public override void ReadXml(XmlReader reader)
{
// Read tag attributes
base.ReadXml(reader);
Fragment = reader.GetAttribute(ATTR.cut);
if (IsFragment)
{
Restrict = reader.GetAttribute(ATTR.no_cut);
Terminus = reader.GetAttribute(ATTR.sense, ToSeqTerminus);
MinFragmentLength = reader.GetNullableIntAttribute(ATTR.min_length) ??
DEFAULT_MIN_FRAGMENT_LENGTH;
}
else
{
var charges = TextUtil.ParseInts(reader.GetAttribute(ATTR.charges)); // Old version?
if (charges.Length > 1)
{
throw new InvalidDataException(Resources.MeasuredIon_ReadXml_Multiple_charge_states_for_custom_ions_are_no_longer_supported_);
}
var parsedIon = CustomIon.Deserialize(reader);
Adduct adduct;
if (charges.Any()) // Old style - fix it up a little for our revised ideas about custom ion ionization
{
adduct = Adduct.FromChargeNoMass(charges[0]);
if (string.IsNullOrEmpty(parsedIon.NeutralFormula)) // Adjust the user-supplied masses
{
SettingsCustomIon = new SettingsCustomIon(parsedIon.NeutralFormula, adduct,
Math.Round(parsedIon.MonoisotopicMass + charges[0] * BioMassCalc.MONOISOTOPIC.GetMass(BioMassCalc.H), SequenceMassCalc.MassPrecision), // Assume user provided neutral mass. Round new value easiest XML roundtripping.
Math.Round(parsedIon.AverageMass + charges[0] * BioMassCalc.AVERAGE.GetMass(BioMassCalc.H), SequenceMassCalc.MassPrecision), // Assume user provided neutral mass. Round new value easiest XML roundtripping.
parsedIon.Name);
}
else // Adjust the formula to include ion atoms
{
if (charges[0] > 1) // XML deserializer will have added an H already
{
var adductProtonated = Adduct.FromChargeProtonated(charges[0] - 1);
var formula = adductProtonated.ApplyToFormula(parsedIon.NeutralFormula);
parsedIon = new CustomIon(formula, adduct, parsedIon.MonoisotopicMass, parsedIon.AverageMass, Name);
}
}
}
else
{
adduct = Adduct.FromStringAssumeChargeOnly(reader.GetAttribute(ATTR.charge)); // Ionization mass is already in formula
}
if (SettingsCustomIon == null)
{
SettingsCustomIon = new SettingsCustomIon(parsedIon.NeutralFormula, adduct,
parsedIon.MonoisotopicMass,
parsedIon.AverageMass,
parsedIon.Name);
}
IsOptional = reader.GetBoolAttribute(ATTR.optional);
}
// Consume tag
reader.Read();
Validate();
}
/// <summary>
/// Constructor for a reporter ion
/// </summary>
/// <param name="name">The name by which it is stored in the settings list</param>
/// <param name="formula">Chemical formula of the ion</param>
/// <param name="monoisotopicMass">Constant monoisotopic mass of the ion, if formula is not given</param>
/// <param name="averageMass">Constant average mass of the ion, if formula is not given</param>
/// <param name="adduct">The charge for this custom ion</param>
/// <param name="isOptional">Whether or not the reporter ion will automatically be added to all proteins</param>
public MeasuredIon(string name,
string formula,
double?monoisotopicMass,
double?averageMass,
Adduct adduct,
bool isOptional = false)
: base(name)
{
SettingsCustomIon = new SettingsCustomIon(formula, adduct, monoisotopicMass, averageMass, name);
IsOptional = isOptional;
Validate();
}
/// <summary>
/// Constructor for a reporter ion
/// </summary>
/// <param name="name">The name by which it is stored in the settings list</param>
/// <param name="formula">Chemical formula of the ion</param>
/// <param name="monoisotopicMass">Constant monoisotopic mass of the ion, if formula is not given</param>
/// <param name="averageMass">Constant average mass of the ion, if formula is not given</param>
/// <param name="charge">The charge for this custom ion</param>
/// <param name="isOptional">Whether or not the reporter ion will automatically be added to all proteins</param>
public MeasuredIon(string name,
string formula,
double?monoisotopicMass,
double?averageMass,
int charge,
bool isOptional = false)
: base(name)
{
SettingsCustomIon = new SettingsCustomIon(formula, monoisotopicMass, averageMass, name); // Like a custom ion, but returns false for IsEditableInstance
Charge = charge;
IsOptional = isOptional;
Validate();
}
public override int GetHashCode()
{
unchecked
{
int result = base.GetHashCode();
result = (result * 397) ^ (Fragment != null ? Fragment.GetHashCode() : 0);
result = (result * 397) ^ (Restrict != null ? Restrict.GetHashCode() : 0);
result = (result * 397) ^ (Terminus.HasValue ? Terminus.Value.GetHashCode() : 0);
result = (result * 397) ^ (MinFragmentLength.HasValue ? MinFragmentLength.Value : 0);
result = (result * 397) ^ (SettingsCustomIon != null ? SettingsCustomIon.GetHashCode() : 0);
result = (result * 397) ^ Charge;
result = (result * 397) ^ IsOptional.GetHashCode();
return(result);
}
}
public override void ReadXml(XmlReader reader)
{
// Read tag attributes
base.ReadXml(reader);
Fragment = reader.GetAttribute(ATTR.cut);
if (IsFragment)
{
Restrict = reader.GetAttribute(ATTR.no_cut);
Terminus = reader.GetAttribute(ATTR.sense, ToSeqTerminus);
MinFragmentLength = reader.GetNullableIntAttribute(ATTR.min_length) ??
