|
public static GetFieldIndicies ( string fieldName, string &condensedFieldName ) : List |
||
| fieldName | string | |
| condensedFieldName | string | |
| return | List |
|
public override void SetValue(string fieldName, string value)
{
if (MzTab.NullFieldText.Equals(value))
{
return;
}
switch (fieldName)
{
case Fields.Identifier:
Identifiers = value.Split('|').ToList(); return;
case Fields.ChemicalFormula:
ChemicalFormula = new ChemicalFormula(value); return;
case Fields.Smiles:
Smiles = value; return;
case Fields.InChIKey:
InChIKeys = value.Split('|').ToList(); return;
case Fields.Description:
Description = value; return;
case Fields.ExperimentMZ:
ExperimentalMZ = double.Parse(value); return;
case Fields.TheoreticalMZ:
TheoreticalMZ = double.Parse(value); return;
case Fields.Charge:
Charge = int.Parse(value); return;
case Fields.RetentionTime:
RetentionTimes = value.Split('|').Select(double.Parse).ToList(); return;
case Fields.TaxID:
TaxID = int.Parse(value); return;
case Fields.Species:
Species = value; return;
case Fields.Database:
Database = value; return;
case Fields.DatabaseVersion:
DatabaseVersion = value; return;
case Fields.Reliability:
Reliability = (MzTab.MetabolomicsReliabilityScore) int.Parse(value); return;
case Fields.Uri:
Uri = new Uri(value); return;
case Fields.SpectralReference:
SpectralReference = value; return;
case Fields.SearchEngine:
SearchEngines = value.Split('|').Select(v => new CVParamater(v)).ToList(); return;
case Fields.Modifications:
Modifications = value; return;
}
if (fieldName.Contains("["))
{
string condensedFieldName;
List <int> indices = MzTab.GetFieldIndicies(fieldName, out condensedFieldName);
switch (condensedFieldName)
{
case Fields.BestSearchEngineScores:
SetListValue(ref _bestSearchEngineScores, indices[0], double.Parse(value)); return;
case Fields.SearchEngineScorePerMsRun:
SetListValue(ref _searchEngineScorePerMsRun, indices[0], indices[1], double.Parse(value)); return;
case Fields.AbundanceAssay:
SetListValue(ref _abundanceAssays, indices[0], double.Parse(value)); return;
case Fields.AbundanceStudyVariable:
SetListValue(ref _abundanceStudyVariables, indices[0], double.Parse(value)); return;
case Fields.AbundanceStDevStudyVariable:
SetListValue(ref _abundanceStdevStudyVariables, indices[0], double.Parse(value)); return;
case Fields.AbudnanceStdErrorStudyVariable:
SetListValue(ref _abundanceStandardErrorStudyVariables, indices[0], double.Parse(value)); return;
}
}
if (fieldName.StartsWith(MzTab.OptionalColumnPrefix))
{
SetOptionalData(fieldName, value); return;
}
throw new ArgumentException("Unexpected field name: " + fieldName);
}
public override void SetValue(string fieldName, string value)
{
if (MzTab.NullFieldText.Equals(value))
{
return;
}
switch (fieldName)
{
case Fields.Accession:
Accession = value;
return;
case Fields.Description:
Description = value;
return;
case Fields.Database:
Database = value;
return;
case Fields.DatabaseVersion:
DatabaseVersion = value;
return;
case Fields.TaxID:
TaxID = int.Parse(value);
return;
case Fields.Species:
Species = value;
return;
case Fields.Modifications:
Modificiations = value;
return;
case Fields.SearchEngine:
SearchEngines = value.Split('|').Select(datum => (CVParamater)datum).ToList();
return;
case Fields.Reliability:
Reliability = (MzTab.ReliabilityScore) int.Parse(value);
return;
case Fields.AmbiguityMembers:
AmbiguityMembers = value.Split(',').ToList();
return;
case Fields.Coverage:
Coverage = double.Parse(value, CultureInfo.CurrentCulture);
return;
case Fields.Uri:
Uri = new Uri(value);
return;
case Fields.GoTerms:
GoTerms = value.Split('|').Select(datum => datum).ToList();
return;
}
if (fieldName.Contains("["))
{
string condensedFieldName;
