/// <summary>
/// Gets the modification array.
/// </summary>
/// <param name="modifications">The modifications.</param>
/// <returns></returns>
/// <exception cref="ArgumentNullException">modifications</exception>
protected void SetupModificationArray(IEnumerable <T> modifications)
{
if (modifications == null)
{
throw new ArgumentNullException(nameof(modifications));
}
var modArray = new IProteoformMassDelta[10000]; // More IDs than will ever exist
int maxId = -1;
foreach (T modification in modifications)
{
IChemicalFormula?chemicalFormula = this.GetChemicalFormula(modification);
int id = Convert.ToInt32(this.RemovePrefix(modification.Id));
if (chemicalFormula != null)
{
modArray[id] = new ModificationWrapper(modification, chemicalFormula);
}
// Keep all the way up to the max passed in, even if it turns out to be NULL
maxId = Math.Max(maxId, id);
}
Array.Resize(ref modArray, maxId + 1);
_modifications = modArray;
}
/// <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 array.
/// </summary>
/// <param name="modifications">The modifications.</param>
/// <returns></returns>
/// <exception cref="ArgumentNullException">modifications</exception>
protected void SetupModificationArray(IEnumerable <T> modifications)
{
if (modifications == null)
{
throw new ArgumentNullException(nameof(modifications));
}
_modificationNames = new Dictionary <string, IProteoformMassDelta>();
var modArray = new IProteoformMassDelta[10000]; // More IDs than will ever exist
int maxId = -1;
foreach (T modification in modifications)
{
IChemicalFormula?chemicalFormula = this.GetChemicalFormula(modification);
int id = Convert.ToInt32(this.RemovePrefix(modification.Id));
if (chemicalFormula != null)
{
modArray[id] = new ModificationWrapper(modification, chemicalFormula);
}
// Keep all the way up to the max passed in, even if it turns out to be NULL
maxId = Math.Max(maxId, id);
if (_modificationNames != null)
{
// HACK for obsolete PSI-MOD terms with same name as something else ... skip
if (modification.Id == "MOD:00949" || modification.Id == "MOD:01966")
{
continue;
}
_modificationNames.Add(modification.Name, modArray[id]);
}
}
Array.Resize(ref modArray, maxId + 1);
_modifications = modArray;
}
public GlobalModification(IProteoformMassDelta modificationDelta, ICollection <char>?targetAminoAcids)
: base(modificationDelta)
{
this.TargetAminoAcids = targetAminoAcids;
}
public TagGroupModification(IProteoformMassDelta modificationDelta, string groupName, IReadOnlyCollection <IProteoformModificationGroupMember> members)
: base(modificationDelta)
{
this.GroupName = groupName;
this.Members = members;
}
public UnlocalizedModification(IProteoformMassDelta modificationDelta, int count, bool isLabile)
: base(modificationDelta)
{
this.Count = count;
this.IsLabile = isLabile;
}
public LocalizedModification(IProteoformMassDelta modificationDelta, int zeroBasedStartIndex, int zeroBasedEndIndex)
: base(modificationDelta)
{
this.ZeroBasedStartIndex = zeroBasedStartIndex;
this.ZeroBasedEndIndex = zeroBasedEndIndex;
}
/// <summary>
/// Initializes a new instance of the <see cref="ProteoformModificationBase"/> class.
/// </summary>
/// <param name="modificationDelta">The modification delta.</param>
public ProteoformModificationBase(IProteoformMassDelta modificationDelta)
{
ModificationDelta = modificationDelta;
}