DEFAULT_MIN_FRAGMENT_LENGTH;
}
else
{
var charges = TextUtil.ParseInts(reader.GetAttribute(ATTR.charges)); // Old version?
if (charges.Count() > 1)
{
throw new InvalidDataException(Resources.MeasuredIon_ReadXml_Multiple_charge_states_for_custom_ions_are_no_longer_supported_);
}
SettingsCustomIon = SettingsCustomIon.Deserialize(reader);
if (charges.Any()) // Old style - fix it up a little for our revised ideas about custom ion ionization
{
Charge = charges[0];
if (string.IsNullOrEmpty(SettingsCustomIon.Formula)) // Adjust the user-supplied masses
{
SettingsCustomIon = new SettingsCustomIon(SettingsCustomIon.Formula,
Math.Round(SettingsCustomIon.MonoisotopicMass + BioMassCalc.MONOISOTOPIC.GetMass(BioMassCalc.H), SequenceMassCalc.MassPrecision), // Assume user provided neutral mass. Round new value easiest XML roundtripping.
Math.Round(SettingsCustomIon.AverageMass + BioMassCalc.AVERAGE.GetMass(BioMassCalc.H), SequenceMassCalc.MassPrecision), // Assume user provided neutral mass. Round new value easiest XML roundtripping.
SettingsCustomIon.Name);
}
}
else
{
Charge = reader.GetIntAttribute(ATTR.charge);
}
IsOptional = reader.GetBoolAttribute(ATTR.optional);
}
// Consume tag
reader.Read();
Validate();
}
public override void ReadXml(XmlReader reader)
{
// Read tag attributes
base.ReadXml(reader);
Fragment = reader.GetAttribute(ATTR.cut);
if (IsFragment)
{
Restrict = reader.GetAttribute(ATTR.no_cut);
Terminus = reader.GetAttribute(ATTR.sense, ToSeqTerminus);
MinFragmentLength = reader.GetNullableIntAttribute(ATTR.min_length) ??
DEFAULT_MIN_FRAGMENT_LENGTH;
}
else
{
var charges = TextUtil.ParseInts(reader.GetAttribute(ATTR.charges)); // Old version?
if (charges.Count() > 1)
throw new InvalidDataException(Resources.MeasuredIon_ReadXml_Multiple_charge_states_for_custom_ions_are_no_longer_supported_);
SettingsCustomIon = SettingsCustomIon.Deserialize(reader);
if (charges.Any()) // Old style - fix it up a little for our revised ideas about custom ion ionization
{
Charge = charges[0];
if (string.IsNullOrEmpty(SettingsCustomIon.Formula)) // Adjust the user-supplied masses
{
SettingsCustomIon = new SettingsCustomIon(SettingsCustomIon.Formula,
Math.Round(SettingsCustomIon.MonoisotopicMass + BioMassCalc.MONOISOTOPIC.GetMass(BioMassCalc.H), SequenceMassCalc.MassPrecision), // Assume user provided neutral mass. Round new value easiest XML roundtripping.
Math.Round(SettingsCustomIon.AverageMass + BioMassCalc.AVERAGE.GetMass(BioMassCalc.H), SequenceMassCalc.MassPrecision), // Assume user provided neutral mass. Round new value easiest XML roundtripping.
SettingsCustomIon.Name);
}
}
else
{
Charge = reader.GetIntAttribute(ATTR.charge);
}
IsOptional = reader.GetBoolAttribute(ATTR.optional);
}
// Consume tag
reader.Read();
Validate();
}
/// <summary>
/// Constructor for a reporter ion
/// </summary>
/// <param name="name">The name by which it is stored in the settings list</param>
/// <param name="formula">Chemical formula of the ion</param>
/// <param name="monoisotopicMass">Constant monoisotopic mass of the ion, if formula is not given</param>
/// <param name="averageMass">Constant average mass of the ion, if formula is not given</param>
/// <param name="charge">The charge for this custom ion</param>
/// <param name="isOptional">Whether or not the reporter ion will automatically be added to all proteins</param>
public MeasuredIon(string name,
string formula,
double? monoisotopicMass,
double? averageMass,
int charge,
bool isOptional = false)
: base(name)
{
SettingsCustomIon = new SettingsCustomIon(formula, monoisotopicMass, averageMass, name); // Like a custom ion, but returns false for IsEditableInstance
Charge = charge;
IsOptional = isOptional;
Validate();
}