List <int> indices = MzTab.GetFieldIndicies(fieldName, out condensedFieldName);
double tempDbl;
switch (condensedFieldName)
{
case Fields.SearchEngine:
SetListValue(ref _searchEngines, indices[0], new CVParamater(value));
return;
case Fields.BestSearchEngineScore:
SetListValue(ref _bestSearchEngineScores, indices[0], double.Parse(value, CultureInfo.CurrentCulture));
return;
case Fields.AbundancePerAssay:
SetListValue(ref _abundanceAssays, indices[0], double.Parse(value, CultureInfo.CurrentCulture));
return;
case Fields.AbundanceStudyVariables:
SetListValue(ref _abundanceStudyVariables, indices[0], double.Parse(value, CultureInfo.CurrentCulture));
return;
case Fields.AbundanceStdevStudyVariables:
SetListValue(ref _abundanceStdevStudyVariables, indices[0], double.Parse(value, CultureInfo.CurrentCulture));
return;
case Fields.AbundanceStandardErrorStudyVariables:
SetListValue(ref _abundanceStandardErrorStudyVariables, indices[0], double.Parse(value, CultureInfo.CurrentCulture));
return;
case Fields.SearchEngineScoreMsRun:
SetListValue(ref _searchEngineScoreMsRun, indices[0], indices[1], double.TryParse(value, out tempDbl) ? tempDbl : default(double?));
return;
case Fields.NumberOfPsmsPerMsRun:
SetListValue(ref _numberOfPsmsPerMsRun, indices[0], int.Parse(value));
return;
case Fields.NumberOfDistinctPeptidesPerMsRun:
SetListValue(ref _numberOfDistinctPeptidesPerMsRun, indices[0], int.Parse(value));
return;
case Fields.NumberOfUniquePeptidesPerMsRun:
SetListValue(ref _numberOfUniquePeptidesPerMsRun, indices[0], int.Parse(value));
return;
}
}
if (fieldName.StartsWith(MzTab.OptionalColumnPrefix))
{
SetOptionalData(fieldName, value);
return;
}
throw new ArgumentException("Unexpected field name: " + fieldName);
}
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 override void SetValue(string fieldName, string value)
{
switch (fieldName)
{
case Fields.Sequence:
Sequence = value; return;
case Fields.ID:
ID = int.Parse(value); return;
case Fields.Accession:
Accession = value; return;
case Fields.Unique:
Unique = value.Equals("1"); return;
case Fields.Database:
Database = value; return;
case Fields.DatabaseVersion:
DatabaseVersion = value; return;
case Fields.SearchEngine:
SearchEngines = value.Split('|').Select(datum => (CVParamater)datum).ToList(); return;
case Fields.Reliability:
Reliability = (MzTab.ReliabilityScore) int.Parse(value); return;
case Fields.Modifications:
Modifications = value; return;
case Fields.RetentionTime:
RetentionTime = value.Split('|').Select(double.Parse).ToList(); return;
case Fields.Charge:
Charge = int.Parse(value); return;
case Fields.ExperimentalMZ:
ExperimentalMZ = double.Parse(value); return;
case Fields.TheoreticalMZ:
TheoreticalMZ = double.Parse(value); return;
case Fields.Uri:
Uri = new Uri(value); return;
case Fields.SpectraReference:
SpectraReference = value; return;
case Fields.PreviousAminoAcid:
PreviousAminoAcid = value[0]; return;
case Fields.FollowingAminoAcid:
FollowingAminoAcid = value[0]; return;
case Fields.StartResidue:
StartResiduePosition = int.Parse(value); return;
case Fields.EndResidue:
EndResiduePosition = int.Parse(value); return;
}
if (fieldName.Contains("["))
{
string condensedFieldName;
List <int> indices = MzTab.GetFieldIndicies(fieldName, out condensedFieldName);
if (condensedFieldName == Fields.SearchEngineScore)
{
SetListValue(ref _searchEngineScores, indices[0], double.Parse(value));
return;
}
}
if (fieldName.StartsWith(MzTab.OptionalColumnPrefix))
{
SetOptionalData(fieldName, value);
return;
}
throw new ArgumentException("Unexpected field name: " + fieldName);
}
public override string GetValue(string fieldName)
{
switch (fieldName)
{
case Fields.Accession:
return(Accession);
