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); }