public void addQuantificationModParam(int id, Param param)
{
AssayQuantificationMod mod = null;
if (quantificationModMap.ContainsKey(id)){
mod = quantificationModMap[id];
}
if (mod == null){
mod = new AssayQuantificationMod(this, id){Param = param};
quantificationModMap.Add(id, mod);
}
else{
mod.Param = param;
}
}
/**
* Defines the used unit for a column in the peptide/protein/small_molecule section.
* The format of the value has to be {column name}={Parameter defining the unit}
*/
internal ColUnit(MZTabColumn column, Param value)
{
if (column == null){
throw new NullReferenceException("MZTabColumn can not set null");
}
if (value == null){
throw new NullReferenceException("Param can not set null");
}
if (column is PluginMzTab.Lib.Model.AbundanceColumn){
throw new Exception("Colunit MUST NOT be used to define a unit for quantification columns.");
}
this.column = column;
this.value = value;
}
public bool AddSearchEngine(Param param)
{
if (param == null){
return false;
}
SplitList<Param> searchParams = SearchEngine;
if (searchParams == null){
searchParams = new SplitList<Param>(MZTabConstants.BAR);
SearchEngine = searchParams;
searchParams.Add(param);
}
else if (! searchParams.Contains(param)){
searchParams.Add(param);
}
return true;
}
public bool AddVariableModParam(int id, Param param)
{
VariableMod mod;
if (_variableModMap.ContainsKey(id)){
mod = _variableModMap[id];
if (mod.Param != null){
return false;
}
mod.Param = param;
return true;
}
mod = new VariableMod(id);
_variableModMap.Add(id, mod);
mod.Param = param;
return true;
}
public void AddSmallMoleculeColUnit(MZTabColumn column, Param param)
{
_smallMoleculeColUnitList.Add(new ColUnit(column, param));
}
public bool AddSampleSpecies(int id, Param species)
{
Sample sample;
if (!_sampleMap.ContainsKey(id)){
sample = new Sample(id);
sample.AddSpecies(species);
_sampleMap.Add(id, sample);
return true;
}
sample = _sampleMap[id];
sample.AddSpecies(species);
return true;
}
public bool AddSampleDisease(int id, Param disease)
{
Sample sample;
if (!_sampleMap.ContainsKey(id)){
sample = new Sample(id);
sample.AddDisease(disease);
_sampleMap.Add(id, sample);
return true;
}
sample = _sampleMap[id];
sample.AddDisease(disease);
return true;
}
public bool AddSampleCellType(int id, Param cellType)
{
Sample sample;
if (!_sampleMap.ContainsKey(id)){
sample = new Sample(id);
sample.AddCellType(cellType);
_sampleMap.Add(id, sample);
return true;
}
sample = _sampleMap[id];
if (sample.CellTypeList.Contains(cellType)){
return false;
}
sample.AddCellType(cellType);
return true;
}
public bool AddFixedModParam(int id, Param param)
{
FixedMod mod;
if (_fixedModMap.ContainsKey(id)){
mod = _fixedModMap[id];
if (mod.Param != null){
return false;
}
mod.Param = param;
return true;
}
mod = new FixedMod(id);
_fixedModMap.Add(id, mod);
mod.Param = param;
return true;
}
public void AddFalseDiscoveryRateParam(Param param)
{
_falseDiscoveryRate.Add(param);
}
public void AddCustom(Param custom)
{
_customList.Add(custom);
}
public bool AddAssayQuantificationReagent(int id, Param quantificationReagent)
{
Assay assay;
if (!_assayMap.ContainsKey(id)){
assay = new Assay(id){QuantificationReagent = quantificationReagent};
_assayMap.Add(id, assay);
return true;
}
assay = _assayMap[id];
if (assay.QuantificationReagent != null){
return false;
}
assay.QuantificationReagent = quantificationReagent;
return true;
}
public void AddAssayQuantificationModParam(int assayId, int quanModId, Param param)
{
Assay assay = _assayMap[assayId];
if (assay == null){
assay = new Assay(assayId);
assay.addQuantificationModParam(quanModId, param);
_assayMap.Add(assayId, assay);
}
else{
assay.addQuantificationModParam(quanModId, param);
}
}
public void AddTissue(Param param)
{
_tissueList.Add(param);
}
public void AddSpecies(Param param)
{
_speciesList.Add(param);
}
public void AddProteinColUnit(MZTabColumn column, Param param)
{
_proteinColUnitList.Add(new ColUnit(column, param));
}
