public static int FindAdductDescription(string line, out Adduct adduct)
{
// Check for adduct description
var chargePos = -1;
adduct = Adduct.EMPTY;
var adductStart = line.LastIndexOf('[');
if (adductStart >= 0)
{
if (adductStart + 2 > line.Length || line[adductStart + 1] == '+')
{
// It was probably a modification like "[+57]", and we're being called by StripChargeIndicators on a peptide
return(chargePos);
}
var adductText = line.Substring(adductStart);
if (adductStart > 0 && line[adductStart - 1] == '(')
{
adductText = adductText.TrimEnd(')', ' ');
adductStart--; // Consider adduct description as beginning at start of enclosing parens
}
if (!Adduct.TryParse(adductText, out adduct))
{
// Whatever it was, it's not an adduct
return(chargePos);
}
chargePos = adductStart;
}
return(chargePos);
}
public static string ValidateAdduct(string adductText)
{
Adduct adduct;
if (!Adduct.TryParse(adductText, out adduct))
{
return(Resources.ValidatingIonMobilityPeptide_ValidateAdduct_A_valid_adduct_description__e_g____M_H____must_be_provided_);
}
return(null);
}
public bool TryGetCharge(long linesRead, out Adduct charge)
{
string chargeString = GetField(Field.charge);
if (chargeString == null)
{
charge = Adduct.EMPTY;
return(false);
}
if (!Adduct.TryParse(chargeString, out charge, Adduct.ADDUCT_TYPE.proteomic)) // Read, for example, "2" as Adduct.DOUBLY_PROTONATED
{
throw new IOException(string.Format(Resources.PeakBoundaryImporter_Import_The_value___0___on_line__1__is_not_a_valid_charge_state_, chargeString, linesRead));
}
return(true);
}
public static bool IsFormulaWithAdduct(string formula, out Molecule molecule, out Adduct adduct, out string neutralFormula)
{
molecule = null;
adduct = Adduct.EMPTY;
neutralFormula = null;
if (string.IsNullOrEmpty(formula))
{
return(false);
}
// Does formula contain an adduct description? If so, pull charge from that.
var parts = formula.Split('[');
if (parts.Length == 2 && parts[1].Count(c => c == ']') == 1)
{
neutralFormula = parts[0];
var adductString = formula.Substring(neutralFormula.Length);
if (Adduct.TryParse(adductString, out adduct))
{
molecule = neutralFormula.Length > 0 ? ApplyAdductToFormula(neutralFormula, adduct) : Molecule.Empty;
return(true);
}
}
return(false);
}
public static string ValidateMeasuredDriftTimeCellValues(string[] values)
{
Adduct tempAdduct;
double tempDouble;
if (values.Length < 3)
{
return(Resources.MeasuredDriftTimeTable_ValidateMeasuredDriftTimeCellValues_The_pasted_text_must_have_three_columns_);
}
// Parse sequence
var sequence = values[EditDriftTimePredictorDlg.COLUMN_SEQUENCE];
if (string.IsNullOrEmpty(sequence))
{
return(Resources.MeasuredDriftTimeTable_ValidateMeasuredDriftTimeCellValues_A_modified_peptide_sequence_is_required_for_each_entry_);
}
if (!FastaSequence.IsExSequence(sequence))
{
return(string.Format(Resources.MeasuredDriftTimeTable_ValidateMeasuredDriftTimeCellValues_The_sequence__0__is_not_a_valid_modified_peptide_sequence_, sequence));
}
try
{
values[EditDriftTimePredictorDlg.COLUMN_SEQUENCE] = SequenceMassCalc.NormalizeModifiedSequence(sequence);
}
catch (Exception x)
{
return(x.Message);
}
// Parse charge
if ((!Adduct.TryParse(values[EditDriftTimePredictorDlg.COLUMN_CHARGE].Trim(), out tempAdduct)) || ValidateCharge(tempAdduct) != null)
{
return(string.Format(Resources.EditDriftTimePredictorDlg_ValidateCharge_The_entry__0__is_not_a_valid_charge__Precursor_charges_must_be_integer_values_between_1_and__1__,
values[EditDriftTimePredictorDlg.COLUMN_CHARGE].Trim(), TransitionGroup.MAX_PRECURSOR_CHARGE));
}
// Parse drift time
if (!double.TryParse(values[EditDriftTimePredictorDlg.COLUMN_ION_MOBILITY].Trim(), out tempDouble))
{
return(string.Format(Resources.MeasuredDriftTimeTable_ValidateMeasuredDriftTimeCellValues_The_value__0__is_not_a_valid_drift_time_, values[EditDriftTimePredictorDlg.COLUMN_ION_MOBILITY].Trim()));
}
if (values.Length > EditDriftTimePredictorDlg.COLUMN_CCS)
