/*string _ProteinName;
string _PeptideSeq;
string _NGlycoSite;
double _PeptideMass;
string _GlycanComposition;
double _GlycanMass;
double _Y1;
double _PPM;*/
public FragEvents()
{
_id = -1;
_TransformResult = new GlypID.HornTransform.clsHornTransformResults();
_cid_intensity_values = new float[1];
_cid_mz_values = new float[1];
_CIDPeaks = new GlypID.Peaks.clsPeak[1];
_hcd_mz_values = new float[1];
_hcd_intensity_values = new float[1];
_HCDPeaks = new GlypID.Peaks.clsPeak[1];
_etd_intensity_values = new float[1];
_etd_mz_values = new float[1];
_ETDPeaks = new GlypID.Peaks.clsPeak[1];
_glycanType = GlypID.enmGlycanType.NA;
_hcdScore = 1;
_etdScore = 0;
_cidScore = 0;
_hcd_scan = 0;
_etd_scan = 0;
_cid_scan = 0;
_fdr = 1.0f;
_cid_sequencing_score = 0;
/*_ProteinName = "";
_PeptideSeq = "";
_NGlycoSite = "";
_PeptideMass = 0;
_GlycanComposition = "";
_GlycanMass = 0;
_PPM = 0;
_Y1 = 0;*/
_gp_record = new GlycopeptideRecord();
_parent_mz = 0;
_parent_scan = 0;
_parent_scan_time = 0;
_FalseHit = false;
/*_hcd_parent_mz = 0;
_etd_parent_mz = 0;
_cid_parent_mz = 0;*/
}
public void ClearGPInfo()
{
_glycanType = GlypID.enmGlycanType.NA;
GP_Record = new GlycopeptideRecord();
}
/// <summary>
/// Function to store glycopeptides
/// </summary>
/// <param name="sequences"> Peptide sequences</param>
/// <param name="glycans"> Glycans</param>
/// <param name="min_mass">Min Mass of the map</param>
/// <param name="max_mass">Max mass of the map</param>
public void SetGlycoPeptides(ref GlypID.Sequence.clsSequence[] sequences, ref GlypID.Glycan.clsGlycan[] glycans)
{
int num_gps = sequences.Length * glycans.Length;
_glycopeptides = new List<GlycopeptideRecord>();
for (int i = 0; i < sequences.Length; i++)
{
for (int j=0 ; j < glycans.Length; j++)
{
GlycopeptideRecord gp = new GlycopeptideRecord();
gp.Sequence = sequences[i];
gp.SequenceAverageMass = sequences[i].CalculateSequenceMass(false) ;
gp.SequenceMonoMass = sequences[i].CalculateSequenceMass(true) ;
gp.Glycan = glycans[j];
gp.GlycanAverageMass = glycans[j].CalculateGlycanMass(false) ;
gp.GlycanMonoMass = glycans[j].CalculateGlycanMass(true) ;
gp.GP_Average_Mass = _utils.CalculateGPMass(gp.SequenceAverageMass, gp.GlycanAverageMass) ;
gp.GP_Mono_Mass = _utils.CalculateGPMass(gp.SequenceMonoMass, gp.GlycanMonoMass) ;
gp.IsDecoy = gp.Glycan.is_decoy | gp.Sequence.is_decoy;
_glycopeptides.Add(gp);
}
}
//-- Sort by mono mass and create a hash table -- //
_glycopeptides.Sort(delegate(GlycopeptideRecord g1, GlycopeptideRecord g2) { return g1.GP_Mono_Mass.CompareTo(g2.GP_Mono_Mass); });
}
public FragEvents(FragEvents e)
{
_id = e._id;
_TransformResult = e._TransformResult;
_parent_mz = e._parent_mz;
_parent_scan = e._parent_scan;
_parent_scan_time = e._parent_scan_time;
_gp_record = e._gp_record;
_glycanType = e._glycanType;
