public List <IqTarget> CreateChargeStateTargets(IqTarget iqTarget, double minMZObs = 400, double maxMZObserved = 1500, int maxChargeStatesToCreate = 100)
{
var minCharge = 1;
var maxCharge = 100;
UpdateTargetMissingInfo(iqTarget);
var targetList = new List <IqTarget>();
for (var charge = minCharge; charge <= maxCharge; charge++)
{
var mz = iqTarget.MonoMassTheor / charge + DeconTools.Backend.Globals.PROTON_MASS;
if (mz < maxMZObserved)
{
if (mz < minMZObs)
{
break;
}
IqTarget chargeStateTarget = new IqChargeStateTarget();
CopyTargetProperties(iqTarget, chargeStateTarget);
//Note - make sure this step is done after the 'CopyTargetProperties'
chargeStateTarget.ChargeState = charge;
//adjust isotope profile to reflect new charge state
if (chargeStateTarget.TheorIsotopicProfile != null && iqTarget.TheorIsotopicProfile != null)
{
chargeStateTarget.TheorIsotopicProfile = AdjustIsotopicProfileMassesFromChargeState(chargeStateTarget.TheorIsotopicProfile, iqTarget.TheorIsotopicProfile.ChargeState, charge);
}
chargeStateTarget.MZTheor = chargeStateTarget.MonoMassTheor / chargeStateTarget.ChargeState +
DeconTools.Backend.Globals.PROTON_MASS;
targetList.Add(chargeStateTarget);
}
}
//sort by charge state (descending). Then take the top N charge states. Then reorder by charge state (ascending).
targetList = targetList.OrderByDescending(p => p.ChargeState).Take(maxChargeStatesToCreate).OrderBy(p => p.ChargeState).ToList();
return(targetList);
}
/// <summary>
/// Expands charge range to cover all instances of a given sequence
/// </summary>
/// <param name="parentTarget"></param>
/// <param name="referenceTarget"></param>
private void ExpandChargeRange(TopDownIqTarget parentTarget, ChromPeakIqTarget referenceTarget)
{
var childWorkflow = new ChargeStateChildTopDownIqWorkflow(Run, WorkflowParameters);
var childTargets = parentTarget.ChildTargets().ToArray();
var fitTolerance = 0.5;
var correlationTolerance = 0.95;
var minCharge = (IqChargeStateTarget)childTargets.First();
var maxCharge = (IqChargeStateTarget)childTargets.Last();
if (minCharge.GetResult().IqResultDetail.Chromatogram != null)
{
var charge = minCharge.ChargeState;
var extendDown = true;
while (extendDown)
{
var extend = new IqChargeStateTarget(childWorkflow);
charge = charge - 1;
extend.ChargeState = charge;
parentTarget.AddTarget(extend);
extend.RefineTarget();
extend.DoWorkflow();
extendDown = ChargeExpansionPeakSelection(parentTarget, referenceTarget, extend, correlationTolerance, fitTolerance);
}
}
if (maxCharge.GetResult().IqResultDetail.Chromatogram != null)
{
var charge = maxCharge.ChargeState;
var extendUp = true;
while (extendUp)
{
var extend = new IqChargeStateTarget(childWorkflow);
charge = charge + 1;
extend.ChargeState = charge;
parentTarget.AddTarget(extend);
extend.RefineTarget();
extend.DoWorkflow();
extendUp = ChargeExpansionPeakSelection(parentTarget, referenceTarget, extend, correlationTolerance, fitTolerance);
}
}
parentTarget.SortChildTargetsByCharge();
}
/// <summary>
/// Removes redundant charge state targets and adds in missing targets within range.
/// </summary>
public override void RefineChildTargets()
{
var chargeStates = new List <int>();
var children = ChildTargets();
var removeList = new List <IqTarget>();
foreach (IqChargeStateTarget child in children)
{
if (!chargeStates.Contains(child.ChargeState))
{
chargeStates.Add(child.ChargeState);
}
else
{
removeList.Add(child);
}
}
foreach (var removal in removeList)
{
RemoveTarget(removal);
}
chargeStates.Sort();
var minCharge = chargeStates.Min() - 3;
var maxCharge = chargeStates.Max() + 3;
for (var charge = minCharge; charge <= maxCharge; charge++)
{
if (!chargeStates.Contains(charge))
{
IqTarget newCharge = new IqChargeStateTarget();
newCharge.ChargeState = charge;
AddTarget(newCharge);
}
}
_childTargets.Sort((target1, target2) => target1.ChargeState.CompareTo(target2.ChargeState));
}
/// <summary>
/// Selects a peak that correlates with the reference target and returns a bool to continue extending the charge range
/// </summary>
/// <param name="parentTarget"></param>
/// <param name="referenceTarget"></param>
/// <param name="chargeTarget"></param>
/// <param name="correlationCutoff"></param>
/// <param name="fitCutoff"></param>
/// <returns></returns>
private bool ChargeExpansionPeakSelection(TopDownIqTarget parentTarget, ChromPeakIqTarget referenceTarget, IqChargeStateTarget chargeTarget, double correlationCutoff, double fitCutoff)
{
var iqChargeCorrelator = ChromatogramCorrelator as IqChargeCorrelator;
var peakTargets = chargeTarget.ChildTargets();
var sortedPeakTargets = peakTargets.OrderBy(x => x.GetResult().FitScore);
foreach (ChromPeakIqTarget target in sortedPeakTargets)
{
if (referenceTarget.ChromPeak != null)
{
var minScan = referenceTarget.ChromPeak.XValue - (0.5 * referenceTarget.ChromPeak.Width);
var maxScan = referenceTarget.ChromPeak.XValue + (0.5 * +referenceTarget.ChromPeak.Width);
if ((target.ChromPeak.XValue > minScan) && (target.ChromPeak.XValue < maxScan))
{
var correlation = iqChargeCorrelator.PairWiseChargeCorrelation(referenceTarget, target, Run, 3);
if (correlation > correlationCutoff && target.GetResult().FitScore < fitCutoff)
{
UpdateSelection(target);
var parentResult = parentTarget.GetResult() as TopDownIqResult;
foreach (var item in parentResult.ChargeCorrelationData.CorrelationData)
{
if (referenceTarget == item.ReferenceTarget)
{
var corrItem = new ChromCorrelationDataItem(0, 0, correlation);
var corr = new ChromCorrelationData();
corr.AddCorrelationData(corrItem);
item.PeakCorrelationData.Add(target, corr);
}
}
return(true);
}
}
}
}
return(false);
}