/// <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>
/// 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));
}
}
