The rankup package and subpackages contain classes and interfaces
implementing the lazy rank updating method to enumerate adjacent modes.
The laziness is reflected by two matrix types:
- {@link ch.javasoft.metabolic.efm.rankup.PreprocessableMatrix PreprocessableMatrix}
reflects a matrix at a certain tree recursion depth, for which the actual
triangularization has not yet been executed. Once triangularization is
{@link ch.javasoft.metabolic.efm.rankup.PreprocessableMatrix#process(ch.javasoft.metabolic.efm.concurrent.RankUpdateToken, ch.javasoft.metabolic.efm.rankup.PreprocessedMatrixFactory) triggered},
a local {@link ch.javasoft.metabolic.efm.rankup.PreprocessedMatrix PreprocessedMatrix}
member contains the calculated values.
- {@link ch.javasoft.metabolic.efm.rankup.PreprocessedMatrix PreprocessedMatrix}
reflects a matrix for which triangularization has been triggered and the
rank for adjacency candidates can be requested.
For implementation details, also see [1].
References
- 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