case Fields.Description:
return(Description);
case Fields.Database:
return(Database);
case Fields.DatabaseVersion:
return(DatabaseVersion);
case Fields.SearchEngine:
return(SearchEngines == null ? MzTab.NullFieldText : string.Join("|", SearchEngines));
case Fields.TaxID:
return(TaxID.ToString());
case Fields.Species:
return(Species);
case Fields.Modifications:
return(Modificiations);
case Fields.AmbiguityMembers:
return(AmbiguityMembers == null ? MzTab.NullFieldText : string.Join(",", AmbiguityMembers));
case Fields.Reliability:
if (Reliability == MzTab.ReliabilityScore.NotSet)
{
return(MzTab.NullFieldText);
}
return(((int)Reliability).ToString());
case Fields.Coverage:
return(Coverage.ToString());
case Fields.Uri:
return(Uri != null?Uri.ToString() : MzTab.NullFieldText);
case Fields.GoTerms:
return(GoTerms == null ? MzTab.NullFieldText : string.Join("|", GoTerms));
}
if (fieldName.Contains("["))
{
string condensedFieldName;
List <int> indices = MzTab.GetFieldIndicies(fieldName, out condensedFieldName);
switch (condensedFieldName)
{
case Fields.SearchEngine:
return(GetListValue(_searchEngines, indices[0]));
case Fields.BestSearchEngineScore:
return(GetListValue(_bestSearchEngineScores, indices[0]));
case Fields.AbundancePerAssay:
return(GetListValue(_abundanceAssays, indices[0]));
case Fields.AbundanceStudyVariables:
return(GetListValue(_abundanceStudyVariables, indices[0]));
case Fields.AbundanceStdevStudyVariables:
return(GetListValue(_abundanceStdevStudyVariables, indices[0]));
case Fields.AbundanceStandardErrorStudyVariables:
return(GetListValue(_abundanceStandardErrorStudyVariables, indices[0]));
case Fields.SearchEngineScoreMsRun:
return(GetListValue(_searchEngineScoreMsRun, indices[0], indices[1]));
case Fields.NumberOfPsmsPerMsRun:
return(GetListValue(_numberOfPsmsPerMsRun, indices[0]));
case Fields.NumberOfDistinctPeptidesPerMsRun:
return(GetListValue(_numberOfDistinctPeptidesPerMsRun, indices[0]));
case Fields.NumberOfUniquePeptidesPerMsRun:
return(GetListValue(_numberOfUniquePeptidesPerMsRun, indices[0]));
}
}
if (fieldName.StartsWith(MzTab.OptionalColumnPrefix))
{
return(GetOptionalData(fieldName));
}
throw new ArgumentException("Unexpected field name: " + fieldName);
}
public override string GetValue(string fieldName)
{
switch (fieldName)
{
case Fields.Sequence:
return(string.IsNullOrEmpty(Sequence) ? MzTab.NullFieldText : Sequence);
case Fields.ID:
return(ID.ToString());
case Fields.Accession:
return(Accession);
case Fields.Unique:
return(Unique ? "1" : "0");
case Fields.Database:
return(string.IsNullOrEmpty(Database) ? MzTab.NullFieldText : Database);
case Fields.DatabaseVersion:
return(string.IsNullOrEmpty(DatabaseVersion) ? MzTab.NullFieldText : DatabaseVersion);
case Fields.SearchEngine:
return(SearchEngines == null ? MzTab.NullFieldText : string.Join("|", SearchEngines));
case Fields.Reliability:
if (Reliability == MzTab.ReliabilityScore.NotSet)
{
return(MzTab.NullFieldText);
}
return(((int)Reliability).ToString());
case Fields.Modifications:
return(string.IsNullOrEmpty(Modifications) ? MzTab.NullFieldText : Modifications);
case Fields.RetentionTime:
return(RetentionTime == null ? MzTab.NullFieldText : string.Join("|", RetentionTime));
case Fields.Charge:
return(Charge.ToString());
case Fields.ExperimentalMZ:
return(ExperimentalMZ.ToString());
case Fields.TheoreticalMZ:
return(TheoreticalMZ.ToString());
case Fields.Uri:
return(Uri == null ? MzTab.NullFieldText : Uri.ToString());
case Fields.SpectraReference:
return(string.IsNullOrEmpty(SpectraReference) ? MzTab.NullFieldText : SpectraReference);
case Fields.PreviousAminoAcid:
return(default(char).Equals(PreviousAminoAcid) ? "-" : PreviousAminoAcid.ToString());
