add gzip support to in/out of SearchMotif

#91 contribution for the SearchMotif tool

CLI
- add new `-z` flag to output options
- update default output to use `.gz` extension
- update script call to include gzip output
script
- update input and output filestream object setup to dynamically handle if input is gzip compressed and gzip compress output if specified
Output
-update output window to add `.gz` extension as appropriate
-update script call to include gzip output
Window
-add gzip output checkbox option
-allow for `fa.gz` extension to be shown as options in the file selector
-update script call to include gzip output

src/cli/Sequence_Analysis/SearchMotifCLI.java

@@ -26,6 +26,8 @@ public class SearchMotifCLI implements Callable<Integer> {
 
 	@Option(names = { "-o", "--output" }, description = "Specify output filename (default = <motif>_<num>Mismatch_<fastaFilename>.bed)")
 	private File output = null;
+	@Option(names = {"-z", "--gzip"}, description = "gzip output (default=false)")
+	private boolean gzOutput = false;
 	@Option(names = { "-m", "--motif" }, required = true, description = "the IUPAC motif to search for")
 	private String motif;
 	@Option(names = { "-n", "--mismatches" }, description = "the number of mismatches allowed (default=0)")
@@ -41,7 +43,7 @@ public Integer call() throws Exception {
 			System.exit(1);
 		}
 
-		SearchMotif script_obj = new SearchMotif(fastaFile, motif, ALLOWED_MISMATCH, output, System.err);
+		SearchMotif script_obj = new SearchMotif(fastaFile, motif, ALLOWED_MISMATCH, output, System.err, gzOutput);
 		script_obj.run();
 
 		System.err.println("Search Complete.");
@@ -63,8 +65,10 @@ private String validateInput() throws IOException {
 		}
 		// set default output filename
 		if (output == null) {
-			output = new File(motif + "_" + Integer.toString(ALLOWED_MISMATCH) + "Mismatch_"
-					+ ExtensionFileFilter.stripExtension(fastaFile) + ".bed");
+			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 {
 			// check ext

src/scripts/Sequence_Analysis/SearchMotif.java

@@ -1,10 +1,11 @@
 package scripts.Sequence_Analysis;
 
+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.InputStream;
 import java.io.InputStreamReader;
 import java.io.PrintStream;
 import java.sql.Timestamp;
@@ -13,23 +14,29 @@
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.zip.GZIPInputStream;
+import java.util.zip.GZIPOutputStream;
+
+import util.GZipUtilities;
 
 public class SearchMotif {
 
 	private int ALLOWED_MISMATCH;
 	private Map<String, String> IUPAC_HASH = new HashMap<>();
 	private Map<String, String> RC_HASH = new HashMap<>();
 	private String motif;
-	private File INPUT = null;
-	private PrintStream OUT;
+	private File input;
+	private File out_filepath;
 	private PrintStream PS;
+	private boolean gzOutput;
 
-	public SearchMotif(File input, String mot, int num, File output, PrintStream ps) throws IOException {
+	public SearchMotif(File i, String mot, int num, File output, PrintStream ps, boolean gz) {
 		ALLOWED_MISMATCH = num;
 		motif = mot;
-		INPUT = input;
-		OUT = new PrintStream(output);
+		input = i;
+		out_filepath = output;
 		PS = ps;
+		gzOutput = gz;
 
 		IUPAC_HASH.put("A", "A");
 		IUPAC_HASH.put("T", "T");
@@ -63,7 +70,7 @@ public SearchMotif(File input, String mot, int num, File output, PrintStream ps)
 	}
 
 	public void run() throws IOException, InterruptedException {
-		PS.println("Searching motif: " + motif + " in " + INPUT.getName());
+		PS.println("Searching motif: " + motif + " in " + input.getName());
 		PS.println("Starting: " + getTimeStamp());
 
 		char[] ORIG = motif.toUpperCase().toCharArray();
@@ -90,10 +97,28 @@ public void run() throws IOException, InterruptedException {
 		int currentEND = 0;
 		String ID;
 
-		InputStream inputStream = new FileInputStream(INPUT);
-		BufferedReader lines = new BufferedReader(new InputStreamReader(inputStream), 100);
-		while (lines.ready()) {
-			String line = lines.readLine().trim();
+		// 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)));
+			}
+		}
+
+		// 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"));
+		}
+		// Initialize line variable to loop through
+		String line = br.readLine();
+		while (line != null) {
+			line = line.trim();
 			if (line.startsWith(">")) {
 				currentChrom = line.substring(1);
 				currentLine = "";
@@ -146,9 +171,10 @@ public void run() throws IOException, InterruptedException {
 				// System.out.println(tmp);
 				currentLine = tmp;
 			}
+			line = br.readLine();
 		}
-		inputStream.close();
-		lines.close();
+		br.close();
+		OUT.close();
 		PS.println("Completing: " + getTimeStamp());
 	}
 

src/window_interface/Sequence_Analysis/SearchMotifOutput.java

@@ -20,10 +20,11 @@ public class SearchMotifOutput extends JFrame {
 	private String motif;
 	private File INPUTFILE = null;
 	private File OUT_DIR;
+	private boolean gzOutput = false;
 
 	private JTextArea textArea;
 
