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In wireless cooperative orthogonal frequency-division multiple-access (OFDMA) networks, it is important to adapt the transmission strategies for each user according to the network channel dynamics in order to optimize the overall system performance. The adaption involves transmission mode selection (a user can choose from direct or cooperative transmission), subcarrier assignment, subcarrier pairing (the incoming and outgoing subcarriers at the relay for cooperative transmission need to be matched), relay selection, as well as power allocation and hence is highly challenging. Many previous works only consider a subset of the adaptation. In this paper, we tackle the joint optimization problem using a network flow approach. Specifically, we first show that for given power allocation, the combinatorial optimization problem of transmission mode selection, subcarrier assignment, relay selection and subcarrier pairing for the system total throughput maximization can be transformed into a minimum cost network flow (MCNF) problem with integer solutions. The linear optimal distribution (LOD) algorithm is applied to find the optimal solution in polynomial time. We then solve the mixed integer programming problem of the joint assignment and power allocation in an asymptotically optimal way in the dual domain. Simulation results show that the proposed algorithms can significantly enhance the overall system throughput.