case Fields.FollowingAminoAcid:
return(default(char).Equals(FollowingAminoAcid) ? "-" : FollowingAminoAcid.ToString());
case Fields.StartResidue:
return(StartResiduePosition.ToString());
case Fields.EndResidue:
return(EndResiduePosition.ToString());
}
if (fieldName.Contains("["))
{
string condensedFieldName;
List <int> indices = MzTab.GetFieldIndicies(fieldName, out condensedFieldName);
if (condensedFieldName == Fields.SearchEngineScore)
{
return(GetListValue(_searchEngineScores, indices[0]));
}
}
if (fieldName.StartsWith(MzTab.OptionalColumnPrefix))
{
return(GetOptionalData(fieldName));
}
throw new ArgumentException("Unexpected field name: " + fieldName);
}
public override void SetValue(string fieldName, string value)
{
if (MzTab.NullFieldText.Equals(value))
{
return;
}
switch (fieldName)
{
case Fields.Sequence:
Sequence = value; return;
case Fields.Accession:
Accession = value; return;
case Fields.Unique:
Unique = value.Equals("1"); return;
case Fields.Database:
Database = value; return;
case Fields.DatabaseVersion:
DatabaseVersion = value; return;
case Fields.SearchEngine:
SearchEngines = value.Split('|').Select(datum => (CVParamater)datum).ToList(); return;
case Fields.Reliability:
Reliability = (MzTab.ReliabilityScore) int.Parse(value); return;
case Fields.Modifications:
Modifications = value; return;
case Fields.RetentionTime:
RetentionTime = value.Split('|').Select(double.Parse).ToList(); return;
case Fields.RetentionTimeWindow:
RetentionTimeWindows = value.Split('|').Select(double.Parse).ToList(); return;
case Fields.Charge:
Charge = int.Parse(value); return;
case Fields.MZ:
MZ = double.Parse(value); return;
case Fields.Uri:
Uri = new Uri(value); return;
case Fields.SpectraReference:
SpectraReference = value; return;
}
if (fieldName.Contains("["))
{
string condensedFieldName;
List <int> indices = MzTab.GetFieldIndicies(fieldName, out condensedFieldName);
switch (condensedFieldName)
{
case Fields.AbundanceAssay:
SetListValue(ref _abundanceAssays, indices[0], double.Parse(value)); return;
case Fields.AbundanceStudyVariable:
SetListValue(ref _abundanceStudyVariables, indices[0], double.Parse(value)); return;
case Fields.AbundanceStDevStudyVariable:
SetListValue(ref _abundanceStdevStudyVariables, indices[0], double.Parse(value)); return;
case Fields.AbudnanceStdErrorStudyVariable:
SetListValue(ref _abundanceStandardErrorStudyVariables, indices[0], double.Parse(value)); return;
case Fields.BestSearchEngineScore:
SetListValue(ref _bestSearchEngineScores, indices[0], double.Parse(value)); return;
}
}
if (fieldName.StartsWith(MzTab.OptionalColumnPrefix))
{
SetOptionalData(fieldName, value);
return;
}
throw new ArgumentException("Unexpected field name: " + fieldName);
}
public override string GetValue(string fieldName)
{
switch (fieldName)
{
case Fields.Sequence:
return(Sequence);
case Fields.Accession:
return(Accession);
case Fields.Unique:
return(Unique ? "1" : "0");
case Fields.Database:
return(Database);
case Fields.DatabaseVersion:
return(DatabaseVersion);
case Fields.SearchEngine:
return(string.Join("|", SearchEngines));
case Fields.Reliability:
if (Reliability == MzTab.ReliabilityScore.NotSet)
{
return(MzTab.NullFieldText);
}
return(((int)Reliability).ToString());
case Fields.Modifications:
return(Modifications);
case Fields.RetentionTime:
return(string.Join("|", RetentionTime));
case Fields.Charge:
return(Charge.ToString());
case Fields.MZ:
return(MZ.ToString());
case Fields.Uri:
return(Uri.ToString());
case Fields.SpectraReference:
return(SpectraReference);
case Fields.RetentionTimeWindow:
return(string.Join("|", RetentionTimeWindows));
}
if (fieldName.Contains("["))
{
string condensedFieldName;
List <int> indices = MzTab.GetFieldIndicies(fieldName, out condensedFieldName);
