ARB
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#include <BI_helix.hxx>
Public Member Functions | |
BI_helix () | |
~BI_helix () | |
GB_ERROR | init (GBDATA *gb_main) |
GB_ERROR | init (GBDATA *gb_main, const char *alignment_name) |
GB_ERROR | init (GBDATA *gb_helix_nr, GBDATA *gb_helix, size_t size) |
GB_ERROR | initFromData (const char *helix_nr, const char *helix, size_t size) |
int | check_pair (char left, char right, BI_PAIR_TYPE pair_type) |
size_t | size () const |
bool | has_entries () const |
const BI_helix_entry & | entry (size_t pos) const |
size_t | opposite_position (size_t pos) const |
BI_PAIR_TYPE | pairtype (size_t pos) const |
const char * | helixNr (size_t pos) const |
long | first_pair_position () const |
long | next_pair_position (size_t pos) const |
long | first_position (const char *helixNr) const |
long | last_position (const char *helixNr) const |
Static Public Member Functions | |
static GB_ERROR | get_error () |
Protected Member Functions | |
bool | is_pairtype (char left, char right, BI_PAIR_TYPE pair_type) |
Protected Attributes | |
char * | pairs [HELIX_MAX] |
char * | char_bind [HELIX_MAX] |
Definition at line 55 of file BI_helix.hxx.
BI_helix::BI_helix | ( | ) |
Definition at line 78 of file BI_helix.cxx.
BI_helix::~BI_helix | ( | ) |
Definition at line 82 of file BI_helix.cxx.
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protected |
Definition at line 321 of file BI_helix.cxx.
References pairs.
Referenced by check_pair(), and AW_helix::get_symbol().
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inlinestatic |
Definition at line 77 of file BI_helix.hxx.
Referenced by SEC_region::align_helix_strands(), init(), initFromData(), and SEC_root::paint().
Definition at line 306 of file BI_helix.cxx.
References GB_await_error(), GBT_get_default_alignment(), get_error(), init, and ta.
Referenced by ARB_main(), ED4_alignment_length_changed(), and reload_helix_cb().
Definition at line 292 of file BI_helix.cxx.
References GBT_get_default_helix(), GBT_get_default_helix_nr(), get_error(), init, and ta.
Definition at line 254 of file BI_helix.cxx.
References GB_read_char_pntr(), get_error(), initFromData(), and ta.
Definition at line 116 of file BI_helix.cxx.
References BI_helix_entry::allocated, ARB_alloc(), ARB_calloc(), bi_assert, BI_helix_check_error(), BI_helix_free_hash(), helix_stack::c, error(), GB_IGNORE_CASE, GBS_create_hash(), GBS_free_hash(), GBS_global_string_copy(), GBS_hash_do_const_loop(), GBS_hash_do_loop(), GBS_read_hash(), GBS_write_hash(), get_error(), HELIX_NO_PAIR, HELIX_NON_STANDARD0, BI_helix_entry::helix_nr, HELIX_PAIR, LEFT_HELIX, LEFT_NONS, helix_stack::next, NULp, BI_helix_entry::pair_pos, BI_helix_entry::pair_type, helix_stack::pos, RIGHT_HELIX, and RIGHT_NONS.
Referenced by init().
int BI_helix::check_pair | ( | char | left, |
char | right, | ||
BI_PAIR_TYPE | pair_type | ||
) |
Definition at line 332 of file BI_helix.cxx.
References HELIX_NO_PAIR, HELIX_PAIR, HELIX_STRONG_PAIR, HELIX_WEAK_PAIR, and is_pairtype().
Referenced by SQ_helix::SQ_calc_helix_layout().
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inline |
Definition at line 89 of file BI_helix.hxx.
Referenced by add_area_for_gde(), AW_helix::is_enabled(), old_decode_xstring_rel_helix(), and AW_helix::seq_2_helix().
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inline |
Definition at line 90 of file BI_helix.hxx.
Referenced by ED4_set_helixnr(), and SQ_helix::SQ_calc_helix_layout().
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inline |
Definition at line 91 of file BI_helix.hxx.
References bi_assert.
Referenced by helixNr(), opposite_position(), and pairtype().
Definition at line 97 of file BI_helix.hxx.
References bi_assert, entry(), HELIX_NONE, BI_helix_entry::pair_pos, and BI_helix_entry::pair_type.
Referenced by SEC_region::align_helix_strands(), ED4_helix_jump_opposite(), ED4_show_helix_on_device(), findLongestHelix(), SEC_root::getHelixPositions(), AW_helix::seq_2_helix(), SQ_helix::SQ_calc_helix_layout(), and SEC_db_interface::update_shown_positions().
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inline |
Definition at line 102 of file BI_helix.hxx.
References entry(), HELIX_NONE, and BI_helix_entry::pair_type.
Referenced by SEC_region::align_helix_strands(), ColumnStat::calculate(), ED4_helix_jump_opposite(), ED4_show_helix_on_device(), SEC_root::getBondtype(), helixNr(), old_decode_xstring_rel_helix(), SEC_xstring_to_foldedHelixList(), AW_helix::seq_2_helix(), SQ_helix::SQ_calc_helix_layout(), and SEC_db_interface::update_shown_positions().
Definition at line 103 of file BI_helix.hxx.
References entry(), HELIX_NONE, BI_helix_entry::helix_nr, NULp, and pairtype().
Referenced by SEC_region::align_helix_strands(), findLongestHelix(), old_decode_xstring_rel_helix(), and SEC_xstring_to_foldedHelixList().
long BI_helix::first_pair_position | ( | ) | const |
Definition at line 358 of file BI_helix.cxx.
References HELIX_NONE, next_pair_position(), and BI_helix_entry::pair_type.
Referenced by findLongestHelix(), and first_position().
Definition at line 362 of file BI_helix.cxx.
References bi_assert, HELIX_NONE, BI_helix_entry::next_pair_pos, and helix_stack::pos.
Referenced by findLongestHelix(), first_pair_position(), first_position(), and last_position().
Definition at line 385 of file BI_helix.cxx.
References first_pair_position(), next_pair_position(), and helix_stack::pos.
Referenced by ED4_set_helixnr(), findLongestHelix(), SEC_root::getHelixPositions(), last_position(), and SEC_foldedHelixList_to_xstring().
Definition at line 393 of file BI_helix.cxx.
References first_position(), next_pair_position(), and helix_stack::pos.
Referenced by findLongestHelix(), SEC_root::getHelixPositions(), and SEC_foldedHelixList_to_xstring().
Definition at line 70 of file BI_helix.hxx.
Referenced by AW_helix::AW_helix(), is_pairtype(), and ~BI_helix().
Definition at line 71 of file BI_helix.hxx.
Referenced by AW_helix::AW_helix(), AW_helix::get_symbol(), and ~BI_helix().