Changes in version 1.2.2 (2024-10-24)                  

Fixed:

  - Using unsigned LenSq in loops.

                 Changes in version 1.2.1 (2024-10-06)                  

Fixed:

  - fixed incorrect codons
  - add explicit casting of alphabet during construction of sequence
    prototype (fixes issues with new implementation of union())
  - add skips for tests that use not available packages from "Suggests"

                        Changes in version 1.2.0                        

New features:

  - write_fasta() and find_motifs() accept data.frame arguments now;
    sequences and their names are taken from specified two columns
  - more descriptive error messages for non-existing generics that print
    out classes of the first parameter

Fixed:

  - return to automatically exported Rcpp catch declaration

Quality of code stuff:

  - added tests and adjusted vignettes for the changes

                 Changes in version 1.1.3 (2022-01-31)                  

Fixed:

  - replaced deprecated use of iterator

                Changes in version 1.1.2-1 (2021-07-27)                 

Fixed:

  - adjusted declaration of function autoexported by Rcpp to match new
    testthat standards

                        Changes in version 1.1.2                        

Fixed:

  - early return now works correctly for remove_ambiguous()
  - ensured correct order of operations during sequence packing
  - changed some values to unsigned wherever there was a mismatch

                        Changes in version 1.1.1                        

Updates for the CRAN god. Fixed random_sq() out-of-bounds possible
problem, so there may be differences in sequences generated using the
same seed in this and previous versions.

Fixed:

  - upper bound for random_sq() correctly ignores now "*" and "-" values
    while computing number of letters to draw from
  - removed default move/copy constructors/assignment operators for
    Sequence and ProtoSequence classes
  - lots of technical files cleanup

                 Changes in version 1.1.0 (2021-03-12)                  

Expanded on v1.0.0, having implemented functions paste() and collapse()
that allow the user to connect multiple sequences into one. Also made
some optimization within C++ using templates, speeding up translate()
and complement() functions significantly. Lastly, added support for
object from bioseq package.

Breaking changes:

  - dropped argument interpret_as_stop from translate() function, as it
    is not feasible to implement well-working translation rules for
    tables with ambiguous codons (27, 28 & 31)

New features:

  - implemented paste() (a method for sq class)
  - implemented collapse()
  - added support for classes from bioseq package, i.e. bioseq_aa,
    bioseq_dna and bioseq_rna

Improved:

  - remade translate() to have codon tables created in compile time;
    this reduced execution time of translate() by 95%
  - remade complement() to have tables created in compile time; this
    reduced execution time of complement() by 85%

Fixed:

  - made random_sq() actually use seed parameter while generating
    sequences

                        Changes in version 1.0.0                        

Initial stable release.