switch (condensedFieldName)
{
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]));
case Fields.BestSearchEngineScore:
return(GetListValue(_bestSearchEngineScores, indices[0]));
}
}
if (fieldName.StartsWith(MzTab.OptionalColumnPrefix))
{
return(GetOptionalData(fieldName));
}
throw new ArgumentException("Unexpected field name: " + fieldName);
}
public override void SetValue(string fieldName, string value)
{
switch (fieldName)
{
case Fields.Mode:
Mode = (MzTab.MzTabMode)Enum.Parse(typeof(MzTab.MzTabMode), value, true);
return;
case Fields.Type:
Type = (MzTab.MzTabType)Enum.Parse(typeof(MzTab.MzTabType), value, true);
return;
case Fields.Description:
Description = value;
return;
case Fields.Title:
Title = value;
return;
case Fields.Version:
Version = value;
return;
case Fields.ID:
ID = value;
return;
case Fields.ProteinQuantificationUnit:
ProteinQuantificationUnit = new CVParamater(value);
return;
}
if (fieldName.Contains("["))
{
string condensedFieldName;
List <int> indices = MzTab.GetFieldIndicies(fieldName, out condensedFieldName);
switch (condensedFieldName)
{
case Fields.FixedMod:
SetListValue(ref _fixedModifications, indices[0], new CVParamater(value));
return;
case Fields.FixedModSite:
SetListValue(ref _fixedModificationSites, indices[0], value);
return;
case Fields.VariableMod:
SetListValue(ref _variableModifications, indices[0], new CVParamater(value));
return;
case Fields.PsmSearchEngineScore:
SetListValue(ref _psmSearchEngineScores, indices[0], new CVParamater(value));
return;
case Fields.ProteinSearchEngineScore:
SetListValue(ref _proteinSearchEngineScores, indices[0], new CVParamater(value));
return;
case Fields.StudyVariableDescription:
SetListValue(ref _studyVariableDescriptions, indices[0], value);
return;
case Fields.MsRunLocation:
SetListValue(ref _msRunLocations, indices[0], value);
return;
case Fields.Software:
SetListValue(ref _software, indices[0], new MzTabSoftware(new CVParamater(value)));
return;
case Fields.SoftwareSettings:
SetFieldValue(ref _software, indices[0], sw => sw.Settings, value);
return;
}
}
//throw new ArgumentException("Unexpected field name: " + fieldName);
}
public override string GetValue(string fieldName)
{
switch (fieldName)
{
case Fields.Mode:
return(Enum.GetName(typeof(MzTab.MzTabMode), Mode));
case Fields.Type:
return(Enum.GetName(typeof(MzTab.MzTabType), Type));
case Fields.Description:
return(Description);
case Fields.Title:
return(Title);
case Fields.Version:
return(Version);
case Fields.ID:
return(ID);
case Fields.ProteinQuantificationUnit:
return(ProteinQuantificationUnit == null ? MzTab.NullFieldText : ProteinQuantificationUnit.ToString());
}
if (fieldName.Contains("["))
{
string condensedFieldName;
List <int> indices = MzTab.GetFieldIndicies(fieldName, out condensedFieldName);
switch (condensedFieldName)
{
case Fields.FixedMod:
return(GetListValue(_fixedModifications, indices[0]));
case Fields.FixedModSite:
return(GetListValue(_fixedModificationSites, indices[0]));
case Fields.VariableMod:
return(GetListValue(_variableModifications, indices[0]));
case Fields.PsmSearchEngineScore:
return(GetListValue(_psmSearchEngineScores, indices[0]));
case Fields.ProteinSearchEngineScore:
return(GetListValue(_proteinSearchEngineScores, indices[0]));
case Fields.StudyVariableDescription:
return(GetListValue(_studyVariableDescriptions, indices[0]));
case Fields.MsRunLocation:
return(GetListValue(_msRunLocations, indices[0]));
case Fields.Software:
return(GetListValue(_software, indices[0]));
case Fields.SoftwareSettings:
return(GetFieldValue(_software, indices[0], sw => sw.Settings, indices[1]));
}
}
throw new ArgumentException("Unexpected field name: " + fieldName);
}