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FJSTransitionController setup and use in View Controller not main app delegate
FJTransitionController* mainTransitionController;

@property (nonatomic,retain) FJTransitionController* mainTransitionController;

@synthesize mainTransitionController

mainTransitionController=[[FJTransitionController alloc] init]; // do I need to instantise?
[self.window addSubview:mainTransitionController.view];

[mainTransitionController setViewControllerClass:[[mainViewController sendMissionsPanelViewController] class] forKey:@"missionView"];

[mainTransitionController setViewController:[mainViewController sendMissionsPanelViewController] forKey:@"missionView"];