public static void DumpTotalTime(ExecutionTimeDto time)
{
Application xlApp = new Application();
if (xlApp == null)
{
return;
}
string excelFile = _directory + "\\Times.xls";
Application oXL;
_Workbook oWB;
_Worksheet oSheet;
Range oRng;
object misvalue = System.Reflection.Missing.Value;
try
{
//Start Excel and get Application object.
oXL = new Microsoft.Office.Interop.Excel.Application();
//oXL.Visible = true;
//Get a new workbook.
oWB = (Microsoft.Office.Interop.Excel._Workbook)(oXL.Workbooks.Add(""));
oSheet = (Microsoft.Office.Interop.Excel._Worksheet)oWB.ActiveSheet;
//Add table headers going cell by cell.
oSheet.Cells[1, 1] = "TotalTime";
oSheet.Cells[1, 2] = "FileReadingTime";
oSheet.Cells[1, 3] = "InsilicoTime";
oSheet.Cells[1, 4] = "MwFilterTime";
oSheet.Cells[1, 5] = "PstTime";
oSheet.Cells[1, 6] = "PtmTime";
oSheet.Cells[1, 7] = "TunerTime";
oSheet.Cells[2, 1] = time.TotalTime;
oSheet.Cells[2, 2] = time.FileReadingTime;
oSheet.Cells[2, 3] = time.InsilicoTime;
oSheet.Cells[2, 4] = time.MwFilterTime;
oSheet.Cells[2, 5] = time.PstTime;
oSheet.Cells[2, 6] = time.PtmTime;
oSheet.Cells[2, 7] = time.TunerTime;
oXL.Visible = false;
oXL.UserControl = false;
oWB.SaveAs(excelFile, Microsoft.Office.Interop.Excel.XlFileFormat.xlWorkbookDefault,
Type.Missing, Type.Missing,
false, false, Microsoft.Office.Interop.Excel.XlSaveAsAccessMode.xlNoChange,
Type.Missing, Type.Missing, Type.Missing, Type.Missing, Type.Missing);
oWB.Close();
}
catch (Exception)
{
}
//...
}
//PST: Peptide Sequence Tags
private void ExecuteDenovoModule(SearchParametersDto parameters, MsPeaksDto massSpectrometryData, List <ProteinDto> candidateProteins,
ExecutionTimeDto executionTimes)
{
Stopwatch moduleTimer = Stopwatch.StartNew();
var pstTags = _pstGenerator.GeneratePeptideSequenceTags(parameters, massSpectrometryData);
//Logging.DumpPstTags(pstTags);
if (candidateProteins.Count > 0)
{
_pstFilter.ScoreProteinsByPst(pstTags, candidateProteins);
}
//Logging.DumpPstScores(candidateProteins);
pstTags.Clear();
moduleTimer.Stop();
executionTimes.PstTime = moduleTimer.Elapsed.ToString();
}
//Peak List: Extracting from data file
private MsPeaksDto PeakListFileReaderModuleModule(SearchParametersDto parameters, int fileNumber, ExecutionTimeDto executionTimes)
{
var moduleTimer = new Stopwatch();
moduleTimer.Start();
var peakData = _peakListFileReader.PeakListReader(parameters, fileNumber);
double maxIntensity = peakData.Intensity.Max();
//DEL ME////Discuss it with Sir. Because during first time reading file I am protonating (FOR MASSES) & normalizing intensities .. #DISCUSSION1(This discussion is Necessary)
//DEL ME//Yehi data hr jagha use hona ha to ... humma hr jgha m/z or nomralized intensities he chahya...??? ---#Compare kr lo with SPECTRUM---
////*************m/z & normalizing for MS2*************////
////After reading peaks(Masses & Intensities) from data file. We converted "*"MS2"*" Masses(monoisotopic masses) into m/z.
//Formula of m/z: m/z = (M+z)/z where M is the monoisotopic mass & z is the mass of proton.
