protected override IqTarget ConvertTextToIqTarget(List <string> processedRow)
{
var target = new IqTargetMsgfFirstHit();
target.ID = ParseIntField(processedRow, TargetIDHeaders, -1);
if (target.ID == -1)
{
target.ID = GetAutoIncrementForTargetID();
}
target.EmpiricalFormula = ParseStringField(processedRow, EmpiricalFormulaHeaders, string.Empty);
target.Code = ParseStringField(processedRow, CodeHeaders, "");
target.ElutionTimeTheor = ParseDoubleField(processedRow, NETHeaders, 0);
target.ScanLC = ParseIntField(processedRow, ScanHeaders, -1);
target.QualityScore = ParseDoubleField(processedRow, QualityScoreHeaders, -1);
target.ChargeState = ParseIntField(processedRow, ChargeStateHeaders, 0);
target.MassError = ParseDoubleField(processedRow, MassErrorHeaders, 0);
target.MZTheor = ParseDoubleField(processedRow, MzHeaders, 0);
target.MonoMassTheor = (target.MZTheor - DeconTools.Backend.Globals.PROTON_MASS) * target.ChargeState;
var targetUtilities = new IqTargetUtilities();
return(target);
}
public override void LoadAndInitializeTargets(string targetsFilePath)
{
if (string.IsNullOrEmpty(targetsFilePath))
{
IqLogger.Log.Info("IqMassAndNetAligner - no alignment targets were loaded. The inputted targets file path is NULL.");
return;
}
if (!File.Exists(targetsFilePath))
{
IqLogger.Log.Info("IqMassAndNetAligner - no alignment targets were loaded. The inputted targets file path is does not exist.");
return;
}
var importer = new IqTargetsFromFirstHitsFileImporter(targetsFilePath);
Targets = importer.Import().Where(p => p.QualityScore < 0.01).OrderBy(p => p.ID).ToList();
//Targets = Targets.Where(p => p.Code.Contains("FEQDGENYTGTIDGNMGAYAR")).ToList();
var filteredList = new List <IqTarget>();
//calculate empirical formula for targets using Code and then monoisotopic mass
foreach (var iqTarget in Targets)
{
iqTarget.Code = _peptideUtils.CleanUpPeptideSequence(iqTarget.Code);
if (_peptideUtils.ValidateSequence(iqTarget.Code))
{
iqTarget.EmpiricalFormula = _peptideUtils.GetEmpiricalFormulaForPeptideSequence(iqTarget.Code, true, true);
var calcMonoMass = EmpiricalFormulaUtilities.GetMonoisotopicMassFromEmpiricalFormula(iqTarget.EmpiricalFormula);
var monoMassFromFirstHitsFile = iqTarget.MonoMassTheor;
var massCalculationsAgree = Math.Abs(monoMassFromFirstHitsFile - calcMonoMass) < 0.02;
if (massCalculationsAgree)
{
iqTarget.MonoMassTheor = calcMonoMass;
iqTarget.ElutionTimeTheor = iqTarget.ScanLC / (double)Run.MaxLCScan;
filteredList.Add(iqTarget);
_targetUtilities.UpdateTargetMissingInfo(iqTarget, true);
var chargeStateTarget = new IqTargetMsgfFirstHit();
_targetUtilities.CopyTargetProperties(iqTarget, chargeStateTarget);
iqTarget.AddTarget(chargeStateTarget);
}
}
}
filteredList = (from n in filteredList
group n by new
{
n.Code,
n.ChargeState
}
into grp
select grp.OrderBy(p => p.QualityScore).First()
).ToList();
Targets = filteredList;
TargetedWorkflowParameters workflowParameters = new BasicTargetedWorkflowParameters();
workflowParameters.ChromNETTolerance = 0.005;
workflowParameters.ChromGenTolerance = 50;
//define workflows for parentTarget and childTargets
var parentWorkflow = new ChromPeakDeciderIqWorkflow(Run, workflowParameters);
var childWorkflow = new ChargeStateChildIqWorkflow(Run, workflowParameters);
var workflowAssigner = new IqWorkflowAssigner();
workflowAssigner.AssignWorkflowToParent(parentWorkflow, Targets);
workflowAssigner.AssignWorkflowToChildren(childWorkflow, Targets);
if (Targets.Count > 0)
{
IqLogger.Log.Info("IqMassAndNetAligner - Loaded " + Targets.Count + " targets for use in mass and net alignment");
}
else
{
IqLogger.Log.Info("IqMassAndNetAligner - NOTE - no targets have been loaded.");
}
//IqWorkflowAssigner workflowAssigner = new IqWorkflowAssigner();
//workflowAssigner.AssignWorkflowToParent(workflow, Targets);
}
