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We consider the offline version of the routing and wavelength assignment problem in transparent all-optical networks. In such networks and in the absence of regenerators, the signal quality of a transmission degrades due to physical layer impairments. Certain physical effects cause choices for one lightpath to affect and be affected by the choices made for other lightpaths. This interference among lightpaths is particularly difficult to formulate in an offline algorithm, since in this version of the problem we start without any established connections, and the utilization of lightpaths are the variables of the problem. For this reason the majority of work performed in this field either neglects lightpath interactions or assumes a worst case interference scenario. In this article we present a way to formulate interlightpath interference as additional constraints on RWA and show how to incorporate these constraints in an IA-RWA algorithm that directly accounts for the most important physical layer impairments. The objective of the resulting cross-layer optimization problem is not only to serve the connection requests using the minimum number of wavelengths (network layer objective), but also to select lightpaths that have acceptable quality of transmission performance (physical layer objective).