Since, the original post created some confusion, i am rephrasing the question to make it understand better.
Lets say I have a series of aperiodic pulses of different energy and shapes coming in from the channel. The pulse widths are 2 ns and pulses are separated by 200 ns. I have used an ADC with enough sampling frequency to digitize the data and they are now in my laptop. I need to measure the energy of the pulses. I can do it say by choosing a window of 200 ns with the pulse at the center, and calculate integration of the samples for that window. I can then move the window 200 ns ahead across time and calculate the integration/energy for the next pulse. However, i was wondering is there a better or easy way to do this?