-	public SearchMotifOutput(File input, String mot, int num, File out_dir) throws IOException {
+	public SearchMotifOutput(File input, String mot, int num, File out_dir, boolean gz) throws IOException {
 		setTitle("Motif Search Progress");
 		setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
 		setBounds(150, 150, 600, 800);
@@ -39,6 +40,7 @@ public SearchMotifOutput(File input, String mot, int num, File out_dir) throws I
 		motif = mot;
 		INPUTFILE = input;
 		OUT_DIR = out_dir;
+		gzOutput = gz;
 	}
 
 	public void run() throws IOException, InterruptedException {
@@ -48,8 +50,9 @@ public void run() throws IOException, InterruptedException {
 		if (OUT_DIR != null) {
 			BASENAME = OUT_DIR.getCanonicalPath() + File.separator + BASENAME;
 		}
+		BASENAME += gzOutput ? ".gz" : "";
 
-		SearchMotif script_obj = new SearchMotif(INPUTFILE, motif, ALLOWED_MISMATCH, new File(BASENAME), PS);
+		SearchMotif script_obj = new SearchMotif(INPUTFILE, motif, ALLOWED_MISMATCH, new File(BASENAME), PS, gzOutput);
 		script_obj.run();
 
 		Thread.sleep(2000);

src/window_interface/Sequence_Analysis/SearchMotifWindow.java

@@ -14,6 +14,7 @@
 
 import javax.swing.DefaultListModel;
 import javax.swing.JButton;
+import javax.swing.JCheckBox;
 import javax.swing.JFileChooser;
 import javax.swing.JFrame;
 import javax.swing.JLabel;
@@ -43,6 +44,7 @@ public class SearchMotifWindow extends JFrame implements ActionListener, Propert
 	private JPanel contentPane;
 	private JTextField txtMotif;
 	private JTextField txtMismatch;
+	private static JCheckBox chckbxGzipOutput;
 	private JProgressBar progressBar;
 
 	public Task task;
@@ -64,7 +66,7 @@ public Void doInBackground() throws IOException, InterruptedException {
 					setProgress(0);
 					for (int gfile = 0; gfile < GenomeFiles.size(); gfile++) {
 						SearchMotifOutput search = new SearchMotifOutput(GenomeFiles.get(gfile), txtMotif.getText(),
-								Integer.parseInt(txtMismatch.getText()), OUT_DIR);
+								Integer.parseInt(txtMismatch.getText()), OUT_DIR, chckbxGzipOutput.isSelected());
 						search.setVisible(true);
 						search.run();
 						int percentComplete = (int) (((double) (gfile + 1) / (GenomeFiles.size())) * 100);
@@ -122,6 +124,11 @@ public void actionPerformed(ActionEvent e) {
 		});
 		contentPane.add(btnOutputDirectory);
 
+		chckbxGzipOutput = new JCheckBox("Output GZIP");
+		sl_contentPane.putConstraint(SpringLayout.NORTH, chckbxGzipOutput, 0, SpringLayout.NORTH, btnOutputDirectory);
+		sl_contentPane.putConstraint(SpringLayout.EAST, chckbxGzipOutput, -10, SpringLayout.EAST, contentPane);
+		contentPane.add(chckbxGzipOutput);
+
 		JLabel lblCurrentOutput = new JLabel("Current Output:");
 		sl_contentPane.putConstraint(SpringLayout.NORTH, lblNewLabel, 5, SpringLayout.SOUTH, lblCurrentOutput);
 		sl_contentPane.putConstraint(SpringLayout.NORTH, lblCurrentOutput, 6, SpringLayout.SOUTH, btnOutputDirectory);
@@ -182,7 +189,7 @@ public void actionPerformed(ActionEvent e) {
 
 		btnLoadFASTA.addActionListener(new ActionListener() {
 			public void actionPerformed(ActionEvent e) {
-				File[] newGenomeFiles = FileSelection.getFiles(fc, "fa");
+				File[] newGenomeFiles = FileSelection.getFiles(fc, "fa", true);
 				if (newGenomeFiles != null) {
 					for (int x = 0; x < newGenomeFiles.length; x++) {
 						GenomeFiles.add(newGenomeFiles[x]);