/// <summary>
/// Copies the target parameter to a new IqTarget.
/// </summary>
/// <param name="target">target parameter</param>
public IqTarget(IqTarget target)
: this()
{
var util = new IqTargetUtilities();
util.CopyTargetProperties(target, this);
}
/// <summary>
/// clones trees for root, parents and children and sets the correct node
/// </summary>
/// <param name="target">target we want to clone</param>
/// <returns></returns>
private static IqTarget CloneIqTrees(IqTarget target)
{
//initialize utilities
var util = new IqTargetUtilities();
//find root
var rootNode = target.RootTarget;
//this returnes the copied tree
var tempTarget = util.Clone(rootNode);
//select current node along the tree. we need to mangle the charge and the ID to ensure uniqueness
var selectID = target.ID;
var selectChargeState = target.ChargeState;
var targetList = new List <IqTarget>();
targetList.Add(tempTarget);
var nodeLevelTargets = util.GetTargetsFromNodelLevel(targetList, target.NodeLevel);
var s = (from n in nodeLevelTargets where n.ID == selectID && n.ChargeState == selectChargeState select n).Take(1).ToList();
return(s[0]);
}
/// <summary>
/// clones simple properties and deeper trees
/// </summary>
/// <param name="target"></param>
/// <returns></returns>
public IqTarget DeepClone(IqTarget target)
{
var util = new IqTargetUtilities();
//basic copy
//TODO: the problem is here is we are creating an IqTargetBasic, which might not fit everyone's liking
IqTarget copiedTarget = new IqTargetBasic();
CopyTargetProperties(target, copiedTarget);
//this returnes the copied tree
var deepCopy = CloneIqTrees(target);
//set root via private set
copiedTarget.RootTarget = deepCopy.RootTarget;
//set parent target
copiedTarget.ParentTarget = deepCopy.ParentTarget;
//set the child targets
var childTargets = deepCopy.ChildTargets().ToList();
if (deepCopy.HasChildren() && childTargets.Count > 0)
{
foreach (var subtarget in childTargets)
{
copiedTarget.AddTarget(subtarget);
}
}
return(copiedTarget);
}
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));
}
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);
}
public ChargeStateChildIqWorkflow(TargetedWorkflowParameters parameters) : base(parameters)
{
TargetUtilities = new IqTargetUtilities();
}
