The tree package and subpackages contain classes implementing different bit pattern tree versions; the trees are stored in-core (in memory) or out-of-core (for instance on disk), and they can be used in combination with any adjacency test method.

Bit pattern trees are used to speed up the enumeration of adjacent modes, usually by applying the recursive enumeration approach described in [1].

Notes
Legacy implementations for bit pattern trees also exist in the {@link ch.javasoft.metabolic.efm.adj.incore.tree adj.incore.tree} package and subpackages.

References

  1. Terzer, M. and Stelling, J., "Large scale computation of elementary flux modes with bit pattern trees",
    Bioinformatics, August 1, 2008, doi:10.1093/bioinformatics/btn401