public override void ValidateResult(DeconTools.Backend.Core.ResultCollection resultColl, DeconTools.Backend.Core.IsosResult currentResult)
{
Check.Require(currentResult is N14N15_TResult, "Currently, this is only implemented for N14N15 results");
var n14n15result = (N14N15_TResult)currentResult;
Check.Require(n14n15result.Target.IsotopicProfileLabelled != null, "Cannot validate labelled isotopic profile. Theoretical profile was not defined.");
// stop, but don't throw an error if there is no labelled isotopic profile.
if (n14n15result.IsotopicProfileLabeled == null)
{
return;
}
var isoN15 = n14n15result.IsotopicProfileLabeled;
var scanPeaks = resultColl.Run.PeakList.Select <Peak, MSPeak>(i => (MSPeak)i).ToList();
// get i_score
n14n15result.InterferenceScoreN15 = getIScore(scanPeaks, isoN15);
// get fit score
var fitval = getFitValue(resultColl.Run.XYData, n14n15result.Target.IsotopicProfileLabelled, isoN15);
n14n15result.ScoreN15 = fitval;
}
public override void MergeAndExport(DeconTools.Backend.Core.ResultCollection resultList)
{
Check.Require(resultList != null, "Scans merger failed. ResultCollection is null");
Check.Require(resultList.ScanResultList != null && resultList.ScanResultList.Count > 0, "Scans merger failed... there's a problem in the ScanResult List");
var sb = new StringBuilder();
var scanresult = resultList.ScanResultList[0]; // we only take the first one since we delete each scanResult after writing it out to file
sb.Append(getScanNumber(scanresult.ScanSet.PrimaryScanNumber));
sb.Append(delimiter);
sb.Append(DblToString(scanresult.ScanTime, 4));
sb.Append(delimiter);
sb.Append(scanresult.SpectrumType);
sb.Append(delimiter);
sb.Append(DblToString(scanresult.BasePeak.Height, 4, true));
sb.Append(delimiter);
sb.Append(DblToString(scanresult.BasePeak.XValue, 5));
sb.Append(delimiter);
sb.Append(DblToString(scanresult.ScanSet.TICValue, 4, true));
sb.Append(delimiter);
sb.Append(scanresult.NumPeaks);
sb.Append(delimiter);
sb.Append(scanresult.NumIsotopicProfiles);
sw.WriteLine(sb.ToString());
resultList.ScanResultList.Clear(); // scanResult List is cleared every time.
runCounter++;
}
protected override void addScanResults(DeconTools.Backend.Core.ResultCollection rc)
{
var myconnection = (SQLiteConnection)cnn;
using (var mytransaction = myconnection.BeginTransaction())
{
using (var mycommand = new SQLiteCommand(myconnection))
{
var frameNumParam = new SQLiteParameter();
var frameTimeParam = new SQLiteParameter();
var typeParam = new SQLiteParameter();
var bpiParam = new SQLiteParameter();
var bpiMZParam = new SQLiteParameter();
var ticParam = new SQLiteParameter();
var num_peaksParam = new SQLiteParameter();
var num_deisotopedParam = new SQLiteParameter();
var framePressureUnsmoothed = new SQLiteParameter();
var framePressureSmoothed = new SQLiteParameter();
mycommand.CommandText = "INSERT INTO T_IMS_Frames ([frame_num],[frame_time],[type],[bpi],[bpi_mz],[tic],[num_peaks],[num_deisotoped],[frame_pressure_unsmoothed],[frame_pressure_smoothed]) VALUES(?,?,?,?,?,?,?,?,?,?)";
mycommand.Parameters.Add(frameNumParam);
mycommand.Parameters.Add(frameTimeParam);
mycommand.Parameters.Add(typeParam);
mycommand.Parameters.Add(bpiParam);
mycommand.Parameters.Add(bpiMZParam);
mycommand.Parameters.Add(ticParam);
mycommand.Parameters.Add(num_peaksParam);
mycommand.Parameters.Add(num_deisotopedParam);
mycommand.Parameters.Add(framePressureUnsmoothed);
mycommand.Parameters.Add(framePressureSmoothed);
for (var n = 0; n < rc.ScanResultList.Count; n++)
{
var r = (UimfScanResult)rc.ScanResultList[n];
frameNumParam.Value = r.LCScanNum;
frameTimeParam.Value = r.ScanTime;
typeParam.Value = r.SpectrumType;
bpiParam.Value = r.BasePeak.Height;
bpiMZParam.Value = r.BasePeak.XValue;
ticParam.Value = r.TICValue;
num_peaksParam.Value = r.NumPeaks;
num_deisotopedParam.Value = r.NumIsotopicProfiles;
framePressureUnsmoothed.Value = r.FramePressureUnsmoothed;
