format numeric literals

Add underscores for readability to numeric literals

Author: owlang

src/main/java/scriptmanager/objects/ArchTEx/CorrParameter.java

@@ -23,7 +23,7 @@ public class CorrParameter {
 	private boolean corrType = false; //Default randomly sample genome
 
 	//Random Sampling Parameters
-	private int windowSize = 50000;	//Default set Window frame for each extraction to 50kb
+	private int windowSize = 50_000;	//Default set Window frame for each extraction to 50kb
 	private int iterations = 10;	//Default set number of random iterations per chromosome
 
 	//TODO if time add resolution and window frame variables

src/main/java/scriptmanager/scripts/BAM_Statistics/BAMGenomeCorrelation.java

@@ -164,13 +164,13 @@ public double correlate(File exp1, File exp2) {
 			//System.err.println("Analyzing: " + seq.getSequenceName());
 
 			//Break chromosome into 100kb chunks and assign to independent nodes
-			int numwindows = (int) (seq.getSequenceLength() / 100000);
+			int numwindows = (int) (seq.getSequenceLength() / 100_000);
 			for(int x = 0; x < numwindows; x++) {
-				int start = x * 100000;
-				int stop = start + 100000;
+				int start = x * 100_000;
+				int stop = start + 100_000;
 				ChromosomeWindows.add(new CorrelationCoord(seq.getSequenceName(), start, stop));
 			}
-			int finalstart = numwindows * 100000;
+			int finalstart = numwindows * 100_000;
 			int finalstop = (seq.getSequenceLength() / BIN) * BIN;
 			ChromosomeWindows.add(new CorrelationCoord(seq.getSequenceName(), finalstart, finalstop));
 

src/main/java/scriptmanager/scripts/BAM_Statistics/CrossCorrelation.java

@@ -121,15 +121,15 @@ public static Component correlate(File bamFile, File output, CorrParameter param
 
 			} else {
 				//Break chromosome into 100kb chunks and assign to independent BLASTNodes
-				int numwindows = (int) (seq.getSequenceLength() / 100000);
+				int numwindows = (int) (seq.getSequenceLength() / 100_000);
 				int Resolution = param.getResolution();	// Resolution controls increment
 				int windowSize = param.getCorrWindow(); // Size of theoretical sliding window
 				for(int x = 0; x < numwindows; x++) {
-					int start = x * 100000;
-					int stop = start + 100000 + windowSize;
+					int start = x * 100_000;
+					int stop = start + 100_000 + windowSize;
 					ChromosomeWindows.add(new CorrNode(seq.getSequenceName(), start, stop));
 				}
-				int finalstart = numwindows * 100000;
+				int finalstart = numwindows * 100_000;
 				int finalstop = (seq.getSequenceLength() / Resolution) * Resolution;
 				ChromosomeWindows.add(new CorrNode(seq.getSequenceName(), finalstart, finalstop));
 			}