@Override
public <G, D, L> void exportParameters(
ParameterHelper helper, DataDocument<G, D, L> document, D dictionary) {
document.addToDictionary(
dictionary, "$name", helper.toClassName(MutableMeasurementProfile.class));
if (intensityDeviation != 0 && !Double.isNaN(intensityDeviation))
document.addToDictionary(dictionary, "intensityDeviation", getIntensityDeviation());
if (getMedianNoiseIntensity() != 0 && !Double.isNaN(getMedianNoiseIntensity()))
document.addToDictionary(dictionary, "medianNoiseIntensity", getMedianNoiseIntensity());
if (formulaConstraints != null)
document.addToDictionary(
dictionary, "formulaConstraints", helper.wrap(document, getFormulaConstraints()));
if (getAllowedMassDeviation() != null)
document.addToDictionary(
dictionary, "allowedMassDeviation", getAllowedMassDeviation().toString());
if (getStandardMs1MassDeviation() != null)
document.addToDictionary(
dictionary, "standardMs1MassDeviation", getStandardMs1MassDeviation().toString());
if (getStandardMs2MassDeviation() != null)
document.addToDictionary(
dictionary, "standardMs2MassDeviation", getStandardMs2MassDeviation().toString());
if (getStandardMassDifferenceDeviation() != null)
document.addToDictionary(
dictionary,
"standardMassDifferenceDeviation",
getStandardMassDifferenceDeviation().toString());
}
@Override
public <G, D, L> void importParameters(
ParameterHelper helper, DataDocument<G, D, L> document, D dictionary) {
final Set<String> keys = document.keySetOfDictionary(dictionary);
if (keys.contains("intensityDeviation"))
setIntensityDeviation(document.getDoubleFromDictionary(dictionary, "intensityDeviation"));
if (keys.contains("medianNoiseIntensity"))
setMedianNoiseIntensity(document.getDoubleFromDictionary(dictionary, "medianNoiseIntensity"));
if (keys.contains("formulaConstraints"))
setFormulaConstraints(
(FormulaConstraints)
helper.unwrap(
document, document.getFromDictionary(dictionary, "formulaConstraints")));
if (keys.contains("allowedMassDeviation"))
allowedMassDeviation =
Deviation.fromString(
document.getStringFromDictionary(dictionary, "allowedMassDeviation"));
if (keys.contains("standardMs1MassDeviation"))
standardMs1MassDeviation =
Deviation.fromString(
document.getStringFromDictionary(dictionary, "standardMs1MassDeviation"));
if (keys.contains("standardMs2MassDeviation"))
standardMs2MassDeviation =
Deviation.fromString(
document.getStringFromDictionary(dictionary, "standardMs2MassDeviation"));
if (keys.contains("standardMassDifferenceDeviation"))
standardMassDifferenceDeviation =
Deviation.fromString(
document.getStringFromDictionary(dictionary, "standardMassDifferenceDeviation"));
}
@Override
public <G, D, L> LinearIntensityDependency readFromParameters(
ParameterHelper helper, DataDocument<G, D, L> document, D dictionary) {
final double zeroIntensity = document.getDoubleFromDictionary(dictionary, "zeroIntensity");
final double fullIntensity = document.getDoubleFromDictionary(dictionary, "fullIntensity");
return new LinearIntensityDependency(fullIntensity, zeroIntensity);
}
@Override
public <G, D, L> void exportParameters(
ParameterHelper helper, DataDocument<G, D, L> document, D dictionary) {
document.addToDictionary(dictionary, "score", penalty);
}
@Override
public <G, D, L> void importParameters(
ParameterHelper helper, DataDocument<G, D, L> document, D dictionary) {
this.penalty = document.getDoubleFromDictionary(dictionary, "score");
}
@Override
public <G, D, L> void exportParameters(
ParameterHelper helper, DataDocument<G, D, L> document, D dictionary) {
document.addToDictionary(dictionary, "zeroIntensity", zeroIntensity);
document.addToDictionary(dictionary, "fullIntensity", fullIntensity);
}