framePressureSmoothed.Value = r.FramePressureSmoothed;
mycommand.ExecuteNonQuery();
}
}
mytransaction.Commit();
}
}
public override void ExportScanResults(DeconTools.Backend.Core.ResultCollection resultList)
{
using (var sw = new StreamWriter(new FileStream(_filename, FileMode.Append,
FileAccess.Write, FileShare.Read)))
{
sw.AutoFlush = true;
foreach (var scanResult in resultList.ScanResultList)
{
var output = buildScansResultOutput(scanResult);
sw.WriteLine(output);
}
}
}
public override void Export(DeconTools.Backend.Core.ResultCollection results)
{
StreamWriter sw;
try
{
sw = new StreamWriter(this.fileName);
}
catch (Exception ex)
{
throw new Exception("Error creating file " + this.fileName + ": " + ex.Message);
}
if (!string.Equals(PNNLOmics.Utilities.StringUtilities.DblToString(3.14159, 4, false, 0.001, false), DblToString(3.14159, 4)))
{
Console.WriteLine("Note: using a period for the decimal point for because the result files are CSV files");
}
sw.WriteLine(headerLine);
foreach (var result in results.ScanResultList)
{
Check.Require(result is UimfScanResult, "UIMF_Scans_Exporter only works on UIMF Scan Results");
var uimfResult = (UimfScanResult)result;
var sb = new StringBuilder();
sb.Append(uimfResult.ScanSet.PrimaryScanNumber);
sb.Append(delimiter);
sb.Append(DblToString(uimfResult.ScanTime, 3));
sb.Append(delimiter);
sb.Append(result.SpectrumType);
sb.Append(delimiter);
sb.Append(DblToString(uimfResult.BasePeak.Height, 4, true));
sb.Append(delimiter);
sb.Append(DblToString(uimfResult.BasePeak.XValue, 5));
sb.Append(delimiter);
sb.Append(DblToString(uimfResult.TICValue, 4, true));
sb.Append(delimiter);
sb.Append(uimfResult.NumPeaks);
sb.Append(delimiter);
sb.Append(uimfResult.NumIsotopicProfiles);
sb.Append(delimiter);
sb.Append(DblToString(uimfResult.FramePressureUnsmoothed, 4));
sb.Append(delimiter);
sb.Append(DblToString(uimfResult.FramePressureSmoothed, 4));
sw.WriteLine(sb.ToString());
}
sw.Close();
}
protected override void addScanResults(DeconTools.Backend.Core.ResultCollection rc)
{
var myconnection = (SQLiteConnection)cnn;
using (var mytransaction = myconnection.BeginTransaction())
{
using (var mycommand = new SQLiteCommand(myconnection))
{
var scanNumParam = new SQLiteParameter();
var scanTimeParam = new SQLiteParameter();
var typeParam = new SQLiteParameter();
var bpiParam = new SQLiteParameter();
var bpiMZParam = new SQLiteParameter();
var ticParam = new SQLiteParameter();
var num_peaksParam = new SQLiteParameter();
var num_deisotopedParam = new SQLiteParameter();
mycommand.CommandText = "INSERT INTO T_MS_ScanSummary ([scan_num],[scan_time],[type],[bpi],[bpi_mz],[tic],[num_peaks],[num_deisotoped]) VALUES(?,?,?,?,?,?,?,?)";
mycommand.Parameters.Add(scanNumParam);
mycommand.Parameters.Add(scanTimeParam);
mycommand.Parameters.Add(typeParam);
mycommand.Parameters.Add(bpiParam);
mycommand.Parameters.Add(bpiMZParam);
mycommand.Parameters.Add(ticParam);
mycommand.Parameters.Add(num_peaksParam);
mycommand.Parameters.Add(num_deisotopedParam);
for (var n = 0; n < rc.ScanResultList.Count; n++)
{
var item = rc.ScanResultList[n];
scanNumParam.Value = item.ScanSet.PrimaryScanNumber;
scanTimeParam.Value = item.ScanTime;
typeParam.Value = item.SpectrumType;
bpiParam.Value = item.BasePeak.Height;
bpiMZParam.Value = item.BasePeak.XValue;
ticParam.Value = item.TICValue;
num_peaksParam.Value = item.NumPeaks;
num_deisotopedParam.Value = item.NumIsotopicProfiles;
mycommand.ExecuteNonQuery();
}
}
mytransaction.Commit();
}
}
public override void Export(DeconTools.Backend.Core.ResultCollection results)
{
try
{
sqliteWriter.CreateNewDB(fileName);
}
catch (Exception)
{
throw;
}
//Insert records to IMS_Frames table
//Insert records in bulk mood, 500 records each time
//this is significantly faster than inserting one record at a time
//500 records are the maximum number sqlite3 can handle
var records = new ArrayList();
