private void ms2mgf_TextChanged(object sender, EventArgs e)
{
firstTitle = Mgfutils.getFirstTitle(this.ms2mgf.Text.Trim());
this.titleLbl.Text = firstTitle;
this.mgfParser.Enabled = true;
}
private void scanFieldsBox_SelectedIndexChanged(object sender, EventArgs e)
{
ListBox.SelectedIndexCollection selection = this.scanFieldsBox.SelectedIndices;
//scanField = new int[selection.Count];
for (int i = 0; i < selection.Count; i++)
{
scanField = (int)selection[i];
}
this.scanNumberResTxt.Text = Mgfutils.getScanNumber(firstTitle, split_chars, scanField).ToString();
locateMS2precMasses = true;
}
public static ArrayList getMHplusFromMgf(ArrayList identifications,
string mgffolder,
char[] split_chars,
int scanField)
{
string titleID = "TITLE";
string chargeID = "CHARGE";
string pepMassID = "PEPMASS";
float protonMass = 1.007F;
//Declaration of a comparer for OutData by key (RAWfilename, ScanNumber, charge)
OutData.OutsComparer cmpKey = new OutData.OutsComparer();
cmpKey.WhichComparison = OutData.OutsComparer.ComparisonType.key;
//Sort up the identifications by the key comparer
identifications.Sort(cmpKey);
ArrayList identificationsWithMassCorrected = new ArrayList();
FileInfo file = new FileInfo(mgffolder);
DirectoryInfo di = new DirectoryInfo(mgffolder);
FileInfo[] files = di.GetFiles("*.mgf");
OutData firstId = (OutData)identifications[0];
string previousMgf = di.FullName + "\\" + firstId.RAWFile;
StreamReader sr = new StreamReader(previousMgf);
string line = "";
for (int i = 0; i < identifications.Count; i++)
{
OutData currId = (OutData)identifications[i];
//Check wether we need to open a new file or not
if (currId.RAWFile != previousMgf)
{
sr.Close();
sr = new StreamReader(di.FullName + "\\" + currId.RAWFile);
previousMgf = di.FullName + "\\" + currId.RAWFile;
//read the file, and locate the desired scannumber (MS2 previous to the id in MS3)
try
{
while (sr.Peek() != -1)
{
line = sr.ReadLine();
if (line.ToUpper().Contains(titleID))
{
//obtain the scannumber of the current spectrum
int tentativeScanNumberMS2 = Mgfutils.getScanNumber(line, split_chars, scanField);
//We need the PREVIOUS scannumber
int tentativeScanNumberMS3 = tentativeScanNumberMS2 + 1;
//get the charge of the spectrum
int charge = 0;
line = sr.ReadLine();
if (line.ToUpper().Contains(chargeID))
{
string[] charge_sp = line.Split('=', '+');
charge = int.Parse(charge_sp[1].Trim());
}
//is this spectrum in our list??
OutData spectrumToFind = new OutData(OutData.databases.Target, OutData.XCorrTypes.normalized);
spectrumToFind.RAWFile = currId.RAWFile;
spectrumToFind.FirstScan = tentativeScanNumberMS3;
spectrumToFind.Charge = currId.Charge;
int specFoundPos = identifications.BinarySearch(spectrumToFind, cmpKey);
if (specFoundPos > -1)
{
bool massLocated = false;
while (!massLocated)
{
line = sr.ReadLine();
if (line.ToUpper().Contains(pepMassID))
{
massLocated = true;
string[] pepMass_split = line.Split('=');
float mz = float.Parse(pepMass_split[1]);
OutData spectrumToSwapMass = (OutData)identifications[specFoundPos];
float MHp = mz * charge - (charge - 1) * protonMass;
spectrumToSwapMass.MHp = MHp;
spectrumToSwapMass.Charge = (short)charge;
identificationsWithMassCorrected.Add(spectrumToSwapMass);
identifications.RemoveAt(specFoundPos);
}
}
}
}
}
}
catch { }
}
}
return(identificationsWithMassCorrected);
}
public static void getMHplusFromMgf(string QuiXMLfile,
string XMLschema,
string mgffolder,
char[] split_chars,
int scanField,
bool swapMgfRaw)
{
string titleID = "TITLE";
string chargeID = "CHARGE";
string pepMassID = "PEPMASS";
float protonMass = 1.007F;
//Open the QuiXML file created
DataSet ds = new DataSet();
ds.ReadXmlSchema(XMLschema);
//ds.ReadXmlSchema(CSVtoQuiXML.Properties.Settings.Default.idSchema);
ds.ReadXml(QuiXMLfile);
DataView dv = new DataView(ds.Tables["peptide_match"]);
DataView dvFiltered = new DataView(ds.Tables["peptide_match"]);
//sort the dataset by RAWfilename, ScanNumber, charge
dv.Sort = "RawFileName, FirstScan, Charge";
DataRowView firstId = dv[0];
FileInfo file = new FileInfo(mgffolder);
DirectoryInfo di = new DirectoryInfo(mgffolder);
FileInfo[] files = di.GetFiles("*.mgf");
string previousMgf = di.FullName + "\\" + dv[0]["RawFileName"].ToString();
StreamReader sr = new StreamReader(previousMgf);
string line = "";
for (int i = 0; i < dv.Count; i++)
{
//Check wether we need to open a new file or not
if (dv[i]["RawFileName"].ToString() != previousMgf)
{
sr.Close();
sr = new StreamReader(di.FullName + "\\" + dv[i]["RawFileName"].ToString());
previousMgf = di.FullName + "\\" + dv[i]["RawFileName"].ToString();
//read the file, and locate the desired scannumber (MS2 previous to the id in MS3)
try
{
while (sr.Peek() != -1)
{
line = sr.ReadLine();
if (line.ToUpper().Contains(titleID))
{
//obtain the scannumber of the current spectrum
int tentativeScanNumberMS2 = Mgfutils.getScanNumber(line, split_chars, scanField);
//We need the PREVIOUS scannumber
int tentativeScanNumberMS3 = tentativeScanNumberMS2 + 1;
//get the charge of the spectrum
int charge = 0;
line = sr.ReadLine();
if (line.ToUpper().Contains(chargeID))
{
string[] charge_sp = line.Split('=', '+');
charge = int.Parse(charge_sp[1].Trim());
}
//is this spectrum in our list??
dvFiltered.RowFilter = "rawfilename = '" + dv[i]["RawFileName"].ToString()
+ "' and firstscan =" + dv[i]["FirstScan"].ToString()
+ " and charge = " + dv[i]["Charge"].ToString();
if (dvFiltered.Count > 0)
{
bool massLocated = false;
while (!massLocated)
{
line = sr.ReadLine();
if (line.ToUpper().Contains(pepMassID))
{
massLocated = true;
string[] pepMass_split = line.Split('=');
float mz = float.Parse(pepMass_split[1]);
float MHp = mz * charge - (charge - 1) * protonMass;
dvFiltered[0]["Charge"] = charge;
dvFiltered[0]["PrecursorMass"] = MHp;
}
}
}
}
}
}
catch { }
}
}
//swapping .mgf to .raw
if (swapMgfRaw)
{
dv.RowFilter = "";
dv.Sort = "";
for (int i = 0; i < dv.Count; i++)
{
string strold = dv[i]["RawFileName"].ToString();
string strnew = strold.Replace(".mgf", ".RAW");
strnew = strnew.Replace(".MGF", ".RAW");
dv[i]["RawFileName"] = strnew;
}
}
ds.WriteXml(QuiXMLfile);
}