//Generates all the combinations of a certain length, except duplicates
private static IEnumerable <PtmSet> combinations(List <Ptm> all_ptms, int combination_length, Dictionary <double, int> modification_ranks, int added_ptm_penalization)
{
Ptm[] result = new Ptm[combination_length];
Stack <int> stack = new Stack <int>();
stack.Push(0);
while (stack.Count > 0)
{
int result_index = stack.Count - 1;
int mod_index = stack.Pop();
while (mod_index < all_ptms.Count)
{
result[result_index] = all_ptms[mod_index];
result_index++;
mod_index++;
if (mod_index < all_ptms.Count)
{
stack.Push(mod_index);
}
if (result_index == combination_length)
{
Ptm[] destinationArray = new Ptm[combination_length];
Array.Copy(result, destinationArray, combination_length);
yield return(new PtmSet(destinationArray.ToList(), modification_ranks, added_ptm_penalization));
break;
}
}
}
}
//Reading in metamopheus excel
public List <TopDownHit> ReadMetamopheusFile(InputFile file)
{
//if neucode labeled, calculate neucode light theoretical AND observed mass! --> better for matching up
//if carbamidomethylated, add 57 to theoretical mass (already in observed mass...)
aaIsotopeMassList = new AminoAcidMasses(Sweet.lollipop.carbamidomethylation, Sweet.lollipop.neucode_labeled).AA_Masses;
List <TopDownHit> td_hits = new List <TopDownHit>();//for one line in excel file
//creates dictionary to find mods
Dictionary <string, Modification> mods = Sweet.lollipop.theoretical_database.all_mods_with_mass.ToDictionary(kv => kv.IdWithMotif, kv => kv);
List <List <string> > cells = ExcelReader.get_cell_strings(file, true);//This returns the entire sheet except for the header. Each row of cells is one List<string>
//get ptms on proteoform -- check for mods. IF not in database, make new topdown mod, show Warning message.
Parallel.ForEach(cells, cellStrings =>
{
bool add_topdown_hit = true; //if PTM or accession not found, will not add (show warning)
if (cellStrings.Count == 55)
{
List <Ptm> new_ptm_list = new List <Ptm>();
//if bad mod itll catch it to add to bad_topdown_ptms
try
{
PeptideWithSetModifications modsIdentifier = new PeptideWithSetModifications(cellStrings[14].Split('|')[0], mods);
var ptm_list = modsIdentifier.AllModsOneIsNterminus;
//for each entry in ptm_list make a new Ptm and add it to the new_ptm_list
foreach (KeyValuePair <int, Proteomics.Modification> entry in ptm_list)
{
Modification mod = Sweet.lollipop.theoretical_database.uniprotModifications.Values.SelectMany(m => m).Where(m => m.IdWithMotif == entry.Value.IdWithMotif).FirstOrDefault();
var Ptm = new Ptm();
if (mod != null)
{
new_ptm_list.Add(new Ptm(entry.Key, entry.Value));
}
else
{
lock (bad_topdown_ptms)
{
//error is somewahre in sequece
bad_topdown_ptms.Add("Mod Name:" + entry.Value.IdWithMotif + " at " + entry.Key);
add_topdown_hit = false;
}
}
}
}
catch (MzLibUtil.MzLibException)
{
lock (bad_topdown_ptms)
{
//error is somewahre in sequece
bad_topdown_ptms.Add("Bad mod at " + cellStrings[0] + " scan " + cellStrings[1]);
add_topdown_hit = false;
}
}
//This is the excel file header:
//cellStrings[0]=File Name
//cellStrings[1]=Scan Number
//cellStrings[2]=Scan Retention Time
//cellStrings[3]=Num Experimental Peaks
