public OutData(OutData.databases db, OutData.XCorrTypes _XCorrType)
{
dbType = db;
FileNameVal = "";
RAWFileVal = "";
ProteinDescriptionVal = "";
SequenceVal = "";
xcorrType = _XCorrType;
Score = double.NaN;
}
//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);
}
