//This is used to read a ResultFile
public List<ResultsGroup> ReadResultsFromFile(String path)
{
//This code looks int, but its just repetitive code. Look for ext and you will understand.
List<ResultsGroup> Ans = new List<ResultsGroup>();
List<String> molnames = new List<String>();
FileStream FS = new FileStream(path, FileMode.Open, FileAccess.Read);
StreamReader read = new StreamReader(FS);
String ext = Path.GetExtension(path).Replace(".", "");
if (ext == "csv")
{
String header = read.ReadLine();
String[] headers = header.Split(',');
List<string> elementIDs = new List<string>();
//This is another older form of data
if (headers[5] != "Hypothesis MW")
{
Boolean moreCompounds = true;
int i = 17;
while (moreCompounds)
{
if (headers[i] != "Hypothesis MW")
{
elementIDs.Add(headers[i]);
i++;
}
else
{
moreCompounds = false;
i++;
}
}
moreCompounds = true;
while (moreCompounds)
{
if (headers[i] != "Adduct/Replacement")
{
molnames.Add(headers[i]);
i++;
}
else
moreCompounds = false;
}
bool firstRow = true;
while (read.Peek() >= 0)
{
//Read data
String Line = read.ReadLine();
String[] Lines = Line.Split(',');
//initialize new gR object
ResultsGroup gR = new ResultsGroup();
DeconRow dR = new DeconRow();
CompositionHypothesisEntry cH = new CompositionHypothesisEntry();
gR.DeconRow = dR;
gR.PredictedComposition = cH;
//Input data
if (!String.IsNullOrEmpty(Lines[0]))
{
if (firstRow)
{
gR.PredictedComposition.ElementNames = elementIDs;
gR.PredictedComposition.MoleculeNames = molnames;
firstRow = false;
}
gR.Score = Convert.ToDouble(Lines[0]);
gR.DeconRow.MonoisotopicMassWeight = Convert.ToDouble(Lines[1]);
gR.PredictedComposition.CompoundComposition = Lines[2];
if (String.IsNullOrEmpty(Lines[2]) || Lines[2] == "0")
gR.Match = false;
else
gR.Match = true;
gR.PredictedComposition.PepSequence = Lines[3];
gR.NumModiStates = Convert.ToDouble(Lines[5]);
gR.NumChargeStates = Convert.ToInt32(Lines[6]);
gR.NumOfScan = Convert.ToDouble(Lines[7]);
gR.ScanDensity = Convert.ToDouble(Lines[8]);
gR.ExpectedA = Convert.ToDouble(Lines[9]);
gR.AvgAA2List = new List<double>();
gR.AvgAA2List.Add(Convert.ToDouble(Lines[10]));
gR.TotalVolume = Convert.ToDouble(Lines[11]);
gR.AvgSigNoise = Convert.ToDouble(Lines[12]);
gR.CentroidScan = Convert.ToDouble(Lines[13]);
gR.DeconRow.ScanNum = Convert.ToInt32(Lines[14]);
gR.MaxScanNum = Convert.ToInt32(Lines[15]);
gR.MinScanNum = Convert.ToInt32(Lines[16]);
gR.PredictedComposition.eqCount = new Dictionary<string, int>();
int sh = 17;
for (int ele = 0; ele < elementIDs.Count(); ele++ )
{
gR.PredictedComposition.ElementAmount.Add(Convert.ToInt32(Lines[sh]));
sh++;
}
gR.PredictedComposition.MassWeight = Convert.ToDouble(Lines[sh]);
sh++;
List<int> eqCoun = new List<int>();
for (int j = 0; j < molnames.Count(); j++)
{
eqCoun.Add(Convert.ToInt32(Lines[sh + j]));
}
gR.PredictedComposition.eqCounts = eqCoun;
gR.PredictedComposition.AddRep = Lines[sh + molnames.Count()];
gR.PredictedComposition.AdductNum = Convert.ToInt32(Lines[sh + molnames.Count() + 1]);
gR.PredictedComposition.PepModification = Lines[sh + molnames.Count() + 2];
gR.PredictedComposition.MissedCleavages = Convert.ToInt32(Lines[sh + molnames.Count() + 3]);
gR.PredictedComposition.NumGlycosylations = Convert.ToInt32(Lines[sh + molnames.Count() + 4]);
gR.PredictedComposition.StartAA = Convert.ToInt32(Lines[sh + molnames.Count() + 5]);
gR.PredictedComposition.EndAA = Convert.ToInt32(Lines[sh + molnames.Count() + 6]);
if (Lines.Count() > sh + molnames.Count() + 7)
{
gR.PredictedComposition.ProteinID = Lines[sh + molnames.Count() + 7];
}
else
{
gR.PredictedComposition.ProteinID = "?";
}
Ans.Add(gR);
}
}
}
//older data format.
