File List

Here is a list of all documented files with brief descriptions:

src/config.h [code]
src/locarna.cc	Defines main function of locarna
src/locarna_p.cc	Defines main function of locarna_p
src/package_constants.hh [code]
src/sparse.cc	Defines main function of SPARSE
src/LocARNA/aligner.hh [code]
src/LocARNA/aligner_impl.hh [code]
src/LocARNA/aligner_n.hh [code]
src/LocARNA/aligner_p.hh [code]
src/LocARNA/aligner_restriction.hh [code]
src/LocARNA/alignment.hh [code]
src/LocARNA/alignment_impl.hh [code]
src/LocARNA/alphabet.hh [code]
src/LocARNA/anchor_constraints.hh [code]
src/LocARNA/arc_matches.hh [code]
src/LocARNA/aux.hh [code]
src/LocARNA/base_pair_filter.hh [code]
src/LocARNA/basepairs.hh [code]
src/LocARNA/confusion_matrix.hh [code]
src/LocARNA/discrete_distribution.hh [code]
src/LocARNA/exact_matcher.hh [code]
src/LocARNA/ext_rna_data.hh [code]
src/LocARNA/ext_rna_data_impl.hh [code]
src/LocARNA/fitonoff.hh [code]
src/LocARNA/global_stopwatch.hh [code]
src/LocARNA/infty_int.hh [code]
src/LocARNA/match_probs.hh [code]
src/LocARNA/matrices.hh [code]
src/LocARNA/matrix.hh [code]
src/LocARNA/mcc_matrices.hh [code]
src/LocARNA/multiple_alignment.hh [code]
src/LocARNA/options.hh [code]	Options -- an interface for getopt_long
src/LocARNA/params.hh [code]
src/LocARNA/pfold_params.hh [code]
src/LocARNA/plusvector.hh [code]
src/LocARNA/ribofit.hh [code]
src/LocARNA/ribosum.hh [code]
src/LocARNA/rna_data.hh [code]
src/LocARNA/rna_data_impl.hh [code]
src/LocARNA/rna_ensemble.hh [code]
src/LocARNA/rna_ensemble_impl.hh [code]
src/LocARNA/rna_structure.hh [code]
src/LocARNA/scoring.hh [code]
src/LocARNA/scoring_fwd.hh [code]
src/LocARNA/sequence.hh [code]
src/LocARNA/sequence_annotation.hh [code]
src/LocARNA/sparse_matrix.hh [code]
src/LocARNA/sparse_vector.hh [code]
src/LocARNA/sparsification_mapper.hh [code]
src/LocARNA/stopwatch.hh [code]
src/LocARNA/stral_score.hh [code]
src/LocARNA/string1.hh [code]
src/LocARNA/trace_controller.hh [code]
src/LocARNA/tuples.hh [code]
src/LocARNA/type_wrapper.hh [code]