Android: Battery usage of each application
Other than the battery usage screen in Settings, there is no API or command-line way to get this information.
How to measure battery usage of my application?
Get a spare device. Load it completely, then run the protocol until shutdown without other interaction (no youtube or anything), note the time it lasted. Repeat with the other protocol. Imho that is a fair way to compare. Note that every device behaves differently and it may or may not be possible to transfer this result to other devices e.g. with different network chips, processors or even firmware versions.
For a more fair comparison I think you should compare how the protocols work. I.e. number of interactions, payload size etc. because the power consumption can only ever be an estimate.
How to find battery usage of an application over time?
The closest you will be able to get to get "accurate battery usage information of a particular application over some period of time" will be to invest in a Qualcomm MDP device and use Trepn. The MDP series have special hardware instrumentation for detailed power measurement; the Trepn software package allows you to collect the results.
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