//// Maximum Intensity selected from the peak data file & Intensities of "*"MS2"*" are normalized by dividing the selected maximum intensity
for (int peakDataindex = 1; peakDataindex <= peakData.Mass.Count - 1; peakDataindex++) //Loop will run only for MS2 so that why its starting from "1".
{
peakData.Mass[peakDataindex] = peakData.Mass[peakDataindex] + 1.00727647; //monoisotopic to m/z value
peakData.Intensity[peakDataindex] = peakData.Intensity[peakDataindex] / maxIntensity; //Normalized by dividing the selected maximum intensity
}
moduleTimer.Stop();
executionTimes.FileReadingTime = moduleTimer.Elapsed.ToString();
return(peakData);
}
//Mass Tunner
private void ExecuteMassTunerModule(SearchParametersDto parameters, MsPeaksDto peakData, ExecutionTimeDto executionTimes)
{
Stopwatch moduleTimer = Stopwatch.StartNew();
if (parameters.Autotune == 1)
{
//double a = parameters.NeutralLoss;
_wholeProteinMassTuner.TuneWholeProteinMass(peakData, parameters.MwTolerance);
}
moduleTimer.Stop();
executionTimes.TunerTime = moduleTimer.Elapsed.ToString();
}
private List <ProteinDto> ExecutePostTranslationalModificationsModule(SearchParametersDto parameters, List <ProteinDto> candidateProteins,
MsPeaksDto massSpectrometryData, ExecutionTimeDto executionTimes)
{
Stopwatch moduleTimer = Stopwatch.StartNew();
List <ProteinDto> proteoformsList;
if (parameters.PtmAllow == 1)
{
proteoformsList = _postTranslationalModificationModule.ExecutePtmModule(candidateProteins,
massSpectrometryData, parameters);
_insilicoFilter.ComputeInsilicoScore(proteoformsList, massSpectrometryData.Mass, parameters.HopThreshhold);
_molecularWeightModule.FilterModifiedProteinsByWholeProteinMass(parameters, proteoformsList,
massSpectrometryData);
}
else
{
proteoformsList = candidateProteins;
foreach (var protein in proteoformsList)
{
protein.PtmParticulars = new List <PostTranslationModificationsSiteDto>();
}
}
moduleTimer.Stop();
executionTimes.PtmTime = moduleTimer.Elapsed.ToString();
return(proteoformsList);
}
//SPECTRAL COMPARISON ALGORITHM:
private void ExecuteSpectralComparisonModule(SearchParametersDto parameters, List <ProteinDto> candidateProteins,
MsPeaksDto massSpectrometryData, ExecutionTimeDto executionTimes)
{
Stopwatch moduleTimer = Stopwatch.StartNew();
/////Starting From Here !!!!
_insilicoFragmentsAdjustment.adjustForFragmentTypeAndSpecialIons(candidateProteins, parameters.InsilicoFragType, parameters.HandleIons);
////
//if (parameters.PtmAllow == 0) // (parameters.PtmAllow == 0)
// _insilicoFragmentsAdjustment.adjustForFragmentTypeAndSpecialIons(candidateProteins, parameters.InsilicoFragType,
// parameters.HandleIons);
////"Module 7 of 9: Insilico Filteration."; //FARHAN
//if (true) // (parameters.PtmAllow == 0)
// _insilicoFilter.ComputeInsilicoScore(candidateProteins, massSpectrometryData.Mass, parameters.HopThreshhold);
moduleTimer.Stop();
executionTimes.InsilicoTime = moduleTimer.Elapsed.ToString();
}
private void StoreSearchResults(SearchParametersDto parameters, List <ProteinDto> candidateProteins, ExecutionTimeDto executionTimes,
int fileNumber)
{
if (candidateProteins.Count > Constants.NumberOfResultsToStore)
{
candidateProteins = candidateProteins.Take(Constants.NumberOfResultsToStore).ToList <ProteinDto>();
}
var final = new SearchResultsDto(parameters.Queryid, candidateProteins, executionTimes);
_dataLayer.StoreResults(final, parameters.PeakListFileName[fileNumber], fileNumber);
