16 #include "../../lib/utils/Matrix.hpp"
23 Opt_general() : sequence_f(
""), domain_f(
""), mda_out_f(
""), msa_out_f(
""), out_msa_format(
""), make_msa(
false), domain_program(
""), domain_database(
""), n_threads(0)
25 std::string sequence_f;
27 std::string mda_out_f;
28 std::string msa_out_f;
29 std::string out_msa_format;
31 std::string domain_program;
32 std::string domain_database;
41 Opt_msa() : gop(0), gep(0), simmat_name(
""), sim_mat(
nullptr)
51 std::string simmat_name;
61 Opt_dom() : use_envelope(
false), no_merging(
false), refine_boundaries(
false), collapse_repeats(
false)
66 bool refine_boundaries;
67 bool collapse_repeats;