public SoftwareParam(Software[] software, CVLookUp cv, Dictionary<string, string> parameters)
: base(null)
{
_count = software.Length;
_cv = cv;
_parameters = parameters;
Value = software;
Default = software;
}
public SoftwarePanel(Software[] value, CVLookUp cv, Dictionary<string, string> parameters)
{
MaxWidth = 800;
_count = value.Length;
_cv = cv;
_parameters = parameters;
defaultName = _cv.GetNameOfTerm("MS:1001583", "MS");
defaultVersion = parameters.ContainsKey("Version") ? parameters["Version"] : null;
InitializeComponent();
Value = value;
}
public void AddSoftwareSetting(int id, string setting)
{
Software software;
if (!_softwareMap.ContainsKey(id)){
software = new Software(id);
_softwareMap.Add(id, software);
}
else{
software = _softwareMap[id];
}
software.AddSetting(setting);
}
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 Metadata CreateMetadataDefault(IMatrixData parameters, IMatrixData experiment, IMatrixData search)
{
Metadata mtd = new Metadata(new MZTabDescription(MzTabMode.Complete, MzTabType.Quantification));
List<MsRunImpl> runs = null;
List<StudyVariable> studyvariables = null;
List<Assay> assays = null;
List<Sample> samples = null;
List<Instrument> instruments = null;
GetExperminetValues(null, null, experiment, search, ref runs, ref studyvariables, ref assays, ref samples,
ref instruments);
foreach (var msRun in runs){
mtd.MsRunMap.Add(msRun.Id, msRun);
}
foreach (var studyvariable in studyvariables){
mtd.StudyVariableMap.Add(studyvariable.Id, studyvariable);
}
foreach (var sample in samples){
mtd.SampleMap.Add(sample.Id, sample);
}
foreach (var assay in assays){
mtd.AssayMap.Add(assay.Id, assay);
}
foreach (var instrument in instruments){
mtd.InstrumentMap.Add(instrument.Id, instrument);
}
SplitList<Lib.Model.Param> sampleProcessing = new SplitList<Lib.Model.Param>{
cv.GetParam("enzyme digestion", "SEP"),
cv.GetParam("reversed-phase chromatography", "SEP")
};
//sampleProcessing.Add(_cv.GetParam("ion-exchange chromatography", "SEP"));
mtd.SampleProcessingMap.Add(1, sampleProcessing);
var paramDict = MzTabMatrixUtils.ConvertToParamDict(parameters);
string key = Constants.GetKeywordName(Utils.parameters.fixedMod, paramDict.Keys.ToArray());
if (key != null){
string[] values = paramDict[key].Split(';');
foreach (var mod in values.Select(x => BaseLib.Mol.Tables.Modifications[x])){
int id = mtd.FixedModMap.Count + 1;
mtd.AddFixedModParam(id, cv.GetModificationParam(mod));
mtd.AddFixedModPosition(id, mod.Position.ToString());
mtd.AddFixedModSite(id, StringUtils.Concat(", ", mod.GetSiteArray()));
}
}
key = Constants.GetKeywordName(Utils.parameters.variableMod, paramDict.Keys.ToArray());
if (key != null){
string[] values = paramDict[key].Split(';');
foreach (var mod in values.Select(x => BaseLib.Mol.Tables.Modifications[x])){
int id = mtd.VariableModMap.Count + 1;
mtd.AddVariableModParam(id, cv.GetModificationParam(mod));
mtd.AddVariableModPosition(id, mod.Position.ToString());
mtd.AddVariableModSite(id, StringUtils.Concat(", ", mod.GetSiteArray()));
}
}
string version = Constants.GetKeywordName(Utils.parameters.version, paramDict.Keys.ToArray());
Software software = new Software(1){
Param = cv.GetParam("MaxQuant", "MS", GetParameterString(parameters, version, null))
};
mtd.SoftwareMap.Add(software.Id, software);
software = new Software(2){
Param = cv.GetParam("Andromeda", "MS", GetParameterString(parameters, version, null))
};
mtd.SoftwareMap.Add(software.Id, software);
if (assays.Count > 0){
var tmp = ArrayUtils.UniqueValues(assays.Select(x => x.QuantificationReagent.Name).ToArray());
if (tmp.Length == 1 && tmp.First().Equals("Unlabeled sample")){
mtd.QuantificationMethod = cv.GetParam("label-free proteingroup level quantitation", "MS");
}
else if (tmp.Any(x => x.Contains("SILAC"))){
mtd.QuantificationMethod = cv.GetParam("SILAC quantitation analysis", "MS");
}
}
return mtd;
}
public override void Clear()
{
Value = new Software[_count];
}