/// \brief TODOCUMENT
void html_ostream_alignment_outputter::do_output_alignment(const alignment_context &arg_alignment_context, ///< TODOCUMENT
ostream &arg_ostream ///< TODOCUMENT
) const {
arg_ostream << html_align_outputter(
arg_alignment_context.get_alignment(),
arg_alignment_context.get_pdbs(),
arg_alignment_context.get_names(),
*colourer_ptr
) << flush;
}
/// \brief TODOCUMENT
void fasta_ostream_alignment_outputter::do_output_alignment(const alignment_context &arg_alignment_context, ///< TODOCUMENT
ostream &arg_ostream ///< TODOCUMENT
) const {
write_alignment_as_fasta_alignment(
arg_ostream,
arg_alignment_context.get_alignment(),
build_protein_list_of_pdb_list_and_names(
arg_alignment_context.get_pdbs(),
arg_alignment_context.get_names()
)
);
}
/// \brief TODOCUMENT
void ssap_ostream_alignment_outputter::do_output_alignment(const alignment_context &arg_alignment_context, ///< TODOCUMENT
ostream &arg_ostream ///< TODOCUMENT
) const {
const alignment the_alignment = arg_alignment_context.get_alignment();
check_alignment_is_a_pair( the_alignment );
const protein_list temp_protein_list = build_protein_list_of_pdb_list_and_names(
arg_alignment_context.get_pdbs(),
arg_alignment_context.get_names()
);
output_alignment_to_cath_ssap_legacy_format(
arg_ostream,
the_alignment,
temp_protein_list[ 0 ],
temp_protein_list[ 1 ]
);
}
/// \brief TODOCUMENT
///
/// \relates viewer
str_vec cath::clean_names_for_viewer(const alignment_context &arg_alignment_context ///< TODOCUMENT
) {
return clean_names_for_viewer( arg_alignment_context.get_names() );
}
