private void loadPP(File file){

		StringBuffer sequence = new StringBuffer();
		String transID = "";
		String geneID = "";

		try {
			Scanner s = new Scanner(file);
			String token;
			int arrowCount = 0;
			int i = 0;
			while(s.hasNextLine()){
				//Ensure that a valid line is coming up next.  THIS IS IMPORTANT****  OTHERWISE IF THE LAST PROTEIN CONTAINS A EVEN NUMBER OF LINES THIS METHOD WILL THROW AN EXCEPTION.
				if(s.hasNext()){
					token = s.next();
				}else{
					break;
				}//else
				

				//Skip header information that is not important
				if(token.contains(">")){
					if(arrowCount < 2){
						arrowCount++;
						s.nextLine();
						continue;
					}//if
					arrowCount = 0;
				}//if

				token = s.nextLine();
				token = token.trim();
				
				transID = token.substring(0, token.indexOf("|"));
				geneID = token.substring(transID.length() + 1, token.length() - 1);

				//Loop through and pull out the protein from the fasta file.
				token = s.nextLine();
				while(token.length() > 0){
					sequence.append(token.toUpperCase());
					token = s.nextLine();
				}//while	

				ppTransList.add(new Translation(geneID, transID, sequence.toString()));
				 	
				sequence = new StringBuffer();
				transID = "";
				geneID = "";
				if(i % 1000 == 0){
					i++;
				}//if
				i++;
			}//while
			
			U.p("Total number of P.P. Translations read in: " + ppTransList.size());
			
		} catch (FileNotFoundException e) {
			e.printStackTrace();
		}//catch
		
		
	}//loadPP