else if (headers[3] == "PeptideSequence")
{
Boolean moreCompounds = true;
int i = 24;
while (moreCompounds)
{
if (headers[i] != "Adduct/Replacement")
{
molnames.Add(headers[i]);
i++;
}
else
moreCompounds = false;
}
bool firstRow = true;
while (read.Peek() >= 0)
{
//Read data
String Line = read.ReadLine();
String[] Lines = Line.Split(',');
//initialize new gR object
ResultsGroup gR = new ResultsGroup();
DeconRow dR = new DeconRow();
CompositionHypothesisEntry cH = new CompositionHypothesisEntry();
gR.DeconRow = dR;
gR.PredictedComposition = cH;
if (firstRow)
{
gR.PredictedComposition.ElementNames.AddRange(new List<string> { "C", "H", "N", "O", "S", "P" });
gR.PredictedComposition.MoleculeNames = molnames;
firstRow = false;
}
//Input data
if (!String.IsNullOrEmpty(Lines[0]))
{
gR.Score = Convert.ToDouble(Lines[0]);
gR.DeconRow.MonoisotopicMassWeight = Convert.ToDouble(Lines[1]);
gR.PredictedComposition.CompoundComposition = Lines[2];
if (String.IsNullOrEmpty(Lines[2]) || Lines[2] == "0")
gR.Match = false;
else
gR.Match = true;
gR.PredictedComposition.PepSequence = Lines[3];
gR.PredictedComposition.MassWeight = Convert.ToDouble(Lines[5]);
gR.NumModiStates = Convert.ToDouble(Lines[6]);
gR.NumChargeStates = Convert.ToInt32(Lines[7]);
gR.NumOfScan = Convert.ToDouble(Lines[8]);
gR.ScanDensity = Convert.ToDouble(Lines[9]);
gR.ExpectedA = Convert.ToDouble(Lines[10]);
gR.AvgAA2List = new List<double>();
gR.AvgAA2List.Add(Convert.ToDouble(Lines[11]));
gR.TotalVolume = Convert.ToDouble(Lines[12]);
gR.AvgSigNoise = Convert.ToDouble(Lines[13]);
gR.CentroidScan = Convert.ToDouble(Lines[14]);
gR.DeconRow.ScanNum = Convert.ToInt32(Lines[15]);
gR.MaxScanNum = Convert.ToInt32(Lines[16]);
gR.MinScanNum = Convert.ToInt32(Lines[17]);
gR.PredictedComposition.eqCount = new Dictionary<string, int>();
for (int k = 18; k < 24; k++)
{
gR.PredictedComposition.ElementAmount.Add(Convert.ToInt32(Lines[k]));
}
List<int> eqCoun = new List<int>();
for (int j = 0; j < molnames.Count(); j++)
{
eqCoun.Add(Convert.ToInt32(Lines[24 + j]));
}
gR.PredictedComposition.eqCounts = eqCoun;
gR.PredictedComposition.AddRep = Lines[24 + molnames.Count()];
gR.PredictedComposition.AdductNum = Convert.ToInt32(Lines[24 + molnames.Count() + 1]);
gR.PredictedComposition.PepModification = Lines[24 + molnames.Count() + 2];
gR.PredictedComposition.MissedCleavages = Convert.ToInt32(Lines[24 + molnames.Count() + 3]);
gR.PredictedComposition.NumGlycosylations = Convert.ToInt32(Lines[24 + molnames.Count() + 4]);
Ans.Add(gR);
}
}
}
//This is supporting an older format of data. Today is Sept 2013, can be deleted after 1 year.
