plot_identity_structure() passes outlines instead of mapped to plot_tRNA_structure()

[jmbilodeaux]

Summary

plot_identity_structure() in R/identity.R correctly computes identity element positions into a mapped object, but then calls plot_tRNA_structure() with outlines = outlines instead of outlines = mapped. This means identity element overlays are either silently dropped (if outlines happens to exist in the local environment) or cause an error (if it does not).

Root cause

The function computes:

mapped <- map_identity_to_trna(...)   # identity element positions

But the downstream call is:

plot_tRNA_structure(..., outlines = outlines)   # wrong variable

outlines is not assigned anywhere in plot_identity_structure(), so this either resolves to an accidental outer-scope binding or throws an object-not-found error.

Suggested fix

Change outlines = outlines to outlines = mapped in the plot_tRNA_structure() call inside plot_identity_structure().

cc @jayhesselberth for review

[jayhesselberth]

This doens't seem broken to me, do you have a reprex for something you're seeing?