public static void testSoftware(List <TheoreticalProtein> database)
{
string[] pepRead = File.ReadAllLines(@"C:\Users\Zach Rolfs\Desktop\Chemistry\Smith Research\Fusion Peptides\Neo\tests\testPepListInput.txt");
int nr = pepRead.Count();
List <PSM> realPSMs = new List <PSM>();
foreach (string s in pepRead)
{
string[] sArray = s.Split('\t');
PSM tempPSM = new PSM(sArray[0], Convert.ToInt16(sArray[1]), Convert.ToDouble(sArray[2]));
}
using (System.IO.StreamWriter file = new System.IO.StreamWriter(@"C:\Users\Zach Rolfs\Desktop\Chemistry\Smith Research\Fusion Peptides\Neo\Results\testPepListOutput.txt"))
{
/* AlternativeSequences altSeq = new AlternativeSequences(new Neo(), new System.ComponentModel.BackgroundWorker());
* altSeq.readProteins(database);
* foreach (string str in pepRead)
* {
* if (altSeq.foundParent(str, ParentInfo.terminal.C,new FusionCandidate(str)))
* {
* file.WriteLine(str + '\t' + "1");
* }
* else
* {
* file.WriteLine(str + '\t' + "0");
* }
* }*/
}
}
private void Button1_Click(object sender, EventArgs e)
{
if (OpenFileDialog1.ShowDialog() == System.Windows.Forms.DialogResult.OK)
{
Index = 0;
Array.Resize(ref PSM_Surface, OpenFileDialog1.FileNames.Length);
for (int i = 0; i <= OpenFileDialog1.FileNames.Length - 1; i++)
{
PSM_Surface[i] = new PSM();
if (OpenFileDialog1.FilterIndex == 1)
{
PSM_Surface[i].LoadPSM(OpenFileDialog1.FileNames[i], CheckBox1.Checked);
}
else if (OpenFileDialog1.FilterIndex == 2)
{
PSM_Surface[i].LoadPTC(OpenFileDialog1.FileNames[i], CheckBox1.Checked);
}
else if (OpenFileDialog1.FilterIndex == 3)
{
PSM_Surface[i].LoadPSF(OpenFileDialog1.FileNames[i], CheckBox1.Checked);
}
}
Label1.Text = (Index + 1).ToString() + @"\" + PSM_Surface.Length.ToString();
GlControl1.Invalidate();
}
}
//public PlotModel display_heatMap()
//{
// var model = new PlotModel();
// model.Title = "Cos Similarity";
// var linearAxis1 = new LinearAxis();
// linearAxis1.Position = AxisPosition.Bottom;
// model.Axes.Add(linearAxis1);
// var linearAxis2 = new LinearAxis();
// model.Axes.Add(linearAxis2);
// return model;
//}
public PlotModel display_heatMap()
{
var model = new PlotModel();
model.Title = "Cos Similarity";
var linearColorAxis1 = new LinearColorAxis();
linearColorAxis1.HighColor = OxyColors.Gray;
linearColorAxis1.LowColor = OxyColors.Black;
linearColorAxis1.Position = AxisPosition.Right;
model.Axes.Add(linearColorAxis1);
var linearAxis1 = new LinearAxis();
linearAxis1.Position = AxisPosition.Bottom;
linearAxis1.Minimum = Min;
linearAxis1.Maximum = Max;
model.Axes.Add(linearAxis1);
var linearAxis2 = new LinearAxis();
linearAxis2.Minimum = Min;
linearAxis2.Maximum = Max;
model.Axes.Add(linearAxis2);
var heatMapSeries1 = new HeatMapSeries();
heatMapSeries1.X0 = 0;
heatMapSeries1.X1 = 1.0;
heatMapSeries1.Y0 = 0;
heatMapSeries1.Y1 = 1.0;
heatMapSeries1.Interpolate = false;
heatMapSeries1.Data = new Double[Scores.Count, Scores.Count];
for (int i = 0; i < Scores.Count; ++i)
{
for (int j = 0; j < Scores.Count; ++j)
{
heatMapSeries1.Data[i, j] = Scores[i][j];
}
}
model.Series.Add(heatMapSeries1);
heatMapSeries1.MouseDown += (s, e) =>
{
DataPoint point = model.Axes[1].InverseTransform(e.Position.X, e.Position.Y, model.Axes[2]);
int x_index = (int)((point.X - this.Min) / this.Width);
int y_index = (int)((point.Y - this.Min) / this.Width);
if (x_index < 0 || x_index >= Ncs.Count || y_index < 0 || y_index >= Ncs.Count)
{
return;
}
string title1 = Ncs[x_index].get_title();