else
{
Boolean moreCompounds = true;
int i = 23;
while (moreCompounds)
{
if (headers[i] != "Adduct/Replacement")
{
molnames.Add(headers[i]);
i++;
}
else
moreCompounds = false;
}
bool firstRow = true;
while (read.Peek() >= 0)
{
//Read data
String Line = read.ReadLine();
String[] Lines = Line.Split(',');
//initialize new gR object
ResultsGroup gR = new ResultsGroup();
if (firstRow)
{
gR.PredictedComposition.ElementNames.AddRange(new List<string> { "C", "H", "N", "O", "S", "P" });
gR.PredictedComposition.MoleculeNames = molnames;
firstRow = false;
}
DeconRow dR = new DeconRow();
CompositionHypothesisEntry cH = new CompositionHypothesisEntry();
gR.DeconRow = dR;
gR.PredictedComposition = cH;
if (!String.IsNullOrEmpty(Lines[0]))
{
//Input data
gR.Score = Convert.ToDouble(Lines[0]);
gR.DeconRow.MonoisotopicMassWeight = Convert.ToDouble(Lines[1]);
gR.PredictedComposition.CompoundComposition = Lines[2].Replace(",", ";");
if (String.IsNullOrEmpty(Lines[2]) || Lines[2] == "0")
gR.Match = false;
else
gR.Match = true;
gR.PredictedComposition.MassWeight = Convert.ToDouble(Lines[4]);
gR.NumModiStates = Convert.ToDouble(Lines[5]);
gR.NumChargeStates = Convert.ToInt32(Lines[6]);
gR.NumOfScan = Convert.ToDouble(Lines[7]);
gR.ScanDensity = Convert.ToDouble(Lines[8]);
gR.ExpectedA = Convert.ToDouble(Lines[9]);
gR.AvgAA2List = new List<double>();
gR.AvgAA2List.Add(Convert.ToDouble(Lines[10]));
gR.TotalVolume = Convert.ToDouble(Lines[11]);
gR.AvgSigNoise = Convert.ToDouble(Lines[12]);
gR.CentroidScan = Convert.ToDouble(Lines[13]);
gR.DeconRow.ScanNum = Convert.ToInt32(Lines[14]);
gR.MaxScanNum = Convert.ToInt32(Lines[15]);
gR.MinScanNum = Convert.ToInt32(Lines[16]);
gR.PredictedComposition.eqCount = new Dictionary<string, int>();
for (int k = 17; k < 23; k++)
{
gR.PredictedComposition.ElementAmount.Add(Convert.ToInt32(Lines[k]));
}
gR.PredictedComposition.eqCount.Add("A", Convert.ToInt32(Lines[23]));
gR.PredictedComposition.eqCount.Add("B", Convert.ToInt32(Lines[24]));
gR.PredictedComposition.eqCount.Add("C", Convert.ToInt32(Lines[25]));
gR.PredictedComposition.eqCount.Add("D", Convert.ToInt32(Lines[26]));
gR.PredictedComposition.eqCount.Add("E", Convert.ToInt32(Lines[27]));
gR.PredictedComposition.eqCount.Add("F", Convert.ToInt32(Lines[28]));
gR.PredictedComposition.eqCount.Add("G", Convert.ToInt32(Lines[29]));
gR.PredictedComposition.eqCount.Add("H", Convert.ToInt32(Lines[30]));
gR.PredictedComposition.eqCount.Add("I", Convert.ToInt32(Lines[31]));
gR.PredictedComposition.eqCount.Add("J", Convert.ToInt32(Lines[32]));
gR.PredictedComposition.eqCount.Add("K", Convert.ToInt32(Lines[33]));
gR.PredictedComposition.eqCount.Add("L", Convert.ToInt32(Lines[34]));
gR.PredictedComposition.eqCount.Add("M", Convert.ToInt32(Lines[35]));
gR.PredictedComposition.eqCount.Add("N", Convert.ToInt32(Lines[36]));
gR.PredictedComposition.eqCount.Add("O", Convert.ToInt32(Lines[37]));
gR.PredictedComposition.eqCount.Add("P", Convert.ToInt32(Lines[38]));
gR.PredictedComposition.eqCount.Add("Q", Convert.ToInt32(Lines[39]));
gR.PredictedComposition.AddRep = Lines[40];
gR.PredictedComposition.AdductNum = Convert.ToInt32(Lines[41]);
gR.PredictedComposition.PepSequence = Lines[42];
gR.PredictedComposition.PepModification = Lines[43];
gR.PredictedComposition.MissedCleavages = Convert.ToInt32(Lines[44]);
gR.PredictedComposition.NumGlycosylations = Convert.ToInt32(Lines[45]);
Ans.Add(gR);
}
}
}
}
//This is gly1 data.
