public override TargetCollection Import()
{
var targetCollection = new TargetCollection();
targetCollection.TargetList.Clear();
GetMassTagDataFromDB(targetCollection, MassTagsToBeRetrieved);
GetModDataFromDB(targetCollection, MassTagsToBeRetrieved);
var peptideUtils = new PeptideUtils();
var troubleSomePeptides = new List <TargetBase>();
foreach (var targetBase in targetCollection.TargetList)
{
var peptide = (PeptideTarget)targetBase;
var baseEmpiricalFormula = peptideUtils.GetEmpiricalFormulaForPeptideSequence(peptide.Code);
if (peptide.ContainsMods)
{
var peptide1 = peptide;
var mods = (from n in _massTagModData where n.Item1 == peptide1.ID select n);
foreach (var tuple in mods)
{
var modString = tuple.Item4;
try
{
baseEmpiricalFormula = EmpiricalFormulaUtilities.AddFormula(baseEmpiricalFormula, modString);
}
catch
{
Console.WriteLine("Failed to calculate empirical formula for the Target " + peptide.ID +
"; Having trouble with the mod: " + modString + "; This Target was NOT imported!!");
troubleSomePeptides.Add(peptide);
}
}
}
try
{
peptide.EmpiricalFormula = baseEmpiricalFormula;
}
catch
{
Console.WriteLine("Failed to calculate empirical formula for the Target " + peptide.ID +
"; Cannot parse this formula: " + peptide.EmpiricalFormula + "; This Target was NOT imported!!");
troubleSomePeptides.Add(peptide);
}
}
var cleanTargetList = new List <TargetBase>();
//filter out the bad peptides (the once with errors during empirical formula parsing)
foreach (var peptide in targetCollection.TargetList)
{
if (!troubleSomePeptides.Contains(peptide))
{
cleanTargetList.Add(peptide);
}
}
targetCollection.TargetList = cleanTargetList;
if (ChargeStateRangeBasedOnDatabase)
{
targetCollection.ApplyChargeStateFilter(ChargeStateFilterThreshold);
}
else
{
var chargeStateTargets = new List <TargetBase>();
foreach (var targetBase in targetCollection.TargetList)
{
var minCharge = 1;
var maxCharge = 100;
for (var charge = minCharge; charge <= maxCharge; charge++)
{
var mz = targetBase.MonoIsotopicMass / charge + Globals.PROTON_MASS;
if (mz < MaxMZForChargeStateRange)
{
if (mz < MinMZForChargeStateRange)
{
break;
}
TargetBase chargeStateTarget = new PeptideTarget((PeptideTarget)targetBase);
chargeStateTarget.ChargeState = (short)charge;
chargeStateTarget.MZ = chargeStateTarget.MonoIsotopicMass / charge + Globals.PROTON_MASS;
chargeStateTarget.ObsCount = -1;
chargeStateTargets.Add(chargeStateTarget);
}
}
}
targetCollection.TargetList = chargeStateTargets.OrderBy(p => p.ID).ThenBy(p => p.ChargeState).ToList();
}
return(targetCollection);
}