string title2 = Ncs[y_index].get_title();
int psm1_index = (int)Psm_hash[title1];
int psm2_index = (int)Psm_hash[title2];
PSM psm1 = MainW.psms[psm1_index];
PSM psm2 = MainW.psms[psm2_index];
PlotModel model0 = display_TwoMS2(psm1, psm2);
Model_Window mw = new Model_Window(model0, psm2.Title + "-" + psm1.Title);
mw.Show();
};
return(model);
}
private static string GetScore(PSM psm, string strScoreName, string strValueIfMissing)
{
if (!psm.TryGetScore(strScoreName, out var strScoreValue))
{
strScoreValue = strValueIfMissing;
}
return(strScoreValue);
}
public LocalizedHit(PSM psm, PeptideIsoform isoform, PeptideIsoform secondIsoform, int numSDFs, int sdfs, int sdfs2, double pvalue, double ascore)
{
PSM = psm;
LocalizedIsoform = isoform;
SecondBestPeptideIsoform = secondIsoform;
NumberOfSiteDeterminingFragments = numSDFs;
BestPeptideSDFCount = sdfs;
SecondBestPeptideSDFCount = sdfs2;
PValue = pvalue;
AScore = ascore;
MatchDifference = isoform.SpectralMatch.Matches - secondIsoform.SpectralMatch.Matches;
}
public LocalizedHit(PSM psm, PeptideIsoform isoform, PeptideIsoform secondIsoform, int numSDFs, int sdfs, int sdfs2, double pvalue, double ascore)
{
PSM = psm;
LocalizedIsoform = isoform;
SecondBestPeptideIsoform = secondIsoform;
NumberOfSiteDeterminingFragments = numSDFs;
BestPeptideSDFCount = sdfs;
SecondBestPeptideSDFCount = sdfs2;
PValue = pvalue;
AScore = ascore;
MatchDifference = isoform.SpectralMatch.Matches - secondIsoform.SpectralMatch.Matches;
}
public PlotModel display_TwoMS2(PSM psm1, PSM psm2)
{
Spectra spec1 = null, spec2 = null;
Peptide pep1 = null, pep2 = null;
MainW.parse_PSM(psm1, ref spec1, ref pep1);
MainW.parse_PSM(psm2, ref spec2, ref pep2);
PlotModel model = new PlotModel();
LinearAxis x_axis = new LinearAxis();
x_axis.Position = AxisPosition.Bottom;
x_axis.Maximum = (spec1.Peaks.Last().Mass > spec2.Peaks.Last().Mass ? spec1.Peaks.Last().Mass : spec2.Peaks.Last().Mass) + 50;
x_axis.Minimum = (spec1.Peaks[0].Mass < spec2.Peaks[0].Mass ? spec1.Peaks[0].Mass : spec2.Peaks[0].Mass) - 50;
x_axis.AbsoluteMaximum = x_axis.Maximum;
x_axis.AbsoluteMinimum = x_axis.Minimum;
x_axis.PositionAtZeroCrossing = true;
x_axis.TickStyle = TickStyle.Crossing;
x_axis.IsAxisVisible = false;
model.Axes.Add(x_axis);
LinearAxis y_axis = new LinearAxis();
y_axis.Minimum = -100;
y_axis.Maximum = 100;
y_axis.IsPanEnabled = false;
y_axis.IsZoomEnabled = false;
y_axis.Title = psm2.Title + "-" + psm1.Title;
model.Axes.Add(y_axis);
LineSeries ls = new LineSeries();
ls.Color = OxyColors.Black;
ls.LineStyle = LineStyle.Solid;
ls.Points.Add(new DataPoint(x_axis.Minimum, 0));
ls.Points.Add(new DataPoint(x_axis.Maximum, 0));
model.Series.Add(ls);
MainW.psm_help.Switch_PSM_Help(spec1, pep1);
MainW.psm_help.Pep.Tag_Flag = int.Parse(psm1.Pep_flag);
MainW.psm_help.Match_BY();
update_peaks(spec1, ref model);
MainW.psm_help.Switch_PSM_Help(spec2, pep2);
MainW.psm_help.Pep.Tag_Flag = int.Parse(psm2.Pep_flag);
MainW.psm_help.Match_BY();
for (int i = 0; i < spec2.Peaks.Count; ++i)
{
spec2.Peaks[i].Intensity = -spec2.Peaks[i].Intensity;
}
update_peaks(spec2, ref model);
return(model);
}
private string GetScore(PSM currentPSM, string scoreColumnName, string alternativeName = "", string valueIfNotFound = "-1")
{
if (currentPSM.TryGetScore(scoreColumnName, out var value))
{
return(value);
}
if (!string.IsNullOrEmpty(alternativeName) && currentPSM.TryGetScore(alternativeName, out var alternativeValue))
{
return(alternativeValue);
