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It is possible to drive actual pipe ranks from jOrgan. Usually you will have a Midi decoder built into your real organ that jOrgan is able to control with Midi messages.
In a common setup each rank is accessible via a fixed Midi channel. For jOrgan this means that you'll have to fix the channel of your ranks accordingly. Only Note played and Note muted messages are required, there's no need to configure a program change or any Midi controller.
To use a real rank accessible under channel 0 you have to setup the channel property of your rank as follows: