--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/datastructures/TargetLine.java	Mon Nov 21 08:12:19 2011 -0500
@@ -0,0 +1,87 @@
+package datastructures;
+
+import java.util.Scanner;
+
+import exceptions.ChromosomeFormatException;
+import exceptions.ChromosomeNotFoundException;
+import exceptions.NullOrNegativeRangeException;
+import exceptions.RangeFormatException;
+import exceptions.RangeLimitNotFoundException;
+
+/**
+ * Represents a target Line from the target file.
+ * 
+ * @author Ali Abdallah
+ * @version 19.07.2011
+ * @since Java 1.6
+ */
+
+public class TargetLine {
+	
+	String line;
+	String chrom;
+	int start, end;
+
+	public TargetLine(String line) throws 	RangeFormatException, 
+											ChromosomeFormatException, 
+											ChromosomeNotFoundException, 
+											RangeLimitNotFoundException, 
+											NullOrNegativeRangeException {
+		this.line = line;
+		Scanner s = new Scanner(line);
+		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 of the target must be a " +
+										 "positive integer.");
+			}
+		}
+		else if(!s.hasNext())
+			throw new RangeLimitNotFoundException("No target range start found!");
+		else	
+			throw new RangeFormatException("Target start position" +
+									 " is not an integer. It must be a positive" +
+									 " integer."+ " Found: "+start);
+		
+		if(s.hasNextInt()){
+			end = s.nextInt();
+			if(end < 0){
+				throw new RangeFormatException("Target end position must be a positive " +
+										 "integer."+ " Found: "+end);
+			}
+		}
+		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.");
+		
+		if(start >= end)
+			throw new NullOrNegativeRangeException("Target line \""+line+"\"");
+	}
+	
+	public String chrom(){
+		return chrom;
+	}
+	
+	public int start(){
+		return start;
+	}
+	
+	public int end(){
+		return end;
+	}
+	
+	public String toString(){
+		return line;
+	}
+	
+}