/// <summary>
/// Create a peptide evidence with the specified values
/// </summary>
/// <param name="dbSeq">Valid <see cref="DbSequenceObj" /> object, not null</param>
/// <param name="peptide">Valid <see cref="PeptideObj" /> object, not null</param>
/// <param name="start">start position of the peptide in the sequence</param>
/// <param name="end">end position of the peptide in the sequence</param>
/// <param name="pre">prefix residue, "." if the beginning of the sequence</param>
/// <param name="post">post/suffix residue, "." if the end of the sequence</param>
/// <param name="isDecoy">true if the peptide is a decoy</param>
public PeptideEvidenceObj(DbSequenceObj dbSeq, PeptideObj peptide, int start, int end,
string pre, string post, bool isDecoy = false) : this()
{
DBSequence = dbSeq ?? throw new ArgumentNullException(nameof(dbSeq), "Argument cannot be null.");
Peptide = peptide ?? throw new ArgumentNullException(nameof(peptide), "Argument cannot be null.");
Start = start;
End = end;
IsDecoy = isDecoy;
Pre = pre;
Post = post;
}
/// <summary>
/// Create a peptide evidence with the specified values
/// </summary>
/// <param name="dbSeq">Valid <see cref="DbSequenceObj" /> object, not null</param>
/// <param name="peptide">Valid <see cref="PeptideObj" /> object, not null</param>
/// <param name="start">start position of the peptide in the sequence</param>
/// <param name="end">end position of the peptide in the sequence</param>
/// <param name="pre">prefix residue, "." if the beginning of the sequence</param>
/// <param name="post">post/suffix residue, "." if the end of the sequence</param>
/// <param name="isDecoy">true if the peptide is a decoy</param>
/// <returns></returns>
public PeptideEvidenceObj(DbSequenceObj dbSeq, PeptideObj peptide, int start, int end,
string pre, string post, bool isDecoy = false) : this()
{
if (dbSeq == null)
{
throw new ArgumentNullException("dbSeq", "Argument cannot be null.");
}
if (peptide == null)
{
throw new ArgumentNullException("peptide", "Argument cannot be null.");
}
DBSequence = dbSeq;
Peptide = peptide;
Start = start;
End = end;
IsDecoy = isDecoy;
Pre = pre;
Post = post;
}
/// <summary>
/// Constructor
/// </summary>
public PeptideEvidenceObj()
{
_dBSequenceRef = null;
_peptideRef = null;
_start = -1;
StartSpecified = false;
_end = -1;
EndSpecified = false;
Pre = null;
Post = null;
_translationTableRef = null;
_frame = -1;
FrameSpecified = false;
IsDecoy = false;
Id = null;
Name = null;
_dBSequence = null;
_peptide = null;
_translationTable = null;
}
/// <summary>
/// Constructor
/// </summary>
public SpectrumIdentificationItemObj()
{
Id = null;
Name = null;
ChargeState = 0;
ExperimentalMassToCharge = -1;
_calculatedMassToCharge = -1;
CalculatedMassToChargeSpecified = false;
_calculatedPI = -1;
CalculatedPISpecified = false;
_peptideRef = null;
Rank = -1;
PassThreshold = false;
_massTableRef = null;
_sampleRef = null;
_peptide = null;
_massTable = null;
_sample = null;
PeptideEvidences = new IdentDataList <PeptideEvidenceRefObj>();
Fragmentations = new IdentDataList <IonTypeObj>();
}
