private List <PstTagsDto> JoinInner(int home_peak, int length_tags, List <PstTagsDto> singleLengthPstTagList, int minusonesingleTagsFound, int plusonemaxpstlength, int length) // Here hop_peak will be considered as home_peak
{
List <PstTagsDto> wholeDatatemporaryListClasswise = new List <PstTagsDto>(); //Full PST data of this Class will be Stored into it
var subtemporaryList = new PstTagsDto(singleLengthPstTagList[home_peak].startIndex, singleLengthPstTagList[home_peak].endIndex, singleLengthPstTagList[home_peak].startIndexMass, singleLengthPstTagList[home_peak].endIndexMass, singleLengthPstTagList[home_peak].massDifferenceBetweenPeaks, singleLengthPstTagList[home_peak].AminoAcidSymbol, singleLengthPstTagList[home_peak].AminoAcidName, singleLengthPstTagList[home_peak].TagError, singleLengthPstTagList[home_peak].averageIntensity);
if (length == plusonemaxpstlength)
{
wholeDatatemporaryListClasswise.Add(subtemporaryList);
}
else
{
int hop_peak;
length = length + 1;
List <PstTagsDto> temporaryList = new List <PstTagsDto>();
temporaryList.Add(subtemporaryList);
wholeDatatemporaryListClasswise.Add(subtemporaryList);
int subindex = 0;
for (int start_peak = home_peak; start_peak <= minusonesingleTagsFound - 2; start_peak++) //
{
hop_peak = start_peak + 1;
if (singleLengthPstTagList[home_peak].endIndex == singleLengthPstTagList[hop_peak].startIndex) // CHECKING "ENDPOSITION" AND "STARTPOSITION" OF SINGLE LENGTH TAGS
{
wholeDatatemporaryListClasswise.Clear();
length_tags = length_tags + 1;
var temporaryListClassData = JoinInner(hop_peak, length_tags, singleLengthPstTagList, minusonesingleTagsFound, plusonemaxpstlength, length); //Here Again, JoinInner function is calling (Working as Recursive Function)
List <PstTagsDto> intersubwholeDatatemporaryListClasswise = new List <PstTagsDto>();
intersubwholeDatatemporaryListClasswise.AddRange(temporaryList);
intersubwholeDatatemporaryListClasswise.AddRange(temporaryListClassData);
List <PstTagsDto> subwholeDatatemporaryListClasswise = new List <PstTagsDto>();
subwholeDatatemporaryListClasswise.AddRange(intersubwholeDatatemporaryListClasswise);
//subwholeDatatemporaryListClasswise.Insert(subindex, temporaryList);
//subwholeDatatemporaryListClasswise.InsertRange(subindex, temporaryListClassData);
wholeDatatemporaryListClasswise.AddRange(subwholeDatatemporaryListClasswise);
subindex = subindex + 1;
}
}
}
return(wholeDatatemporaryListClasswise);
}
private List <List <PstTagsDto> > GenerateMultipleLenghtPstList(SearchParametersDto parameters, List <PstTagsDto> singleLengthPstTagList)
{ //FIGURE 6: STEP 3:::: OBTAIN AMINO ACIDS CORRESPONDING TO FRAGMENT-PAIR DIFFERENCES
//Hops having equal starting peak and ending peak values were joined together to form PST ladders
List <List <PstTagsDto> > wholeDatatemporaryList = new List <List <PstTagsDto> >(); //Full PST data will be Stored into it //LadderRaw
int hop_peak;
int length_tags = 0; //Indexing start from 0 so that why its "0"
int minusonesingleTagsFound = singleLengthPstTagList.Count - 1;
for (int home_peak = 0; home_peak <= minusonesingleTagsFound - 2; home_peak++)//HERE IS THE STARTING OF MAKING MORE THAN ON PST TAGS...
