Possible bug in hard-coded magic constant

[PMSeitzer]

void PeakGroup::updateQuality() {
    maxQuality=0;
    goodPeakCount=0;
    for(unsigned int i=0; i< peaks.size(); i++) {
        if(peaks[i].quality > maxQuality) maxQuality = peaks[i].quality;
        if(peaks[i].quality > 0.5) goodPeakCount++;
    }
}

Note the hard-coded 0.5. Instead, this should be whatever the qualityThreshold is, which is usually a parameter.

[PMSeitzer]

This same magic constant is used in PeakGroup::groupStatistics():

...
        if(peaks[i].quality > 0.5) goodPeakCount++;
...

[PMSeitzer]

This isn't a bug, exactly, just confusing. There should probably be a parameter like goodPeakQualityThreshold which is tunable but takes a default value of 0.5

A parameter should be added to the Peaks dialog, not to mention, all other places where peak grouping takes place.