Document highlighter plot code locations

[Copilot]

The issue requested locating the highlighter plot code in the repository. This PR documents all files containing highlighter plot implementation and integration.

Key Files Located

Core implementation:

• phylobook/projects/utils/highlighter.py (951 lines)
  • Highlighter class: sequence alignment analysis, mismatch/match detection, APOBEC/G→A mutations, stop codons, glycosylation sites
  • HighlighterPlot class: SVG/PNG generation via ReportLab, LANL/ML color schemes, tree-based sorting

Django integration:

• phylobook/projects/models.py: file naming methods, has_svg_highlighter() plot generation
• phylobook/projects/views.py: highlighter data parsing and serving
• phylobook/projects/templates/displayproject.html: plot rendering with legends
• phylobook/projects/utils/tree.py: SVG generation utilities
• phylobook/projects/management/commands/prerun_svgs.py: batch SVG pregeneration

Architecture

The highlighter plot system analyzes sequence alignments against reference sequences and visualizes mutations as colored marks. Supports both nucleotide and amino acid sequences with configurable color schemes, sorting strategies (similarity/tree-based), and special mutation markers (circles for APOBEC, diamonds for G→A).

# Core usage pattern from models.py:742-778
mutation_plot = highlighter.HighlighterPlot(alignment, seq_type=seq_type, tree=tree)
mutation_plot.draw_mismatches(output_file, apobec=True, g_to_a=True, 
                               glycosylation=True, sort="tree", scheme="LANL")

Original prompt

Search this repo for the code for the highlighter plot

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