}
return(valueIfNotFound);
}
internal void AddReference(POI connectedEntity)
{
string value = PSM.ReadPropertyString(Owner, DriGraph.ConnectedEntities);
//Avoid duplicate connections on con strings
//Or filter the connections by their type
//if (regex.IsMatch(value))
//{
// var matches = regex.Matches(value);
// foreach (Match match in matches)
// if (match.Groups["Handle"].Value == connectedEntity.Owner.Handle.ToString())
// //Do not add a reference if it already exists in the connection string
// return;
//}
value += $"{(int)EndType}:{(int)connectedEntity.EndType}:{connectedEntity.Owner.Handle};";
PSM.WritePropertyString(DriGraph.ConnectedEntities, value);
}
private static string GetCorrectedMassErrorPPM(PSM psm, out int intIsotopeError)
{
const double MASS_C13 = 1.00335483;
double dblMassErrorPPM = 0;
intIsotopeError = 0;
if (double.TryParse(psm.MassErrorDa, out var dblDelM))
{
// Examine dblDelM to determine which isotope was chosen
if (dblDelM >= -0.5)
{
// This is the typical case
while (dblDelM > 0.5)
{
dblDelM -= MASS_C13;
intIsotopeError += 1;
}
}
else
{
// This happens less often; but we'll still account for it
// In this case, intCorrectionCount will be negative
while (dblDelM < -0.5)
{
dblDelM += MASS_C13;
intIsotopeError -= 1;
}
}
dblMassErrorPPM = PeptideMassCalculator.MassToPPM(dblDelM, psm.PrecursorNeutralMass);
}
return(dblMassErrorPPM.ToString("0.0000"));
}
static void ClientThreadProc(object obj)
{
System.Net.Sockets.Socket dllclientSock = null;
byte[] buf = new byte[0x400 * 4];
try
{
dllclientSock = (System.Net.Sockets.Socket)obj;
System.Net.Sockets.NetworkStream netstm = new System.Net.Sockets.NetworkStream(dllclientSock);
for (bool run = true; run; )
{
int ich = -1;
try
{
ich = netstm.ReadByte();
}
catch
{
}
if (ich == -1)
{
break;
}
switch (ich)
{
case 'p': // Pin shared memory.
{
try
{
string smname = XContent.ReceiveXString(netstm, buf);
IntPtr hf = INVALID_HANDLE_VALUE;
IntPtr hmap = CreateFileMapping(hf, IntPtr.Zero, PAGE_READWRITE, 1, @"Global\" + smname);
int lasterror = Marshal.GetLastWin32Error();
if (IntPtr.Zero == hmap)
{
if (8 == lasterror)
{
throw new Exception("Shared memory segment named '" + smname + "' cannot be allocated; CreateFileMapping failed with ERROR_NOT_ENOUGH_MEMORY",
new OutOfMemoryException());
}
throw new Exception("Shared memory segment named '" + smname + "' cannot be allocated; CreateFileMapping failed with GetLastWin32Error=" + lasterror);
}
if (ERROR_ALREADY_EXISTS != lasterror)
{
throw new Exception("Shared memory segment named '" + smname + "' not found");
}
IntPtr ipview = MapViewOfFile(hmap, FILE_MAP_ALL_ACCESS, 0, 0, 0);
if (IntPtr.Zero == ipview)
{
lasterror = Marshal.GetLastWin32Error();
CloseHandle(hmap);
if (8 == lasterror)
{
throw new Exception("Shared memory segment named '" + smname + "' cannot be mapped into memory; MapViewOfFile failed with ERROR_NOT_ENOUGH_MEMORY",
new OutOfMemoryException());
}
throw new Exception("Shared memory segment named '" + smname + "' cannot be mapped into memory; MapViewOfFile failed with GetLastWin32Error=" + lasterror);
}
PSM psm;
psm.hmap = hmap;
psm.ipview = ipview;
psm.name = smname;
lock (pins)
{
pins.Add(psm);
}
netstm.WriteByte((byte)'+');
}
catch(Exception e)
{
try
{
netstm.WriteByte((byte)'-');
XContent.SendXContent(netstm, e.ToString());
}
catch
{
throw new Exception("Unable to report exception to caller (pin shared memory)", e);
}
}
}
break;
case 'u': // Unpin shared memory.
