Screen pop up application is developed on JTapi.Window pops up on ringing event on agent console.

This is the following scenario:
Agent X has answered the call.He is on the line with Customer
IVR tries to dial the same X agent's extension in the mean time.Will the ringing event be caught at agent Jtapi applicaion?
If yes how to avoid screen popping up until agent hungs up the call.

In this situation the Agents would usually be signed into a skill, and the IVR would dial a VDN or a hunt group directly. Then the next available agent would take the call. So if an agent is busy on a call the Communication Manager will not try to send a call to that agent at all. If a station is able to be alerted by Communication Manager then a delivered event will occur. If the extension is busy then the station can't be alerted and no delivered event will occur.

a screen pop is something the JTAPI Client application controls (i.e. your code) The sample application available in the SDK/on the DevConnect portal is one implementation. You should implement the application per your requirements. In the scenario you describe a call by an IVR to the agent's extension (i.e. the AgentID) is a direct agent seeking call, and will be handled per the configuration of Communication manager. As Craig indicates a number of possible outcomes may occur (ring a free call appearance at the extension the agent is logged in at, or receive busy). Assuming the IVR call is offered to the extension the agent is logged in at, an event indicating a call has been delivered will be passed to the TSAPI Client and thus the application. At that point how the application reacts to it is up to you. All JTAPI is responsible for is delivering the notification.