/// <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>
/// Object hash code
/// </summary>
public override int GetHashCode()
{
unchecked
{
var hashCode = Name?.GetHashCode() ?? 0;
return((hashCode * 397) ^ (CVParams?.GetHashCode() ?? 0));
}
}
/// <summary>
/// Object hash code
/// </summary>
public override int GetHashCode()
{
unchecked
{
var hashCode = Code?.GetHashCode() ?? 0;
hashCode = (hashCode * 397) ^ (CVParams?.GetHashCode() ?? 0);
hashCode = (hashCode * 397) ^ (UserParams?.GetHashCode() ?? 0);
return(hashCode);
}
}
/// <summary>
/// Object hash code
/// </summary>
/// <returns></returns>
public override int GetHashCode()
{
unchecked
{
var hashCode = CVParams != null?CVParams.GetHashCode() : 0;
hashCode = (hashCode * 397) ^ (UserParams != null ? UserParams.GetHashCode() : 0);
return(hashCode);
}
}
/// <summary>
/// Creates a DB sequence object with the specified values
/// </summary>
/// <param name="searchDb">Valid <see cref="SearchDatabaseInfo" /> object, not null</param>
/// <param name="length">length of the protein</param>
/// <param name="accession">protein identifier</param>
/// <param name="description">description of the protein</param>
public DbSequenceObj(SearchDatabaseInfo searchDb, int length, string accession, string description = "") : this()
{
Length = length;
SearchDatabase = searchDb;
Accession = accession;
if (!string.IsNullOrWhiteSpace(description))
{
CVParams.Add(new CVParamObj(CV.CV.CVID.MS_protein_description, description));
}
}
/// <summary>
/// Object hash code
/// </summary>
/// <returns></returns>
public override int GetHashCode()
{
unchecked
{
var hashCode = AvgMassDelta.GetHashCode();
hashCode = (hashCode * 397) ^ MonoisotopicMassDelta.GetHashCode();
hashCode = (hashCode * 397) ^ Location;
hashCode = (hashCode * 397) ^ (Residues != null ? Residues.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (CVParams != null ? CVParams.GetHashCode() : 0);
return(hashCode);
}
}
/// <summary>
/// Object hash code
/// </summary>
/// <returns></returns>
public override int GetHashCode()
{
unchecked
{
var hashCode = FixedMod.GetHashCode();
hashCode = (hashCode * 397) ^ MassDelta.GetHashCode();
hashCode = (hashCode * 397) ^ (Residues != null ? Residues.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (SpecificityRules != null ? SpecificityRules.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (CVParams != null ? CVParams.GetHashCode() : 0);
return(hashCode);
}
}
/// <summary>
/// Object hash code
/// </summary>
/// <returns></returns>
public override int GetHashCode()
{
unchecked
{
var hashCode = Name != null?Name.GetHashCode() : 0;
hashCode = (hashCode * 397) ^ (ProteinDetectionHypotheses != null ? ProteinDetectionHypotheses.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (CVParams != null ? CVParams.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (UserParams != null ? UserParams.GetHashCode() : 0);
return(hashCode);
}
}
/// <summary>
/// Object hash code
/// </summary>
/// <returns></returns>
public override int GetHashCode()
{
unchecked
{
var hashCode = Name != null?Name.GetHashCode() : 0;
hashCode = (hashCode * 397) ^ (Parent != null ? Parent.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (CVParams != null ? CVParams.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (UserParams != null ? UserParams.GetHashCode() : 0);
return(hashCode);
}
}
/// <summary>
/// Object hash code
/// </summary>
/// <returns></returns>
public override int GetHashCode()
{
unchecked
{
var hashCode = Name != null?Name.GetHashCode() : 0;
hashCode = (hashCode * 397) ^ (ProteinAmbiguityGroups != null ? ProteinAmbiguityGroups.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (CVParams != null ? CVParams.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (UserParams != null ? UserParams.GetHashCode() : 0);
return(hashCode);
}
}
/// <summary>
/// Object hash code
/// </summary>
/// <returns></returns>
public override int GetHashCode()
{
unchecked
{
var hashCode = (Name != null ? Name.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ PassThreshold.GetHashCode();
hashCode = (hashCode * 397) ^ (DBSequence != null ? DBSequence.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (PeptideHypotheses != null ? PeptideHypotheses.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (CVParams != null ? CVParams.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (UserParams != null ? UserParams.GetHashCode() : 0);
return(hashCode);
}
}
/// <summary>
/// Object hash code
/// </summary>
/// <returns></returns>
public override int GetHashCode()
{
unchecked
{
var hashCode = Name != null?Name.GetHashCode() : 0;
hashCode = (hashCode * 397) ^ (ContactRoles != null ? ContactRoles.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (SubSamples != null ? SubSamples.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (CVParams != null ? CVParams.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (UserParams != null ? UserParams.GetHashCode() : 0);
return(hashCode);
}
}
/// <summary>
/// Object hash code
/// </summary>
/// <returns></returns>
public override int GetHashCode()
{
unchecked
{
var hashCode = Name != null?Name.GetHashCode() : 0;
hashCode = (hashCode * 397) ^ (ExternalFormatDocumentation != null ? ExternalFormatDocumentation.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (Location != null ? Location.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (FileFormat != null ? FileFormat.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (CVParams != null ? CVParams.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (UserParams != null ? UserParams.GetHashCode() : 0);
return(hashCode);
}
}
/// <summary>
/// Object hash code
/// </summary>
/// <returns></returns>
public override int GetHashCode()
{
unchecked
{
var hashCode = Name != null?Name.GetHashCode() : 0;
hashCode = (hashCode * 397) ^ (Residues != null ? Residues.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (AmbiguousResidues != null ? AmbiguousResidues.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (MsLevels != null ? MsLevels.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (CVParams != null ? CVParams.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (UserParams != null ? UserParams.GetHashCode() : 0);
return(hashCode);
}
}
/// <summary>
/// Object hash code
/// </summary>
/// <returns></returns>
public override int GetHashCode()
{
unchecked
{
var hashCode = Name != null?Name.GetHashCode() : 0;
hashCode = (hashCode * 397) ^ (PeptideSequence != null ? PeptideSequence.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (Modifications != null ? Modifications.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (SubstitutionModifications != null ? SubstitutionModifications.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (CVParams != null ? CVParams.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (UserParams != null ? UserParams.GetHashCode() : 0);
return(hashCode);
}
}
/// <summary>
/// Object hash code
/// </summary>
/// <returns></returns>
public override int GetHashCode()
{
unchecked
{
var hashCode = Name != null?Name.GetHashCode() : 0;
hashCode = (hashCode * 397) ^ NumSequencesSearched.GetHashCode();
hashCode = (hashCode * 397) ^ (FragmentationTables != null ? FragmentationTables.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (SpectrumIdentificationResults != null ? SpectrumIdentificationResults.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (CVParams != null ? CVParams.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (UserParams != null ? UserParams.GetHashCode() : 0);
return(hashCode);
}
}
/// <summary>
/// Object hash code
/// </summary>
/// <returns></returns>
public override int GetHashCode()
{
unchecked
{
var hashCode = Name != null?Name.GetHashCode() : 0;
hashCode = (hashCode * 397) ^ (SpectrumID != null ? SpectrumID.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (SpectrumIdentificationItems != null ? SpectrumIdentificationItems.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (SpectraData != null ? SpectraData.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (CVParams != null ? CVParams.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (UserParams != null ? UserParams.GetHashCode() : 0);
return(hashCode);
}
}
/// <summary>
/// Object hash code
/// </summary>
/// <returns></returns>
public override int GetHashCode()
{
unchecked
{
var hashCode = Name != null?Name.GetHashCode() : 0;
