public ExperimentalProteoform(string accession, ExperimentalProteoform temp, List <IAggregatable> candidate_observations, bool is_target, bool neucode_labeled)
: base(accession) //this is for first mass of aggregate components. uses a temporary component
{
if (neucode_labeled)
{
NeuCodePair ncRoot = new NeuCodePair();
ncRoot.weighted_monoisotopic_mass = temp.agg_mass;
ncRoot.intensity_sum = temp.agg_intensity;
ncRoot.rt_apex = temp.agg_rt;
ncRoot.lysine_count = temp.lysine_count;
this.root = ncRoot;
this.aggregated.AddRange(candidate_observations.Where(p => includes(p, this.root)));
this.calculate_properties();
this.root = this.aggregated.OrderByDescending(a => a.intensity_sum).FirstOrDefault(); //reset root to component with max intensity
}
else
{
Component cRoot = new Component();
cRoot.weighted_monoisotopic_mass = temp.agg_mass;
cRoot.intensity_sum = temp.agg_intensity;
cRoot.rt_apex = temp.agg_rt;
this.root = cRoot;
this.aggregated.AddRange(candidate_observations.Where(p => includes(p, this.root)));
calculate_properties();
this.root = this.aggregated.OrderByDescending(a => a.intensity_sum).FirstOrDefault(); //reset root to component with max intensity
}
}
private bool tolerable_lysCt(NeuCodePair candidate, int lysine_count)
{
int max_missed_lysines = Convert.ToInt32(SaveState.lollipop.missed_lysines);
List <int> acceptable_lysineCts = Enumerable.Range(lysine_count - max_missed_lysines, max_missed_lysines * 2 + 1).ToList();
return(acceptable_lysineCts.Contains(candidate.lysine_count));
}
private bool tolerable_lysCt(NeuCodePair candidate, int lysine_count)
{
List <int> acceptable_lysineCts = Enumerable.Range(lysine_count - Sweet.lollipop.maximum_missed_lysines, Sweet.lollipop.maximum_missed_lysines * 2 + 1).ToList();
return(acceptable_lysineCts.Contains(candidate.lysine_count));
}
