// Special implementation to be called by custom comparer
public int CompareTo(
OutData rhs,
OutData.OutsComparer.ComparisonType which)
{
switch (which)
{
case OutData.OutsComparer.ComparisonType.Xcorr1:
return(this.Xcorr1.CompareTo(rhs.Xcorr1));
case OutData.OutsComparer.ComparisonType.XcorrRandomVSXcorr1:
return(this.Xcorr1.CompareTo(rhs.XcorrRandom));
case OutData.OutsComparer.ComparisonType.XcorrRandomVSXcorrRandom:
return(this.XcorrRandom.CompareTo(rhs.XcorrRandom));
case OutData.OutsComparer.ComparisonType.pRatio:
return(this.pRatio.CompareTo(rhs.pRatio));
case OutData.OutsComparer.ComparisonType.FDR:
return(this.FDR.CompareTo(rhs.FDR));
case OutData.OutsComparer.ComparisonType.RAWfile:
return(this.RAWFile.CompareTo(rhs.RAWFile));
case OutData.OutsComparer.ComparisonType.key:
{
int result = 0;
result = this.RAWFile.CompareTo(rhs.RAWFile);
if (result != 0)
{
return(result);
}
result = this.FirstScan.CompareTo(rhs.FirstScan);
if (result != 0)
{
return(result);
}
result = this.Charge.CompareTo(rhs.Charge);
if (result != 0)
{
return(result);
}
return(result);
}
case OutData.OutsComparer.ComparisonType.RnkXc1:
return(this.rnkXc1.CompareTo(rhs.rnkXc1));
}
return(0);
}
public static ArrayList substituteExtension(ArrayList _identifications,
string _oldExtension,
string _newExtension)
{
ArrayList substituted = new ArrayList(_identifications.Count);
for (int i = 0; i < _identifications.Count; i++)
{
OutData currId = (OutData)_identifications[i];
currId.RAWFile = currId.RAWFile.Replace(_oldExtension, _newExtension);
substituted.Add(currId);
}
return(substituted);
}
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 test()
//{
// string[] txtFiles = new string[1];
// txtFiles[0] = "I:\\wrk\\iTRAQ_estadistica\\samples\\datos_abian\\Salida_Peptidos_Filtrados.txt";
// OutData.databases whichDB = OutData.databases.Target;
// ArrayList testing = readTXT(txtFiles, whichDB);
//}
public static ArrayList readTXT(string[] txtFiles,
string[] readingOrder,
OutData.databases whichDB)
{
ArrayList outsList = new ArrayList();
//FormHeaderSelection frmHeader = new FormHeaderSelection();
//frmHeader.Show();
foreach (string file in txtFiles)
{
try
{
StreamReader sr = new StreamReader(File.OpenRead(file));
ArrayList myAL = new ArrayList();
try
{
while (sr.Peek() != -1) //equivalente a feof en C
{
myAL.Add(sr.ReadLine());
}
}
catch
{
//Console.WriteLine(" Parse error: " + e);
}
//int r = myAL.Count;
//object ob = (object)myAL[0];
//myAL.Remove(ob);
foreach (object o in myAL)
{
try
{
OutData sd = new OutData(whichDB, OutData.XCorrTypes.regular);
int RAWFilePos = findInArray(readingOrder, "*RAW file name");
int FirstScanPos = findInArray(readingOrder, "*FirstScan [- LastScan]");
int LastScanPos = findInArray(readingOrder, "LastScan");
int ProteinDescriptionPos = findInArray(readingOrder, "*Protein description");
int MHpPos = findInArray(readingOrder, "MH+");
int deltaMPos = findInArray(readingOrder, "DeltaM");
int ChargePos = findInArray(readingOrder, "*Charge");
int SequencePos = findInArray(readingOrder, "*Sequence");
int PpepPos = findInArray(readingOrder, "P (pep)");
int Xcorr1Pos = findInArray(readingOrder, "Xcorr1");
//int Xcorr2Pos = findInArray(readingOrder, "Xcorr2");
int DeltaCnPos = findInArray(readingOrder, "DeltaCn");
int SpPos = findInArray(readingOrder, "Sp");
int SpRankPos = findInArray(readingOrder, "Sp Rank");
int ionsPos = findInArray(readingOrder, "Ions");
int XcTeoricPos = findInArray(readingOrder, "XcTeoric");
int ScorePos = findInArray(readingOrder, "Score");
sd.FileName = file;
string[] str;
str = Regex.Split(o.ToString(), "\t");
sd.RAWFile = str[RAWFilePos];
string[] scans = Regex.Split(str[FirstScanPos], "-");
sd.FirstScan = int.Parse(scans[0]);
if (scans.Length > 1)
{
sd.LastScan = int.Parse(scans[scans.Length - 1]);
}
else
{
sd.LastScan = sd.FirstScan;
}
// If there is a specific column for the LastScan, then it is overwritten in next file
if (LastScanPos != -1)
{
sd.LastScan = int.Parse(str[LastScanPos]);
}
sd.ProteinDescription = str[ProteinDescriptionPos];
if (MHpPos != -1)
{
sd.MHp = float.Parse(str[MHpPos]);
}
sd.PrecursorMass = float.Parse(str[MHpPos]);
if (deltaMPos != -1)
{
sd.deltaM = float.Parse(str[deltaMPos]);
}
sd.Charge = short.Parse(str[ChargePos]);
// Sequence is written only if selected
if (SequencePos != -1)
{
sd.Sequence = str[SequencePos];
}
if (PpepPos != -1)
{
sd.Ppep = float.Parse(str[PpepPos]);
}
if (Xcorr1Pos != -1)
{
sd.Xcorr1 = float.Parse(str[Xcorr1Pos]);
}
if (DeltaCnPos != -1)
{
sd.DeltaCn = float.Parse(str[DeltaCnPos]);
sd.Xcorr2 = sd.Xcorr1Search * (1 - sd.DeltaCn);
sd.XcorrRandom = sd.Xcorr2;
}
if (SpPos != -1)
{
sd.Sp = float.Parse(str[SpPos]);
}
if (SpRankPos != -1)
{
sd.SpRank = short.Parse(str[SpRankPos]);
}
if (ionsPos != -1)
{
string[] ions = str[ionsPos].Split('/');
sd.IonsMatched = short.Parse(ions[0]);
if (ions.Length > 1)
{
sd.IonsCompared = short.Parse(ions[ions.Length - 1]);
}
}
if (ScorePos != -1)
{
sd.Score = double.Parse(str[ScorePos]);
}
if (XcTeoricPos != -1)
{
sd.XcTeoric = float.Parse(str[XcTeoricPos]);
}
// Here to implement redundances
//int numOfReds = 3;
//Redundance[] allReds = new Redundance[numOfReds];
//Redundance myRed = new Redundance();
//allReds[0].FASTAIndex = 12345;
//allReds[0].FASTAProteinDescription = "la proteina que le falta al Marco";
//sd.Redundances = (Redundance[]) allReds.Clone();
outsList.Add(sd);
}
catch { }
}
sr.Close();
}
catch
{
}
}
return(outsList);
}
public int CompareTo(Object rhs)
{
OutData r = (OutData)rhs;
return(this.Xcorr1.CompareTo(r.Xcorr1));
}