hashCode = (hashCode * 397) ^ (Accession != null ? Accession.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ Length;
hashCode = (hashCode * 397) ^ (Seq != null ? Seq.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (SearchDatabase != null ? SearchDatabase.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (CVParams != null ? CVParams.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (UserParams != null ? UserParams.GetHashCode() : 0);
return(hashCode);
}
}
/// <summary>
/// Object hash code
/// </summary>
/// <returns></returns>
public override int GetHashCode()
{
unchecked
{
var hashCode = Name != null?Name.GetHashCode() : 0;
hashCode = (hashCode * 397) ^ (LastName != null ? LastName.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (FirstName != null ? FirstName.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (MidInitials != null ? MidInitials.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (Affiliations != null ? Affiliations.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (CVParams != null ? CVParams.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (UserParams != null ? UserParams.GetHashCode() : 0);
return(hashCode);
}
}
/// <summary>
/// Object hash code
/// </summary>
/// <returns></returns>
public override int GetHashCode()
{
unchecked
{
var hashCode = Name != null?Name.GetHashCode() : 0;
hashCode = (hashCode * 397) ^ (Version != null ? Version.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ NumDatabaseSequences.GetHashCode();
hashCode = (hashCode * 397) ^ NumResidues.GetHashCode();
hashCode = (hashCode * 397) ^ (ExternalFormatDocumentation != null ? ExternalFormatDocumentation.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (Location != null ? Location.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (DatabaseName != null ? DatabaseName.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (FileFormat != null ? FileFormat.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (CVParams != null ? CVParams.GetHashCode() : 0);
return(hashCode);
}
}
/// <summary>
/// Object hash code
/// </summary>
/// <returns></returns>
public override int GetHashCode()
{
unchecked
{
var hashCode = Name != null?Name.GetHashCode() : 0;
hashCode = (hashCode * 397) ^ IsDecoy.GetHashCode();
hashCode = (hashCode * 397) ^ Start;
hashCode = (hashCode * 397) ^ End;
hashCode = (hashCode * 397) ^ Pre.GetHashCode();
hashCode = (hashCode * 397) ^ Post.GetHashCode();
hashCode = (hashCode * 397) ^ Frame;
hashCode = (hashCode * 397) ^ (TranslationTable != null ? TranslationTable.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (Peptide != null ? Peptide.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (DBSequence != null ? DBSequence.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (CVParams != null ? CVParams.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (UserParams != null ? UserParams.GetHashCode() : 0);
return(hashCode);
}
}
/// <summary>
/// Object hash code
/// </summary>
/// <returns></returns>
public override int GetHashCode()
{
unchecked
{
var hashCode = Name != null?Name.GetHashCode() : 0;
hashCode = (hashCode * 397) ^ ChargeState;
hashCode = (hashCode * 397) ^ ExperimentalMassToCharge.GetHashCode();
hashCode = (hashCode * 397) ^ CalculatedMassToCharge.GetHashCode();
hashCode = (hashCode * 397) ^ CalculatedPI.GetHashCode();
hashCode = (hashCode * 397) ^ Rank;
hashCode = (hashCode * 397) ^ PassThreshold.GetHashCode();
hashCode = (hashCode * 397) ^ (Peptide != null ? Peptide.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (MassTable != null ? MassTable.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (Sample != null ? Sample.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (PeptideEvidences != null ? PeptideEvidences.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (Fragmentations != null ? Fragmentations.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (CVParams != null ? CVParams.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (UserParams != null ? UserParams.GetHashCode() : 0);
return(hashCode);
}
}
/// <summary>
/// Get the SpecEValue of this identification
/// </summary>
/// <returns></returns>
public double GetSpecEValue()
{
return(CVParams.GetCvParam(CV.CV.CVID.MS_MS_GF_SpecEValue, "1").ValueAs <double>());
}