var count = 0;
foreach (var result in results.ScanResultList)
{
Check.Require(result is UimfScanResult, "UIMF_Scans_Exporter only works on UIMF Scan Results");
var uimfResult = (UimfScanResult)result;
var fp = new IMS_Frames();
fp.frame_num = (ushort)uimfResult.ScanSet.PrimaryScanNumber;
fp.frame_time = (float)uimfResult.ScanTime;
fp.type = (ushort)uimfResult.SpectrumType;
fp.bpi = uimfResult.BasePeak.Height;
fp.bpi_mz = (float)uimfResult.BasePeak.XValue;
fp.tic = uimfResult.TICValue;
fp.num_peaks = (uint)uimfResult.NumPeaks;
fp.num_deisotoped = (uint)uimfResult.NumIsotopicProfiles;
fp.frame_pressure_front = (float)uimfResult.FramePressureUnsmoothed;
fp.frame_pressure_back = (float)uimfResult.FramePressureSmoothed;
records.Add(fp);
count++;
if (count == 500)
{
sqliteWriter.InsertIMSFrames(records);
count = 0;
records = new ArrayList();
}
}
//Insert the rest of the records to IMS_Frames table
sqliteWriter.InsertIMSFrames(records);
sqliteWriter.CloseDB(fileName);
}
public override void Export(DeconTools.Backend.Core.ResultCollection results)
{
StreamWriter sw;
try
{
sw = new StreamWriter(this.fileName);
}
catch (Exception)
{
throw;
}
sw.WriteLine(headerLine);
writeUIMFIsosResults(sw, results);
sw.Close();
}
public override void ValidateResult(DeconTools.Backend.Core.ResultCollection resultColl, DeconTools.Backend.Core.IsosResult currentResult)
{
if (currentResult.IsotopicProfile == null)
{
return;
}
Check.Require(currentResult != null, String.Format("{0} failed. CurrentResult has not been defined.", this.Name));
if (resultColl.Run.PeakList == null || resultColl.Run.PeakList.Count == 0)
{
currentResult.InterferenceScore = -1;
return;
}
var monoPeak = currentResult.IsotopicProfile.getMonoPeak();
var lastPeak = currentResult.IsotopicProfile.Peaklist[currentResult.IsotopicProfile.Peaklist.Count - 1];
var leftMZBoundary = monoPeak.XValue - 1.1;
var rightMZBoundary = lastPeak.XValue + lastPeak.Width / 2.35 * 2; // 2 sigma
double interferenceVal = -1;
if (UsePeakBasedInterferenceValue)
{
var scanPeaks = resultColl.Run.PeakList.Select <Peak, MSPeak>(i => (MSPeak)i).ToList();
interferenceVal = m_scorer.GetInterferenceScore(scanPeaks, currentResult.IsotopicProfile.Peaklist, leftMZBoundary, rightMZBoundary);
}
else
{
var startIndexOfXYData = MathUtils.BinarySearchWithTolerance(resultColl.Run.XYData.Xvalues, monoPeak.XValue - 3, 0, (resultColl.Run.XYData.Xvalues.Length - 1), 2);
if (startIndexOfXYData < 0)
{
startIndexOfXYData = 0;
}
interferenceVal = m_scorer.GetInterferenceScore(resultColl.Run.XYData, currentResult.IsotopicProfile.Peaklist, leftMZBoundary, rightMZBoundary, startIndexOfXYData);
}
currentResult.InterferenceScore = interferenceVal;
}
public override void Export(DeconTools.Backend.Core.ResultCollection results)
{
StreamWriter sw;
try
{
sw = new StreamWriter(this.fileName);
}
catch (Exception)
{
throw;
}
sw.WriteLine(headerLine);
//OriginalIntensitiesExtractor origIntensExtractor = new OriginalIntensitiesExtractor(results);
//List<OriginalIntensitiesDTO> origIntensitiesCollection = origIntensExtractor.ExtractOriginalIntensities();
//writeUIMFIsosResults(sw, results, origIntensitiesCollection);
sw.Close();
}
public override void ValidateResult(DeconTools.Backend.Core.ResultCollection resultColl, IsosResult currentResult)
{
Check.Require(currentResult != null, String.Format("{0} failed. CurrentResult has not been defined.", this.Name));
if (currentResult.IsotopicProfile == null)
{
return;
}
var monoPeak = currentResult.IsotopicProfile.getMonoPeak();
var peakToTheLeft = LookforPeakToTheLeftOfMonoPeak(monoPeak, currentResult.IsotopicProfile.ChargeState, resultColl.Run.PeakList);
if (peakToTheLeft == null)
{
return; // no peak found... so no problem.
}
if (peakToTheLeft.Height > monoPeak.Height * MinRatioToGiveFlag) //if peak-to-the-left exceeds min Ratio, then flag it
{
currentResult.Flags.Add(new PeakToTheLeftResultFlag());
}
}
