public void ReadInMLNFile(string filename, int _numdatasets)
{
// Read in MultiAlign file
// Note : sep 26, 2011 - This will need to be updated when the new MLN format comes out
CSVFileHandler CsvFileHandler2 = new CSVFileHandler(filename, CSVFileHandler.READ_ONLY);
CsvFileHandler2.openFile();
String[] Attributes2;
CsvFileHandler2.readLine();
while ((Attributes2 = CsvFileHandler2.readLine()) != null)
{
MultiAlignRecord mrecord = new MultiAlignRecord();
mrecord.ID = int.Parse(Attributes2[0]);
mrecord.Size = int.Parse(Attributes2[1]);
mrecord.Mass = double.Parse(Attributes2[2]);
mrecord.NET = double.Parse(Attributes2[3]);
mrecord.AllocateNumberDatasets(_numdatasets);
int n_dataset = 0;
for (int i = 4; i < Attributes2.Length; i += 4)
{
UMCRecord u = new UMCRecord();
if (Attributes2[i] != "")
{
u.ScanRep = int.Parse(Attributes2[i]);
u.Abundance = double.Parse(Attributes2[i + 1]);
u.ScanStart = int.Parse(Attributes2[i + 2]);
u.ScanEnd = int.Parse(Attributes2[i + 3]);
}
mrecord._AssociatedUMCRecords.Add(u);
n_dataset++;
}
AddRecord(mrecord);
}
}
public void ReanInMLNV2File(string filename, int _numdatasets)
{
// Read in new version of MLN file
CSVFileHandler CsvFileHandler2 = new CSVFileHandler(filename, CSVFileHandler.READ_ONLY);
CsvFileHandler2.openFile();
String[] Attributes2;
CsvFileHandler2.readLine();
while ((Attributes2 = CsvFileHandler2.readLine()) != null)
{
MultiAlignRecord mrecord = new MultiAlignRecord();
mrecord.ID = int.Parse(Attributes2[0]);
mrecord.Mass = double.Parse(Attributes2[1]);
mrecord.NET = double.Parse(Attributes2[2]);
int numDatasetsToAllocate = 0;
if (mrecord.Mass < _MAP_MIN_MASS)
_MAP_MIN_MASS = mrecord.Mass;
if (mrecord.Mass > _MAP_MAX_MASS)
_MAP_MAX_MASS = mrecord.Mass;
if ((Attributes2.Length-5) / 8 != _numdatasets)
numDatasetsToAllocate = (Attributes2.Length -5) / 8;
else
numDatasetsToAllocate = _numdatasets;
mrecord.AllocateNumberDatasets(numDatasetsToAllocate);
for (int i = 5; i < Attributes2.Length; i += 8)
{
UMCRecord u = new UMCRecord();
if (Attributes2[i] != "")
{
u.ID = int.Parse(Attributes2[i]);
u.DatasetID = int.Parse(Attributes2[i + 1]);
u.MW = double.Parse(Attributes2[i + 2]);
u.Abundance = double.Parse(Attributes2[i + 4]);
u.ScanRep = int.Parse(Attributes2[i + 5]);
u.ScanStart = int.Parse(Attributes2[i + 6]);
u.ScanEnd = int.Parse(Attributes2[i + 7]);
mrecord._AssociatedUMCRecords.Add(u);
}
}
AddRecord(mrecord);
if (mrecord._AssociatedUMCRecords.Count > 10)
{
bool debig = true;
}
}
}
/// <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();
}