--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/datastructures/ReducedReadLine.java	Mon Nov 21 08:12:19 2011 -0500
@@ -0,0 +1,89 @@
+package datastructures;
+
+import java.util.Scanner;
+import exceptions.ChromosomeFormatException;
+import exceptions.ChromosomeNotFoundException;
+import exceptions.RangeFormatException;
+import exceptions.RangeLimitNotFoundException;
+
+/**
+ * Represents a read Line from the read alignment file.
+ * 
+ * @author Ali Abdallah
+ * @version 22.07.2011
+ * @since Java 1.6
+ */
+public class ReducedReadLine implements Line{
+
+	String line;
+	String rName;
+	String chrom;
+	int start, end;
+	
+	public ReducedReadLine(String line) throws ChromosomeFormatException, 
+										ChromosomeNotFoundException, 
+										RangeFormatException, 
+										RangeLimitNotFoundException{
+		this.line = line;
+		Scanner s = new Scanner(line);
+		if(s.hasNext())
+			rName = s.next();
+		if(s.hasNext()){
+			chrom = s.next(); 
+			if(!(chrom.toLowerCase().startsWith("chr") || chrom.equals("*")))
+				throw new ChromosomeFormatException(chrom);
+		}
+		else
+			throw new ChromosomeNotFoundException();
+		
+		if(s.hasNextInt()){
+			start = s.nextInt();
+			if(start < 0){
+				throw new RangeFormatException("Start position must be a positive integer.");
+			}
+		}
+		else if(!s.hasNext())
+			throw new RangeLimitNotFoundException("No range start found!");
+		else	
+			throw new RangeFormatException("Found: "+start+". Start position ist not an integer. " +
+									 "It must be a positive integer.");
+		
+		if(s.hasNextInt()){
+			end = s.nextInt();
+			if(end < 0){
+				throw new RangeFormatException("End position must be a positive integer.");
+			}
+		}
+		else if(!s.hasNext())
+			throw new RangeLimitNotFoundException("No range end found!");
+		else	
+			throw new RangeFormatException("Found: "+end+". End position ist not an integer. " +
+									 "It must be a positive integer.");
+	}
+	
+	public String chrom(){
+		return chrom;
+	}
+	
+	public int start(){
+		return start;
+	}
+	
+	public int end(){
+		return end;
+	}
+	
+	public String toString(){
+		return line;
+	}
+	
+	public boolean isForwardRead(){
+		return start <= end;
+	}
+
+	public String name() {
+		// TODO Auto-generated method stub
+		return rName;
+	}
+	
+}