else
{
String header = read.ReadLine();
String[] headers = header.Split('\t');
while (read.Peek() >= 0)
{
//Read data
String Line = read.ReadLine();
String[] Lines = Line.Split('\t');
//initialize new gR object
ResultsGroup gR = new ResultsGroup();
DeconRow dR = new DeconRow();
CompositionHypothesisEntry cH = new CompositionHypothesisEntry();
gR.DeconRow = dR;
gR.PredictedComposition = cH;
if (!String.IsNullOrEmpty(Lines[0]))
{
//Input data
gR.PredictedComposition.MoleculeNames = molnames;
gR.Score = Convert.ToDouble(Lines[0]);
gR.DeconRow.MonoisotopicMassWeight = Convert.ToDouble(Lines[1]);
gR.PredictedComposition.CompoundComposition = Lines[2].Replace(",", ";");
if (String.IsNullOrEmpty(Lines[2]) || Lines[2] == "0")
{
gR.Match = false;
gR.PredictedComposition.MassWeight = 0;
}
else
{
gR.Match = true;
gR.PredictedComposition.MassWeight = Convert.ToDouble(Lines[4]);
}
gR.NumModiStates = Convert.ToDouble(Lines[5]);
gR.NumChargeStates = Convert.ToInt32(Lines[6]);
gR.NumOfScan = Convert.ToDouble(Lines[7]);
gR.ScanDensity = Convert.ToDouble(Lines[8]);
gR.ExpectedA = Convert.ToDouble(Lines[9]);
gR.AvgAA2List = new List<double>();
gR.AvgAA2List.Add(Convert.ToDouble(Lines[10]));
gR.TotalVolume = Convert.ToDouble(Lines[11]);
gR.AvgSigNoise = Convert.ToDouble(Lines[12]);
gR.CentroidScan = Convert.ToDouble(Lines[13]);
gR.DeconRow.ScanNum = Convert.ToInt32(Convert.ToDouble(Lines[14]));
Ans.Add(gR);
}
}
}
return Ans;
}
public List<DeconRow> getdata(String DeconData)
{
ParametersForm parad = new ParametersForm();
ParametersForm.ParameterSettings paradata = parad.GetParameters();
//try
// {
FileStream fileinput = new FileStream(DeconData, FileMode.Open, FileAccess.Read);
StreamReader readdata = new StreamReader(fileinput);
//The first line in the file contains the column names, we don't need it.
readdata.ReadLine();
while (readdata.Peek() >= 0)
{
DeconRow Row = new DeconRow();
String Line = readdata.ReadLine();
String[] column = Line.Split(',');
Row.ScanNum = Convert.ToInt32(column[0]);
Row.charge = Convert.ToInt32(column[1]);
Row.abundance = Convert.ToInt32(column[2]);
Row.mz = Convert.ToDouble(column[3]);
Row.fit = Convert.ToDouble(column[4]);
Row.average_mw = Convert.ToDouble(column[5]);
Row.MonoisotopicMassWeight = Convert.ToDouble(column[6]);
Row.mostabundant_mw = Convert.ToDouble(column[7]);
Row.fwhm = Convert.ToDouble(column[8]);
Row.SignalNoiseRatio = Convert.ToDouble(column[9]);
Row.MonoisotopicAbundance = Convert.ToInt32(column[10]);
Double mp2a = Convert.ToDouble(column[11]);
Row.MonoisotopicPlus2Abundance = Convert.ToInt32(mp2a);
//Flag maybe empty, so, special treatment.
if (column[12] == "")
{ Row.flag = 0; }
else
{ Row.flag = Convert.ToInt32(column[12]); }
if (Convert.ToInt32(column.Count()) == 14)
Row.interference_sore = Convert.ToDouble(column[13]);
else
Row.interference_sore = 0;
//Check if the data are within the boundaries of the Parameters
if (Row.abundance >= paradata.DataNoiseTheshold)
{
if (Row.MonoisotopicMassWeight <= paradata.MolecularWeightUpperBound)
{
if (Row.MonoisotopicMassWeight >= paradata.MolecularWeightLowerBound)
{
DeconDATA.Add(Row);
}
}
}
}
fileinput.Close();
// }
// catch(Exception ex)
// {
// MessageBox.Show("Error: Could not read DeconTools Data file from disk. Original error: " + ex.Message);
// }
return DeconDATA;
}
