public List <PstTagList> GeneratePeptideSequenceTags(SearchParametersDto parameters, MsPeaksDto peakData)
{
//Converting Peak List Data into 2D List
var peakDatalist = new List <peakData2Dlist>(); //Making a 2D list(peakDatalist) in which Mass & Intensity includes {{FARHAN!! ITS NOT AN EFFICIENT WAY}} NOt NEEDED THIS IF ONCE MsPeaksDto.cs is modified
for (int row = 0; row <= peakData.Mass.Count - 1; row++)
{
var dataforpeakDatalist = new peakData2Dlist(peakData.Mass[row], peakData.Intensity[row]);
peakDatalist.Add(dataforpeakDatalist);
}
var peakDatalistsort = peakDatalist.OrderBy(n => n.Mass).ToArray();
double[] MassPeakData = peakDatalistsort.Select(n => n.Mass).ToArray();
double[] IntensityPeakData = peakDatalistsort.Select(n => n.Intensity).ToArray();
var pstList = new List <NewPstTagsDtoGpu>();
GeneratePstGpu(MassPeakData, pstList, parameters.HopThreshhold, IntensityPeakData);
//if (IsFilterPstByLength(parameters))
// pstList = pstList.Where(t => t.AminoAcidTag.Length >= parameters.MinimumPstLength && t.AminoAcidTag.Length <= parameters.MaximumPstLength).ToList();
//FilterTagsWithMultipleOccurences(pstList);
////////////var PstTagListGpu = AccomodateIsoforms(pstList, parameters);
//AccomodateIsoforms(pstList);
//return pstList;
var pstList2 = new List <PstTagList>();
return(pstList2);
}
// Extracts a list Peptide Sequence Tags from the MS/MS peaklist
public List <PstTagList> GeneratePeptideSequenceTags(SearchParametersDto parameters, MsPeaksDto peakData)
{
List <PstTagList> PstTagCPU = new List <PstTagList>();
//////// ************* FARHAN!!! WHAT IF THERE WILL BE NO PST TAGS FOUND THEN, WHAT COULD HAPPENED...?????
//////// ************* FARHAN!!! WHAT IF THERE WILL BE NO PST TAGS FOUND THEN, WHAT COULD HAPPENED...?????
//////// ************* FARHAN!!! WHAT IF THERE WILL BE NO PST TAGS FOUND THEN, WHAT COULD HAPPENED...?????
//Making a 2D list(peakDatalist) in which Mass & Intensity includes
var peakDatalist = new List <peakData2Dlist>();
for (int row = 0; row <= peakData.Mass.Count - 1; row++)
{
var dataforpeakDatalist = new peakData2Dlist(peakData.Mass[row], peakData.Intensity[row]);
peakDatalist.Add(dataforpeakDatalist);
}
//Sort the peakDatalist with respect to the Mass in ascending order
var peakDatalistsort = peakDatalist.OrderBy(n => n.Mass).ToList();
var singleLengthPstTagList = GenerateSingleLengthPstList(parameters, peakDatalistsort); // This method will extract Single Length PST Tags
var multipleLenghtTagList = GenerateMultipleLenghtPstList(parameters, singleLengthPstTagList); // This method will extract Multiple Length PST Tags
//var pstTagsdata = multipleLenghtTagList; // Multiple Tags
//////// ************* FARHAN!!! WHAT IF THERE WILL BE NO PST TAGS FOUND THEN, WHAT COULD HAPPENED...?????
if (multipleLenghtTagList.Count != 0) // Here filtering out tags according to MIN & MAX threshold of PST lengths...
{
List <List <PstTagsDto> > TrimPstTagsList = PSTCpuGpuCombineMethod.TrimPstTags(multipleLenghtTagList, parameters); // Break the larger Tags into all possible smaller tags &&& Filtering the Tags according to Minimum-Maximum Range Length of PST
var FinalPstTagList = PSTCpuGpuCombineMethod.PstTagInfoList(TrimPstTagsList, parameters); //Calculating PST Tag Error, PST intensity, & Root Mean Square Error etc. && Finding the Unique PSTs: Remove all other redundant PSTs but keep only one having lowest Root Mean Square Error(RMSE)
//If 2 or more Tags are same then also keep just one
if (FinalPstTagList.Count != 0)
{
//var AccoFinalPstTagList = AccomodateIsoforms(FinalPstTagList, parameters); // Its Accomodated Isoforms also, considered... COMMENT ME MORE
List <PstTagList> PstTags = PSTCpuGpuCombineMethod.AccomodateIsoforms(FinalPstTagList, parameters);
PstTagCPU = PstTags;
}
}
return(PstTagCPU);
}
public void TuneWholeProteinMass(MsPeaksDto peakData, double molTolerance)
{ //Making a 2D list(peakDatalist) in which Mass & Intensity includes
var peakDatalist = new List<peakData2Dlist>();
for (int row = 0; row <= peakData.Mass.Count - 1; row++)
{
var dataforpeakDatalist = new peakData2Dlist(peakData.Mass[row], peakData.Intensity[row]);
peakDatalist.Add(dataforpeakDatalist);
}
//Sort the peakDatalist with respect to the Mass in ascending order
var peakDatalistsort = peakDatalist.OrderBy(n => n.Mass).ToList();
//FIGURE 5: STEP 2:::: SUMMATIONS FOR EACH M/Z I,J IN MS2 DATA [REF: SPCTRUM PAPER]
//Description::: Calculate Peak Sums and shortlist those falling within user specified tolerance.
