public static string GetHeader(IndexedElement element, string value)
{
StringBuilder sb = new StringBuilder();
sb.Append(OPT).Append("_").Append(element == null ? GLOBAL : element.Reference);
sb.Append("_").Append(value.Replace(" ", "_"));
return sb.ToString();
}
public static string GetHeader(IndexedElement element, CVParam param)
{
StringBuilder sb = new StringBuilder();
sb.Append(OPT).Append("_").Append(element == null ? GLOBAL : element.Reference);
sb.Append("_").Append(CV).Append(param.Accession).Append("_").Append(param.Name.Replace(" ", "_"));
return sb.ToString();
}
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;
}
private AbundanceColumn(Section section, Field field, IndexedElement element, int offset)
: base(translate(section.Name) + "_" + field.name, field.columnType, true, offset + field.position + "")
{
Element = element;
}
public OptionColumn(IndexedElement element, string value, System.Type columnType, int offset)
: base(GetHeader(element, value), columnType, true, offset + 1 + "")
{
}
public CVParamOptionColumn(IndexedElement element, CVParam param, System.Type columnType, int offset)
: base(element, CV + param.Accession + "_" + param.Name.Replace(" ", "_"), columnType, offset)
{
this.param = param;
}