Update scripts to check GZip using MAGIC bytes

Use the new GZipUtilities class to check for GZip file format in both ShiftInterval/Shift coord tool and the Two-color heatmap tool (#88). Remove unnecessary imports along the way.

Author: owlang

src/scripts/Coordinate_Manipulation/ShiftCoord.java

@@ -11,7 +11,8 @@
 import java.util.Arrays;
 import java.util.zip.GZIPInputStream;
 import java.util.zip.GZIPOutputStream;
-import java.util.zip.ZipException;
+
+import util.GZipUtilities;
 
 /**
  * This class contains scripts for shifting coordinate intervals (BED/GFF) by a user-defined direction and distance.
@@ -43,9 +44,9 @@ public static void shiftBEDInterval(File out_filepath, File input, int SHIFT, bo
 		}
 		// Assume file is gzipped and create normal BufferedReader if not
 		BufferedReader br;
-		try {
+		if(GZipUtilities.isGZipped(input)) {
 			br = new BufferedReader(new InputStreamReader(new GZIPInputStream(new FileInputStream(input)), "UTF-8"));
-		} catch (ZipException e) {
+		} else {
 			br = new BufferedReader(new InputStreamReader(new FileInputStream(input), "UTF-8"));
 		}
 		// Initialize line variable to loop through
@@ -112,9 +113,9 @@ public static void shiftGFFInterval(File out_filepath, File input, int SHIFT, bo
 		}
 		// Assume file is gzipped and create normal BufferedReader if not
 		BufferedReader br;
-		try {
+		if(GZipUtilities.isGZipped(input)) {
 			br = new BufferedReader(new InputStreamReader(new GZIPInputStream(new FileInputStream(input)), "UTF-8"));
-		} catch (ZipException e) {
+		} else {
 			br = new BufferedReader(new InputStreamReader(new FileInputStream(input), "UTF-8"));
 		}
 		// Initialize line variable to loop through

src/scripts/Figure_Generation/TwoColorHeatMap.java

@@ -13,16 +13,15 @@
 import java.io.InputStreamReader;
 import java.io.UnsupportedEncodingException;
 import java.util.ArrayList;
-import java.util.Arrays;
 import java.util.Collections;
-import java.util.Scanner;
 import java.util.zip.GZIPInputStream;
-import java.util.zip.ZipException;
 
 import javax.imageio.ImageIO;
 import javax.swing.ImageIcon;
 import javax.swing.JLabel;
 
+import util.GZipUtilities;
+
 public class TwoColorHeatMap {
 
 	protected static File SAMPLE = null;
@@ -370,9 +369,9 @@ public static ArrayList<double[]> loadMatrix(File input) throws UnsupportedEncod
 		int currentRow = 0;
 		// Assume file is gzipped and create normal BufferedReader if not
 		BufferedReader br;
-		try {
+		if(GZipUtilities.isGZipped(input)) {
 			br = new BufferedReader(new InputStreamReader(new GZIPInputStream(new FileInputStream(input)), "UTF-8"));
-		} catch (ZipException e) {
+		} else {
 			br = new BufferedReader(new InputStreamReader(new FileInputStream(input), "UTF-8"));
 		}
 		// Initialize line variable to loop through