1. A method for generating playback instructions for playback of a recorded presentation layer protocol data stream transmitted from an application server (i) executing an application for a client and (ii) streaming the output display generated by the application to the client, the method comprising: (a) receiving, by a protocol engine executing on a computing device, a recorded presentation layer protocol data stream comprising a plurality of packets representing display data generated by an application program executing on an application server; (b) determining, by the protocol engine, to render the contents of a first packet having content identifying a window having input focus, the window associated with the application; (c) determining, by the protocol engine, not to render the contents of a second packet having content identifying the window lacks input focus; and (c) storing, by the protocol engine, the determination for the first packet and for the second packet of the recorded presentation layer protocol data stream in a playback data structure.