Closed tonyelewis closed 6 years ago
I've investigated why this is a problem for cath-refine-align
but not cath-superpose
and I've found that it's because the alignment_context
passed to use_all_alignment_outputters()
by cath_superposer::superpose()
here is restricted to the relevant regions, whereas the one passed (to the same function) by cath_align_refiner::refine()
here isn't.
Recent commits (eg 8078efce5f8a29af24c423c15d7b5a68f2658f67) that make this clearer and make it easy to now switch cath-refine-align
over to passing a restricted alignment_context
.
But this raises the issue of why the relevant alignment outputter isn't just getting this right using the alignment_context
it gets given...
Resolved by 3c2c54954f0ee99313fab00dcd42735e3ec06081 and 363bdb0b00ee6e46548fcae09bf23070f6d96382.
But see #48 for other issues arising from this.
Performing the following:
...generates a second alignment file in which the numbering starts at 1, not at the start of the specified domain.