/// <summary>Gets the modification.</summary>
/// <param name="descriptor">The descriptor.</param>
/// <returns></returns>
public IProteoformMassDelta?GetModification(IProFormaDescriptor descriptor)
{
if (double.TryParse(descriptor.Value, out double mass))
{
return(new MassModification(mass));
}
else
{
throw new ProteoformModificationLookupException($"Could not parse mass string for descriptor {descriptor}");
}
}
/// <summary>Gets the modification.</summary>
/// <param name="descriptor">The descriptor.</param>
/// <returns></returns>
public IProteoformMassDelta?GetModification(IProFormaDescriptor descriptor)
{
if (ChemicalFormula.TryParseString(descriptor.Value, this._elementProvider, out IChemicalFormula chemicalFormula))
{
return(new FormulaModification(chemicalFormula));
}
else
{
throw new ProteoformModificationLookupException($"Could not parse formula string for descriptor {descriptor}");
}
}
/// <summary>
/// Gets the modification.
/// </summary>
/// <param name="descriptor">The descriptor.</param>
/// <returns></returns>
public IProteoformMassDelta?GetModification(IProFormaDescriptor descriptor)
{
foreach (var lookup in _lookups)
{
if (lookup.CanHandleDescriptor(descriptor))
{
return(lookup.GetModification(descriptor));
}
}
throw new ProteoformGroupCreateException($"Couldn't handle value for descriptor {descriptor}.");
}
/// <summary>
/// Determines whether this instance [can handle descriptor] the specified descriptor.
/// </summary>
/// <param name="descriptor">The descriptor.</param>
/// <returns>
/// <c>true</c> if this instance [can handle descriptor] the specified descriptor; otherwise, <c>false</c>.
/// </returns>
public virtual bool CanHandleDescriptor(IProFormaDescriptor descriptor)
{
var nonDefault = descriptor.EvidenceType == this.EvidenceType &&
(descriptor.Key == ProFormaKey.Name || descriptor.Key == ProFormaKey.Identifier);
if (!this.IsDefaultModificationType || nonDefault)
{
return(nonDefault);
}
// If this is the default modification type, allow no evidence name check.
return(_modificationNames?.ContainsKey(descriptor.Value) ?? false);
}
/// <summary>
/// Determines whether this instance [can handle descriptor] the specified descriptor.
/// </summary>
/// <param name="descriptor">The descriptor.</param>
/// <returns>
/// <c>true</c> if this instance [can handle descriptor] the specified descriptor; otherwise, <c>false</c>.
/// </returns>
public virtual bool CanHandleDescriptor(IProFormaDescriptor descriptor)
{
var nonDefault = descriptor.EvidenceType == this.EvidenceType &&
(descriptor.Key == ProFormaKey.Name || descriptor.Key == ProFormaKey.Identifier);
if (!this.IsDefaultModificationType)
{
return(nonDefault);
}
// If this is the default modification type, allow one more condition.
return(nonDefault ||
(descriptor.Key == ProFormaKey.Name && descriptor.EvidenceType == ProFormaEvidenceType.None));
}
/// <summary>
/// Gets the modification.
/// </summary>
/// <param name="descriptor">The descriptor.</param>
/// <returns></returns>
public virtual IProteoformMassDelta GetModification(IProFormaDescriptor descriptor)
{
if (_modifications == null)
{
throw new Exception("Modification array in not initialized.");
}
if (descriptor.Value == null)
{
throw new ProteoformModificationLookupException($"Value is NULL in descriptor {descriptor}.");
}
if (descriptor.Key == ProFormaKey.Name)
{
string value = descriptor.Value;
IProteoformMassDelta modification = _modifications
.SingleOrDefault(x => x != null && ((ModificationWrapper)x).Modification.Name == value);
if (modification == null)
{
throw new ProteoformModificationLookupException($"Could not find modification using Name in descriptor {descriptor}.");
}
return(modification);
}
else if (descriptor.Key == ProFormaKey.Identifier)
{
string value = this.RemovePrefix(descriptor.Value);
if (int.TryParse(value, out int id))
{
if (id < 0 || id > _modifications.Length - 1 || _modifications[id] == null)
{
throw new ProteoformModificationLookupException($"Could not find modification using ID in descriptor {descriptor}.");
}
return(_modifications[id]);
}
throw new ProteoformModificationLookupException($"Invalid integer in descriptor {descriptor}.");
}
throw new ProteoformModificationLookupException($"Couldn't handle value for descriptor {descriptor}.");
}
/// <summary>
/// Gets the modification.
