private void uploadBedFile(){
		File peptideFile = new File(bedFile);
		//
		int id = 0;
		int chromosomeName = -1;
		int startLocation = -1;
		int stopLocation = -1;
		String sequence = "";
		String score = "";
		int strand = -1;
		String color = "";
		String blockCount = "";
		String blockSize = "";
		String blockStart = "";
		
		
		//Parse each line of the file and save it
		try{
			Scanner s = new Scanner(peptideFile);
			String token;
			
			//Parse each Line, one at a time
			while(s.hasNextLine()){
				
				if(!s.hasNext()){
					break;
				}
				 token = s.next();
				 /*Plug values from the fields array into variables*/
				if(token.equalsIgnoreCase("chrM")){
					chromosomeName = Definitions.chromosomeM;
				}else if(token.equalsIgnoreCase("chrX")){
					chromosomeName = Definitions.chromosomeX;
				}else if(token.equalsIgnoreCase("chrY")){
					chromosomeName = Definitions.chromosomeY;
				}else{
					chromosomeName = Integer.parseInt(token.substring(token.indexOf('r') + 1));
					
				}
					
				
				token = s.next();
				//Get the start location
				startLocation = Integer.parseInt(token);
				
				token = s.next();
				//Get the stop location
				stopLocation = Integer.parseInt(token);
				 
				//Get the amino acid sequence from the file
				token = s.next();
				sequence = token;
				
				//Get the first score from the file
				token = s.next();
				score = token;
				
				
				//Determine genomic strand
				token = s.next();
				if(token.equalsIgnoreCase("+")){
					strand = Definitions.genomicStrandPOSITIVE;
				}else {
					strand = Definitions.genomicStrandNEGATIVE;
				}
				
				//Skip the repeated start and stop location
				token = s.next();
				token = s.next();
				
				token = s.next();
				color = token;
				
				
				token = s.next();
				blockCount = token;
				
				token = s.next();
				blockSize = token;
				
				token = s.next();
				blockStart = token;
				
				//Add the newly read line into the peptideLocationList
				BEDlist.add(new BedFileLine(id ,chromosomeName, startLocation, stopLocation, sequence, score, strand, color, blockCount, blockSize, blockStart));
				
				id++;
				 //Reset all variables
				chromosomeName = -1;
				startLocation = -1;
				stopLocation = -1;
				sequence = "";
				score = "";
				strand = -1;
				color = "";
				blockCount = "";
				blockSize = "";
				blockStart = "";
				

			}//while

		//Let the user know if the bed file is not found	
		}catch(FileNotFoundException e){
			U.p("Error populating Bed File List: " + e);

		}//catch
	}//upLoadBedFile