{
for (int startIndexmultiple = 0; startIndexmultiple <= minusonesingleTagsFound - 2; startIndexmultiple++)
{
hop_peak = startIndexmultiple + 1;
if (singleLengthPstTagList[home_peak].endIndex == singleLengthPstTagList[hop_peak].startIndex) // CHECKING "ENDPOSITION" AND "STARTPOSITION" OF SINGLE LENGTH TAGS
{
List <PstTagsDto> temporaryList = new List <PstTagsDto>();
var subtemporaryList = new PstTagsDto(singleLengthPstTagList[home_peak].startIndex, singleLengthPstTagList[home_peak].endIndex, singleLengthPstTagList[home_peak].startIndexMass, singleLengthPstTagList[home_peak].endIndexMass, singleLengthPstTagList[home_peak].massDifferenceBetweenPeaks, singleLengthPstTagList[home_peak].AminoAcidSymbol, singleLengthPstTagList[home_peak].AminoAcidName, singleLengthPstTagList[home_peak].TagError, singleLengthPstTagList[home_peak].averageIntensity); //Home Peak will be attached with everyone...
temporaryList.Add(subtemporaryList);
var temporaryListClassData = Join(hop_peak, length_tags, singleLengthPstTagList, minusonesingleTagsFound, parameters);
for (int index = 0; index <= temporaryListClassData.Count - 1; index++)
{
List <PstTagsDto> subwholeDatatemporaryList = new List <PstTagsDto>();
subwholeDatatemporaryList.Add(subtemporaryList); // Willl be start here
subwholeDatatemporaryList.AddRange(temporaryListClassData[index]);
wholeDatatemporaryList.Insert(length_tags, subwholeDatatemporaryList);
length_tags = length_tags + 1;
}
}
if (singleLengthPstTagList[home_peak].endIndex < singleLengthPstTagList[hop_peak].startIndex)
{
break;
}
}
}
return(wholeDatatemporaryList);
}
private List <PstTagsDto> GenerateSingleLengthPstList(SearchParametersDto parameters, List <peakData2Dlist> peakDatalistsort)
{
// SINGLE LENGTH PSTs
var GenerateSingleLengthPstList = new List <PstTagsDto>();
//m/z(of MS2) value differences for each Fragment-pair
//startIndex and endIndex are selecting upper triangle(in Matrix) for calculation to avoid Mirror Image Values {Means: startIndex = 1(means peak 1) and endIndex = 2 (means peak 2) is Equal to startIndex = 2(means peak 2) and endIndex = 1 (means peak 1) WHEN GIVING differences}
for (var home_peakIndexsingle = 0; home_peakIndexsingle <= peakDatalistsort.Count - 2; home_peakIndexsingle++) // startIndex=0 so that's why its "-1" and according to formula "n-1" which gives us peakData.Mass.Count - 2 //Starting from peak 1(startIndex = 0)
{
// for each element of peaklist after ith element
for (var hop_peakIndexsingle = home_peakIndexsingle + 1; hop_peakIndexsingle <= peakDatalistsort.Count - 1; hop_peakIndexsingle++) //endIndex starts from 0 so that's why peakData.Mass.Count - 1 and according to Formula just "n"
{
var massDifferenceBetweenPeaks = peakDatalistsort[hop_peakIndexsingle].Mass - peakDatalistsort[home_peakIndexsingle].Mass; //Mass difference between two peaks
for (int AminoAcidIndex = 0; AminoAcidIndex <= AminoAcidMasses.Length - 1; AminoAcidIndex++) //Taking 21 amino acids
{
var TagError = Math.Abs(massDifferenceBetweenPeaks - AminoAcidMasses[AminoAcidIndex]);
if (TagError <= parameters.HopThreshhold)
{
var aminoAcid = AminoAcidSymbol[AminoAcidIndex];
double avgIntensityList = (peakDatalistsort[home_peakIndexsingle].Intensity + peakDatalistsort[hop_peakIndexsingle].Intensity) / 2;
var singleLengthPstTag = new PstTagsDto(home_peakIndexsingle, hop_peakIndexsingle, peakDatalistsort[home_peakIndexsingle].Mass, peakDatalistsort[hop_peakIndexsingle].Mass, massDifferenceBetweenPeaks, AminoAcidSymbol[AminoAcidIndex], AminoAcidName[AminoAcidIndex], TagError, avgIntensityList);