{
try
{
string smname = XContent.ReceiveXString(netstm, buf);
bool found = false;
PSM psm = new PSM();
lock (pins)
{
int ipsm = IndexOfPSM_unlocked(smname);
if (-1 != ipsm)
{
psm = pins[ipsm];
pins.RemoveAt(ipsm);
found = true;
}
}
if (found)
{
UnmapViewOfFile(psm.ipview);
CloseHandle(psm.hmap);
netstm.WriteByte((byte)'+');
}
else
{
netstm.WriteByte((byte)'-');
XContent.SendXContent(netstm, "Cannot unpin; shared memory segment not pinned: " + smname);
}
}
catch (Exception e)
{
try
{
netstm.WriteByte((byte)'-');
XContent.SendXContent(netstm, e.ToString());
}
catch
{
throw new Exception("Unable to report exception to caller (unpin shared memory)", e);
}
}
}
break;
case 'c': // Close.
run = false;
break;
}
}
netstm.Close();
dllclientSock.Close();
}
catch (Exception e)
{
XLog.errorlog("ClientThreadProc exception: " + e.ToString());
try
{
dllclientSock.Close();
}
catch (Exception e2)
{
}
}
}
static void ClientThreadProc(object obj)
{
System.Net.Sockets.Socket dllclientSock = null;
byte[] buf = new byte[0x400 * 4];
try
{
dllclientSock = (System.Net.Sockets.Socket)obj;
System.Net.Sockets.NetworkStream netstm = new System.Net.Sockets.NetworkStream(dllclientSock);
for (bool run = true; run;)
{
int ich = -1;
try
{
ich = netstm.ReadByte();
}
catch
{
}
if (ich == -1)
{
break;
}
switch (ich)
{
case 'p': // Pin shared memory.
{
try
{
string smname = XContent.ReceiveXString(netstm, buf);
IntPtr hf = INVALID_HANDLE_VALUE;
IntPtr hmap = CreateFileMapping(hf, IntPtr.Zero, PAGE_READWRITE, 1, @"Global\" + smname);
int lasterror = Marshal.GetLastWin32Error();
if (IntPtr.Zero == hmap)
{
if (8 == lasterror)
{
throw new Exception("Shared memory segment named '" + smname + "' cannot be allocated; CreateFileMapping failed with ERROR_NOT_ENOUGH_MEMORY",
new OutOfMemoryException());
}
throw new Exception("Shared memory segment named '" + smname + "' cannot be allocated; CreateFileMapping failed with GetLastWin32Error=" + lasterror);
}
if (ERROR_ALREADY_EXISTS != lasterror)
{
throw new Exception("Shared memory segment named '" + smname + "' not found");
}
IntPtr ipview = MapViewOfFile(hmap, FILE_MAP_ALL_ACCESS, 0, 0, 0);
if (IntPtr.Zero == ipview)
{
lasterror = Marshal.GetLastWin32Error();
CloseHandle(hmap);
if (8 == lasterror)
{
throw new Exception("Shared memory segment named '" + smname + "' cannot be mapped into memory; MapViewOfFile failed with ERROR_NOT_ENOUGH_MEMORY",
new OutOfMemoryException());
}
throw new Exception("Shared memory segment named '" + smname + "' cannot be mapped into memory; MapViewOfFile failed with GetLastWin32Error=" + lasterror);
}
PSM psm;
psm.hmap = hmap;
psm.ipview = ipview;
psm.name = smname;
lock (pins)
{
pins.Add(psm);
}
netstm.WriteByte((byte)'+');
}
catch (Exception e)
{
try
{
netstm.WriteByte((byte)'-');
XContent.SendXContent(netstm, e.ToString());
}
catch
{
throw new Exception("Unable to report exception to caller (pin shared memory)", e);
}
}
}
break;
case 'u': // Unpin shared memory.
