The adj.incore.tree package and subpackages contain classes implementing different bit pattern tree versions; all those trees are stored in-core (in memory).

Bit pattern trees are used to speed up the enumeration of adjacent modes. All tree implementations are similar, most use the recursive enumeration approach described in [1].

The main difference between the various tree versions in the subpackages are the use of different adjacency tests.

Notes
More recent bit pattern tree implementations are contained in the {@link ch.javasoft.metabolic.efm.tree} package. Those classes support different memory types, that is, storage of the trees in-core (in memory) or out-of-core (for instance on disk). Those implementations generally offer higher flexibility, for instance, the same tree implementation can be used in combination with various adjacency test methods.

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