GenerateSingleLengthPstList.Add(singleLengthPstTag);
}
else
{
if (TagError < -parameters.HopThreshhold)
{
break;
}
}
}
}
}
return(GenerateSingleLengthPstList);
}
private List <List <PstTagsDto> > Join(int home_peak, int length_tags, List <PstTagsDto> singleLengthPstTagList, int minusonesingleTagsFound, SearchParametersDto parameters) // IN ABOVE METHOD's PARAMETERS, hop_peak now will be USED as home_peak
{
int plusonemaxpstlength = parameters.MaximumPstLength + 1;
int length = 1; //Change my Name
int hop_peak;
int subindex = 0;
List <List <PstTagsDto> > wholeDatatemporaryListClasswise = new List <List <PstTagsDto> >(); //Full PST data of this Class will be Stored into it
List <List <PstTagsDto> > sub = new List <List <PstTagsDto> >();
List <List <PstTagsDto> > subData = new List <List <PstTagsDto> >();
List <PstTagsDto> temporaryList = new List <PstTagsDto>();
int checkpoint = 0;// We want to mimic Join.m of lines(17,18 and 24, 25, 26). So, that if for loop iterate and gave AA_Next{iter,1} = Hop_Info{Home_peak} while if statement(line 19) is FALSE then, what can we do in Perceptron....? {Introduced: checkpoint variable}
for (int start_peak = home_peak; start_peak <= minusonesingleTagsFound - 1; start_peak++)
{
hop_peak = start_peak + 1;
if (start_peak == home_peak) // New addition not in SPECTRUM. Now just one time value will be assigned...
{
var subtemporaryList = new PstTagsDto(singleLengthPstTagList[home_peak].startIndex, singleLengthPstTagList[home_peak].endIndex, singleLengthPstTagList[home_peak].startIndexMass, singleLengthPstTagList[home_peak].endIndexMass, singleLengthPstTagList[home_peak].massDifferenceBetweenPeaks, singleLengthPstTagList[home_peak].AminoAcidSymbol, singleLengthPstTagList[home_peak].AminoAcidName, singleLengthPstTagList[home_peak].TagError, singleLengthPstTagList[home_peak].averageIntensity);
temporaryList.Add(subtemporaryList); //Dear! make it more computationally efficient
sub.Add(temporaryList);
}
checkpoint = 0;
if (singleLengthPstTagList[home_peak].endIndex == singleLengthPstTagList[hop_peak].startIndex) // CHECKING "ENDPOSITION" AND "STARTPOSITION" OF SINGLE LENGTH TAGS
{
List <List <PstTagsDto> > subwholeDatatemporaryListClasswise = new List <List <PstTagsDto> >();
length_tags = length_tags + 1;
var temporaryListClassData = JoinInner(hop_peak, length_tags, singleLengthPstTagList, minusonesingleTagsFound, plusonemaxpstlength, length);
List <PstTagsDto> intersubwholeDatatemporaryListClasswise = new List <PstTagsDto>();
intersubwholeDatatemporaryListClasswise.AddRange(temporaryList);
intersubwholeDatatemporaryListClasswise.AddRange(temporaryListClassData);
subwholeDatatemporaryListClasswise.Insert(0, intersubwholeDatatemporaryListClasswise);
subData.InsertRange(subindex, subwholeDatatemporaryListClasswise);
subindex = subindex + 1;
checkpoint = 1; // "checkpoint" is used to check after reaching this point at which "subData populated" whether its go back and populate "sub" due to for loop...?
}
}
if (subData.Count != 0 && checkpoint == 0)
{
wholeDatatemporaryListClasswise.AddRange(subData);
wholeDatatemporaryListClasswise.AddRange(sub);
}
else if (subData.Count != 0 && checkpoint == 1)
{
wholeDatatemporaryListClasswise.AddRange(subData);
}
else
{
wholeDatatemporaryListClasswise.AddRange(sub);
}
return(wholeDatatemporaryListClasswise);
}