public void Input_Order_Is_Sorted()
{
string formula = "N4O4C2H4";
var chem = new ChemicalFormula(formula);
Assert.AreEqual("C2H4N4O4", chem.ToString());
}
public void Generate_Correct_Instance_From_String()
{
string formula = "C6H12O6";
var glucoseTest = new ChemicalFormula(formula);
// TODO: implement comparator for chemical formulas
Assert.AreEqual(glucose.ToString(), glucoseTest.ToString());
}
public override string GetValue(string fieldName)
{
switch (fieldName)
{
case Fields.Identifier:
return(Identifiers == null ? MzTab.NullFieldText : string.Join("|", Identifiers));
case Fields.ChemicalFormula:
return(ChemicalFormula.ToString());
case Fields.Smiles:
return(Smiles ?? MzTab.NullFieldText);
case Fields.InChIKey:
return(InChIKeys == null ? MzTab.NullFieldText : string.Join("|", InChIKeys));
case Fields.Description:
return(Description ?? MzTab.NullFieldText);
case Fields.ExperimentMZ:
return(ExperimentalMZ.ToString());
case Fields.TheoreticalMZ:
return(TheoreticalMZ.ToString());
case Fields.Charge:
return(Charge.ToString());
case Fields.RetentionTime:
return(RetentionTimes == null ? MzTab.NullFieldText : string.Join("|", RetentionTimes));
case Fields.TaxID:
return(TaxID.ToString());
case Fields.Species:
return(Species ?? MzTab.NullFieldText);
case Fields.Database:
return(Database ?? MzTab.NullFieldText);
case Fields.DatabaseVersion:
return(DatabaseVersion ?? MzTab.NullFieldText);
case Fields.Reliability:
return((Reliability == MzTab.MetabolomicsReliabilityScore.NotSet) ? MzTab.NullFieldText : ((int)Reliability).ToString());
case Fields.Uri:
return(Uri == null ? MzTab.NullFieldText : Uri.ToString());
case Fields.SpectralReference:
return(SpectralReference ?? MzTab.NullFieldText);
case Fields.SearchEngine:
return(SearchEngines == null ? MzTab.NullFieldText : string.Join("|", SearchEngines));
case Fields.Modifications:
return(Modifications ?? MzTab.NullFieldText);
}
if (fieldName.Contains("["))
{
string condensedFieldName;
List <int> indices = MzTab.GetFieldIndicies(fieldName, out condensedFieldName);
switch (condensedFieldName)
{
case Fields.BestSearchEngineScores:
return(GetListValue(_bestSearchEngineScores, indices[0]));
case Fields.SearchEngineScorePerMsRun:
return(GetListValue(_searchEngineScorePerMsRun, indices[0], indices[1]));
case Fields.AbundanceAssay:
return(GetListValue(_abundanceAssays, indices[0]));
case Fields.AbundanceStudyVariable:
return(GetListValue(_abundanceStudyVariables, indices[0]));
case Fields.AbundanceStDevStudyVariable:
return(GetListValue(_abundanceStdevStudyVariables, indices[0]));
case Fields.AbudnanceStdErrorStudyVariable:
return(GetListValue(_abundanceStandardErrorStudyVariables, indices[0]));
}
}
if (fieldName.StartsWith(MzTab.OptionalColumnPrefix))
{
return(GetOptionalData(fieldName));
}
throw new ArgumentException("Unexpected field name: " + fieldName);
}
public void Generates_Correct_Formula_String()
{
Assert.AreEqual("C6H12O6", glucose.ToString());
Assert.AreEqual("C16H18N2O4S", penicillin.ToString());
}