/// <summary>
/// Create an object using the contents of the corresponding MzIdentML object
/// </summary>
/// <param name="sip"></param>
/// <param name="idata"></param>
public SpectrumIdentificationProtocolObj(SpectrumIdentificationProtocolType sip, IdentDataObj idata)
: base(idata)
{
Id = sip.id;
Name = sip.name;
AnalysisSoftwareRef = sip.analysisSoftware_ref;
_searchType = null;
_additionalSearchParams = null;
_enzymes = null;
_threshold = null;
_databaseTranslation = null;
ModificationParams = new IdentDataList <SearchModificationObj>(1);
MassTables = new IdentDataList <MassTableObj>(1);
FragmentTolerances = new IdentDataList <CVParamObj>(1);
ParentTolerances = new IdentDataList <CVParamObj>(1);
DatabaseFilters = new IdentDataList <FilterInfo>(1);
if (sip.SearchType != null)
{
_searchType = new ParamObj(sip.SearchType, IdentData);
}
if (sip.AdditionalSearchParams != null)
{
_additionalSearchParams = new ParamListObj(sip.AdditionalSearchParams, IdentData);
}
if (sip.ModificationParams?.Count > 0)
{
ModificationParams.AddRange(sip.ModificationParams, mp => new SearchModificationObj(mp, IdentData));
}
if (sip.Enzymes != null)
{
_enzymes = new EnzymeListObj(sip.Enzymes, IdentData);
}
if (sip.MassTable?.Count > 0)
{
MassTables.AddRange(sip.MassTable, mt => new MassTableObj(mt, IdentData));
}
if (sip.FragmentTolerance?.Count > 0)
{
FragmentTolerances.AddRange(sip.FragmentTolerance, ft => new CVParamObj(ft, IdentData));
}
if (sip.ParentTolerance?.Count > 0)
{
ParentTolerances.AddRange(sip.ParentTolerance, pt => new CVParamObj(pt, IdentData));
}
if (sip.Threshold != null)
{
_threshold = new ParamListObj(sip.Threshold, IdentData);
}
if (sip.DatabaseFilters?.Count > 0)
{
DatabaseFilters.AddRange(sip.DatabaseFilters, df => new FilterInfo(df, IdentData));
}
if (sip.DatabaseTranslation != null)
{
_databaseTranslation = new DatabaseTranslationObj(sip.DatabaseTranslation, IdentData);
}
}
/// <summary>
/// Create an object using the contents of the corresponding MzIdentML object
/// </summary>
/// <param name="sip"></param>
/// <param name="idata"></param>
public SpectrumIdentificationProtocolObj(SpectrumIdentificationProtocolType sip, IdentDataObj idata)
: base(idata)
{
Id = sip.id;
Name = sip.name;
AnalysisSoftwareRef = sip.analysisSoftware_ref;
_searchType = null;
_additionalSearchParams = null;
_modificationParams = null;
_enzymes = null;
_massTables = null;
_fragmentTolerances = null;
_parentTolerances = null;
_threshold = null;
_databaseFilters = null;
_databaseTranslation = null;
if (sip.SearchType != null)
_searchType = new ParamObj(sip.SearchType, IdentData);
if (sip.AdditionalSearchParams != null)
_additionalSearchParams = new ParamListObj(sip.AdditionalSearchParams, IdentData);
if ((sip.ModificationParams != null) && (sip.ModificationParams.Count > 0))
{
ModificationParams = new IdentDataList<SearchModificationObj>();
foreach (var mp in sip.ModificationParams)
ModificationParams.Add(new SearchModificationObj(mp, IdentData));
}
if (sip.Enzymes != null)
_enzymes = new EnzymeListObj(sip.Enzymes, IdentData);
if ((sip.MassTable != null) && (sip.MassTable.Count > 0))
{
MassTables = new IdentDataList<MassTableObj>();
foreach (var mt in sip.MassTable)
MassTables.Add(new MassTableObj(mt, IdentData));
}
if ((sip.FragmentTolerance != null) && (sip.FragmentTolerance.Count > 0))
{
FragmentTolerances = new IdentDataList<CVParamObj>();
foreach (var ft in sip.FragmentTolerance)
FragmentTolerances.Add(new CVParamObj(ft, IdentData));
}
if (sip.ParentTolerance != null)
{
ParentTolerances = new IdentDataList<CVParamObj>();
