/// <summary>
/// Add another evidence of the ConsensusTarget
/// </summary>
/// <param name="evidence"></param>
public void AddEvidence(Evidence evidence)
{
Evidences.Add(evidence);
if (Sequence == null)
{
Sequence = evidence.Sequence;
}
evidence.Sequence = Sequence;
if (Math.Abs(PredictedNet) < double.Epsilon)
{
PredictedNet = evidence.PredictedNet;
}
// For rebuilding and getting the predicted NET into Evidence
// when reloading back into the data objects
evidence.PredictedNet = PredictedNet;
if (MultiProteinCount == 0)
{
MultiProteinCount = evidence.MultiProteinCount;
}
evidence.MultiProteinCount = MultiProteinCount;
if (string.IsNullOrWhiteSpace(ModificationDescription))
{
ModificationDescription = evidence.ModificationDescription;
}
evidence.ModificationDescription = ModificationDescription;
if (ModificationCount == 0)
{
ModificationCount = evidence.ModificationCount;
}
evidence.ModificationCount = ModificationCount;
if (evidence.Ptms.Count != 0 && Ptms.Count == 0)
{
foreach (var ptm in evidence.Ptms)
{
Ptms.Add(ptm);
ptm.Parent = this;
}
}
var tempList = Ptms.ToList();
tempList.Sort((x, y) => x.Location.CompareTo(y.Location));
// Copy sequence as is up until you hit a modification
//For numeric, add a bracket add +/- and copy the mass
//For non numeric, add a bracket add +/- and copy the formula
var numeric = "";
var nonNumeric = "";
var cleanSeq = "";
var sequencePos = 0;
var symbolsRemoved = 0;
string partialSeq;
foreach (var ptm in tempList)
{
partialSeq = Sequence.Substring(sequencePos, (ptm.Location + PreCharCount + symbolsRemoved) - sequencePos);
cleanSeq += partialSeq;
numeric += partialSeq + string.Format("[{0}{1}]", ((ptm.Mass > 0) ? "+" : "-"), ptm.Mass);
nonNumeric += partialSeq + string.Format("[{0}{1}]", ((ptm.Mass > 0) ? "+" : "-"), ptm.Formula);
sequencePos = ptm.Location + PreCharCount;
// To skip over non-alphanumeric characters in the sequence such as "*" or "&"
// which can be used to denote ptms in .txt files, but not skip over "." or "-"
// which are standard characters in peptide sequences to separate peptide from
// pre/post residues and to denote the lack of a pre/post residue respectively
int indexCheck = sequencePos + symbolsRemoved;
if ((Sequence[indexCheck] != 46 && Sequence[indexCheck] != 45) &&
(Sequence[indexCheck] < 65 || Sequence[indexCheck] > 90))
{
sequencePos += ++symbolsRemoved;
}
}
partialSeq = Sequence.Substring(sequencePos);
cleanSeq += partialSeq;
numeric += partialSeq;
nonNumeric += partialSeq;
StrippedSequence = cleanSeq;
var pieces = cleanSeq.Split('.');
if (pieces.Count() != 1)
{
PrefixResidue = pieces[0].First();
StrippedSequence = pieces[1];
SuffixResidue = pieces[2].First();
}
if (string.IsNullOrWhiteSpace(evidence.CleanPeptide))
{
//evidence.CleanPeptide = cleanSeq;
evidence.CleanPeptide = StrippedSequence;
}
CleanSequence = cleanSeq;
if (string.IsNullOrWhiteSpace(evidence.EncodedNonNumericSequence))
{
evidence.EncodedNonNumericSequence = nonNumeric;
}
EncodedNonNumericSequence = nonNumeric;
if (string.IsNullOrWhiteSpace((evidence.SeqWithNumericMods)))
{
evidence.SeqWithNumericMods = numeric;
}
EncodedNumericSequence = numeric;
if (!Charges.Contains(evidence.Charge))
{
Charges.Add(evidence.Charge);
}
evidence.Parent = this;
}