanager/window_interface/Sequence_Analysis/DNAShapefromBEDWindow.java

@@ -63,6 +63,7 @@ public class DNAShapefromBEDWindow extends JFrame implements ActionListener, Pro
 
 	private JCheckBox chckbxStrand;
 	private JCheckBox chckbxAll;
+	private JCheckBox chckbxGzipOutput;
 	private JCheckBox chckbxMinorGrooveWidth;
 	private JCheckBox chckbxRoll;
 	private JCheckBox chckbxHelicalTwist;
@@ -93,7 +94,7 @@ public Void doInBackground() throws IOException {
 					OUTPUT_TYPE[3] = chckbxRoll.isSelected();
 
 					DNAShapefromBEDOutput signal = new DNAShapefromBEDOutput(INPUT, BEDFiles, OUT_DIR, OUTPUT_TYPE,
-							chckbxStrand.isSelected());
+							chckbxStrand.isSelected(), chckbxGzipOutput.isSelected());
 
 					signal.addPropertyChangeListener("fa", new PropertyChangeListener() {
 						public void propertyChange(PropertyChangeEvent propertyChangeEvent) {
@@ -182,6 +183,11 @@ public void actionPerformed(ActionEvent arg0) {
 		sl_contentPane.putConstraint(SpringLayout.SOUTH, btnCalculate, -10, SpringLayout.SOUTH, contentPane);
 		contentPane.add(btnCalculate);
 
+		chckbxGzipOutput = new JCheckBox("Output Gzip");
+		sl_contentPane.putConstraint(SpringLayout.NORTH, chckbxGzipOutput, 0, SpringLayout.NORTH, btnCalculate);
+		sl_contentPane.putConstraint(SpringLayout.WEST, chckbxGzipOutput, 30, SpringLayout.WEST, contentPane);
+		contentPane.add(chckbxGzipOutput);
+
 		progressBar = new JProgressBar();
 		sl_contentPane.putConstraint(SpringLayout.SOUTH, progressBar, -10, SpringLayout.SOUTH, contentPane);
 		sl_contentPane.putConstraint(SpringLayout.EAST, progressBar, 0, SpringLayout.EAST, scrollPane);

src/main/java/scriptmanager/window_interface/Sequence_Analysis/DNAShapefromFASTAOutput.java

@@ -30,6 +30,7 @@ public class DNAShapefromFASTAOutput extends JFrame {
 	private File OUT_DIR = null;
 	private boolean[] OUTPUT_TYPE = null;
 	private ArrayList<File> FASTA = null;
+	private boolean OUTPUT_GZIP;
 
 	final JLayeredPane layeredPane;
 	final JTabbedPane tabbedPane;
@@ -43,8 +44,9 @@ public class DNAShapefromFASTAOutput extends JFrame {
 	 * @param fa the FASTA-formatted sequences to generate the shape scores from
 	 * @param out_dir the output directory to save output files to
 	 * @param type the shape types to generate
+	 * @param gzOutput Whether to output compressed file
 	 */
-	public DNAShapefromFASTAOutput(ArrayList<File> fa, File out_dir, boolean[] type) {
+	public DNAShapefromFASTAOutput(ArrayList<File> fa, File out_dir, boolean[] type, boolean gzOutput) {
 		setTitle("DNA Shape Prediction Composite");
 		setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
 		setBounds(150, 150, 800, 600);
@@ -70,6 +72,7 @@ public DNAShapefromFASTAOutput(ArrayList<File> fa, File out_dir, boolean[] type)
 		FASTA = fa;
 		OUT_DIR = out_dir;
 		OUTPUT_TYPE = type;
+		OUTPUT_GZIP = gzOutput;
 	}
 
 	/**
@@ -122,7 +125,7 @@ public void run() throws IOException, InterruptedException {
 			}
 
 			// Initialize Script Object and execute calculations
-			DNAShapefromFASTA script_obj = new DNAShapefromFASTA(FASTA.get(x), BASENAME, OUTPUT_TYPE, PS);
+			DNAShapefromFASTA script_obj = new DNAShapefromFASTA(FASTA.get(x), BASENAME, OUTPUT_TYPE, PS, OUTPUT_GZIP);
 			script_obj.run();
 
 			// Convert average and statistics to output tabs panes