public void addSearchEngineScoreOptionalColumn(MZTabColumn column, Integer id, MsRun msRun) {
String position = column.getLogicPosition();
if (optionalColumnMapping.containsKey(position)) {
throw new IllegalArgumentException(
"There exists column "
+ optionalColumnMapping.get(position)
+ " in position "
+ position);
}
MZTabColumn newColumn = null;
switch (section) {
case Protein_Header:
if (column.getName().equals(ProteinColumn.SEARCH_ENGINE_SCORE.getName())) {
newColumn = MZTabColumn.createOptionalColumn(section, column, id, msRun);
}
break;
case Peptide_Header:
if (column.getName().equals(PeptideColumn.SEARCH_ENGINE_SCORE.getName())) {
newColumn = MZTabColumn.createOptionalColumn(section, column, id, msRun);
}
break;
case Small_Molecule_Header:
if (column.getName().equals(SmallMoleculeColumn.SEARCH_ENGINE_SCORE.getName())) {
newColumn = MZTabColumn.createOptionalColumn(section, column, id, msRun);
}
break;
case PSM_Header:
if (column.getName().equals(PSMColumn.SEARCH_ENGINE_SCORE.getName())) {
newColumn = MZTabColumn.createOptionalColumn(section, column, id, null);
}
break;
}
if (newColumn != null) {
optionalColumnMapping.put(newColumn.getLogicPosition(), newColumn);
columnMapping.put(newColumn.getLogicPosition(), newColumn);
}
}
/**
* Judge the column is optional or not, based one its header name.
*
* @param header SHOULD NOT be null!
*/
public boolean isOptionalColumn(String header) {
header = header.trim().toLowerCase();
switch (section) {
case Protein_Header:
if (header.startsWith(ProteinColumn.SEARCH_ENGINE_SCORE.getName())
|| header.startsWith(ProteinColumn.NUM_PSMS.getName())
|| header.startsWith(ProteinColumn.NUM_PEPTIDES_DISTINCT.getName())
|| header.startsWith(ProteinColumn.NUM_PEPTIDES_UNIQUE.getName())
|| header.startsWith("protein_abundance_assay")
|| header.startsWith("protein_abundance_study_variable")
|| header.startsWith("protein_abundance_stdev_study_variable")
|| header.startsWith("protein_abundance_std_error_study_variable")) {
return true;
}
break;
case Peptide_Header:
if (header.startsWith(PeptideColumn.SEARCH_ENGINE_SCORE.getName())
|| header.startsWith("peptide_abundance_assay")
|| header.startsWith("peptide_abundance_study_variable")
|| header.startsWith("peptide_abundance_stdev_study_variable")
|| header.startsWith("peptide_abundance_std_error_study_variable")) {
return true;
}
break;
case Small_Molecule_Header:
if (header.startsWith(SmallMoleculeColumn.SEARCH_ENGINE_SCORE.getName())
|| header.startsWith("smallmolecule_abundance_assay")
|| header.startsWith("smallmolecule_abundance_study_variable")
|| header.startsWith("smallmolecule_abundance_stdev_study_variable")
|| header.startsWith("smallmolecule_abundance_std_error_study_variable")) {
return true;
}
break;
}
return header.startsWith("opt_");
}
