private void Normalize()
{
foreach (var groupParameter in GroupParameter.GetAllFragmentGroupParameters(_maxCharge))
{
if (!IsotopeIntensityCorrProbDictionary.ContainsKey(groupParameter))
{
IsotopeIntensityCorrProbDictionary[groupParameter] = new Dictionary <IonType, Dictionary <int, double> >();
}
var si = IsotopeIntensityCorrProbDictionary[groupParameter];
foreach (var ionType in _ionTypes[groupParameter])
{
if (!si.ContainsKey(ionType))
{
si[ionType] = new Dictionary <int, double>();
}
var ssi = si[ionType];
var sum = 0.0;
foreach (var score in SubScoreFactory.GetAllCorrIntScore())
{
if (!ssi.ContainsKey(score))
{
ssi[score] = 1.0;
}
sum = sum + ssi[score];
}
var keys = new List <int>(ssi.Keys);
foreach (var score in keys)
{
ssi[score] = Math.Max(double.MinValue, ssi[score] / sum);
}
}
}
}
public ValueParameter <T> CreateValueParameter <T>(string label = "", GroupParameter group = null)
{
var datatype = TypeDefinition.GetDatatype(typeof(T));
var param = CreateParameter(datatype, label, group) as ValueParameter <T>;
return(AddAndReturn(param, label, group));
}
public ArrayParameter <T> CreateArrayParameter <T>(string label = "", GroupParameter group = null, int[] structure = null)
{
var elementType = TypeDefinition.GetDatatype(typeof(T));
var param = Parameter.Create(this, FIdCounter++, RcpTypes.Datatype.Array, elementType, structure) as ArrayParameter <T>;
return(AddAndReturn(param, label, group));
}
public NumberParameter <T> CreateNumberParameter <T>(string label = "", GroupParameter group = null) /*where T : struct*/
{
var datatype = TypeDefinition.GetDatatype(typeof(T));
var param = (NumberParameter <T>)CreateParameter(datatype, label, group);
return(AddAndReturn(param, label, group));
}
private void GetIonTypes()
{
foreach (var groupParameter in GroupParameter.GetAllFragmentGroupParameters(_maxCharge))
{
IonTypes[groupParameter] = new List <IonType>();
if (!_ionFrequencyFunction.ContainsKey(groupParameter))
{
continue;
}
var subIonFrequencyFunction = _ionFrequencyFunction[groupParameter];
var subIonTypes = IonTypes[groupParameter];
var offsets = new List <double>(subIonFrequencyFunction.Values);
offsets.Sort();//ascending
foreach (var ionType in subIonFrequencyFunction.Keys)
{
if (offsets.Count <= NumberPerGroup || subIonFrequencyFunction[ionType] < offsets[offsets.Count - NumberPerGroup])
{
continue;
}
if (subIonTypes.Count < NumberPerGroup)
{
subIonTypes.Add(ionType);
}
}
}
}
public void AddParameter(Parameter param, GroupParameter group)
{
base.AddParameter(param);
if (group == null)
{
group = Root;
}
group.AddParameter(param);
}
private void Normalize()
{
foreach (var groupParameter in GroupParameter.GetAllFragmentGroupParameters(_maxCharge))
{
if (!RatioProbDictionary.ContainsKey(groupParameter))
{
RatioProbDictionary[groupParameter] = new Dictionary <Tuple <IonType, IonType>, Dictionary <int, double> >();
}
if (!_allNumberDictionary.ContainsKey(groupParameter))
{
_allNumberDictionary[groupParameter] = 1.0;
}
if (!NoIonProbDictionary.ContainsKey(groupParameter))
{
NoIonProbDictionary[groupParameter] = 1.0;
}
NoIonProbDictionary[groupParameter] = NoIonProbDictionary[groupParameter] /
Math.Max(_allNumberDictionary[groupParameter], 1.0);
var sr = RatioProbDictionary[groupParameter];
foreach (var ionType in _ionTypes[groupParameter])
{
foreach (var ionType2 in _ionTypes[groupParameter])
{
var sum = 0.0;
var ionTypes = new Tuple <IonType, IonType> (ionType, ionType2);
if (!sr.ContainsKey(ionTypes))
{
sr[ionTypes] = new Dictionary <int, double>();
}
var ssr = sr[ionTypes];
foreach (var ratio in FeatureEdge.GetAllRatioIndices())
{
if (!ssr.ContainsKey(ratio))
{
ssr[ratio] = 1.0;
}
sum = sum + ssr[ratio];
}
var keys = new List <int> (ssr.Keys);
foreach (var ratio in keys)
{
ssr[ratio] = Math.Max(Double.MinValue, ssr[ratio] / sum);
}
}
}
}
}
public UriParameter CreateUriParameter(string label = "", GroupParameter group = null)
{
var param = CreateParameter(RcpTypes.Datatype.Uri, label, group) as UriParameter;
return(AddAndReturn(param, label, group));
}
public Parameter CreateRangeParameter(RcpTypes.Datatype elementType, string label = "", GroupParameter group = null)
{
var param = Parameter.Create(this, FIdCounter++, RcpTypes.Datatype.Range, elementType);
return(AddAndReturn(param, label, group));
}
public Parameter CreateBangParameter(string label = "", GroupParameter group = null)
{
var param = Parameter.Create(this, FIdCounter++, RcpTypes.Datatype.Bang);
return(AddAndReturn(param, label, group));
}
TParameter AddAndReturn <TParameter>(TParameter param, string label, GroupParameter group) where TParameter : Parameter
{
param.Label = label;
AddParameter(param, group);
return(param);
}
public PrecursorFeatureNode(IsotopomerFeatures isotopomerFeatures, GroupParameter parameter, SubScoreFactory scoringParams)
: base(isotopomerFeatures, null, isotopomerFeatures.GetMostAbundantFeature(), parameter)
{
_scoringParams = scoringParams;
Score = GetScore();
}
public PrecursorFeatureNode(IsotopomerFeatures isotopomerFeatures, GroupParameter parameter, SubScoreFactory scoringParams)
: base(isotopomerFeatures, null, isotopomerFeatures.GetMostAbundantFeature(), parameter)
{
_scoringParams = scoringParams;
Score = GetScore();
}
public ClientServerBase()
{
FContext = SynchronizationContext.Current;
Root = new GroupParameter(0, this, new GroupDefinition());
}