foreach (var pt in sip.ParentTolerance)
ParentTolerances.Add(new CVParamObj(pt, IdentData));
}
if (sip.Threshold != null)
_threshold = new ParamListObj(sip.Threshold, IdentData);
if ((sip.DatabaseFilters != null) && (sip.DatabaseFilters.Count > 0))
{
DatabaseFilters = new IdentDataList<FilterInfo>();
foreach (var df in sip.DatabaseFilters)
DatabaseFilters.Add(new FilterInfo(df, IdentData));
}
if (sip.DatabaseTranslation != null)
_databaseTranslation = new DatabaseTranslationObj(sip.DatabaseTranslation, IdentData);
}
/// <summary>
/// Constructor
/// </summary>
public ProteinDetectionProtocolObj()
{
Id = null;
Name = null;
_analysisSoftwareRef = null;
_analysisSoftware = null;
_analysisParams = null;
_threshold = null;
}
/// <summary>
/// Constructor
/// </summary>
public EnzymeObj()
{
Id = null;
Name = null;
SiteRegexp = null;
NTermGain = null;
CTermGain = null;
_semiSpecific = false;
SemiSpecificSpecified = false;
_missedCleavages = -1;
MissedCleavagesSpecified = false;
_minDistance = -1;
MinDistanceSpecified = false;
_enzymeName = null;
}
/// <summary>
/// Constructor
/// </summary>
public SpectrumIdentificationProtocolObj()
{
Id = null;
Name = null;
_analysisSoftwareRef = null;
_analysisSoftware = null;
_searchType = null;
_additionalSearchParams = null;
ModificationParams = new IdentDataList <SearchModificationObj>(1);
_enzymes = null;
MassTables = new IdentDataList <MassTableObj>(1);
FragmentTolerances = new IdentDataList <CVParamObj>(1);
ParentTolerances = new IdentDataList <CVParamObj>(1);
_threshold = null;
DatabaseFilters = new IdentDataList <FilterInfo>(1);
_databaseTranslation = null;
}
/// <summary>
/// Create an object using the contents of the corresponding MzIdentML object
/// </summary>
/// <param name="pdp"></param>
/// <param name="idata"></param>
public ProteinDetectionProtocolObj(ProteinDetectionProtocolType pdp, IdentDataObj idata)
: base(idata)
{
Id = pdp.id;
Name = pdp.name;
AnalysisSoftwareRef = pdp.analysisSoftware_ref;
_analysisParams = null;
_threshold = null;
if (pdp.AnalysisParams != null)
{
_analysisParams = new ParamListObj(pdp.AnalysisParams, IdentData);
}
if (pdp.Threshold != null)
{
_threshold = new ParamListObj(pdp.Threshold, IdentData);
}
}
/// <summary>
/// Create an object using the contents of the corresponding MzIdentML object
/// </summary>
/// <param name="f"></param>
/// <param name="idata"></param>
public FilterInfo(FilterType f, IdentDataObj idata)
: base(idata)
{
_filterType = null;
_include = null;
_exclude = null;
if (f.FilterType1 != null)
{
_filterType = new ParamObj(f.FilterType1, IdentData);
}
if (f.Include != null)
{
_include = new ParamListObj(f.Include, IdentData);
}
if (f.Exclude != null)
{
_exclude = new ParamListObj(f.Exclude, IdentData);
}
}
/// <summary>
/// Create an object using the contents of the corresponding MzIdentML object
/// </summary>
/// <param name="e"></param>
/// <param name="idata"></param>
public EnzymeObj(EnzymeType e, IdentDataObj idata)
: base(idata)
{
Id = e.id;
Name = e.name;
SiteRegexp = e.SiteRegexp;
NTermGain = e.nTermGain;
CTermGain = e.cTermGain;
_semiSpecific = e.semiSpecific;
SemiSpecificSpecified = e.semiSpecificSpecified;
_missedCleavages = e.missedCleavages;
MissedCleavagesSpecified = e.missedCleavagesSpecified;
_minDistance = e.minDistance;
MinDistanceSpecified = e.minDistanceSpecified;
_enzymeName = null;
if (e.EnzymeName != null)
{
_enzymeName = new ParamListObj(e.EnzymeName, IdentData);
}
}
/// <summary>
/// Constructor
/// </summary>
public FilterInfo()
{
_filterType = null;
_include = null;
_exclude = null;
}