private void parseUnMod(){
		//Only read in lines up to the breakAt point.  This is useful for debugging.
		int breakAt = -1;
		int count = 0;
		
		try {
			Scanner s = new Scanner(new File(inputFile));
			String token = "";
			//Skip the header
			for(int i = 0; i < 4; i++){
				token = s.nextLine();
			}
			
			
			//Parse information for each line
			int index = 0;
			int ID = -1;
			int SpectrumID = -1;
			String MD5 = "";
			String FileName = "";
			double score = -1;
			double PrecursorMZ = -1;
			double PrecursorNeutralMass = -1;
			double eValue = -1;
			String peptideSequence = "";
			int start = -1;
			int stop = -1;
			String sequenceFile = "";
			String sequenceDescription = "";
			int intronStart = -1;
			int intronStop = -1;
			int strand = -1;
			boolean isSpliced = false;
			int matchRank = -1;
			int RankCount = -1;
			int IonCount = -1;
			boolean labeled = false;
			int charge = -1; 
			int cleavageAcidCount = -1;
			boolean inORF = false;
			double hydrophobic = -1;
			double hydrophilic = -1;
			boolean isModified = false;
			double modMass = 0;
			int modIndex = -1;

			/*Parse each line*/
			while(s.hasNextLine()){
				
				//Once a line without any content on it is reached, consider the file over
				if(!s.hasNext()){
					break;
				}
				//Get the ID
				token = s.next();
				ID = Integer.parseInt(token);
				
				//Get the SpectrumID
				token = s.next();
				SpectrumID = Integer.parseInt(token);
				
				//Get the MD5
				token = s.next();
				MD5 = token;
				
				//Get the fileName
				token = s.next();
				FileName = token;

				//Get the score
				token = s.next();
				score = Double.parseDouble(token);

				//Get the PrecursorMZ
				token = s.next();
				PrecursorMZ = Double.parseDouble(token);

				//Get the PrecursorNeutralMass
				token = s.next();
				PrecursorNeutralMass = Double.parseDouble(token);

				//Get the eValue
				token = s.next();
				eValue = Double.parseDouble(token);

				//Get the peptideSequence
				token = s.next();
				peptideSequence = token;

				
				//Get the start
				token = s.next();
				start = Integer.parseInt(token);

				
				//Get the stop
				token = s.next();
				stop = Integer.parseInt(token);

				
				
				//Get the sequence File
				token = s.next();
				sequenceFile = token;

				
				//Get the sequence description
				token = s.next();
				sequenceDescription = token;

				
				
				//Get the Intron-Start
				token = s.next();
				intronStart = Integer.parseInt(token);

				
				//Get the Intron-Stop
				token = s.next();
				intronStop = Integer.parseInt(token);

				
				//Get the Strand
				token = s.next();
				if(token.equals("+")){
					strand = Definitions.genomicStrandPOSITIVE;
				}else{
					strand = Definitions.genomicStrandNEGATIVE;
				}

				
				//Get the isSpliced
				token = s.next();
				isSpliced = Boolean.valueOf(token);

				
				//Get the matchRank
				token = s.next();
				matchRank = Integer.parseInt(token);

				//Get the RankCount
				token = s.next();
				RankCount = Integer.parseInt(token);
				
				//Get the IonCount
				token = s.next();
				IonCount = Integer.parseInt(token);
				
				
				//Get the labeled column value
				token = s.next();
				labeled = Boolean.valueOf(token);
				
				//Get the charge
				token = s.next();
				charge = Integer.parseInt(token);
				
				//Get the cleavage acid count
				token = s.next();
				cleavageAcidCount = Integer.parseInt(token);
				
				//Get the inORF
				token = s.next();
				inORF = Boolean.valueOf(token);
				
				//Get the hydrophobic
				token = s.next();
				hydrophobic = Double.valueOf(token);
				
				//Get the Hydrophilic
				token = s.next();
				hydrophilic = Double.valueOf(token);
				
				//get the isModified
				token = s.next();
				isModified = Boolean.valueOf(token);
				
				//get the modMass
				token = s.next();
				modMass = Double.valueOf(token);
				
				
				//get the mod Index
				token = s.next();
				modIndex = Integer.valueOf(token);
				
				s.nextLine();
				
				
				if(matchRank <= maxMatchRank){
					//List of the peppy input file lines
					PeppyLine pl = new PeppyLine(ID, SpectrumID, MD5, FileName, score, PrecursorMZ, PrecursorNeutralMass, eValue, peptideSequence, start, stop, sequenceFile, sequenceDescription, intronStart, intronStop, strand, isSpliced, matchRank, RankCount, IonCount, labeled, charge,
					        cleavageAcidCount, inORF, hydrophobic, hydrophilic, isModified, modMass, modIndex);
					pl.setIndex(index);
					pl.setDna(true);
					PeppyList.add(pl);
					index++;
//					U.p(index);
				}else{
					matchRankFiltered.add(new PeppyLine(ID, SpectrumID, MD5, FileName, score, PrecursorMZ, PrecursorNeutralMass, eValue, peptideSequence, start, stop, sequenceFile, sequenceDescription, intronStart, intronStop, strand, isSpliced, matchRank, RankCount, IonCount, labeled, charge,
							        cleavageAcidCount, inORF, hydrophobic, hydrophilic, isModified, modMass, modIndex));
				}
				
//				U.p(PeppyList.get(PeppyList.size() - 1).toString());
				//Reset the default values
				ID = -1;
				SpectrumID = -1;
				MD5 = "";
				FileName = "";
				score = -1;
				PrecursorMZ = -1;
				PrecursorNeutralMass = -1;
				eValue = -1;
				peptideSequence = "";
				start = -1;
				stop = -1;
				sequenceFile = "";
				sequenceDescription = "";
				intronStart = -1;
				intronStop = -1;
				strand = -1;
				isSpliced = false;
				matchRank = -1;
				RankCount = -1;
				IonCount = -1;
				labeled = false;
				charge = -1; 
				cleavageAcidCount = -1;
				inORF = false;
				hydrophobic = -1;
				hydrophilic = -1;
				isModified = false;
				modMass = 0;
				modIndex = -1;
				
				//DEBUGGING BREAK
				if(count == breakAt){
					U.p("Breaking early in the peptide list, with a break early value of " + breakAt);
					break;
				}
				
				count++;
			}//While has next line
			
		//File is not found.
		} catch (FileNotFoundException e) {
			// TODO Auto-generated catch block
			e.printStackTrace();
		//Throw an error when a unparsable token is read in.
		} catch (NoSuchElementException e) {
			U.p("Invalid file.  Unable to completely parse input.  Output will not contain all peptides.");
		}//catch
		
	}//parseUnMod