The ProtocolAnalyzer constantly samples the analog input signal, trying to recreate any digital pulses found in the signal. The so called flank detector uses a quite simple algorithm to find the flanks of the pulses:
Find sequences where the sampled value changed significanlty (Flank Swing) over a short period of time (Flank Length)
To avoid the same flank being counted twice if it is large, we wait a while (Flank Holdoff) after finding a flank until we accept a new flank. This picture shows the meaning of the settings on a real sampled signal. The red line is the analog value (where the sample points are marked with black dots). The blue line is the flank detectors interpretation of the signal:
In the example Flank Swing was set at 50 and Flank Length set to 3, so when the signal changed more than 50 over 3 samples, the flank was detected (see the blue line). Note that the signal changed more than 50 in the following samples as well, but since this was within Flank Holdoff, this was not counted.