public BoundAggregatedValue(ValueSlot output, AggregateSymbol aggregate, IAggregatable aggregatable, BoundExpression argument)
{
Output = output;
Aggregate = aggregate;
Aggregatable = aggregatable;
Argument = argument;
}
public ExperimentalProteoform(string accession, IAggregatable root, bool is_target)
: base(accession)
{
quant = new QuantitativeProteoformValues(this);
this.root = root;
this.is_target = is_target;
}
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
}
}
public void AggregateTest()
{
IAggregatable duck = DuckTyping.Aggregate <IAggregatable>(new AggregateClass1(), new AggregateClass2());
Assert.IsNotNull(duck);
Assert.AreEqual(1, duck.Method1());
Assert.AreEqual(2, duck.Method2());
// It is still possible to get access
// to an interface of an underlying object.
//
IClass2 cls2 = DuckTyping.Implement <IClass2>(duck);
Assert.IsNotNull(cls2);
Assert.AreEqual(2, cls2.Method2());
// Even to switch from one aggregated object to another
//
IClass1 cls1 = DuckTyping.Implement <IClass1>(cls2);
Assert.IsNotNull(cls1);
Assert.AreEqual(1, cls1.Method1());
Assert.AreEqual(3, cls1.Method3());
}
public void aggregate()
{
ExperimentalProteoform temp_pf = new ExperimentalProteoform("tbd", root, new List <IAggregatable>(Sweet.lollipop.remaining_to_aggregate), true); //first pass returns temporary proteoform
ExperimentalProteoform new_pf = new ExperimentalProteoform("tbd", temp_pf, new List <IAggregatable>(Sweet.lollipop.remaining_to_aggregate), true, Sweet.lollipop.neucode_labeled); //second pass uses temporary protoeform from first pass.
copy_aggregate(new_pf); //doesn't copy quant on purpose
root = temp_pf.root; //maintain the original component root
}
public AvgAggregatable(IAggregatable sumAggregatable, IAggregatable countAggregatable, Expression <object> divisionExpression, VariableSymbol sumArgument, VariableSymbol countArgument)
{
_sumAggregatable = sumAggregatable;
_countAggregatable = countAggregatable;
_divisionExpression = divisionExpression;
_sumArgument = sumArgument;
_countArgument = countArgument;
}
public ExperimentalProteoform(string accession, IAggregatable root, List <IAggregatable> candidate_observations, bool is_target)
: base(accession)
{
quant = new QuantitativeProteoformValues(this);
this.root = root;
this.aggregated.AddRange(candidate_observations.Where(p => this.includes(p, this.root)));
this.calculate_properties();
this.root = this.aggregated.OrderByDescending(a => a.intensity_sum).FirstOrDefault();
}
public BoundAggregateExpression Update(AggregateSymbol aggregate, IAggregatable aggregatable, BoundExpression argument)
{
if (aggregate == Symbol && aggregatable == Aggregatable && argument == Argument)
{
return(this);
}
return(new BoundAggregateExpression(aggregate, aggregatable, argument));
}
public void choose_next_agg_component()
{
Component c = new Component();
Component d = new Component();
Component e = new Component();
Component f = new Component();
c.weighted_monoisotopic_mass = 100;
d.weighted_monoisotopic_mass = 119;
e.weighted_monoisotopic_mass = 121;
f.weighted_monoisotopic_mass = 122;
c.intensity_sum = 1;
d.intensity_sum = 2;
e.intensity_sum = 3;
f.intensity_sum = 4;
List <IAggregatable> ordered = new List <IAggregatable> {
c, d, e, f
}.OrderByDescending(cc => cc.intensity_sum).ToList();
Component is_running = new Component();
is_running.weighted_monoisotopic_mass = 100;
is_running.intensity_sum = 100;
//Based on components
List <IAggregatable> active = new List <IAggregatable> {
is_running
};
IAggregatable next = Sweet.lollipop.find_next_root(ordered, active);
Assert.True(Math.Abs(next.weighted_monoisotopic_mass - is_running.weighted_monoisotopic_mass) > 2 * (double)Sweet.lollipop.maximum_missed_monos);
Assert.AreEqual(4, next.intensity_sum);
//Based on experimental proteoforms
ExperimentalProteoform exp = ConstructorsForTesting.ExperimentalProteoform("E");
exp.root = is_running;
List <ExperimentalProteoform> active2 = new List <ExperimentalProteoform> {
exp
};
IAggregatable next2 = Sweet.lollipop.find_next_root(ordered, active2);
