/// <summary>
/// Create a modification with the specified values
/// </summary>
/// <param name="unimodCv">CV term for the modification, if available; otherwise, use CVID.MS_unknown_modification</param>
/// <param name="modificationName">
/// Name of the modification, if a CV term for the modification is not available or unknown.
/// If this matches an Unimod modification name, the Unimod CV term will be used.
/// </param>
/// <param name="location">
/// location of the modification, using '0' for N-term and length+1 for C-term, and otherwise
/// 1-based indexing
/// </param>
/// <param name="monoMassDelta">monoisotopic mass delta</param>
/// <returns></returns>
public ModificationObj(CV.CV.CVID unimodCv, string modificationName = "", int location = int.MinValue, double monoMassDelta = double.NaN) : this()
{
if (!monoMassDelta.Equals(double.NaN))
{
MonoisotopicMassDelta = monoMassDelta;
}
if (location != int.MinValue)
{
Location = location;
}
if ((unimodCv != CV.CV.CVID.CVID_Unknown) && (unimodCv != CV.CV.CVID.MS_unknown_modification))
{
CVParams.Add(new CVParamObj(unimodCv));
}
else if (!string.IsNullOrWhiteSpace(modificationName))
{
var result = SearchForUnimodMod(modificationName);
if (result != CV.CV.CVID.MS_unknown_modification)
{
CVParams.Add(new CVParamObj(result));
}
else
{
CVParams.Add(new CVParamObj(CV.CV.CVID.MS_unknown_modification, modificationName));
}
}
}
/// <summary>
/// Add information about the spectra input to the search
/// </summary>
/// <param name="location"></param>
/// <param name="name"></param>
/// <param name="spectrumIdFormat"></param>
/// <param name="fileFormatCvid"></param>
/// <returns></returns>
public SpectraDataObj AddSpectraData(string location, string name, CV.CV.CVID spectrumIdFormat,
CV.CV.CVID fileFormatCvid = CV.CV.CVID.CVID_Unknown)
{
var dataFile = new SpectraDataObj
{
Id = "SD_" + specDataCounter++,
Location = location,
Name = name,
SpectrumIDFormat = new SpectrumIDFormatObj()
{
CVParam = new CVParamObj(spectrumIdFormat),
},
};
if (fileFormatCvid != CV.CV.CVID.CVID_Unknown)
{
dataFile.FileFormat = new FileFormatInfo()
{
CVParam = new CVParamObj(fileFormatCvid),
};
}
if (identData.DataCollection.Inputs == null)
{
identData.DataCollection.Inputs = new InputsObj();
}
if (identData.DataCollection.Inputs.SpectraDataList == null)
{
identData.DataCollection.Inputs.SpectraDataList = new IdentDataList <SpectraDataObj>();
}
identData.DataCollection.Inputs.SpectraDataList.Add(dataFile);
return(dataFile);
}
/// <summary>
/// Constructor
/// </summary>
/// <param name="cvid"></param>
/// <param name="value"></param>
public CVParamObj(CV.CV.CVID cvid = CV.CV.CVID.CVID_Unknown, string value = null)
{
_cvRef = null;
//this._name = null;
//this._accession = null;
_value = value;
Cvid = cvid;
}
/// <summary>
/// Constructor
/// </summary>
protected ParamBaseObj()
{
//this._unitAccession = null;
//this._unitName = null;
_unitCvRef = null;
_unitsSet = false;
_unitCvid = CV.CV.CVID.CVID_Unknown;
}
/// <summary>
/// Adds information about a search database to the IdentData
/// </summary>
/// <remarks>
/// <para>
/// Valid CVParams to add:
/// </para>
/// <para>
/// CVID.MS_MD5
/// CVID.MS_SHA_1
/// </para>
/// <para>
/// CVID.MS_database_source
/// CVID.MS_database_name
/// CVID.MS_database_local_file_path_OBSOLETE
/// CVID.MS_database_original_uri
/// CVID.MS_database_version_OBSOLETE
/// CVID.MS_database_release_date_OBSOLETE
/// CVID.MS_database_type
/// CVID.MS_database_filtering
/// CVID.MS_translation_frame
/// CVID.MS_translation_table
/// CVID.MS_number_of_peptide_seqs_compared_to_each_spectrum
/// CVID.MS_database_sequence_details
/// CVID.MS_database_file_formats
/// CVID.MS_translation_start_codon,
/// CVID.MS_translation_table_description
/// CVID.MS_decoy_DB_details
/// CVID.MS_number_of_decoy_sequences
/// </para>
/// <para>
/// CVID.MS_decoy_DB_type_reverse
/// CVID.MS_decoy_DB_type_randomized
/// CVID.MS_DB_composition_target_decoy
/// CVID.MS_decoy_DB_accession_regexp
/// CVID.MS_decoy_DB_derived_from_OBSOLETE
/// </para>
/// </remarks>
/// <param name="location">Path to the database (absolute path)</param>
/// <param name="numberOfSequences">Number of sequences in the database</param>
/// <param name="databaseName">Name of the database (can be the filename)</param>
/// <param name="publicDatabaseName">Name of the database, if it maps exactly to a CV term; otherwise use CVID_Unknown</param>
/// <param name="fileFormatCvid">The format of the database, if it exists in the CV</param>
/// <returns>An initialized and added database, can add CVParams that add details about the database. See remarks.</returns>
public SearchDatabaseInfo AddSearchDatabase(
string location,
long numberOfSequences,
string databaseName,
CV.CV.CVID publicDatabaseName = CV.CV.CVID.CVID_Unknown,
CV.CV.CVID fileFormatCvid = CV.CV.CVID.CVID_Unknown)
{
var db = new SearchDatabaseInfo
{
Id = "SearchDB_" + dbCounter++,
Location = location,
Name = databaseName,
NumDatabaseSequences = numberOfSequences,
DatabaseName = new ParamObj(),
};
if (publicDatabaseName != CV.CV.CVID.CVID_Unknown)
{
db.DatabaseName.Item = new CVParamObj(publicDatabaseName);
}
else
{
db.DatabaseName.Item = new UserParamObj()
{
Name = databaseName,
};
}
if (fileFormatCvid != CV.CV.CVID.CVID_Unknown)
{
db.FileFormat = new FileFormatInfo
{
CVParam = new CVParamObj(fileFormatCvid)
};
}
if (identData.DataCollection.Inputs == null)
{
identData.DataCollection.Inputs = new InputsObj();
}
if (identData.DataCollection.Inputs.SearchDatabases == null)
{
identData.DataCollection.Inputs.SearchDatabases = new IdentDataList <SearchDatabaseInfo>();
}
identData.DataCollection.Inputs.SearchDatabases.Add(db);
return(db);
}
/// <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);
}
/// <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);
}
/// <summary>
/// Get the CVParam that matches the specified CV term, defaulting to the value provided if not found.
/// </summary>
/// <param name="paramList"></param>
/// <param name="cvid"></param>
/// <param name="valueIfNotFound"></param>
/// <returns></returns>
public static CVParamObj GetCvParam(this IdentDataList <ParamBaseObj> paramList, CV.CV.CVID cvid, string valueIfNotFound)
{
var defaultCvParam = new CVParamObj(CV.CV.CVID.CVID_Unknown, valueIfNotFound);
if (paramList == null || paramList.Count == 0)
{
return(defaultCvParam);
}
foreach (var p in paramList)
{
var cvp = p as CVParamObj;
if (cvp != null && cvp.Cvid == cvid)
{
return(cvp);
}
}
return(defaultCvParam);
}
