Changes in version 2025-10-21 (2025-10-21)               

Fixed

  - Example and test errors related to internal helpers
    (compareAndColorSequences(), compute_cache()) now handled safely
    using \dontrun{} and updated documentation.
  - Removed outdated License stub issue and corrected DESCRIPTION
    metadata formatting.
  - Corrected internal tests referencing deprecated
    testthat::local_null_device().

Improved

  - CountSNPs() re-implementation: directly computes pairwise SNP counts
    without relying on model-based rounding (e.g., from MSA2dist). No
    rounding artifacts

               Changes in version 2025-10-01 (2025-10-01)               

Added

  - New function: alignToRefs(), which aligns user sequences to the
    packaged rhinovirus prototype references using msa::msa() (ClustalW,
    ClustalOmega, or MUSCLE), with an option to trim alignments to the
    non-gap span of a chosen reference.

Improved

  - SNPeek() and plotAA(): now support zooming to specific genomic
    regions and highlighting individual sequences of interest.
  - assignTypes(): now reports the genetic distance to the nearest
    prototype even when the query is "unassigned".
  - Distance calculation: switched to using MSA2dist for pairwise
    distance computation. This provides broader model support — access
    to all substitution models in ape::dist.dna, in addition to the
    "IUPAC" model.
  - Data access: prototype and example datasets are now exported as
    packaged objects (rhinovirusVP4, rhinovirusPrototypesVP4) instead of
    being accessed via system.file(), simplifying workflows.
  - Improved documentation:
      - Improved explanations and runnable examples added where
        feasible.
      - Visualization functions return results invisibly to avoid
        console clutter, while still allowing advanced users to capture
        outputs.
  - Code style and formatting improved (e.g.,consistent internal
    helpers).

                        Changes in version 0.1.0                        

  - First public release of rhinotypeR.
  - Implements VP4/2-based rhinovirus genotyping workflow.
  - Provides bundled prototype reference sequences and example datasets.