Counting the notes in the MIDI file should be fairly straightforward since a MIDI file is more or less just a sequence of instructions of which notes to play. However, I've no idea if there's a MIDI file decoder implemented in matlab. If not, there might be something on the FileExchange.
For the wav file, that's going to be significantly harder since it's just a sound recording. There's no note information embedded in the file. I guess for drums the start of a drum beat is a note, so you could probably detect sudden increases in sound amplitude. But what you're asking is akin to asking someone to listen to some drub and transcribe what they hear into notes. Not easy!
