protected TargetCollection GetMassTagTargets(string massTagFileName, List <int> targetIDsToFilterOn)
{
if (String.IsNullOrEmpty(massTagFileName) || !File.Exists(massTagFileName))
{
return(new TargetCollection());
}
if (massTagFileName.ToLower().Contains("_msgfplus.tsv"))
{
var iqTargetImporter = new BasicIqTargetImporter(massTagFileName);
var iqTargets = iqTargetImporter.Import();
var targetUtilities = new IqTargetUtilities();
var targetCollection = new TargetCollection
{
TargetList = new List <TargetBase>()
};
foreach (var iqTarget in iqTargets)
{
if (iqTarget.QualityScore > MsgfFdrScoreCutoff)
{
continue;
}
targetUtilities.UpdateTargetMissingInfo(iqTarget);
TargetBase oldStyleTarget = new PeptideTarget();
oldStyleTarget.ChargeState = (short)iqTarget.ChargeState;
oldStyleTarget.Code = iqTarget.Code;
oldStyleTarget.EmpiricalFormula = iqTarget.EmpiricalFormula;
oldStyleTarget.ID = iqTarget.ID;
oldStyleTarget.MZ = iqTarget.MZTheor;
oldStyleTarget.MonoIsotopicMass = iqTarget.MonoMassTheor;
oldStyleTarget.ScanLCTarget = iqTarget.ScanLC;
oldStyleTarget.NormalizedElutionTime = (float)iqTarget.ElutionTimeTheor;
oldStyleTarget.ElutionTimeUnit = DeconTools.Backend.Globals.ElutionTimeUnit.ScanNum;
targetCollection.TargetList.Add(oldStyleTarget);
}
return(targetCollection);
}
var importer = new MassTagFromTextFileImporter(massTagFileName);
return(importer.Import(targetIDsToFilterOn));
}
public override void LoadAndInitializeTargets(string targetsFilePath)
{
if (TargetImporter == null)
{
TargetImporter = new MSAlignIqTargetImporter(targetsFilePath);
}
Targets = TargetImporter.Import();
foreach (TopDownIqTarget target in Targets)
{
setParentNetFromChildren(target);
_targetUtilities.UpdateTargetMissingInfo(target);
target.RefineChildTargets();
target.SetChildrenFromParent();
}
}
protected virtual TargetCollection GetLcmsFeatureTargets(string targetsFilePath)
{
if (targetsFilePath.ToLower().Contains("_msgf"))
{
var iqTargetImporter = new BasicIqTargetImporter(targetsFilePath);
var iqTargets = iqTargetImporter.Import();
var targetUtilities = new IqTargetUtilities();
var targetCollection = new TargetCollection();
targetCollection.TargetList = new List <TargetBase>();
foreach (var iqTarget in iqTargets)
{
if (iqTarget.QualityScore > MsgfFdrScoreCutoff)
{
continue;
}
targetUtilities.UpdateTargetMissingInfo(iqTarget);
TargetBase oldStyleTarget = new LcmsFeatureTarget();
oldStyleTarget.ChargeState = (short)iqTarget.ChargeState;
oldStyleTarget.Code = iqTarget.Code;
oldStyleTarget.EmpiricalFormula = iqTarget.EmpiricalFormula;
oldStyleTarget.ID = iqTarget.ID;
oldStyleTarget.MZ = iqTarget.MZTheor;
oldStyleTarget.MonoIsotopicMass = iqTarget.MonoMassTheor;
oldStyleTarget.ScanLCTarget = iqTarget.ScanLC;
oldStyleTarget.NormalizedElutionTime = (float)iqTarget.ElutionTimeTheor;
oldStyleTarget.ElutionTimeUnit = DeconTools.Backend.Globals.ElutionTimeUnit.ScanNum;
targetCollection.TargetList.Add(oldStyleTarget);
}
return(targetCollection);
}
var importer =
new LcmsTargetFromFeaturesFileImporter(targetsFilePath);
var lcmsTargetCollection = importer.Import();
return(lcmsTargetCollection);
}