Todo List

Class LocARNA::AlignerN

implement noLP in sparse algorithm

Member LocARNA::AlignerP::compute_arcmatch_probabilities ()

check: why is that long double? do we need it? should we rather use pf_t?

Member LocARNA::AnchorConstraints::allowed_del_unopt (size_type i, size_type j) const

profile and potentially optimize

Class LocARNA::MultipleAlignment

constructors ensure name uniqueness; if constructing as alignment of alignments, names are made unique if needed.

because this class does not know whether it contains RNA, it would be useful to have a derived class RNAMultipleAlignment. This class could guarantee that its sequences are normalized RNA sequences. Consequently, we could enforce by the type system that RnaEnsemble is generated only from RNAMultipleAlignment etc.

automatically adapt output width for sequence names to longest name

Member LocARNA::MultipleAlignment::set_annotation (const AnnoType::type &annotype, const SequenceAnnotation &annotation)

check that annotation is valid for multiple alignment; throw failure if annotation is not valid

Member LocARNA::RnaData::read_old_pp (const std::string &filename)

move implementation to impl class

Member LocARNA::RnaData::read_ps (const std::string &filename)

move implementation to impl class

Member LocARNA::RnaData::RnaData (const std::string &filename, double p_bpcut, double max_bps_length_ratio, const PFoldParams &pfoldparams)

consider to allow reading from istream; use istream::seekg(0) to reset stream to beginning (needed for format autodetect.) Is there a problem due to fail on eofbit in C++98?

filter by maxBPspan when reading base pair probabilities from file. currently maxBPspan in pfoldparams is only respected when folding

Member LocARNA::RnaDataImpl::RnaDataImpl (RnaData *self, const RnaData &rna_dataA, const RnaData &rna_dataB, const Alignment::edges_t &alignment, double p_expA, double p_expB)

this constant should be configurable

Class LocARNA::RnaEnsemble

support constraints for in loop probabilities

split up RnaEnsemble into two classes; one with and one without in-loop probabilities (like RnaData and ExtRnaData)

Class LocARNA::RnaStructure

read structure in ct format from stream

Class LocARNA::Scoring

check proper use of unpaired penalty; e.g. is correction needed for arc match (like for lambda)??

Class LocARNA::SparseVector< T >

this code is basically a stripped down version of the SparseMatrix code; likely one could reduce redundancy

Member main (int argc, char **argv)

currently not a command line option of locarna_p

File options.hh

replace by gengetopt