Assert.True(Math.Abs(next.weighted_monoisotopic_mass - is_running.weighted_monoisotopic_mass) > 2 * (double)Sweet.lollipop.maximum_missed_monos);
Assert.AreEqual(4, next.intensity_sum);
}
public string find_manual_inspection_component(IEnumerable <IAggregatable> components)
{
IAggregatable intense = components.OrderByDescending(c => c.intensity_sum).FirstOrDefault();
if (intense == null)
{
return("");
}
ChargeState intense_cs = intense.charge_states.OrderByDescending(c => c.intensity).FirstOrDefault();
if (intense_cs == null)
{
return("");
}
return("File: " + intense.input_file.filename
+ "; Scan Range: " + intense.min_scan + "-" + intense.max_scan
+ "; Charge State m/z (+" + intense_cs.charge_count.ToString() + "): " + intense_cs.mz_centroid + "; RT (min): " + intense.rt_apex);
}
private void copy_aggregate(ExperimentalProteoform e)
{
root = e.root;
//doesn't copy quant on purpose
agg_intensity = e.agg_intensity;
agg_mass = e.agg_mass;
modified_mass = e.modified_mass;
agg_rt = e.agg_rt;
lysine_count = e.lysine_count;
is_target = e.is_target;
family = e.family;
aggregated = new List <IAggregatable>(e.aggregated);
lt_quant_components = new List <Component>(e.lt_quant_components);
lt_verification_components = new List <Component>(e.lt_verification_components);
hv_quant_components = new List <Component>(e.hv_quant_components);
hv_verification_components = new List <Component>(e.hv_verification_components);
biorepIntensityList = new List <BiorepIntensity>(e.biorepIntensityList);
manual_validation_id = e.manual_validation_id;
manual_validation_verification = e.manual_validation_verification;
manual_validation_quant = e.manual_validation_quant;
}
public BoundAggregatedValue Update(ValueSlot output, AggregateSymbol aggregate, IAggregatable aggregatable, BoundExpression argument)
{
if (output == Output && aggregate == Aggregate && aggregatable == Aggregatable && argument == Argument)
{
return(this);
}
return(new BoundAggregatedValue(output, aggregate, aggregatable, argument));
}
private bool tolerable_rt(IAggregatable candidate, double rt_apex)
{
return(candidate.rt_apex >= rt_apex - Sweet.lollipop.retention_time_tolerance &&
candidate.rt_apex <= rt_apex + Sweet.lollipop.retention_time_tolerance);
}
//This aggregates based on lysine count, mass, and retention time all at the same time. Note that in the past we aggregated based on
//lysine count first, and then aggregated based on mass and retention time afterwards, which may give a slightly different root for the
//experimental proteoform because the precursor aggregation may shuffle the intensity order slightly. We haven't observed any negative
//impact of this difference as of 160812. -AC
public bool includes(IAggregatable candidate, IAggregatable root)
{
return(tolerable_rt(candidate, root.rt_apex) && tolerable_mass(candidate.weighted_monoisotopic_mass, root.weighted_monoisotopic_mass) &&
(candidate as NeuCodePair == null || tolerable_lysCt(candidate as NeuCodePair, (root as NeuCodePair).lysine_count)));
}
public static ExperimentalProteoform ExperimentalProteoform(string accession, IAggregatable root, List <IAggregatable> candidate_observations, List <Component> quantitative_observations, bool is_target)
{
ExperimentalProteoform e = new ExperimentalProteoform(accession, root, is_target);
e.aggregated.AddRange(candidate_observations.Where(p => e.includes(p, e.root)));
e.calculate_properties();
if (quantitative_observations.Count > 0)
{
e.lt_quant_components.AddRange(quantitative_observations.Where(r => e.includes_neucode_component(r, e, true)));
if (Sweet.lollipop.neucode_labeled)
{
e.hv_quant_components.AddRange(quantitative_observations.Where(r => e.includes_neucode_component(r, e, false)));
}
}
e.root = e.aggregated.OrderByDescending(a => a.intensity_sum).FirstOrDefault();
return(e);
}
public BoundAggregateExpression(AggregateSymbol aggregate, IAggregatable aggregatable, BoundExpression argument)
{
Symbol = aggregate;
Aggregatable = aggregatable;
Argument = argument;
}
