internal static Target FromHandle(LLVMTargetRef targetHandle)
{
targetHandle.ValidateNotDefault(nameof(targetHandle));
lock ( TargetMap )
{
if (TargetMap.TryGetValue(targetHandle, out Target retVal))
{
return(retVal);
}
retVal = new Target(targetHandle);
TargetMap.Add(targetHandle, retVal);
return(retVal);
}
}
public static List <IrtStandard> BestMatch(ICollection <SpectrumMzInfo> targets)
{
var potentialMatches = BestMatch(targets.Select(t => t.Key.Target)).ToList();
var matches = new List <IrtStandard>();
foreach (var standard in potentialMatches)
{
var doc = standard.GetDocument();
if (doc == null || doc.Peptides.All(nodePep => nodePep.ExplicitModsHeavy.Count == 0))
{
matches.Add(standard);
continue;
}
// Compare precursor m/zs in document (heavy label check)
var docPeps = new TargetMap <PeptideDocNode>(doc.Peptides.Select(pep => new KeyValuePair <Target, PeptideDocNode>(pep.ModifiedTarget, pep)));
var matchTargets = doc.Peptides.Select(pep => pep.ModifiedTarget).ToHashSet();
foreach (var target in targets)
{
if (!docPeps.TryGetValue(target.Key.Target, out var nodePep))
{
continue;
}
var nodeTranGroup = nodePep.TransitionGroups.FirstOrDefault(precursor => precursor.PrecursorCharge == target.Key.Charge);
if (nodeTranGroup != null && Math.Abs(nodeTranGroup.PrecursorMz - target.PrecursorMz) < 1)
{
matchTargets.Remove(nodePep.ModifiedTarget);
}
}
if (matchTargets.Count == 0)
{
matches.Add(standard);
}
}
if (matches.Contains(BIOGNOSYS_10) && matches.Contains(BIOGNOSYS_11))
{
matches.Remove(BIOGNOSYS_10);
}
return(matches);
}
public IEnumerable <PeptideDocNode> FindInDocument(SrmDocument document)
{
var standardDoc = GetDocument();
var docPeps = new TargetMap <Dictionary <int, SignedMz> >(standardDoc != null
? standardDoc.Peptides.Select(pep =>
new KeyValuePair <Target, Dictionary <int, SignedMz> >(pep.ModifiedTarget,
pep.TransitionGroups.ToDictionary(nodeTranGroup => nodeTranGroup.PrecursorCharge, nodeTranGroup => nodeTranGroup.PrecursorMz)))
: Peptides.Select(pep => new KeyValuePair <Target, Dictionary <int, SignedMz> >(pep.ModifiedTarget, null)));
// Compare precursor m/z to see if heavy labeled
foreach (var nodePep in document.Peptides)
{
if (docPeps.TryGetValue(nodePep.ModifiedTarget, out var precursors) &&
(precursors == null || nodePep.TransitionGroups.Any(nodeTranGroup => precursors.TryGetValue(nodeTranGroup.PrecursorCharge, out var mz) && Math.Abs(mz - nodeTranGroup.PrecursorMz) < 1)))
{
yield return(nodePep);
}
}
}
public double?CirtIrt(Target target)
{
return(_cirtAll.TryGetValue(target, out var irt) ? irt : (double?)null);
}
public void OkDialog()
{
var reader = new StringReader(textPeptides.Text);
var standardPeptides = new List <DbIrtPeptide>();
var invalidLines = new List <string>();
string line;
while ((line = reader.ReadLine()) != null)
{
line = line.Trim();
// Skip blank lines
if (string.IsNullOrEmpty(line))
{
continue;
}
DbIrtPeptide peptide = null;
var target = TargetResolver.ResolveTarget(line);
if (target == null || !_dictSequenceToPeptide.TryGetValue(target, out peptide)) // CONSIDER(bspratt) - small molecule equivalent?
{
invalidLines.Add(line);
}
standardPeptides.Add(peptide);
}
if (invalidLines.Count > 0)
{
string message;
if (invalidLines.Count == 1)
{
message = ModeUIAwareStringFormat(Resources.ChangeIrtPeptidesDlg_OkDialog_The_sequence__0__is_not_currently_in_the_database,
invalidLines[0]);
MessageBox.Show(this, message, Program.Name);
}
else
{
message = TextUtil.LineSeparate(GetModeUIHelper().Translate(Resources.ChangeIrtPeptidesDlg_OkDialog_The_following_sequences_are_not_currently_in_the_database),
string.Empty,
TextUtil.LineSeparate(invalidLines),
string.Empty,
GetModeUIHelper().Translate(Resources.ChangeIrtPeptidesDlg_OkDialog_Standard_peptides_must_exist_in_the_database));
MessageBox.Show(this, message, Program.Name);
}
return;
}
ReplacementProtein = null;
var selected = (ComboBoxProtein)comboProteins.SelectedItem;
if (selected.IsNotNull)
{
var removedPeptides = selected.RemovedPeptides(TargetResolver, textPeptides.Lines).ToArray();
if (removedPeptides.Any())
{
switch (MultiButtonMsgDlg.Show(this, TextUtil.LineSeparate(
Resources.ChangeIrtPeptidesDlg_OkDialog_The_following_peptides_were_removed_,
TextUtil.LineSeparate(removedPeptides.Select(nodePep => nodePep.ModifiedSequenceDisplay)),
Resources.ChangeIrtPeptidesDlg_OkDialog_Would_you_like_to_remove_them_from_the_document_),
MultiButtonMsgDlg.BUTTON_YES, MultiButtonMsgDlg.BUTTON_NO, true))
{
case DialogResult.Yes:
ReplacementProtein = selected.RemovePeptides(TargetResolver, textPeptides.Lines);
break;
case DialogResult.No:
break;
case DialogResult.Cancel:
return;
}
}
}
_standardPeptides = standardPeptides.ToArray();
DialogResult = DialogResult.OK;
}