public override void GetTIC(DeconTools.Backend.Core.ResultCollection resultList)
{
Check.Require(resultList.Run is UIMFRun, "UIMF_TIC_Extractor only works on UIMF files");
var uimfRun = (UIMFRun)resultList.Run;
var ticValue = uimfRun.GetTIC(uimfRun.CurrentScanSet.PrimaryScanNumber, uimfRun.CurrentIMSScanSet.PrimaryScanNumber);
uimfRun.CurrentIMSScanSet.TICValue = ticValue;
}
public override void Export(DeconTools.Backend.Core.ResultCollection results)
{
StringBuilder sb;
StreamWriter sw;
try
{
sw = new StreamWriter(this.fileName);
}
catch (Exception)
{
throw new System.IO.IOException("Could not access the output file. Check to see if it is already open.");
}
sw.WriteLine(headerLine);
foreach (var isosResult in results.ResultList)
{
var result = (StandardIsosResult)isosResult;
sb = new StringBuilder();
sb.Append(getScanNumber(result.ScanSet.PrimaryScanNumber));
sb.Append(delimiter);
sb.Append(result.IsotopicProfile.ChargeState);
sb.Append(delimiter);
sb.Append(DblToString(result.IsotopicProfile.GetAbundance(), 4, true));
sb.Append(delimiter);
sb.Append(DblToString(result.IsotopicProfile.GetMZ(), 5));
sb.Append(delimiter);
sb.Append(DblToString(result.IsotopicProfile.Score, 4)); // Fit Score
sb.Append(delimiter);
sb.Append(DblToString(result.IsotopicProfile.AverageMass, 5));
sb.Append(delimiter);
sb.Append(DblToString(result.IsotopicProfile.MonoIsotopicMass, 5));
sb.Append(delimiter);
// this.headerLine = "scan_num,charge,abundance,mz,fit,average_mw,monoisotopic_mw,mostabundant_mw,fwhm,signal_noise,mono_abundance,mono_plus2_abundance";
sb.Append(DblToString(result.IsotopicProfile.MostAbundantIsotopeMass, 5));
sb.Append(delimiter);
sb.Append(DblToString(result.IsotopicProfile.GetFWHM(), 4));
sb.Append(delimiter);
sb.Append(DblToString(result.IsotopicProfile.GetSignalToNoise(), 2));
sb.Append(delimiter);
sb.Append(DblToString(result.IsotopicProfile.GetMonoAbundance(), 4, true));
sb.Append(delimiter);
sb.Append(DblToString(result.IsotopicProfile.GetMonoPlusTwoAbundance(), 4, true));
// Uncomment to write out the fit_count_basis
//sb.Append(delimiter);
//sb.Append(result.IsotopicProfile.ScoreCountBasis); // Number of points used for the fit score
sw.WriteLine(sb.ToString());
}
sw.Close();
}
public override void Deconvolute(DeconTools.Backend.Core.ResultCollection resultList)
{
//do nothing
}
protected override void addResults(DeconTools.Backend.Core.ResultCollection rc)
{
var myconnection = (SQLiteConnection)cnn;
using (var mytransaction = myconnection.BeginTransaction())
{
using (var mycommand = new SQLiteCommand(myconnection))
{
var featureIDParam = new SQLiteParameter();
var scanNumParam = new SQLiteParameter();
var chargeParam = new SQLiteParameter();
var abundanceParam = new SQLiteParameter();
var mzParam = new SQLiteParameter();
var fitParam = new SQLiteParameter();
var averageMWParam = new SQLiteParameter();
var monoIsotopicMWParam = new SQLiteParameter();
var mostAbundantMWParam = new SQLiteParameter();
var fwhmParam = new SQLiteParameter();
var sigNoiseParam = new SQLiteParameter();
var monoAbundanceParam = new SQLiteParameter();
var monoPlus2AbundParam = new SQLiteParameter();
var netParam = new SQLiteParameter();
var massTagIDParam = new SQLiteParameter();
var massTagMZParam = new SQLiteParameter();
var massTagNETParam = new SQLiteParameter();
var massTagSequenceParam = new SQLiteParameter();
mycommand.CommandText = @"INSERT INTO T_MassTagResults ([feature_id],[scan_num],[charge],[abundance],[mz],[fit],
[net],[mass_tag_id],[mass_tag_mz],[mass_tag_NET],[mass_tag_sequence],
[average_mw],[monoisotopic_mw],[mostabundant_mw],[fwhm],[signal_noise],[mono_abundance],[mono_plus2_abundance]) VALUES(?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?)";
mycommand.Parameters.Add(featureIDParam);
mycommand.Parameters.Add(scanNumParam);
mycommand.Parameters.Add(chargeParam);
mycommand.Parameters.Add(abundanceParam);
mycommand.Parameters.Add(mzParam);
mycommand.Parameters.Add(fitParam);
mycommand.Parameters.Add(netParam);
mycommand.Parameters.Add(massTagIDParam);
mycommand.Parameters.Add(massTagMZParam);
mycommand.Parameters.Add(massTagNETParam);
mycommand.Parameters.Add(massTagSequenceParam);
mycommand.Parameters.Add(averageMWParam);
mycommand.Parameters.Add(monoIsotopicMWParam);
mycommand.Parameters.Add(mostAbundantMWParam);
mycommand.Parameters.Add(fwhmParam);
mycommand.Parameters.Add(sigNoiseParam);
mycommand.Parameters.Add(monoAbundanceParam);
mycommand.Parameters.Add(monoPlus2AbundParam);
foreach (var item in rc.MassTagResultList)
{
featureIDParam.Value = item.Value.MSFeatureID;
fitParam.Value = item.Value.Score;
if (item.Value.ScanSet != null)
{
scanNumParam.Value = item.Value.ScanSet.PrimaryScanNumber;
}
netParam.Value = item.Value.GetNET();
massTagIDParam.Value = item.Value.Target.ID;
massTagMZParam.Value = item.Value.Target.MZ;
massTagNETParam.Value = item.Value.Target.NormalizedElutionTime;
massTagSequenceParam.Value = item.Value.Target.Code;
if (item.Value.IsotopicProfile != null)
{
chargeParam.Value = item.Value.IsotopicProfile.ChargeState;
abundanceParam.Value = item.Value.IsotopicProfile.GetAbundance();
mzParam.Value = item.Value.IsotopicProfile.GetMZ();
averageMWParam.Value = item.Value.IsotopicProfile.AverageMass;
monoIsotopicMWParam.Value = item.Value.IsotopicProfile.MonoIsotopicMass;
//mostAbundantMWParam.Value = item.Value.IsotopicProfile.getMostIntensePeak().XValue;
fwhmParam.Value = item.Value.IsotopicProfile.GetFWHM();
sigNoiseParam.Value = item.Value.IsotopicProfile.GetSignalToNoise();
monoAbundanceParam.Value = item.Value.IsotopicProfile.GetMonoAbundance();
monoPlus2AbundParam.Value = item.Value.IsotopicProfile.GetMonoPlusTwoAbundance();
}
mycommand.ExecuteNonQuery();
}
}
mytransaction.Commit();
}
}
public override void ExportMassTagResults(DeconTools.Backend.Core.ResultCollection resultColl)
{
addResults(resultColl);
resultColl.MassTagResultList.Clear();
}
protected abstract void addScanResults(DeconTools.Backend.Core.ResultCollection resultList);
public override void ExportScanResults(DeconTools.Backend.Core.ResultCollection resultList)
{
addScanResults(resultList);
}
