public SQTLight(SQTScan scn)
{
if (scn == null)
{
}
else
{
ScanNumber = scn.ScanNumber;
Z = scn.ChargeState;
PeptideSequenceCleaned = scn.PeptideSequenceCleaned;
PrimaryScore = scn.PrimaryScore;
MeasuredMH = scn.MeasuredMH;
TheoreticalMH = scn.TheoreticalMH;
}
}
public SQTParser(string fileName)
{
int matchesToConsider = 2;
//Scan Example
//scan number, scan number, charge state, time used for search, computer name, measured M+H, total ion intensity, probability value, number of singleSearchCandidates,
//Match, primary rank, secondary rank, calculated M+H, delta CN, Primary Score, Secondary Score, peaks matched, peaks considered, peptide sequence, Manual Validation Status
//S 198 198 2 172 blacknote 1491.6589 39274362.53 0.0129 60284
//M 1 5 1491.6505 0.0000 1.4029 10.368 8 23 F.GAGLGGGYGGGFGSGFSS.S U
//L Reverse_contaminant_KERATIN08 PositionInAASequence
//L Reverse_contaminant_KERATIN05 PositionInAASequence
//M 2 21 1491.6789 0.0982 1.2651 6.559 5 15 S.LNQDSMLHYLEE.I U
//L Reverse_YLR398C PositionInAASequence
//M 155 1 1491.7039 0.5606 0.6164 11.649 8 17 F.DLKSDNSVKNNSGN.N U
//L Reverse_YKL112W PositionInAASequence
StreamReader sr = new StreamReader(fileName);
List <SQTScan> scanArray = new List <SQTScan>();
SQTScan s = new SQTScan();
//Used to make sure that we are only keeping the IDs from the first match
int lastMatch = 0;
int lineCounter = 0;
string[] scans = Ssplitter.Split(sr.ReadToEnd());
foreach (string scan in scans)
{
lineCounter++;
//try
//{
int matchOneCounter = 0;
List <string> line = Regex.Split(scan, "\r\n|\r|\n").ToList();;
line.RemoveAll(a => a.Equals(""));
for (int l = 0; l < line.Count; l++)
{
string[] cols = TabSplitter.Split(line[l]);
if (cols.Length == 1)
{
continue;
}
if (cols[0].Equals("H"))
{
if (cols[1].Equals("Database"))
{
database = cols[2];
continue;
}
else
{
continue;
}
}
if (l == 0)
{
scanArray.Add(s);
if (cols.Length < 8)
{
Console.WriteLine("Breaking on line " + lineCounter);
break;
}
s = new SQTScan(int.Parse(cols[1]), 0);
s.ChargeState = int.Parse(cols[3]);
s.ProbabilityValue = double.Parse(cols[8]);
s.MeasuredMH = double.Parse(cols[6]);
int numbOfCandidates;
if (int.TryParse(cols[9], out numbOfCandidates))
{
s.NumberOfCandidates = numbOfCandidates;
}
else
{
s.NumberOfCandidates = int.MaxValue;
}
}
else if (cols[0].Equals("M"))
{
int matchNo = int.Parse(cols[1]);
lastMatch = matchNo;
if (matchNo == 1)
{
matchOneCounter++;
s.PrimaryRank = int.Parse(cols[1]);
s.SecondaryRank = int.Parse(cols[2]);
s.TheoreticalMH = double.Parse(cols[3]);
s.DeltaCN = 0;
s.PrimaryScore = double.Parse(cols[5]);
s.SecondaryScore = double.Parse(cols[6]);
s.PeaksMatched = int.Parse(cols[7]);
s.PeaksConsidered = int.Parse(cols[8]);
s.PeptideSequence = cols[9].Replace(" ", "");
}
else if (matchNo > 1)
{
if (cols.Length == 11)
{
s.DeltaCN = double.Parse(cols[4]);
}
}
if (matchNo > matchesToConsider + 1)
{
break;
}
}
else if (cols[0].Equals("L"))
{
//Problematic line
//L Reverse_contaminant_gi|625237 15 DFV.TYYQRIFVD.GLI
if (lastMatch == 1)
{
string identificationName = cols[1];
//Column 1 holds the Locci
if (identificationName.StartsWith("IPI"))
{
string[] cols2 = Regex.Split(identificationName, " ");
identificationName = cols2[0];
}
s.IdentificationNames.Add(identificationName);
}
}
else if (cols[0].Length == 0)
{
//Skip this line
}
else
{
Console.WriteLine("Problematic line in sqt file " + fileName + "\nline content: " + line[l] + "\nLine # " + lineCounter);
Console.Beep();
//throw new Exception("Unrecognized line");
}
}
s.IdentificationNames = s.IdentificationNames.Distinct().ToList();
//This is to make sure that we don't have different peptides tied in first place
if (matchOneCounter == 1)
{
theScans.Add(s);
}
//}
//catch (Exception e7)
//{
// Console.WriteLine("Problem parsing scan.");
// Console.WriteLine(lineCounter);
//}
}
//The first index is bogus so we should remove it
scanArray.RemoveAll(a => string.IsNullOrEmpty(a.PeptideSequence));
}