}
private void PerformSearch(SearchParametersDto parameters)
{
//Logging.CreateDirectory();
//Logging.DumpParameters(parameters);
//var counter = 0;
var numberOfPeaklistFiles = parameters.PeakListFileName.Length; //Number of files uploaded by user
for (var fileNumber = 0; fileNumber < numberOfPeaklistFiles; fileNumber++)
{
//Logging.CreatePeakFileDirectory(fileNumber);
try
{
var executionTimes = new ExecutionTimeDto();
var pipeLineTimer = new Stopwatch();
pipeLineTimer.Start();
//Step 0 - Read the Peaklist File
var massSpectrometryData = PeakListFileReaderModuleModule(parameters, fileNumber, executionTimes);
// Logging.DumpMsData(massSpectrometryData);
//Step 1 - 1st Algorithm - Mass Tuner
var old = massSpectrometryData.WholeProteinMolecularWeight;
ExecuteMassTunerModule(parameters, massSpectrometryData, executionTimes);
if (massSpectrometryData.WholeProteinMolecularWeight == 0)
{
massSpectrometryData.WholeProteinMolecularWeight = old;
}
//Logging.DumpMwTunerResult(massSpectrometryData);
//Step 2 - 1st Candidate Protein List --- (In SPECTRUM: Score_Mol_Weight)
var candidateProteins = GetCandidateProtein(parameters, massSpectrometryData);
double mass, error, mw_score;
for (var i = 0; i < candidateProteins.Count; ++i)
{
mass = candidateProteins[i].Mw;
error = Math.Abs(mass - massSpectrometryData.WholeProteinMolecularWeight);
if (error == 0)
{
mw_score = 1;
}
else
{
mw_score = 1 / (Math.Pow(2, error));
}
candidateProteins[i].MwScore = mw_score;
}
//Logging.DumpCandidateProteins(candidateProteins);
//Step 3 - 2nd Algorithm - Peptide Sequence Tags (PSTs)
if (parameters.DenovoAllow == 1)
{
ExecuteDenovoModule(parameters, massSpectrometryData, candidateProteins, executionTimes);
}
var t = 0;
double score = 0;
string lol;
//Logging.DumpModifiedProteins(candidateProteins);
//Step X - ??? Algorithm - Post Translational Modifications (PTMs) {{*****FARHAN!!! FOR THE TIME BEING ITS PTM IS AFTER INSILICO COMPARISON*****}}
//string candidateProteins = "xyz";
candidateProteins = ExecutePostTranslationalModificationsModule(parameters, candidateProteins, massSpectrometryData, executionTimes);
for (var i = 0; i < candidateProteins.Count; ++i)
{
if (candidateProteins[i].PstScore > score)
{
score = candidateProteins[i].PstScore;
lol = candidateProteins[i].Header;
t = i;
}
}
//Step 4 - ??? Algorithm - Spectral Comparison
ExecuteSpectralComparisonModule(parameters, candidateProteins, massSpectrometryData, executionTimes);
//Logging.DumpInsilicoScores(candidateProteins);
score = 0;
for (var i = 0; i < candidateProteins.Count; ++i)
{
if (candidateProteins[i].PstScore + candidateProteins[i].MwScore + candidateProteins[i].PtmScore > score)
{
score = candidateProteins[i].PstScore + candidateProteins[i].MwScore + candidateProteins[i].PtmScore;
lol = candidateProteins[i].Header;
t = i;
}
}
candidateProteins = ExecuteProteoformScoringModule(parameters, candidateProteins);
//Logging.DumpTotalScores(candidateProteins);
pipeLineTimer.Stop();
executionTimes.TotalTime = pipeLineTimer.Elapsed.ToString();
StoreSearchResults(parameters, candidateProteins, executionTimes, fileNumber);
}
catch (Exception r)
{
string k = r.Message;
System.Diagnostics.Debug.WriteLine(r.Message);
}
//Logging.DumpTotalTime(executionTimes);
//Logging.ExitPeakFileDirectory();
}
Send_Results_Link(parameters);
_dataLayer.Set_Progress(parameters.Queryid, 100);
}