internal static MZTabColumn CreateOptionalColumn(Section section, MZTabColumn column, Integer id, IndexedElement element)
{
if (! column.isOptional()){
throw new ArgumentException(column + " is not optional column!");
}
MZTabColumn optionColumn = null;
if (section.Equals(Section.Protein_Header)){
optionColumn = new ProteinColumn(column.Name, column.Type, column.isOptional(), column.Order, id);
}
else if (section.Equals(Section.Peptide_Header)){
optionColumn = new PeptideColumn(column.Name, column.Type, column.isOptional(), column.Order, id);
}
else if (section.Equals(Section.PSM_Header)){
optionColumn = new PSMColumn(column.Name, column.Type, column.isOptional(), column.Order, id);
}
else if (section.Equals(Section.Small_Molecule_Header)){
optionColumn = new SmallMoleculeColumn(column.Name, column.Type, column.isOptional(), column.Order, id);
}
if (optionColumn != null && element != null){
optionColumn.Element = element;
}
return optionColumn;
}
/**
* Translate the data line to a {@link MZTabRecord}.
*
* NOTICE: Normally, we suggest user do convert operation after validate successfully.
*
* @see #parse(int, string, uk.ac.ebi.pride.jmztab.utils.errors.MZTabErrorList)
*/
protected MZTabRecord getRecord(Section section, string line)
{
MZTabRecord record = null;
if (section.Equals(Section.Protein)){
record = new Protein(factory);
}
else if (section.Equals(Section.Peptide)){
record = new Peptide(factory, metadata);
}
else if (section.Equals(Section.PSM)){
record = new PSM(factory, metadata);
}
else if (section.Equals(Section.Small_Molecule)){
record = new SmallMolecule(factory, metadata);
}
int offset = loadStableData(record, line);
if (offset == _items.Length - 1){
return record;
}
loadOptionalData(record, offset);
return record;
}
/**
* Based on {@link #section} to generate stable columns, and store them into {@link #stableColumnMapping} and
* {@link #columnMapping} which maintain all columns in the factory.
*
* @param section SHOULD be {@link Section#Protein_Header}, {@link Section#Peptide_Header} {@link Section#PSM_Header}
* or {@link Section#Small_Molecule_Header}.
*/
public static MZTabColumnFactory GetInstance(Section section)
{
section = Section.toHeaderSection(section);
if (section == null){
throw new ArgumentException(
"Section should use Protein_Header, Peptide_Header, PSM_Header or Small_Molecule_Header.");
}
MZTabColumnFactory factory = new MZTabColumnFactory();
if (section.Equals(Section.Protein_Header)){
AddStableColumn(factory, ProteinColumn.ACCESSION);
AddStableColumn(factory, ProteinColumn.DESCRIPTION);
AddStableColumn(factory, ProteinColumn.TAXID);
AddStableColumn(factory, ProteinColumn.SPECIES);
AddStableColumn(factory, ProteinColumn.DATABASE);
AddStableColumn(factory, ProteinColumn.DATABASE_VERSION);
AddStableColumn(factory, ProteinColumn.SEARCH_ENGINE);
AddStableColumn(factory, ProteinColumn.AMBIGUITY_MEMBERS);
AddStableColumn(factory, ProteinColumn.MODIFICATIONS);
AddStableColumn(factory, ProteinColumn.PROTEIN_COVERAGE);
}
else if (section.Equals(Section.Peptide_Header)){
AddStableColumn(factory, PeptideColumn.SEQUENCE);
AddStableColumn(factory, PeptideColumn.ACCESSION);
AddStableColumn(factory, PeptideColumn.UNIQUE);
AddStableColumn(factory, PeptideColumn.DATABASE);
AddStableColumn(factory, PeptideColumn.DATABASE_VERSION);
AddStableColumn(factory, PeptideColumn.SEARCH_ENGINE);
AddStableColumn(factory, PeptideColumn.MODIFICATIONS);
AddStableColumn(factory, PeptideColumn.RETENTION_TIME);
AddStableColumn(factory, PeptideColumn.RETENTION_TIME_WINDOW);
AddStableColumn(factory, PeptideColumn.CHARGE);
AddStableColumn(factory, PeptideColumn.MASS_TO_CHARGE);
AddStableColumn(factory, PeptideColumn.SPECTRA_REF);
}
else if (section.Equals(Section.PSM_Header)){
AddStableColumn(factory, PSMColumn.SEQUENCE);
AddStableColumn(factory, PSMColumn.PSM_ID);
AddStableColumn(factory, PSMColumn.ACCESSION);
AddStableColumn(factory, PSMColumn.UNIQUE);
AddStableColumn(factory, PSMColumn.DATABASE);
AddStableColumn(factory, PSMColumn.DATABASE_VERSION);
AddStableColumn(factory, PSMColumn.SEARCH_ENGINE);
AddStableColumn(factory, PSMColumn.MODIFICATIONS);
AddStableColumn(factory, PSMColumn.RETENTION_TIME);
AddStableColumn(factory, PSMColumn.CHARGE);
AddStableColumn(factory, PSMColumn.EXP_MASS_TO_CHARGE);
AddStableColumn(factory, PSMColumn.CALC_MASS_TO_CHARGE);
AddStableColumn(factory, PSMColumn.SPECTRA_REF);
AddStableColumn(factory, PSMColumn.PRE);
AddStableColumn(factory, PSMColumn.POST);
AddStableColumn(factory, PSMColumn.START);
AddStableColumn(factory, PSMColumn.END);
}
else if (section.Equals(Section.Small_Molecule_Header)){
AddStableColumn(factory, SmallMoleculeColumn.IDENTIFIER);
AddStableColumn(factory, SmallMoleculeColumn.CHEMICAL_FORMULA);
AddStableColumn(factory, SmallMoleculeColumn.SMILES);
AddStableColumn(factory, SmallMoleculeColumn.INCHI_KEY);
AddStableColumn(factory, SmallMoleculeColumn.DESCRIPTION);
AddStableColumn(factory, SmallMoleculeColumn.EXP_MASS_TO_CHARGE);
AddStableColumn(factory, SmallMoleculeColumn.CALC_MASS_TO_CHARGE);
AddStableColumn(factory, SmallMoleculeColumn.CHARGE);
AddStableColumn(factory, SmallMoleculeColumn.RETENTION_TIME);
AddStableColumn(factory, SmallMoleculeColumn.TAXID);
AddStableColumn(factory, SmallMoleculeColumn.SPECIES);
AddStableColumn(factory, SmallMoleculeColumn.DATABASE);
AddStableColumn(factory, SmallMoleculeColumn.DATABASE_VERSION);
AddStableColumn(factory, SmallMoleculeColumn.SPECTRA_REF);
AddStableColumn(factory, SmallMoleculeColumn.SEARCH_ENGINE);
AddStableColumn(factory, SmallMoleculeColumn.BEST_SEARCH_ENGINE_SCORE);
AddStableColumn(factory, SmallMoleculeColumn.MODIFICATIONS);
}
else{
throw new NotImplementedException("Section should be Protein, Peptide or " +
"Small_Molecule. Others can not setting. ");
}
foreach (var column in factory.StableColumnMapping){
factory.ColumnMapping.Add(column.Key, column.Value);
}
factory.section = section;
return factory;
}