public override bool Equals(object o)
{
ModificationMotif m = o as ModificationMotif;
return(m != null &&
m.motifString == motifString);
}
public ModificationWithLocation(string id, Tuple <string, string> accession, ModificationMotif motif, ModificationSites terminusLocalization, IDictionary <string, IList <string> > linksToOtherDbs, string modificationType) : base(id, modificationType)
{
this.accession = accession;
this.motif = motif;
this.terminusLocalization = terminusLocalization;
this.linksToOtherDbs = linksToOtherDbs;
}
public ModificationWithLocation(string id, string modificationType, ModificationMotif motif, TerminusLocalization terminusLocalization, IDictionary <string, IList <string> > linksToOtherDbs = null, List <string> keywords = null) : base(id, modificationType)
{
this.motif = motif;
this.terminusLocalization = terminusLocalization;
// Optional
this.linksToOtherDbs = linksToOtherDbs ?? new Dictionary <string, IList <string> >();
this.keywords = keywords ?? new List <string>();
}
/// <summary>
/// Only upper and lower case letters allowed, must have a single upper case letter
/// </summary>
/// <param name="motifString"></param>
/// <param name="motif"></param>
/// <returns></returns>
public static bool TryGetMotif(string motifString, out ModificationMotif motif)
{
motif = null;
if (ModificationMotifRegex.IsMatch(motifString) && motifString.Count(b => char.IsUpper(b)) == 1)
{
motif = new ModificationMotif(motifString);
return(true);
}
return(false);
}
public ModificationWithMass(string id, Tuple <string, string> accession, ModificationMotif motif, ModificationSites modificationSites, double monoisotopicMass, IDictionary <string, IList <string> > externalDatabaseReferences, IEnumerable <double> neutralLosses, IEnumerable <double> diagnosticIons, string modificationType)
: base(id, accession, motif, modificationSites, externalDatabaseReferences, modificationType)
{
this.monoisotopicMass = monoisotopicMass;
if (neutralLosses == null || neutralLosses.Count() == 0)
{
neutralLosses = new List <double> {
0
}
}
;
this.neutralLosses = neutralLosses;
this.diagnosticIons = diagnosticIons;
}
public ModificationWithMass(string id, string modificationType, ModificationMotif motif, TerminusLocalization terminusLocalization, double monoisotopicMass, IDictionary <string, IList <string> > externalDatabaseReferences = null, List <string> keywords = null, List <double> neutralLosses = null, List <double> diagnosticIons = null)
: base(id, modificationType, motif, terminusLocalization, externalDatabaseReferences, keywords)
{
this.monoisotopicMass = monoisotopicMass;
// Optional
this.neutralLosses = neutralLosses ?? new List <double> {
0
};
this.diagnosticIons = diagnosticIons ?? new List <double>();
this.neutralLosses = this.neutralLosses.OrderBy(b => b).ToList();
this.diagnosticIons = this.diagnosticIons.OrderBy(b => b).ToList();
}
public Modification(string _originalId = null, string _accession = null, string _modificationType = null, string _featureType = null,
ModificationMotif _target = null, string _locationRestriction = "Unassigned.", ChemicalFormula _chemicalFormula = null,
double?_monoisotopicMass = null, Dictionary <string, IList <string> > _databaseReference = null,
Dictionary <string, IList <string> > _taxonomicRange = null, List <string> _keywords = null,
Dictionary <DissociationType, List <double> > _neutralLosses = null, Dictionary <DissociationType, List <double> > _diagnosticIons = null,
string _fileOrigin = null)
{
if (_originalId != null)
{
if (_originalId.Contains(" on "))
{
this.IdWithMotif = _originalId;
this.OriginalId = _originalId.Split(new[] { " on " }, StringSplitOptions.None)[0];
}
else if (_originalId.Contains(" of "))
{
this.IdWithMotif = _originalId.Replace(" of ", " on ");
this.OriginalId = _originalId.Split(new[] { " of ", " on " }, StringSplitOptions.None)[0];
}
else if (_target != null)
{
this.IdWithMotif = _originalId + " on " + _target.ToString();
this.OriginalId = _originalId;
}
else
{
this.OriginalId = _originalId;
}
}
this.Accession = _accession;
this.ModificationType = _modificationType;
this.FeatureType = _featureType;
this.Target = _target;
this.LocationRestriction = ModLocationOnPeptideOrProtein(_locationRestriction);
this.ChemicalFormula = _chemicalFormula;
this.MonoisotopicMass = _monoisotopicMass;
this.DatabaseReference = _databaseReference;
this.TaxonomicRange = _taxonomicRange;
this.Keywords = _keywords;
this.NeutralLosses = _neutralLosses;
this.DiagnosticIons = _diagnosticIons;
this.FileOrigin = _fileOrigin;
if (this.MonoisotopicMass == null && this.ChemicalFormula != null)
{
this.MonoisotopicMass = this.ChemicalFormula.MonoisotopicMass;
}
}
public ModificationWithMassAndCf(string id, string modificationType, ModificationMotif motif, TerminusLocalization terminusLocalization, ChemicalFormula chemicalFormula, double?mm = null, IDictionary <string, IList <string> > linksToOtherDbs = null, List <string> keywords = null, List <double> neutralLosses = null, List <double> diagnosticIons = null)
: base(id, modificationType, motif, terminusLocalization, mm ?? chemicalFormula.MonoisotopicMass, linksToOtherDbs, keywords, neutralLosses, diagnosticIons)
{
this.chemicalFormula = chemicalFormula;
}
public ModificationWithMassAndCf(string id, Tuple <string, string> accession, ModificationMotif motif, ModificationSites site, ChemicalFormula chemicalFormula, double mm, IDictionary <string, IList <string> > linksToOtherDbs, IEnumerable <double> neutralLosses, IEnumerable <double> diagnosticIons, string modificationType)
: base(id, accession, motif, site, mm, linksToOtherDbs, neutralLosses, diagnosticIons, modificationType)
{
this.chemicalFormula = chemicalFormula;
}