--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/middlewares/ReadCounter.java	Mon Nov 21 08:12:19 2011 -0500
@@ -0,0 +1,33 @@
+package middlewares;
+/**
+ * Counter for the reads on targets (+/- 0/100/200) and the reads overlapping 
+ * targets (+/- 0/100/200).
+ *  
+ * @author Ali Abdallah
+ * @version 14.07.2011
+ * @since jdk 1.6.0
+ */
+public class ReadCounter {
+
+	// Self explanatory.
+	private int on, on100, on200, over, over100, over200;
+
+	public ReadCounter(){on=0; on100=0; on200=0; over=0; over100=0; over200=0;}
+	
+	public void incOn(){on++;}
+	public void incOn100(){on100++;}
+	public void incOn200(){on200++;}
+	
+	public void incOver(){over++;}
+	public void incOver100(){over100++;}
+	public void incOver200(){over200++;}
+	
+	public int on(){return on;}
+	public int on100(){return on100;}
+	public int on200(){return on200;}
+
+	public int over(){return over;}
+	public int over100(){return over100;}
+	public int over200(){return over200;}
+
+}