var summationMassandaverageintensity = new List<peakData2Dlist>();
for (int i = 0; i <= peakDatalistsort.Count - 2; i++) //i starts from 0 so that's why "peakDatalistsort.Count - 1" and according to Formula "n-1" gives peakDatalistsort.Count - 2
{
for (int j = i + 1; j <= peakDatalistsort.Count - 1; j++)//j starts from 0 so that's why peakDatalistsort.Count - 1 and according to Formula just "n"
{
double cpusummationMassData = peakDatalistsort[i].Mass + peakDatalistsort[j].Mass; //Making Tuple sums of MS2 masses
if (peakData.WholeProteinMolecularWeight - molTolerance <= cpusummationMassData && cpusummationMassData <= peakData.WholeProteinMolecularWeight + molTolerance)//Masses & Intensities filter out due to the selected RANGE OF INTACT MASS +/- PROTEIN MASS TOLERANCE
{
double cpuaverageIntensityData = (peakDatalistsort[i].Intensity + peakDatalistsort[j].Intensity) / 2;
var dataforsummationMassandaverageintensity = new peakData2Dlist(cpusummationMassData, cpuaverageIntensityData);
summationMassandaverageintensity.Add(dataforsummationMassandaverageintensity); //Making 2D list for Mass & Intensity
}
}
}
//FIGURE 5: STEP 3 Running window have size of Proton (and starts from smallest mass of FIGURE 5: STEP 2 list) [REF: SPCTRUM PAPER]
double windowposition = summationMassandaverageintensity[0].Mass; //Smallest mass selected from Tuple Sums for creating a window positon
const double proton = 1.00727647; //Mass of proton
var windowcapturedelementsold = new List<peakData2Dlist>();
var oldindex = new List<int>(); //CHANGE MY NAME...
var count = new List<int>(); //CHANGE MY NAME...
double olddiff = 1, newdiff = 0;
//Add here SliderValue(BELOW)
double SliderValue = 0.5699; //HARD CODE NOW FOR WORKING WILL ADD THIS FEATURE INTO THE FRONTEND FOR USER DEFINED #FutureWork3b(CPU)
int summationMassandaverageintensityindex = summationMassandaverageintensity.Count - 1;
while (windowposition < summationMassandaverageintensity[summationMassandaverageintensityindex].Mass)
{
var newindex = new List<int>(); //CHANGE MY NAME...
var windowcapturedelementsnew = new List<peakData2Dlist>();
for (int i = 0; i <= summationMassandaverageintensityindex; i++)
{
if (windowposition <= summationMassandaverageintensity[i].Mass && summationMassandaverageintensity[i].Mass < windowposition + proton)//#DISCUSSION
{
var dataforwindowcapturedelementsnew = new peakData2Dlist(summationMassandaverageintensity[i].Mass, summationMassandaverageintensity[i].Intensity);
windowcapturedelementsnew.Add(dataforwindowcapturedelementsnew);
newindex.Add(i);
}
else if (summationMassandaverageintensity[i].Mass >= windowposition + proton)
{
break;
}
}
count.Add(windowcapturedelementsnew.Count);
int a = oldindex.Count;//count.Count;///DEL ME AFTER TESTING!!! :)
if (windowcapturedelementsnew.Count > windowcapturedelementsold.Count)
{
windowcapturedelementsold = windowcapturedelementsnew;
oldindex = newindex;
}
else if (windowcapturedelementsnew.Count == windowcapturedelementsold.Count)
{
olddiff = Math.Abs((windowcapturedelementsold[windowcapturedelementsold.Count - 1].Mass) - peakData.WholeProteinMolecularWeight);
newdiff = Math.Abs((windowcapturedelementsnew[windowcapturedelementsnew.Count -1].Mass) - peakData.WholeProteinMolecularWeight);
if (olddiff >= newdiff)
{
windowcapturedelementsold = windowcapturedelementsnew;
oldindex = newindex;
}
}
windowposition = windowposition + SliderValue;
}
//FIGURE 5: STEP 5:::: Applying formula [REF: SPCTRUM PAPER]
double[] dataforsumoftunedmassesandintensities = new double[windowcapturedelementsold.Count];//Its tunedmassnominator according to SPECTRUM's formula for TunedMass
double sumoftunedmassesandintensities = 0;
double sumoftunedintensities = 0;
for (int i = 0; i <= windowcapturedelementsold.Count - 1; i++)
{
dataforsumoftunedmassesandintensities[i] = windowcapturedelementsold[i].Mass * windowcapturedelementsold[i].Intensity;
sumoftunedmassesandintensities = sumoftunedmassesandintensities + dataforsumoftunedmassesandintensities[i];
//Actually, ""intensities are not tuned"" (there isn't any terminology in OUR Mass Tuner Algorithm) according to the algorithm but just for the sake of UNDERSTANDING variable names are "dataforsumoftunedintensities" & "sumoftunedintensities".
sumoftunedintensities = sumoftunedintensities + windowcapturedelementsold[i].Intensity;//Its tunedmassdenominator according to SPECTRUM's formula for TunedMass
}
peakData.WholeProteinMolecularWeight = sumoftunedmassesandintensities / sumoftunedintensities;// NOW, Tuned Mass will be consider as Intact Mass(WholeProteinMolecularWeight)
}