public void AddPSMColUnit(MZTabColumn column, Param param)
{
_psmColUnitList.Add(new ColUnit(column, param));
}
public bool AddInstrumentAnalyzer(int id, Param analyzer)
{
Instrument instrument;
if (!_instrumentMap.ContainsKey(id)){
instrument = new Instrument(id){Analyzer = analyzer};
_instrumentMap.Add(id, instrument);
return true;
}
instrument = _instrumentMap[id];
if (instrument.Analyzer != null){
return false;
}
instrument.Analyzer = analyzer;
return true;
}
public bool AddSampleCustom(int id, Param custom)
{
Sample sample;
if (!_sampleMap.ContainsKey(id)){
sample = new Sample(id);
sample.AddCustom(custom);
_sampleMap.Add(id, sample);
return true;
}
sample = _sampleMap[id];
sample.AddCustom(custom);
return true;
}
public bool AddInstrumentDetector(int id, Param detector)
{
Instrument instrument;
if (!_instrumentMap.ContainsKey(id)){
instrument = new Instrument(id){Detector = detector};
_instrumentMap.Add(id, instrument);
return true;
}
instrument = _instrumentMap[id];
if (instrument.Detector != null){
return false;
}
instrument.Detector = detector;
return true;
}
public bool AddSampleProcessingParam(int id, Param param)
{
if (!_sampleProcessingMap.ContainsKey(id)){
_sampleProcessingMap.Add(id, new SplitList<Param>(MZTabConstants.BAR){param});
}
else{
_sampleProcessingMap[id].Add(param);
}
return true;
}
public bool AddInstrumentName(int id, Param name)
{
Instrument instrument;
if (!_instrumentMap.ContainsKey(id)){
instrument = new Instrument(id){Name = name};
_instrumentMap.Add(id, instrument);
return true;
}
instrument = _instrumentMap[id];
if (instrument.Name != null){
return false;
}
instrument.Name = name;
return true;
}
public bool AddSampleTissue(int id, Param tissue)
{
Sample sample;
if (!_sampleMap.ContainsKey(id)){
sample = new Sample(id);
sample.AddTissue(tissue);
_sampleMap.Add(id, sample);
return true;
}
sample = _sampleMap[id];
sample.AddTissue(tissue);
return true;
}
public bool AddInstrumentSource(int id, Param source)
{
Instrument instrument;
if (!_instrumentMap.ContainsKey(id)){
instrument = new Instrument(id){Source = source};
_instrumentMap.Add(id, instrument);
return true;
}
instrument = _instrumentMap[id];
if (instrument.Source != null){
return false;
}
instrument.Source = source;
return true;
}
public bool AddSoftwareParam(int id, Param param)
{
Software software;
if (!_softwareMap.ContainsKey(id)){
software = new Software(id){Param = param};
_softwareMap.Add(id, software);
return true;
}
software = _softwareMap[id];
if (software.Param != null){
return false;
}
software.Param = param;
return true;
}
public bool AddMsRunFragmentationMethod(int id, Param fragmentationMethod)
{
MsRun msRun;
if (!_msRunMap.ContainsKey(id)){
msRun = new MsRun(id){FragmentationMethod = fragmentationMethod};
_msRunMap.Add(id, msRun);
return true;
}
msRun = _msRunMap[id];
if (msRun.FragmentationMethod != null){
return false;
}
msRun.FragmentationMethod = fragmentationMethod;
return true;
}
public bool AddBestSearchEngineScore(Param param)
{
if (param == null){
return false;
}
SplitList<Param> searchparams = BestSearchEngineScore;
if (searchparams == null){
searchparams = new SplitList<Param>(MZTabConstants.BAR);
BestSearchEngineScore = (searchparams);
}
searchparams.Add(param);
return true;
}
public bool AddMsRunIdFormat(int id, Param idFormat)
{
MsRun msRun;
if (!_msRunMap.ContainsKey(id)){
msRun = new MsRun(id){IdFormat = idFormat};
_msRunMap.Add(id, msRun);
return true;
}
msRun = _msRunMap[id];
if (msRun.IdFormat != null){
return false;
}
msRun.IdFormat = idFormat;
return true;
}
public bool addSearchEngineParam(Param param)
{
if (param == null){
return false;
}
SplitList<Param> paramList = SearchEngine;
if (paramList == null){
paramList = new SplitList<Param>(MZTabConstants.BAR);
SearchEngine = paramList;
}
paramList.Add(param);
return true;
}
public void AddPeptideColUnit(MZTabColumn column, Param param)
{
_peptideColUnitList.Add(new ColUnit(column, param));
}
