/// <summary>
/// Adds information about the analysis software to the file
/// </summary>
/// <param name="id">Unique identifier for the entry</param>
/// <param name="name">Name of the analysis software</param>
/// <param name="version">Version of the analysis software</param>
/// <param name="cvid">CVID (if it exists) for the analysis software</param>
/// <param name="userParamSoftwareName">Long name of the Analysis software. Not used unless cvid is "CVID_Unknown"</param>
/// <returns>The analysis software object to further modify, if needed.</returns>
public AnalysisSoftwareObj AddAnalysisSoftware(string id, string name, string version, CV.CV.CVID cvid,
string userParamSoftwareName = "")
{
var software = new AnalysisSoftwareObj
{
Name = name,
Id = id,
Version = version,
SoftwareName = new ParamObj(),
};
if (cvid != CV.CV.CVID.CVID_Unknown)
{
software.SoftwareName.Item = new CVParamObj(cvid);
}
else
{
software.SoftwareName.Item = new UserParamObj()
{
Name = userParamSoftwareName,
};
}
identData.AnalysisSoftwareList.Add(software);
return(software);
}
public MsgfMzidFull(string mzidFilePath) : base(mzidFilePath, false)
{
// load mzid file;
// obviously won't have a 'Job' number available
identData = IdentDataReaderWriter.Read(mzidFilePath);
identData.Version = "1.2"; // Instruct the output to use MzIdentML 1.2 schema and namespace
var ascoreSoftware = new AnalysisSoftwareObj()
{
Id = "AScore_software",
Name = "AScore",
Version = System.Reflection.Assembly.GetExecutingAssembly().GetName().Version.ToString(),
SoftwareName = new ParamObj()
{
Item = new CVParamObj(CV.CVID.MS_Ascore_software)
},
};
identData.AnalysisSoftwareList.Add(ascoreSoftware);
identData.AnalysisProtocolCollection.SpectrumIdentificationProtocols.First().AdditionalSearchParams.Items.Add(new CVParamObj(CV.CVID.MS_modification_localization_scoring));
foreach (var peptide in identData.SequenceCollection.Peptides)
{
var modIndex = 1;
foreach (var mod in peptide.Modifications)
{
mod.CVParams.Add(new CVParamObj(CV.CVID.MS_modification_index, modIndex.ToString()));
modIndex++;
}
}
foreach (var list in identData.DataCollection.AnalysisData.SpectrumIdentificationList)
{
foreach (var result in list.SpectrumIdentificationResults)
{
foreach (var ident in result.SpectrumIdentificationItems)
{
data.Add(new SpectrumIdentificationItemWrapper(result, ident));
}
}
}
AssignSymbolsToMods(identData.AnalysisProtocolCollection.SpectrumIdentificationProtocols.SelectMany(x => x.ModificationParams)); // TODO
// maxSteps normally set using DataTable information in base constructor
maxSteps = data.Count;
}
/// <summary>
/// Add the settings used with the software "analysisSoftwareInfo"
/// </summary>
/// <param name="analysisSoftwareInfo">The object returned by <see cref="AddAnalysisSoftware"/></param>
/// <param name="name">The name of the set of settings</param>
/// <param name="searchType">The type of search performed:
/// CVID.MS_de_novo_search
/// CVID.MS_spectral_library_search
/// CVID.MS_spectral_library_search
/// CVID.MS_pmf_search
/// CVID.MS_tag_search
/// CVID.MS_ms_ms_search
/// CVID.MS_combined_pmf___ms_ms_search
/// CVID.MS_special_processing
/// CVID.MS_peptide_level_scoring
/// CVID.MS_modification_localization_scoring
/// CVID.MS_consensus_scoring
/// CVID.MS_sample_pre_fractionation
/// CVID.MS_cross_linking_search
/// CVID.MS_no_special_processing
/// </param>
/// <returns>An object that needs multiple items set - add CV/User params to AdditionalSearchParams, ModificationParams, Enzymes, FragmentTolerances, ParentTolerances, and Threshold</returns>
public SpectrumIdentificationProtocolObj AddAnalysisSettings(AnalysisSoftwareObj analysisSoftwareInfo, string name, CV.CV.CVID searchType)
{
var settings = new SpectrumIdentificationProtocolObj
{
Id = "SearchProtocol_" + searchProtocolCounter++,
AnalysisSoftware = analysisSoftwareInfo,
Name = name,
SearchType = new ParamObj(),
};
if (searchType != CV.CV.CVID.CVID_Unknown)
{
settings.SearchType.Item = new CVParamObj(searchType);
}
settings.AdditionalSearchParams = new ParamListObj()
{
Items = new IdentDataList <ParamBaseObj>()
};
settings.ModificationParams = new IdentDataList <SearchModificationObj>();
settings.Enzymes = new EnzymeListObj()
{
Enzymes = new IdentDataList <EnzymeObj>(),
};
settings.FragmentTolerances = new IdentDataList <CVParamObj>();
settings.ParentTolerances = new IdentDataList <CVParamObj>();
settings.Threshold = new ParamListObj()
{
Items = new IdentDataList <ParamBaseObj>(),
};
if (identData.AnalysisProtocolCollection.SpectrumIdentificationProtocols == null)
{
identData.AnalysisProtocolCollection.SpectrumIdentificationProtocols = new IdentDataList <SpectrumIdentificationProtocolObj>();
}
identData.AnalysisProtocolCollection.SpectrumIdentificationProtocols.Add(settings);
return(settings);
}
