QTClusterFinder::QTClusterFinder() :
BaseGroupFinder(), feature_distance_(FeatureDistance())
{
setName(getProductName());
defaults_.setValue("use_identifications", "false", "Never link features that are annotated with different peptides (only the best hit per peptide identification is taken into account).");
defaults_.setValidStrings("use_identifications", StringList::create("true,false"));
defaults_.insert("", feature_distance_.getDefaults());
defaultsToParam_();
}
StablePairFinder::StablePairFinder() :
Base()
{
//set the name for DefaultParamHandler error messages
Base::setName(getProductName());
defaults_.setValue("second_nearest_gap", 2.0, "Only link features whose distance to the second nearest neighbors (for both sides) is larger by 'second_nearest_gap' than the distance between the matched pair itself.");
defaults_.setMinFloat("second_nearest_gap", 1.0);
defaults_.setValue("use_identifications", "false", "Never link features that are annotated with different peptides (features without ID's always match; only the best hit per peptide identification is considered).");
defaults_.setValidStrings("use_identifications", ListUtils::create<String>("true,false"));
defaults_.insert("", FeatureDistance().getDefaults());
Base::defaultsToParam_();
}
StablePairFinder::StablePairFinder() :
Base()
{
//set the name for DefaultParamHandler error messages
Base::setName(getProductName());
defaults_.setValue("second_nearest_gap", 2.0, "The distance to the second nearest neighbors must be larger by this factor than the distance to the matching element itself.");
defaults_.setMinFloat("second_nearest_gap", 1.0);
defaults_.setValue("use_identifications", "false", "Never link features that are annotated with different peptides (only the best hit per peptide identification is taken into account).");
defaults_.setValidStrings("use_identifications", ListUtils::create<String>("true,false"));
defaults_.insert("", FeatureDistance().getDefaults());
Base::defaultsToParam_();
}
void QTClusterFinder::setParameters_(DoubleReal max_intensity,
DoubleReal max_mz)
{
if (max_mz < 1e-16 || max_mz > 1e16 || max_intensity < -1e16 || max_intensity > 1e16)
{
throw Exception::IllegalArgument(__FILE__, __LINE__, __PRETTY_FUNCTION__,
"Maximum mz or intensity out of range (mz,intensity): " + String(max_mz) + ", " + String(max_intensity));
}
use_IDs_ = String(param_.getValue("use_identifications")) == "true";
max_diff_rt_ = param_.getValue("distance_RT:max_difference");
max_diff_mz_ = param_.getValue("distance_MZ:max_difference");
// compute m/z tolerance in Da (if given in ppm; for the hash grid):
if (param_.getValue("distance_MZ:unit") == "ppm")
{
max_diff_mz_ *= max_mz * 1e-6;
}
Param distance_params = param_.copy("");
distance_params.remove("use_identifications");
feature_distance_ = FeatureDistance(max_intensity, true);
feature_distance_.setParameters(distance_params);
}
