public PositionMapping(MZTabColumnFactory factory, String[] headerList) {
String header;
for (int physicalPosition = 0; physicalPosition < headerList.length; physicalPosition++) {
header = headerList[physicalPosition];
MZTabColumn column = factory.findColumnByHeader(header);
if (column != null) {
put(physicalPosition, column.getLogicPosition());
}
}
}
/**
* 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 IllegalArgumentException(
"Section should use Protein_Header, Peptide_Header, PSM_Header or Small_Molecule_Header.");
}
MZTabColumnFactory factory = new MZTabColumnFactory();
switch (section) {
case 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);
break;
case 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);
break;
case 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);
break;
case 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.MODIFICATIONS);
break;
default:
throw new IllegalArgumentException("Can not use Comment, Metadata section.");
}
factory.columnMapping.putAll(factory.stableColumnMapping);
factory.section = section;
return factory;
}
@Test
public void testUnique() throws Exception {
pepParser.checkUnique(pehFactory.findColumnByHeader("unique"), "x");
assertError(FormatErrorType.MZBoolean);
}