_cid_scan = e._cid_scan;
_cid_intensity_values = e._cid_intensity_values;
_cid_mz_values = e._cid_mz_values;
_CIDPeaks = e._CIDPeaks;
_cidProfileType = e._cidProfileType;
_cidScore = e._cidScore;
// _cid_parent_mz = e._cid_parent_mz;
_hcd_scan = e._hcd_scan;
_hcd_intensity_values = e._hcd_intensity_values;
_hcd_mz_values = e._hcd_mz_values;
_HCDPeaks = e._HCDPeaks;
_hcdProfileType = e._hcdProfileType;
_hcdScore = e._hcdScore;
// _hcd_parent_mz = e._hcd_parent_mz;
_etd_scan = e._etd_scan;
_etd_intensity_values = e._etd_intensity_values;
_etd_mz_values = e._etd_mz_values;
_ETDPeaks = e._ETDPeaks;
_etdProfileType = e._etdProfileType;
_etdScore = e._etdScore;
// _etd_parent_mz = e._etd_parent_mz;
_fdr = e._fdr;
_cid_sequencing_score = e._cid_sequencing_score;
_FalseHit = e._FalseHit;
}
/// <summary>
/// Function to read in glycopeptides dictionary from file
/// </summary>
/// <param name="infile"></param>
public void LoadGlycopeptidesFromFile(string infile, double min_mass, double max_mass, bool create_hash)
{
CSVFileHandler CsvFileHandler2 = new CSVFileHandler(infile, CSVFileHandler.READ_ONLY);
CsvFileHandler2.openFile();
String[] Attributes2;
CsvFileHandler2.readLine();
if (create_hash)
_dGlycopeptides = new Dictionary<int, List<GlycopeptideRecord>>();
else
_glycopeptides = new List<GlycopeptideRecord>();
while ((Attributes2 = CsvFileHandler2.readLine()) != null)
{
double gpmass = double.Parse(Attributes2[0]);
if (gpmass >= min_mass && gpmass <= max_mass)
{
GlycopeptideRecord gp = new GlycopeptideRecord();
gp.GP_Mono_Mass = gpmass ;
gp.GP_Average_Mass = double.Parse(Attributes2[1]) ;
gp.Sequence.proteinName = Attributes2[2] ;
gp.Sequence.sequence = Attributes2[3];
gp.Sequence.is_decoy = bool.Parse(Attributes2[4]);
gp.Sequence.nGlycoSite = Attributes2[5] ;
gp.SequenceMonoMass = double.Parse(Attributes2[6]) ;
gp.SequenceAverageMass = double.Parse(Attributes2[7]) ;
gp.Glycan.SetMonosaccharideCompostion(Attributes2[8]) ;
gp.Glycan.composition = Attributes2[8];
gp.Glycan.is_decoy = bool.Parse(Attributes2[9]) ;
gp.GlycanMonoMass = double.Parse(Attributes2[10]) ;
gp.GlycanAverageMass = double.Parse(Attributes2[11]) ;
gp.IsDecoy = gp.Sequence.is_decoy | gp.Glycan.is_decoy;
if (create_hash)
{
List<GlycopeptideRecord> value_gp_list = new List<GlycopeptideRecord>();
int key_mass = (int)Math.Floor(gp.GP_Mono_Mass);
int min_mass_int = (int)Math.Floor(min_mass);
int max_mass_int = (int)Math.Floor(max_mass);
if (!_dGlycopeptides.ContainsKey(key_mass))
{
if (value_gp_list.Count > 0)
value_gp_list.Clear();
value_gp_list.Add(gp);
_dGlycopeptides.Add(key_mass, value_gp_list);
}
else
{
value_gp_list.Clear();
value_gp_list = _dGlycopeptides[key_mass];
value_gp_list.Add(gp);
_dGlycopeptides[key_mass] = value_gp_list;
}
}
else
_glycopeptides.Add(gp);
}
}
CsvFileHandler2.closeFile();
}