public MZTabColumn(string name, Type type, bool optional, string order, Integer id)
{
_name = name;
if (type == null) {
throw new NullReferenceException("Column data type should not set null!");
}
_type = type;
_optional = optional;
_order = order;
_id = id;
_header = generateHeader(name);
_logicPosition = generateLogicalPosition();
}
internal SmallMoleculeColumn(string name, Type columnType, bool optional, string order,Integer id)
: base(name, columnType, optional, order, id)
{
}
/**
* The search engine score for the given protein in the defined ms run. The type of score
* MUST be defined in the metadata section. If the protein was not identified by the specified
* search engine “null” must be reported
*
* @param id protein_search_engine_score[id] which MUST be defined in the metadata section.
* @param msRun SHOULD NOT set null
*/
public void setSearchEngineScore(Integer id, MsRun msRun, double searchEngineScore)
{
setValue(getLogicalPosition(PeptideColumn.SEARCH_ENGINE_SCORE, id, msRun), searchEngineScore);
}
/**
* The best search engine score (for this type of score) for the given protein across
* all replicates reported. The type of score MUST be defined in the metadata section.
* If the protein was not identified by the specified search engine “null” must be reported
*
* @param id protein_search_engine_score[id] which MUST be defined in the metadata section.
*/
public void setBestSearchEngineScore(Integer id, double bestSearchEngineScore)
{
setValue(getLogicalPosition(PeptideColumn.BEST_SEARCH_ENGINE_SCORE, id, null), bestSearchEngineScore);
}
/**
* The search engine score for the given protein in the defined ms run. The type of score
* MUST be defined in the metadata section. If the protein was not identified by the specified
* search engine “null” must be reported
*
* @param id protein_search_engine_score[id] which MUST be defined in the metadata section.
* @param msRun SHOULD NOT set null
*/
public Double getSearchEngineScore(Integer id, MsRun msRun)
{
return getDouble(getLogicalPosition(PeptideColumn.SEARCH_ENGINE_SCORE, id, msRun));
}
/**
* The best search engine score (for this type of score) for the given protein across
* all replicates reported. The type of score MUST be defined in the metadata section.
* If the protein was not identified by the specified search engine “null” must be reported
*
* @param id protein_search_engine_score[id] which MUST be defined in the metadata section.
*/
public Double getBestSearchEngineScore(Integer id)
{
return getDouble(getLogicalPosition(PeptideColumn.BEST_SEARCH_ENGINE_SCORE, id, null));
}
internal ProteinColumn(string name, Type columnType, bool optional, string order, Integer id)
: base(name, columnType, optional, order, id)
{
}
public void setNumPeptidesDistinct(MsRun msRun, Integer numPeptidesDistinct)
{
setNumPeptidesDistinct(getPosition(ProteinColumn.NUM_PEPTIDES_DISTINCT, msRun), numPeptidesDistinct);
}
/**
* The search engine score for the given protein in the defined ms run. The type of score
* MUST be defined in the metadata section. If the protein was not identified by the specified
* search engine “null” must be reported
*
* @param id protein_search_engine_score[id] which MUST be defined in the metadata section.
* @param msRun SHOULD NOT set null
*/
public Double getSearchEngineScore(Integer id)
{
return getDouble(getLogicalPosition(PSMColumn.SEARCH_ENGINE_SCORE, id, null));
}
/** Add {@link SearchEngineScore} followed by {@link MsRun} (MsRun will be null in the PSM section) which has stable order and name,
* into {@link #optionalColumnMapping} and {@link #columnMapping}.
*
* @param column search_engine_score column to add. SHOULD NOT set null.
* @param id of the {section}_search_engine_score[id] param defined in {@link Metadata} for this column. SHOULD NOT set null.
* @param msRun {@link MsRun} for this search_engine_score
*
* The header will be represented as: search_engine_score[id]{_ms_run[1-n]}
*/
public void AddSearchEngineScoreOptionalColumn(MZTabColumn column, Integer id, MsRun msRun)
{
String position = column.LogicPosition;
if (optionalColumnMapping.ContainsKey(position)) {
throw new ArgumentOutOfRangeException("There exists column " + optionalColumnMapping[position] + " in position " + position);
}
MZTabColumn newColumn = null;
if (section.Equals(Section.Protein_Header)){
if (column.Name.Equals(ProteinColumn.SEARCH_ENGINE_SCORE.Name)) {
newColumn = MZTabColumn.CreateOptionalColumn(section, column, id, msRun);
}
} else if (section.Equals(Section.Peptide_Header)){
if (column.Name.Equals(PeptideColumn.SEARCH_ENGINE_SCORE.Name)) {
newColumn = MZTabColumn.CreateOptionalColumn(section, column, id, msRun);
}
}else if (section.Equals(Section.Small_Molecule_Header)){
if (column.Name.Equals(SmallMoleculeColumn.SEARCH_ENGINE_SCORE.Name)) {
newColumn = MZTabColumn.CreateOptionalColumn(section, column, id, msRun);
}
}else if (section.Equals(Section.PSM_Header)){
if (column.Name.Equals(PSMColumn.SEARCH_ENGINE_SCORE.Name)) {
newColumn = MZTabColumn.CreateOptionalColumn(section, column, id, null);
}
}
if (newColumn != null) {
optionalColumnMapping.Add(newColumn.LogicPosition, newColumn);
columnMapping.Add(newColumn.LogicPosition, newColumn);
}
}
public void setNumPSMs(MsRun msRun, Integer numPSMs)
{
setNumPSMs(getLogicalPosition(ProteinColumn.NUM_PSMS, null, msRun), numPSMs.ToString());
}
public void setNumPSMs(string logicalPosition, Integer numPSMs)
{
setValue(logicalPosition, numPSMs);
}
public void setNumPeptidesUnique(MsRun msRun, Integer numPeptidesUnique)
{
setNumPeptidesUnique(getPosition(ProteinColumn.NUM_PEPTIDES_UNIQUE, msRun), numPeptidesUnique);
}
public void setNumPeptidesUnique(string logicalPosition, Integer numPeptidesUnique)
{
setValue(logicalPosition, numPeptidesUnique);
}
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;
}
/**
* The search engine score for the given protein in the defined ms run. The type of score
* MUST be defined in the metadata section. If the protein was not identified by the specified
* search engine “null” must be reported
*
* @param id protein_search_engine_score[id] which MUST be defined in the metadata section.
* @param msRun SHOULD NOT set null
*/
public void setSearchEngineScore(Integer id, double searchEngineScore)
{
setValue(getLogicalPosition(PSMColumn.SEARCH_ENGINE_SCORE, id, null), searchEngineScore);
}
public void setNumPeptidesDistinct(string logicalPosition, Integer numPeptidesDistinct)
{
setValue(logicalPosition, numPeptidesDistinct);
}
