public AnalysisRow (object queryRow, DataFilter dataFilter)
{
DataFilter = dataFilter;
Analysis = (DataModel.Analysis) queryRow;
}
public AnalysisRow(object queryRow, DataFilter dataFilter)
{
DataFilter = dataFilter;
Analysis = (DataModel.Analysis)queryRow;
}
public PeptideSpectrumMatchRow(object[] queryRow, DataFilter dataFilter, IList<Grouping<GroupBy>> checkedGroupings)
{
DataFilter = dataFilter;
int column = -1;
Spectrum = (DataModel.Spectrum) queryRow[++column];
Source = (DataModel.SpectrumSource) queryRow[++column];
Group = (DataModel.SpectrumSourceGroup) queryRow[++column];
Analysis = (DataModel.Analysis) queryRow[++column];
PeptideSpectrumMatchId = Convert.ToInt64(queryRow[++column]);
Rank = Convert.ToInt32(queryRow[++column]);
Charge = Convert.ToInt32(queryRow[++column]);
QValue = Convert.ToDouble(queryRow[++column]);
ObservedMass = Convert.ToDouble(queryRow[++column]);
double monoisotopicError = Convert.ToDouble(queryRow[++column]);
double averageError = Convert.ToDouble(queryRow[++column]);
// if absolute value of monoisotopic error is less than absolute value of average error
// or if the monoisotopic error is nearly a multiple of a neutron mass,
// then treat the mass as monoisotopic
if (PeptideSpectrumMatch.GetSmallerMassError(monoisotopicError, averageError) == monoisotopicError)
ExactMass = ObservedMass - monoisotopicError;
else
ExactMass = ObservedMass - averageError;
string modificationString = (string) queryRow[++column];
ModifiedSequence = (string) queryRow[++column];
if (!String.IsNullOrEmpty(modificationString) && modificationString.Contains('@'))
{
// build modified sequence
var modifications = modificationString.Split(' ').Last()
.Split(',')
.Select(o => o.Split('@'))
.Select(o => new { Offset = Convert.ToInt32(o[1]), DeltaMass = Convert.ToDouble(o[0]) })
.OrderByDescending(o => o.Offset);
var sb = new StringBuilder(ModifiedSequence);
string formatString = "[{0}]";
foreach (var mod in modifications)
if (mod.Offset == int.MinValue)
sb.Insert(0, String.Format(formatString, mod.DeltaMass));
else if (mod.Offset == int.MaxValue)
sb.AppendFormat(formatString, mod.DeltaMass);
else
sb.Insert(mod.Offset + 1, String.Format(formatString, mod.DeltaMass));
ModifiedSequence = sb.ToString();
}
// if not grouping by Spectrum, use Spectrum as the key column
if (checkedGroupings.Count(o => o.Mode == GroupBy.Spectrum) == 0)
{
Key = Spectrum.NativeID;
// try to abbreviate, e.g. "controllerType=0 controllerNumber=1 scan=123" -> "0.1.123"
try { Key = pwiz.CLI.msdata.id.abbreviate(Key); }
catch { }
// if not grouping by Source, prepend Spectrum.Source to the NativeID
if (checkedGroupings.Count(o => o.Mode == GroupBy.Source) == 0)
Key = (Group.Name + "/" + Source.Name + "/" + Key).Replace("//", "/");
}
else
Key = Rank.ToString();
}
