--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/datastructures/GenomeFrame.java	Mon Nov 21 08:12:19 2011 -0500
@@ -0,0 +1,87 @@
+package datastructures;
+
+import java.util.Vector;
+
+/**
+ * @author Ali Abdallah
+ * @version 01.2011
+ * @since jdk 1.6.0
+ */
+
+public class GenomeFrame extends Frame{
+	
+	int limit;
+	Vector<Integer> hits;
+
+	public GenomeFrame(int start, int length) {
+		super(start, length);
+		limit = end;
+		hits = new Vector<Integer>(length);
+		hits.setSize(length);
+		for(int i = 0; i < length; i++){
+			hits.set(i, 0);
+		}
+	}
+	
+	public int getHit(int base){
+		if(base-start < hits.size())
+			return hits.get(base-start);
+		else
+			return -1;
+	}
+	
+	public void setHit(int base, int bhits){
+		if(base-start < hits.size()){
+			hits.set(base-start, bhits);
+		}
+	}
+	
+	public boolean contains(ReadFrame r){
+		return (start <= r.start() && end >= r.end());
+	}
+	
+	public boolean overlaps(ReadFrame r){
+		return (end >= r.start() && end < r.end());
+	}
+	
+	
+	
+	public void addBases(int nr){
+		for(int i = 0; i < nr; i++){
+			hits.add(1);
+		}
+	}
+	
+	public String toString(){
+		return start+":"+end+" ("+limit+")";
+	}
+
+
+	public void updateHits(ReadFrame read) {
+		for(int base = read.start(); base <= read.end(); base++){
+			setHit(base, getHit(base)+1);
+		}
+	}
+
+	public void updateFrameFromRightEnd(ReadFrame readF) {
+		// TODO Auto-generated method stub
+		for(int i = end+1; i <= readF.end(); i++)
+			hits.add(0);
+		end = readF.end();	
+	}
+
+	public boolean limitExceeded(ReadFrame readF) {
+		return readF.start() > limit;
+	}
+
+	public void updateFrameFromBothEnds(ReadFrame readF, int length) {
+		for(int i = end-readF.start()+1; i < length; i++ )
+			hits.add(0);
+		for(int i = 0; i < readF.start()-start; i++)
+			hits.remove(0);
+		start = readF.start();
+		end = start+length-1;
+		limit = end;
+	}
+	
+}