public void OkDialog()
{
var peptide = NodePeptide.Peptide;
var explicitModsCurrent = NodePeptide.ExplicitMods;
var modsDoc = DocSettings.PeptideSettings.Modifications;
var implicitMods = new ExplicitMods(NodePeptide,
modsDoc.StaticModifications, Settings.Default.StaticModList,
modsDoc.GetHeavyModifications(), Settings.Default.HeavyModList);
// Get static modifications from the dialog, and check for equality with
// the document implicit modifications.
TypedExplicitModifications staticTypedMods = null;
bool isVariableStaticMods = false;
var staticMods = GetExplicitMods(_listComboStatic, Settings.Default.StaticModList);
if (ArrayUtil.EqualsDeep(staticMods, implicitMods.StaticModifications))
{
if (!NodePeptide.HasVariableMods)
staticMods = null; // Use implicit modifications
else
{
staticMods = explicitModsCurrent.StaticModifications;
isVariableStaticMods = true;
}
}
else if (explicitModsCurrent != null &&
ArrayUtil.EqualsDeep(staticMods, explicitModsCurrent.StaticModifications))
{
staticMods = explicitModsCurrent.StaticModifications;
}
if (staticMods != null)
{
staticTypedMods = new TypedExplicitModifications(peptide,
IsotopeLabelType.light, staticMods);
}
var listHeavyTypedMods = new List<TypedExplicitModifications>();
for (int i = 0; i < _listLabelTypeHeavy.Count; i++)
{
var labelType = _listLabelTypeHeavy[i];
var heavyMods = GetExplicitMods(_listListComboHeavy[i], Settings.Default.HeavyModList);
if (ArrayUtil.EqualsDeep(heavyMods, implicitMods.GetModifications(labelType)))
continue;
var heavyTypedMods = new TypedExplicitModifications(peptide, labelType, heavyMods);
listHeavyTypedMods.Add(heavyTypedMods.AddModMasses(staticTypedMods));
}
ExplicitMods explicitMods = null;
if (staticMods != null || listHeavyTypedMods.Count > 0)
explicitMods = new ExplicitMods(peptide, staticMods, listHeavyTypedMods, isVariableStaticMods);
Helpers.AssignIfEquals(ref explicitMods, explicitModsCurrent);
ExplicitMods = explicitMods;
DialogResult = DialogResult.OK;
Close();
}
public ExplicitSequenceMassCalc(ExplicitMods mods, SequenceMassCalc massCalcBase, IsotopeLabelType labelType)
{
_massCalcBase = massCalcBase;
_mods = new ExplicitSequenceMods
{
Mods = mods.GetModifications(labelType),
StaticBaseMods = mods.GetStaticBaseMods(labelType),
ModMasses = mods.GetModMasses(_massCalcBase.MassType, labelType),
RequiresAllCalcMods = mods.IsVariableStaticMods
};
}
public RelativeRT GetRelativeRT(IsotopeLabelType labelType, string seq, ExplicitMods mods)
{
if (labelType.IsLight)
return RelativeRT.Matching;
// Default is matching
RelativeRT relativeRT = RelativeRT.Matching;
// One unkown modification makes everything unknown
// One preceding modification with no unknowns make relative RT preceding
// Overlapping overrides matching
if (mods != null && mods.IsModified(labelType))
{
foreach (var mod in mods.GetModifications(labelType))
{
if (mod.Modification.RelativeRT == RelativeRT.Unknown)
return RelativeRT.Unknown;
if (mod.Modification.RelativeRT == RelativeRT.Preceding)
relativeRT = RelativeRT.Preceding;
else if (mod.Modification.RelativeRT == RelativeRT.Overlapping &&
relativeRT == RelativeRT.Matching)
relativeRT = RelativeRT.Overlapping;
}
}
else
{
foreach (var mod in PeptideSettings.Modifications.GetModifications(labelType))
{
if (!mod.IsMod(seq))
continue;
if (mod.RelativeRT == RelativeRT.Unknown)
return RelativeRT.Unknown;
if (mod.RelativeRT == RelativeRT.Preceding)
relativeRT = RelativeRT.Preceding;
else if (mod.RelativeRT == RelativeRT.Overlapping &&
relativeRT == RelativeRT.Matching)
relativeRT = RelativeRT.Overlapping;
}
}
return relativeRT;
}
public PeptideDocNode EnsureMods(PeptideModifications source, PeptideModifications target,
MappedList<string, StaticMod> defSetStat, MappedList<string, StaticMod> defSetHeavy)
{
// Create explicit mods matching the implicit mods on this peptide for each document.
var sourceImplicitMods = new ExplicitMods(this, source.StaticModifications, defSetStat, source.GetHeavyModifications(), defSetHeavy);
var targetImplicitMods = new ExplicitMods(this, target.StaticModifications, defSetStat, target.GetHeavyModifications(), defSetHeavy);
// If modifications match, no need to create explicit modifications for the peptide.
if (sourceImplicitMods.Equals(targetImplicitMods))
return this;
// Add explicit mods if static mods not implicit in the target document.
IList<ExplicitMod> newExplicitStaticMods = null;
bool preserveVariable = HasVariableMods;
// Preserve non-variable explicit modifications
if (!preserveVariable && HasExplicitMods && ExplicitMods.StaticModifications != null)
{
// If they are not the same as the implicit modifications in the new document
if (!ArrayUtil.EqualsDeep(ExplicitMods.StaticModifications, targetImplicitMods.StaticModifications))
newExplicitStaticMods = ExplicitMods.StaticModifications;
}
else if (!ArrayUtil.EqualsDeep(sourceImplicitMods.StaticModifications, targetImplicitMods.StaticModifications))
{
preserveVariable = false;
newExplicitStaticMods = sourceImplicitMods.StaticModifications;
}
else if (preserveVariable)
{
newExplicitStaticMods = ExplicitMods.StaticModifications;
}
// Drop explicit mods if matching implicit mods are found in the target document.
IList<TypedExplicitModifications> newExplicitHeavyMods = new List<TypedExplicitModifications>();
// For each heavy label type, add explicit mods if static mods not found in the target document.
var newTypedStaticMods = newExplicitStaticMods != null
? new TypedExplicitModifications(Peptide, IsotopeLabelType.light, newExplicitStaticMods)
: null;
foreach (TypedExplicitModifications targetDocMod in targetImplicitMods.GetHeavyModifications())
{
// Use explicit modifications when available. Otherwise, compare against new implicit modifications
IList<ExplicitMod> heavyMods = (HasExplicitMods ? ExplicitMods.GetModifications(targetDocMod.LabelType) : null) ??
sourceImplicitMods.GetModifications(targetDocMod.LabelType);
if (heavyMods != null && !ArrayUtil.EqualsDeep(heavyMods, targetDocMod.Modifications) && heavyMods.Count > 0)
{
var newTypedHeavyMods = new TypedExplicitModifications(Peptide, targetDocMod.LabelType, heavyMods);
newTypedHeavyMods = newTypedHeavyMods.AddModMasses(newTypedStaticMods);
newExplicitHeavyMods.Add(newTypedHeavyMods);
}
}
if (newExplicitStaticMods != null || newExplicitHeavyMods.Count > 0)
return ChangeExplicitMods(new ExplicitMods(Peptide, newExplicitStaticMods, newExplicitHeavyMods, preserveVariable));
return ChangeExplicitMods(null);
}