/// </summary>
/// <param name="descriptor">The descriptor.</param>
/// <returns></returns>
public virtual IProteoformMassDelta GetModification(IProFormaDescriptor descriptor)
{
if (_modifications == null)
{
throw new Exception("Modification array in not initialized.");
}
if (descriptor.Value == null)
{
throw new ProteoformModificationLookupException($"Value is NULL in descriptor {descriptor}.");
}
if (descriptor.Key == ProFormaKey.Name)
{
string value = descriptor.Value;
if (_modificationNames != null)
{
if (!_modificationNames.ContainsKey(value))
{
throw new ProteoformModificationLookupException($"Could not find modification using Name in descriptor {descriptor}.");
}
return(_modificationNames[value]);
}
}
else if (descriptor.Key == ProFormaKey.Identifier)
{
string value = this.RemovePrefix(descriptor.Value);
if (int.TryParse(value, out int id))
{
if (id < 0 || id > _modifications.Length - 1 || _modifications[id] == null)
{
throw new ProteoformModificationLookupException($"Could not find modification using ID in descriptor {descriptor}.");
}
return(_modifications[id]);
}
throw new ProteoformModificationLookupException($"Invalid integer in descriptor {descriptor}.");
}
throw new ProteoformModificationLookupException($"Couldn't handle value for descriptor {descriptor}.");
}
private string CreateDescriptorText(IProFormaDescriptor descriptor)
{
return(descriptor.Key switch
{
ProFormaKey.Formula => $"Formula:{descriptor.Value}",
ProFormaKey.Glycan => $"Glycan:{descriptor.Value}",
ProFormaKey.Info => $"Info:{descriptor.Value}",
var x when x == ProFormaKey.Name || x == ProFormaKey.Mass => descriptor.EvidenceType switch
{
ProFormaEvidenceType.None => descriptor.Value, // We assume the name is enough
ProFormaEvidenceType.Observed => $"Obs:{descriptor.Value}",
ProFormaEvidenceType.Unimod => $"U:{descriptor.Value}",
ProFormaEvidenceType.Resid => $"R:{descriptor.Value}",
ProFormaEvidenceType.PsiMod => $"M:{descriptor.Value}",
ProFormaEvidenceType.XlMod => $"X:{descriptor.Value}",
ProFormaEvidenceType.Gno => $"G:{descriptor.Value}",
ProFormaEvidenceType.Brno => $"B:{descriptor.Value}",
_ => throw new Exception($"Can't handle {descriptor.Key} with evidence type: {descriptor.EvidenceType}.")
},
/// <summary>
/// Gets the modification.
/// </summary>
/// <param name="descriptor">The descriptor.</param>
/// <returns></returns>
public IProteoformMassDelta GetModification(IProFormaDescriptor descriptor)
{
string abbreviation = descriptor.Value;
switch (abbreviation)
{
case "ac": return(_modifications[0]);
case "me1": return(_modifications[1]);
case "me2s": return(_modifications[2]);
case "me2a": return(_modifications[3]);
case "me2": return(_modifications[4]);
case "me3": return(_modifications[5]);
case "ph": return(_modifications[6]);
default:
throw new ProteoformModificationLookupException($"Couldn't handle value for descriptor {descriptor}.");
}
}
/// <summary>
/// Determines whether this instance [can handle descriptor] the specified descriptor.
/// </summary>
/// <param name="descriptor">The descriptor.</param>
/// <returns>
/// <c>true</c> if this instance [can handle descriptor] the specified descriptor; otherwise, <c>false</c>.
/// </returns>
public bool CanHandleDescriptor(IProFormaDescriptor descriptor)
{
return(descriptor.Key == ProFormaKey.Name &&
descriptor.EvidenceType == ProFormaEvidenceType.Brno &&
descriptor.Value != null);
}
/// <summary>
/// Determines whether this instance [can handle descriptor] the specified descriptor.
/// </summary>
/// <param name="descriptor">The descriptor.</param>
/// <returns>
/// <c>true</c> if this instance [can handle descriptor] the specified descriptor; otherwise, <c>false</c>.
/// </returns>
public bool CanHandleDescriptor(IProFormaDescriptor descriptor)
{
return(_lookups.Any(x => x.CanHandleDescriptor(descriptor)));
}
/// <summary> /// Gets the modification. /// </summary> /// <param name="descriptor">The descriptor.</param> /// <returns></returns> public IProteoformMassDelta?GetModification(IProFormaDescriptor descriptor) => null;
/// <summary>
/// Determines whether this instance [can handle descriptor] the specified descriptor.
/// </summary>
/// <param name="descriptor">The descriptor.</param>
/// <returns>
/// <c>true</c> if this instance [can handle descriptor] the specified descriptor; otherwise, <c>false</c>.
/// </returns>
public bool CanHandleDescriptor(IProFormaDescriptor descriptor)
{
return(descriptor.Key == _key);
}
/// <summary>Determines whether this instance [can handle descriptor] the specified descriptor.</summary>
/// <param name="descriptor">The descriptor.</param>
/// <returns>
/// <c>true</c> if this instance [can handle descriptor] the specified descriptor; otherwise, <c>false</c>.</returns>
public bool CanHandleDescriptor(IProFormaDescriptor descriptor)
{
return(descriptor.Key == ProFormaKey.Mass);
}
