Since their inception in the 30s by von Neumann, operator algebras have been used in shedding light in many mathematical theories. Classification results for self-adjoint and non-self-adjoint operator algebras manifest this approach, but a clear connection between the two was sought since their emergence in the late 60s. We connect these seemingly separate type of results by uncovering a hierarchy of classification for non-self-adjoint operator algebras and $C^*$-algebras with additional $C^*$-algebraic structure. Our approach naturally applies to algebras arising from $C^*$-correspondences to resolve self-adjoint and non-self-adjoint isomorphism problems in the literature. We apply our strategy to completely elucidate this newly found hierarchy for operator algebras arising from directed graphs.