//cellStrings[4]=Total Ion Current
//cellStrings[5]=Precursor Scan Number
//cellStrings[6]=Precursor Charge
//cellStrings[7]=Precursor MZ
//cellStrings[8]=Precursor Mass
//cellStrings[9]=Score
//cellStrings[10]=Delta Score
//cellStrings[11]=Notch
//cellStrings[12]=Different Peak Matches
//cellStrings[13]=Base Sequence
//cellStrings[14]=Full Sequence
//cellStrings[15]=Essential Sequence
//cellStrings[16]=PSM Count
//cellStrings[17]=Mods
//cellStrings[18]=Mods Chemical Formulas
//cellStrings[19]=Mods Combined Chemical Formula
//cellStrings[20]=Num Variable Mods
//cellStrings[21]=Missed Cleavages
//cellStrings[22]=Peptide Monoisotopic Mass
//cellStrings[23]=Mass Diff (Da)
//cellStrings[24]=Mass Diff (ppm)
//cellStrings[25]=Protein Accession
//cellStrings[26]=Protein Name
//cellStrings[27]=Gene Name
//cellStrings[28]=Organism Name
//cellStrings[29]=Intersecting Sequence Variations
//cellStrings[30]=Identified Sequence Variations
//cellStrings[31]=Splice Sites
//cellStrings[32]=Contaminant
//cellStrings[33]=Decoy
//cellStrings[34]=Peptide Description
//cellStrings[35]=Start and End Residues In Protein
//cellStrings[36]=Previous Amino Acid
//cellStrings[37]=Next Amino Acid
//cellStrings[38]=All Scores
//cellStrings[39]=Theoreticals Searched
//cellStrings[40]=Decoy/Contaminant/Target
//cellStrings[41]=Matched Ion Series
//cellStrings[42]=Matched Ion Mass-To-Charge Ratios
//cellStrings[43]=Matched Ion Mass Diff (Da)
//cellStrings[44]=Matched Ion Mass Diff (Ppm)
//cellStrings[45]=Matched Ion Intensities
//cellStrings[46]=Matched Ion Counts
//cellStrings[47]=Localized Scores
//cellStrings[48]=Improvement Possible
//cellStrings[49]=Cumulative Target
//cellStrings[50]=Cumulative Decoy
//cellStrings[51]=QValue
//cellStrings[52]=Cumulative Target Notch
//cellStrings[53]=Cumulative Decoy Notch
//cellStrings[54]=QValue Notch
//cellStrings[55]=eValue
//cellStrings[56]=eScore
if (cellStrings[35].Length > 0)
{
string[] ids = cellStrings[35].Split('|');
//splits the string to get the value of starting index
string[] index = ids[0].Split(' ');
string[] startIndexValue = index[0].Split('[');
string startResidues = startIndexValue[1];
//splits string to get value of ending index
string[] endIndexValue = index[2].Split(']');
string endResidues = endIndexValue[0];
if (add_topdown_hit)
{
//if bad mod u want td hit to be false
TopDownHit td_hit = new TopDownHit(aaIsotopeMassList, file, TopDownResultType.TightAbsoluteMass, cellStrings[25], cellStrings[14], cellStrings[25], cellStrings[26], cellStrings[13],
Int32.TryParse(startResidues, out int j) ? j : 0, Int32.TryParse(endResidues, out int i) ? i : 0, new_ptm_list, Double.TryParse(cellStrings[8], out double d) ? d : 0, Double.TryParse(cellStrings[22], out d) ? d : 0,
Int32.TryParse(cellStrings[1], out i) ? i : 0, Double.TryParse(cellStrings[2], out d) ? d : 0, cellStrings[0].Split('.')[0], Double.TryParse(cellStrings[8], out d) ? d : 0, Sweet.lollipop.min_score_td + 1);
if (td_hit.begin > 0 && td_hit.end > 0 && td_hit.theoretical_mass > 0 && td_hit.pscore > 0 && td_hit.reported_mass > 0 && td_hit.score > 0 &&
td_hit.ms2ScanNumber > 0 && td_hit.ms2_retention_time > 0)
{
lock (td_hits) td_hits.Add(td_hit);
}
}
}
}
});
return(td_hits);
}
