Enhance auto layout with RNApuzzler, covariation rectangles, and font adjustments#209
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AntonPetrov merged 7 commits intomainfrom Mar 29, 2026
Merged
Enhance auto layout with RNApuzzler, covariation rectangles, and font adjustments#209AntonPetrov merged 7 commits intomainfrom
AntonPetrov merged 7 commits intomainfrom
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Run RNApuzzler as part of the template-free auto layout selection and adjust ordering/selection logic. The puzzler run is now executed (with work/result folders created and exceptions handled), its overlap count compared alongside R2R and RNArtist, and candidate ordering/printing updated. The CLI --auto option is changed to --auto/--no-auto and defaults to true; auto mode only runs when no specific engine is chosen. Added example input (examples/rnapuzzler-auto.fasta) and expected SVG fixture (tests/examples/rnapuzzler-auto/9ZCC.colored.svg) and updated tests accordingly.
Draw coloured rectangles spanning both nucleotides of a base pair instead of per-nucleotide circles. Dual rectangles are drawn when a pair has both pair-level (dark green) and helix-level (light green) covariation signals.
Scale nucleotide font size based on median nearest-neighbour spacing: new_font = max(current, min(20, max(2, 0.56 * median_nn))) Never decreases existing fonts. Replaces the old nucleotide-count heuristic that only ran for Rfam/GtRNAdb.
Update documentation to describe rectangle-based visualization. Regenerate 9LEL images with rectangles and adjusted font size (14px).
ViennaRNA's RNA.svg_rna_plot produces nan coordinates for hairpin loops with fewer than 3 unpaired bases (e.g. '()' or '(.)'). Add _remove_small_hairpins() to iteratively strip such pairs before layout generation. Both template and target FASTA files are kept in sync so Traveler does not attempt to draw pairs without coordinates. Add _write_linear_colored_svg() fallback for when hairpin removal strips all base pairs, producing a Traveler-compatible SVG directly from ViennaRNA coordinates. Update 9MME reference SVG to reflect font-size adjustment.
Split normalization into two structures: layout_structure (all bracket types mapped to () for ViennaRNA coordinate generation) and template_structure (only original () retained; other brackets become dots so Traveler sees the same pair-tree topology). Apply small-hairpin removal to both, detect removed pairs by comparing against the original ()-only template, and write the template FASTA using template_structure. This preserves pseudoknot rendering in the final target while ensuring coordinates and template topology match.
Improve R-scape alignment processing
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