{
try
{
string smname = XContent.ReceiveXString(netstm, buf);
bool found = false;
PSM psm = new PSM();
lock (pins)
{
int ipsm = IndexOfPSM_unlocked(smname);
if (-1 != ipsm)
{
psm = pins[ipsm];
pins.RemoveAt(ipsm);
found = true;
}
}
if (found)
{
UnmapViewOfFile(psm.ipview);
CloseHandle(psm.hmap);
netstm.WriteByte((byte)'+');
}
else
{
netstm.WriteByte((byte)'-');
XContent.SendXContent(netstm, "Cannot unpin; shared memory segment not pinned: " + smname);
}
}
catch (Exception e)
{
try
{
netstm.WriteByte((byte)'-');
XContent.SendXContent(netstm, e.ToString());
}
catch
{
throw new Exception("Unable to report exception to caller (unpin shared memory)", e);
}
}
}
break;
case 'c': // Close.
run = false;
break;
}
}
netstm.Close();
dllclientSock.Close();
}
catch (Exception e)
{
XLog.errorlog("ClientThreadProc exception: " + e.ToString());
try
{
dllclientSock.Close();
}
catch (Exception e2)
{
}
}
}
public void Read(IList<Modification> fixedModifications, int numberOfTopHits = 1, bool higherScoresAreBetter = false)
{
_data.Clear();
bool first = true;
using (CsvReader reader = new CsvReader(new StreamReader(FilePath), true))
{
string[] headers = reader.GetFieldHeaders();
HasPPMInfo = headers.Contains("Precursor Mass Error (ppm)");
while (reader.ReadNextRecord())
{
if (first)
{
RawFileName = reader["Filename/id"].Split('.')[0];
first = false;
}
int scanNumber = int.Parse(reader["Spectrum number"]);
PSM psm = new PSM(scanNumber) {Score = double.Parse(reader["E-value"])};
SortedMaxSizedContainer<PSM> peptides;
if (!_data.TryGetValue(scanNumber, out peptides))
{
peptides = new SortedMaxSizedContainer<PSM>(numberOfTopHits);
_data.Add(scanNumber, peptides);
}
if (!peptides.Add(psm))
continue;
psm.FileName = reader["Filename/id"];
psm.Charge = int.Parse(reader["Charge"]);
psm.IsDecoy = reader["Defline"].StartsWith("DECOY_");
if (HasPPMInfo)
psm.PrecursorMassError = double.Parse(reader["Precursor Mass Error (ppm)"]);
psm.SetSequenceAndMods(reader["Peptide"].ToUpper(), fixedModifications, reader["Mods"]);
}
}
PeptideSpectralMatches.Clear();
foreach (SortedMaxSizedContainer<PSM> set in _data.Values)
{
PeptideSpectralMatches.AddRange(set);
}
}
/// <summary>
/// Loads all the unique peptide sequences (L / I ambiguous) from the OMSSA csv files
/// supplied. Keeps track of all the psms for those peptides as well.
/// </summary>
/// <param name="csvFiles">The OMSSA .csv Files to read the PSMs from</param>
/// <returns>A Dictionary of all unique peptide sequences with values of all the PSMs</returns>
private Dictionary<string, Peptide> GetAllUniquePeptides(IEnumerable<CsvFile> csvFiles)
{
Log("Reading in unique peptides sequences from all .csv files...");
Dictionary<string, Peptide> peptides = new Dictionary<string, Peptide>(1 << 16);
Proteases = new HashSet<Protease>();
int psmCount = 0;
// Loop over each input file and read its contents
foreach (CsvFile csvfile in csvFiles)
{
// Keep a list of all the proteases used
Proteases.Add(Protease.GetProtease(csvfile.Protease));
// Counter for the number of PSMs loaded in this csvfile
int csvPsmCount = 0;
string sequenceString = "Peptide";
string pvalueString = "P-value";
bool proteomeDiscover = false;
// Open up the csvfile and read its contents, skipping the header
using (CsvReader reader = new CsvReader(new StreamReader(csvfile.FilePath), true))
{
if (reader.GetFieldHeaders().Contains("XCorr"))
{
sequenceString = "Sequence";
pvalueString = "PEP";
proteomeDiscover = true;
}
// Read each line of the csv
while (reader.ReadNextRecord())
{
// Remove leucine / isoleucine ambiguity
string leuSeq = reader[sequenceString].ToUpper().Replace('I', 'L');
