public void addBestSearchEngineScoreOptionalColumn(MZTabColumn column, Integer id) {
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.BEST_SEARCH_ENGINE_SCORE.getName())) {
newColumn = MZTabColumn.createOptionalColumn(section, column, id, null);
}
break;
case Peptide_Header:
if (column.getName().equals(PeptideColumn.BEST_SEARCH_ENGINE_SCORE.getName())) {
newColumn = MZTabColumn.createOptionalColumn(section, column, id, null);
}
break;
case Small_Molecule_Header:
if (column.getName().equals(SmallMoleculeColumn.BEST_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);
}
}
/**
* Add {@link AbundanceColumn} into {@link AbundanceColumn}, {@link #optionalColumnMapping} and
* {@link #columnMapping}. The header like: {Section}_abundance_assay[1]
*
* @see AbundanceColumn#createOptionalColumn(Section, Assay, int)
* @param assay SHOULD NOT empty.
*/
public String addAbundanceOptionalColumn(Assay assay) {
MZTabColumn column =
AbundanceColumn.createOptionalColumn(
section, assay, new Integer(getColumnOrder(columnMapping.lastKey())));
abundanceColumnMapping.put(column.getLogicPosition(), column);
return addOptionColumn(column);
}
private String addOptionColumn(MZTabColumn column) {
String logicalPosition = column.getLogicPosition();
optionalColumnMapping.put(logicalPosition, column);
columnMapping.put(column.getLogicPosition(), column);
return logicalPosition;
}
/** @return tab split column header string list. */
public SplitList<String> getHeaderList() {
SplitList<String> headerList = new SplitList<String>(TAB);
for (MZTabColumn mzTabColumn : columnMapping.values()) {
headerList.add(mzTabColumn.getHeader());
}
return headerList;
}
/**
* Add {@link ProteinColumn#GO_TERMS} into {@link #optionalColumnMapping} and {@link
* #columnMapping}.
*
* <p>Notice: this function only used in {@link Section#Protein_Header}
*/
public void addGoTermsOptionalColumn() {
if (section != Section.Protein_Header) {
throw new IllegalArgumentException(
"go_terms optional column only add into the protein section.");
}
MZTabColumn column = ProteinColumn.GO_TERMS;
optionalColumnMapping.put(column.getLogicPosition(), column);
columnMapping.put(column.getLogicPosition(), column);
}
/**
* Query the MZTabColumn in factory, based on column header with case-insensitive. Notice: for
* optional columns, header name maybe flexible. For example, num_psms_ms_run[1]. At this time,
* user SHOULD BE provide the full header name to query MZTabColumn. If just provide
* num_psms_ms_run, return null.
*/
public MZTabColumn findColumnByHeader(String header) {
header = header.trim();
for (MZTabColumn column : columnMapping.values()) {
if (header.equalsIgnoreCase(column.getHeader())) {
return column;
}
}
return null;
}
/** Add URI optional column into {@link #optionalColumnMapping} and {@link #columnMapping}. */
public void addURIOptionalColumn() {
MZTabColumn column = null;
switch (section) {
case Protein_Header:
column = ProteinColumn.URI;
break;
case Peptide_Header:
column = PeptideColumn.URI;
break;
case Small_Molecule_Header:
column = SmallMoleculeColumn.URI;
break;
case PSM_Header:
column = PSMColumn.URI;
break;
}
if (column != null) {
optionalColumnMapping.put(column.getLogicPosition(), column);
columnMapping.put(column.getLogicPosition(), column);
}
}
/**
* Add a optional column which has stable order and name, into {@link #optionalColumnMapping} and
* {@link #columnMapping}.
*
* @see MZTabColumn#createOptionalColumn(Section, MZTabColumn, Integer, IndexedElement)
* @exception IllegalArgumentException: If user would like to add duplicate optional columns.
* @param column SHOULD NOT set null.
* @param msRun SHOULD NOT set null.
*/
public void addOptionalColumn(MZTabColumn column, 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.NUM_PSMS.getName()) ||
// column.getName().equals(ProteinColumn.NUM_PEPTIDES_DISTINCT.getName())
// ||
// column.getName().equals(ProteinColumn.NUM_PEPTIDES_UNIQUE.getName()))
// {
// newColumn = MZTabColumn.createOptionalColumn(section, column, msRun);
// }
//
// if (position.equals(ProteinColumn.SEARCH_ENGINE_SCORE.getOrder()) ||
// position.equals(ProteinColumn.NUM_PSMS.getOrder()) ||
// position.equals(ProteinColumn.NUM_PEPTIDES_DISTINCT.getOrder()) ||
// position.equals(ProteinColumn.NUM_PEPTIDES_UNIQUE.getOrder())) {
// newColumn = MZTabColumn.createOptionalColumn(section, column, msRun);
// }
// break;
// case Peptide_Header:
// if (position.equals(PeptideColumn.SEARCH_ENGINE_SCORE.getOrder())) {
// newColumn = MZTabColumn.createOptionalColumn(section, column, msRun);
// }
// break;
// case Small_Molecule_Header:
// if (position.equals(SmallMoleculeColumn.SEARCH_ENGINE_SCORE.getOrder())) {
// newColumn = MZTabColumn.createOptionalColumn(section, column, msRun);
// }
// break;
// }
if (section == Section.Protein_Header) {
if (column.getName().equals(ProteinColumn.NUM_PSMS.getName())
|| column.getName().equals(ProteinColumn.NUM_PEPTIDES_DISTINCT.getName())
|| column.getName().equals(ProteinColumn.NUM_PEPTIDES_UNIQUE.getName())) {
newColumn = MZTabColumn.createOptionalColumn(section, column, null, msRun);
}
}
if (newColumn != null) {
optionalColumnMapping.put(newColumn.getLogicPosition(), newColumn);
columnMapping.put(newColumn.getLogicPosition(), newColumn);
}
}
private static void addStableColumn(MZTabColumnFactory factory, MZTabColumn column) {
factory.stableColumnMapping.put(column.getLogicPosition(), column);
}