public ViewLibraryPepInfo AssociateMatchingPeptide(ViewLibraryPepInfo pepInfo, int charge, SrmSettingsDiff settingsDiff)
{
var key = pepInfo.Key;
var settings = _chargeSettingsMap[charge];
// Change current document settings to match the current library and change the charge filter to
// match the current peptide.
if (settings == null)
{
settings = _document.Settings;
var rankId = settings.PeptideSettings.Libraries.RankId;
if (rankId != null && !_selectedSpec.PeptideRankIds.Contains(rankId))
{
settings = settings.ChangePeptideLibraries(lib => lib.ChangeRankId(null));
}
settings = settings.ChangePeptideLibraries(
lib => lib.ChangeLibraries(new[] { _selectedSpec }, new[] { _selectedLibrary })
.ChangePick(PeptidePick.library))
.ChangeTransitionFilter(
filter => filter.ChangePrecursorCharges(new[] { charge }).ChangeAutoSelect(true))
.ChangeMeasuredResults(null);
_chargeSettingsMap[charge] = settings;
}
var nodePep = _matcher.GetModifiedNode(key, pepInfo.GetAASequence(_lookupPool), settings, settingsDiff);
if (nodePep != null)
{
pepInfo.PeptideNode = nodePep;
}
return(pepInfo);
}
public ViewLibraryPepInfo AssociateMatchingPeptide(ViewLibraryPepInfo pepInfo, Adduct charge, SrmSettingsDiff settingsDiff)
{
var key = pepInfo.Key;
if (key.IsPrecursorKey)
{
return(pepInfo);
}
var settings = _chargeSettingsMap[charge];
// Change current document settings to match the current library and change the charge filter to
// match the current peptide.
if (settings == null)
{
settings = _document.Settings;
var rankId = settings.PeptideSettings.Libraries.RankId;
if (rankId != null && !_selectedSpec.PeptideRankIds.Contains(rankId))
{
settings = settings.ChangePeptideLibraries(lib => lib.ChangeRankId(null));
}
var isProteomic = pepInfo.Target.IsProteomic;
settings = settings.ChangePeptideLibraries(
lib => lib.ChangeLibraries(new[] { _selectedSpec }, new[] { _selectedLibrary })
.ChangePick(PeptidePick.library))
.ChangeTransitionFilter(
filter => (isProteomic ?
filter.ChangePeptidePrecursorCharges(new[] { charge }) :
filter.ChangeSmallMoleculePrecursorAdducts(new[] { charge }))
.ChangeAutoSelect(true))
.ChangeMeasuredResults(null);
var staticMods = settings.PeptideSettings.Modifications.StaticModifications.ToList();
foreach (var crosslinkMod in Properties.Settings.Default.StaticModList.Where(mod =>
null != mod.CrosslinkerSettings))
{
if (!staticMods.Any(mod => mod.Name == crosslinkMod.Name))
{
staticMods.Add(crosslinkMod);
}
}
settings = settings.ChangePeptideSettings(
settings.PeptideSettings.ChangeModifications(
settings.PeptideSettings.Modifications.ChangeStaticModifications(staticMods)));
_chargeSettingsMap[charge] = settings;
}
var nodePep = _matcher.GetModifiedNode(key, settings, settingsDiff);
if (nodePep != null)
{
pepInfo = pepInfo.ChangePeptideNode(nodePep);
}
return(pepInfo);
}
public ViewLibraryPepInfo AssociateMatchingPeptide(ViewLibraryPepInfo pepInfo, Adduct charge, SrmSettingsDiff settingsDiff)
{
var key = pepInfo.Key;
if (key.IsPrecursorKey)
{
return(pepInfo);
}
var settings = _chargeSettingsMap[charge];
// Change current document settings to match the current library and change the charge filter to
// match the current peptide.
if (settings == null)
{
settings = _document.Settings;
var rankId = settings.PeptideSettings.Libraries.RankId;
if (rankId != null && !_selectedSpec.PeptideRankIds.Contains(rankId))
{
settings = settings.ChangePeptideLibraries(lib => lib.ChangeRankId(null));
}
var isProteomic = pepInfo.Target.IsProteomic;
settings = settings.ChangePeptideLibraries(
lib => lib.ChangeLibraries(new[] { _selectedSpec }, new[] { _selectedLibrary })
.ChangePick(PeptidePick.library))
.ChangeTransitionFilter(
filter => (isProteomic ?
filter.ChangePeptidePrecursorCharges(new[] { charge }) :
filter.ChangeSmallMoleculePrecursorAdducts(new[] { charge }))
.ChangeAutoSelect(true))
.ChangeMeasuredResults(null);
_chargeSettingsMap[charge] = settings;
}
var nodePep = _matcher.GetModifiedNode(key, settings, settingsDiff);
if (nodePep != null)
{
pepInfo = pepInfo.ChangePeptideNode(nodePep);
}
return(pepInfo);
}