{
// Parse CCS, if any
if (!string.IsNullOrEmpty(values[EditDriftTimePredictorDlg.COLUMN_CCS]) &&
!double.TryParse(values[EditDriftTimePredictorDlg.COLUMN_CCS].Trim(), out tempDouble))
{
return(string.Format(Resources.MeasuredDriftTimeTable_ValidateMeasuredDriftTimeCellValues_The_value__0__is_not_a_valid_collisional_cross_section_, values[EditDriftTimePredictorDlg.COLUMN_CCS].Trim()));
}
}
if (values.Length > EditDriftTimePredictorDlg.COLUMN_HIGH_ENERGY_OFFSET)
{
// Parse high energy offset, if any
if (!string.IsNullOrEmpty(values[EditDriftTimePredictorDlg.COLUMN_HIGH_ENERGY_OFFSET]) &&
!double.TryParse(values[EditDriftTimePredictorDlg.COLUMN_HIGH_ENERGY_OFFSET].Trim(), out tempDouble))
{
return(string.Format(Resources.MeasuredDriftTimeTable_ValidateMeasuredDriftTimeCellValues_The_value__0__is_not_a_valid_high_energy_offset_, values[EditDriftTimePredictorDlg.COLUMN_HIGH_ENERGY_OFFSET].Trim()));
}
}
return(null);
}
private void UpdateAverageAndMonoTextsForFormula()
{
bool valid;
try
{
var formula = Formula; // Get current formula and adduct
var userinput = textFormula.Text.Trim();
if (_editMode == EditMode.adduct_only)
{
if (!string.IsNullOrEmpty(userinput) && !userinput.StartsWith(@"["))
{
// Assume they're trying to type an adduct
userinput = @"[" + userinput + @"]";
}
if (string.IsNullOrEmpty(NeutralFormula))
{
formula = null; // Parent molecule was described as mass only
}
else
{
formula = NeutralFormula + userinput; // Try to apply this new adduct to parent molecule
}
}
else
{
formula = userinput;
}
string neutralFormula;
Molecule ion;
Adduct adduct;
if (!IonInfo.IsFormulaWithAdduct(formula, out ion, out adduct, out neutralFormula))
{
neutralFormula = formula;
if (!Adduct.TryParse(userinput, out adduct))
{
adduct = Adduct.EMPTY;
}
}
if (_editMode != EditMode.adduct_only)
{
NeutralFormula = neutralFormula;
}
if (_editMode != EditMode.formula_only)
{
Adduct = adduct;
}
// Update mass/mz displays
if (string.IsNullOrEmpty(neutralFormula))
{
if (!adduct.IsEmpty)
{
// No formula, but adduct changed
Adduct = adduct;
// ReSharper disable once PossibleNullReferenceException
GetTextFromMass(_neutralMonoMass, MassType.Monoisotopic); // Just to see if it throws or not
GetTextFromMass(_neutralAverageMass, MassType.Average); // Just to see if it throws or not
}
}
else
{
// Is there an isotopic label we should apply to get the mass?
if (IsotopeLabelsForMassCalc != null && (Adduct.IsEmpty || !Adduct.HasIsotopeLabels)) // If adduct declares an isotope, that takes precedence
{
neutralFormula = IsotopeLabelsForMassCalc.Aggregate(neutralFormula, (current, kvp) => current.Replace(kvp.Key, kvp.Value));
}
var monoMass = SequenceMassCalc.FormulaMass(BioMassCalc.MONOISOTOPIC, neutralFormula, SequenceMassCalc.MassPrecision);
var averageMass = SequenceMassCalc.FormulaMass(BioMassCalc.AVERAGE, neutralFormula, SequenceMassCalc.MassPrecision);
GetTextFromMass(monoMass, MassType.Monoisotopic); // Just to see if it throws or not
GetTextFromMass(averageMass, MassType.Average); // Just to see if it throws or not
MonoMass = monoMass;
AverageMass = averageMass;
}
valid = true; // If we got here, formula parsed OK, or adduct did
textFormula.ForeColor = Color.Black;
if (_editMode == EditMode.adduct_only)
{
textFormula.Text = userinput; // Enforce proper adduct formatting
if (adduct.IsEmpty)
{
valid = false; // Adduct did not parse
}
}
else if (_editMode == EditMode.formula_only)
{
valid &= adduct.IsEmpty; // Should not have anything going on with adduct here
}
}
catch (InvalidOperationException)
{
valid = false;
}
catch (ArgumentException)
{
valid = false;
}
if (valid)
{
textFormula.ForeColor = Color.Black;
}
else
{
textFormula.ForeColor = Color.Red;
textMono.Text = textAverage.Text = string.Empty;
}
// Allow direct editing of masses if direct editing of formula is allowed, but formula is empty
MassEnabled = _editMode != EditMode.adduct_only && string.IsNullOrEmpty(_neutralFormula);
}