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;
}
_standardPeptides = standardPeptides.ToArray();
DialogResult = DialogResult.OK;
}
public Dictionary <LibKey, IonMobilityAndCCS> GetTableMeasuredIonMobility(bool useHighEnergyOffsets, eIonMobilityUnits units)
{
var e = new CancelEventArgs();
var dict = new Dictionary <LibKey, IonMobilityAndCCS>();
foreach (DataGridViewRow row in _gridMeasuredDriftTimePeptides.Rows)
{
if (row.IsNewRow)
{
continue;
}
string seq;
if (!ValidateSequence(e, row.Cells[EditDriftTimePredictorDlg.COLUMN_SEQUENCE], out seq))
{
return(null);
}
// OK, we have a non-empty "sequence" string, but is that actually a peptide or a molecule?
// See if there's anything in the document whose text representation matches what's in the list
var target = _targetResolver.ResolveTarget(seq);
if (target == null || target.IsEmpty)
{
return(null);
}
Adduct charge;
if (!ValidateCharge(e, row.Cells[EditDriftTimePredictorDlg.COLUMN_CHARGE], target.IsProteomic, out charge))
{
return(null);
}
double mobility;
if (!ValidateDriftTime(e, row.Cells[EditDriftTimePredictorDlg.COLUMN_ION_MOBILITY], out mobility))
{
return(null);
}
double?ccs;
if (!ValidateCCS(e, row.Cells[EditDriftTimePredictorDlg.COLUMN_CCS], out ccs))
{
return(null);
}
double highEnergyOffset = 0; // Set default value in case user does not provide one
if (useHighEnergyOffsets && !ValidateHighEnergyDriftTimeOffset(e, row.Cells[EditDriftTimePredictorDlg.COLUMN_HIGH_ENERGY_OFFSET], out highEnergyOffset))
{
return(null);
}
var ionMobility = IonMobilityValue.GetIonMobilityValue(mobility, units);
try
{
dict.Add(new LibKey(target, charge), IonMobilityAndCCS.GetIonMobilityAndCCS(ionMobility, ccs, highEnergyOffset));
}
// ReSharper disable once EmptyGeneralCatchClause
catch
{
// just take the first seen
}
}
return(dict);
}
private static TargetMap <bool> TextTargets(TargetResolver targetResolver, IEnumerable <string> pepLines)
{
return(new TargetMap <bool>(pepLines.Select(line => line.Trim())
.Where(line => !string.IsNullOrEmpty(line))
.Select(line => new KeyValuePair <Target, bool>(targetResolver.ResolveTarget(line), true))));
}
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;
}
