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We examine the freight transportation problem which occurs when the same authority controls and plans both the supply of transportation services (modes, routes, frequencies for the services and classification, consolidation, transfer policies for terminals) and the routing of freight. We present a general modeling framework, based on a network optimization model, which may be used to assist and enhance the tactical and strategic planning process for such a system. The problem is solved by means of an algorithm, described in some detail, based on decomposition and column generation principles. We also present detailed results on the behaviour and performance of the algorithm, as observed during experimentation with a specific rail application.