public static List <PstTagList> PstTagInfoList(List <List <PstTagsDto> > LadderList, SearchParametersDto parameters)
{
string psttags;
int psttaglength;
double PstTagErrorSum;
double pstintensity;
double rootmeansquareerror;
var psttaginfolist = new List <Psts>();
for (int indexouterLadderList = 0; indexouterLadderList <= LadderList.Count - 1; indexouterLadderList++)
{
psttaglength = LadderList[indexouterLadderList].Count;
psttags = "";
PstTagErrorSum = 0;
pstintensity = 0;
for (int indexinnerLadderList = 0; indexinnerLadderList <= LadderList[indexouterLadderList].Count - 1; indexinnerLadderList++)
{
psttags = psttags + LadderList[indexouterLadderList][indexinnerLadderList].AminoAcidSymbol;
PstTagErrorSum = PstTagErrorSum + Math.Pow(LadderList[indexouterLadderList][indexinnerLadderList].TagError, 2);
pstintensity = pstintensity + LadderList[indexouterLadderList][indexinnerLadderList].averageIntensity; //averageIntensity= mean intensity of 2 peaks(home peak and hop peak)
}
rootmeansquareerror = (Math.Pow(PstTagErrorSum, .5) / psttaglength) * 10;
pstintensity = pstintensity / psttaglength; ///Panga Modlsdajl
var psttaginfo = new Psts(psttaglength, psttags, PstTagErrorSum, rootmeansquareerror, pstintensity);
psttaginfolist.Add(psttaginfo);
}
//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
var uniquepst = psttaginfolist.Select(test => test.psttags).Distinct().ToList();
var UniquePstTagInfoList = new List <Psts>(); //This will store data about Unique Pst Tag Information ////////IF POSSIBLE ASSIGN THE SIZE OF "uniquepst.Count"
for (int indexuniquepst = 0; indexuniquepst <= uniquepst.Count - 1; indexuniquepst++) // This loop will run on the Unique(distinct) PSTTAGS
{
var uniquepsttag = uniquepst[indexuniquepst]; //Each Unique(distinct) PSTTAG will be taken for selecting all corresponding data against this PSTTAG
var UniquePstTagMinError = (from c in psttaginfolist
group c by c.psttags into g
where g.Key == uniquepsttag
select new { psttags = g.Key, MinPstTagErrorSum = g.Select(m => m.PstTagErrorSum).Min() }).ToList(); // PSTTAG SELECTED; Select That list's Row which have Minimum "PST TAG ERROR SUM"
for (int indexpsttaginfolist = 0; indexpsttaginfolist <= psttaginfolist.Count - 1; indexpsttaginfolist++)
{
if (psttaginfolist[indexpsttaginfolist].psttags == uniquepsttag && psttaginfolist[indexpsttaginfolist].PstTagErrorSum == UniquePstTagMinError[0].MinPstTagErrorSum)
{
var temporaryData = psttaginfolist[indexpsttaginfolist];
UniquePstTagInfoList.Add(psttaginfolist[indexpsttaginfolist]);
break; //If 2 or more Tags are same then, keep just one AND BREAK THE LOOP...
}
}
}
//Filter tags according to fulltag error threshold
var FilteredTagList = new List <Psts>();
List <PstTagList> FinalPstTagList = new List <PstTagList>();
for (int indexUniquePstTagInfoList = 0; indexUniquePstTagInfoList <= UniquePstTagInfoList.Count - 1; indexUniquePstTagInfoList++)
{
// Filtering tags According to PST Tolerance & Scoring Tag Length
if (UniquePstTagInfoList[indexUniquePstTagInfoList].rootmeansquareerror <= parameters.PSTTolerance)
{
var ScoreError = Math.Exp(-2 * UniquePstTagInfoList[indexUniquePstTagInfoList].rootmeansquareerror);
double ScoreForLength = Math.Pow(UniquePstTagInfoList[indexUniquePstTagInfoList].psttaglength, 2);
double PstTagFrequency = UniquePstTagInfoList[indexUniquePstTagInfoList].PstTagIntensity * ScoreForLength;
var tempList = new PstTagList(UniquePstTagInfoList[indexUniquePstTagInfoList].psttaglength, UniquePstTagInfoList[indexUniquePstTagInfoList].psttags, ScoreError, PstTagFrequency);
FinalPstTagList.Add(tempList);
}
}
return(FinalPstTagList);
}
public static List <PstTagList> AccomodateIsoforms(List <PstTagList> FinalPstTagList, SearchParametersDto parameters)
{
char[] ResidueForReplacement = { 'L', 'D', 'N', 'E', 'Q' };
string newResidue;
List <PstTagList> NewAccomodatedPstTagList = new List <PstTagList>();
for (int indexFinalPstTagList = 0; indexFinalPstTagList <= FinalPstTagList.Count - 1; indexFinalPstTagList++) //Pura Chlana ha islya...
{
List <PstTagList> RowofFinalPstTagList = new List <PstTagList>();
RowofFinalPstTagList.Add(FinalPstTagList[indexFinalPstTagList]);
for (int indexResidueAA = 0; indexResidueAA <= ResidueForReplacement.Length - 1; indexResidueAA++) //ResidueForReplacement wise Chlana ha islya
{
char OldResidue = ResidueForReplacement[indexResidueAA];
string BeforeAccomodatePst = RowofFinalPstTagList[0].PstTags;
if (BeforeAccomodatePst.Contains(OldResidue))
{
newResidue = " ";
if (OldResidue == 'L')//Here I think Switch Case will be more better....!!!!
{
newResidue = "I";
}
else if (OldResidue == 'D')
{
newResidue = "B";
}
else if (OldResidue == 'N')
{
newResidue = "B";
}
else if (OldResidue == 'E')
{
newResidue = "Z";
}
else if (OldResidue == 'Q' && parameters.HopThreshhold <= 1.5)
{
newResidue = "Z";
}
else if (OldResidue == 'Q' && parameters.HopThreshhold > 1.5)
{
newResidue = "K";
}
for (int iter = 0; iter <= BeforeAccomodatePst.Length - 1; iter++)
{
if (BeforeAccomodatePst[iter] == OldResidue)
{
var ResidueRemoved = BeforeAccomodatePst.Remove(iter, 1);
var ResidueInserted = ResidueRemoved.Insert(iter, newResidue);
var AccomodatedPstTag = ResidueInserted;
var tempD = new PstTagList(FinalPstTagList[indexFinalPstTagList].PstTagLength, AccomodatedPstTag, FinalPstTagList[indexFinalPstTagList].PstErrorScore, FinalPstTagList[indexFinalPstTagList].PstFrequency);
NewAccomodatedPstTagList.Add(tempD);
BeforeAccomodatePst = AccomodatedPstTag;// Just for using same PST Tag for further Accommodation.......
}
}
}
}
}
FinalPstTagList.AddRange(NewAccomodatedPstTagList);
return(FinalPstTagList);
}
