The graph layout problem arises frequently in the conceptual stage of mechanism design, specially in the enumeration process where a large number of topological solutions must be analyzed. Two main objectives of graph layout are the avoidance or minimization of edge crossings and the aesthetics. Edge crossings cannot be always avoided by force-directed algorithms since they reach a minimum of the energy in dependence with the initial position of the vertices, often randomly generated. Combinatorial algorithms based on the properties of the graph representation of the kinematic chain can be used to find an adequate initial position of the vertices with minimal edge crossings. To select an initial layout, the minimal independent loops of the graph can be drawn as circles followed by arcs, in all forms. The computational cost of this algorithm grows as factorial with the number of independent loops. This paper presents a combination of two algorithms: a combinatorial algorithm followed by a force-directed algorithm based on spring repulsion and electrical attraction, including a new concept of vertex-to-edge repulsion to improve aesthetics and minimize crossings. Atlases of graphs of complex kinematic chains are used to validate the results. The layouts obtained have good quality in terms of minimization of edge crossings and maximization of aesthetic characteristics.
Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes