public PositionMapping(MZTabColumnFactory factory, string[] headerList)
{
for (int physicalPosition = 0; physicalPosition < headerList.Length; physicalPosition++){
string header = headerList[physicalPosition];
MZTabColumn column = factory.FindColumnByHeader(header);
if (column != null){
put(physicalPosition, column.LogicPosition);
}
}
}
/**
* valueLabel pattern like: column_name=param_string
*/
private MZTabError checkColUnit(string valueLabel, MZTabColumnFactory factory)
{
string[] items = valueLabel.Split('=');
string columnName = items[0].Trim();
string value = items[1].Trim();
MZTabColumn column = factory.FindColumnByHeader(columnName);
if (column == null){
// column_name not exists in the factory.
return new MZTabError(FormatErrorType.ColUnit, _lineNumber, valueLabel, columnName);
}
Param param = MZTabUtils.ParseParam(value);
if (param == null){
return new MZTabError(FormatErrorType.Param, _lineNumber, valueLabel, value);
}
if (factory.Section.Equals(Section.Protein_Header)){
_metadata.AddProteinColUnit(column, param);
}
else if (factory.Section.Equals(Section.Peptide_Header)){
_metadata.AddPeptideColUnit(column, param);
}
else if (factory.Section.Equals(Section.PSM_Header)){
_metadata.AddPSMColUnit(column, param);
}
else if (factory.Section.Equals(Section.Small_Molecule_Header)){
_metadata.AddSmallMoleculeColUnit(column, param);
}
return null;
}