double rt = 0;
int specNum = 0;
if (proteomeDiscover)
{
if (ProteinsPerMinute)
rt = double.Parse(reader["RT [min]"]);
}
else
{
specNum = int.Parse(reader["Spectrum number"]);
if (ProteinsPerMinute)
rt = double.Parse(omssaRTRegex.Match(reader["Filename/id"]).Groups[1].Value);
}
double pvalue = double.Parse(reader[pvalueString]);
// Create a new peptide spectral match
PSM psm = new PSM(csvfile, specNum, rt, pvalue);
// Add to the list of the all the unique peptides
Peptide realPep;
if (peptides.TryGetValue(leuSeq, out realPep)) // Faster than contains key since you only try to hash once
{
realPep.PSMs.Add(psm);
}
else
{
realPep = new Peptide(leuSeq);
realPep.PSMs.Add(psm);
peptides.Add(leuSeq, realPep);
// Check to see if the peptide was the biggest or smallest
if (leuSeq.Length < _smallestPeptide)
{
_smallestPeptide = leuSeq.Length;
}
if (leuSeq.Length > _largestPeptide)
{
_largestPeptide = leuSeq.Length;
}
}
// General psm counters;
csvPsmCount++;
}
}
// Total psms loaded
psmCount += csvPsmCount;
Log("{0:N0} PSMs were loaded from {1}", csvPsmCount, csvfile);
}
Log("{0:N0} unique peptides were found from the {1:N0} PSMs loaded ({2:F1}%). (I/L ambiguity removed)", peptides.Count, psmCount, 100.0 * ((double)peptides.Count / psmCount));
return peptides;
}
private bool CheckPsm( PSM psm )
{
if( psm.Peptide == null )
return false;
return CheckPsm( psm.passThreshold, psm.Rank, psm.Confidence, psm.Score, psm.ScoreType );
}
private void LoadRelations(
SortedList<string,string> SortedAccession, SortedList<string,Peptide> SortedPeptides)
{
if( m_mzid.Data.DataCollection.AnalysisData.SpectrumIdentificationList.Length != 1 )
throw new ApplicationException( "Multiple spectrum identification lists not supported" );
SortedList<string,PeptideEvidenceType> SortedEvidences = new SortedList<string, PeptideEvidenceType>();
foreach( PeptideEvidenceType evidence in m_mzid.Data.SequenceCollection.PeptideEvidence )
SortedEvidences.Add( evidence.id, evidence );
int SpectrumID = 1;
int PsmID = 1;
double score;
string type;
Peptide.ConfidenceType confidence;
foreach( SpectrumIdentificationResultType idres in
m_mzid.Data.DataCollection.AnalysisData.SpectrumIdentificationList[0].SpectrumIdentificationResult ) {
Spectrum spectrum = new Spectrum();
spectrum.ID = SpectrumID++;
spectrum.File = idres.spectraData_ref;
spectrum.SpectrumID = idres.spectrumID;
spectrum.Psm = new List<PSM>();
Spectra.Add(spectrum);
foreach( SpectrumIdentificationItemType item in idres.SpectrumIdentificationItem ) {
//Console.Out.WriteLine(item.id);
GetPsmScore( item, out score, out type, out confidence );
PSM psm = new PSM();
psm.ID = PsmID++;
psm.Charge = item.chargeState;
psm.Mz = item.experimentalMassToCharge;
psm.Rank = item.rank;
psm.Score = score;
psm.ScoreType = type;
psm.Confidence = confidence;
psm.passThreshold = item.passThreshold;
psm.Spectrum = spectrum;
spectrum.Psm.Add(psm);
if( item.PeptideEvidenceRef == null )
continue;
foreach( PeptideEvidenceRefType evref in item.PeptideEvidenceRef ) {
//Console.Out.WriteLine(evref.peptideEvidence_ref);
PeptideEvidenceType evidence = SortedEvidences[evref.peptideEvidence_ref];
Peptide pep = SortedPeptides[evidence.peptide_ref];
if( pep.Sequence == null || pep.Sequence.Length == 0 ) { // ProCon 0.9.348 bug
//Notify( "Skiped peptide with empty sequence: " + pep.DBRef );
continue;
}
pep.Decoy = evidence.isDecoy;
psm.Peptide = pep;
//pep.Psm.Add(psm);
Protein prot = m_SortedProteins[SortedAccession[evidence.dBSequence_ref]];
if( pep.Proteins.Contains(prot) )
continue;
prot.Peptides.Add( pep );
pep.Proteins.Add( prot );
}
}
}
}
