ARB
Public Member Functions | Static Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
BI_helix Class Reference

#include <BI_helix.hxx>

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Public Member Functions

 BI_helix ()
 
 ~BI_helix ()
 
const char * init (GBDATA *gb_main)
 
const char * init (GBDATA *gb_main, const char *alignment_name)
 
const char * init (GBDATA *gb_helix_nr, GBDATA *gb_helix, size_t size)
 
const char * 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 char * get_error ()
 
static void clear_error ()
 
static void set_error (const char *err)
 

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]
 

Detailed Description

Definition at line 55 of file BI_helix.hxx.

Constructor & Destructor Documentation

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.

References char_bind, HELIX_MAX, and pairs.

Member Function Documentation

bool BI_helix::is_pairtype ( char  left,
char  right,
BI_PAIR_TYPE  pair_type 
)
protected

Definition at line 311 of file BI_helix.cxx.

References pairs.

Referenced by check_pair(), and AW_helix::get_symbol().

static char* BI_helix::get_error ( )
inlinestatic

Definition at line 74 of file BI_helix.hxx.

Referenced by SEC_region::align_helix_strands(), BI_helix_check_error(), init(), initFromData(), and SEC_root::paint().

static void BI_helix::clear_error ( )
inlinestatic

Definition at line 75 of file BI_helix.hxx.

Referenced by init(), and initFromData().

static void BI_helix::set_error ( const char *  err)
inlinestatic

Definition at line 76 of file BI_helix.hxx.

Referenced by BI_helix_check_error(), and init().

const char * BI_helix::init ( GBDATA *  gb_main)

Definition at line 301 of file BI_helix.cxx.

References GBT_get_default_alignment(), init, and ta.

Referenced by ARB_main(), ED4_alignment_length_changed(), and reload_helix_cb().

const char * BI_helix::init ( GBDATA *  gb_main,
const char *  alignment_name 
)

Definition at line 287 of file BI_helix.cxx.

References GBT_get_default_helix(), GBT_get_default_helix_nr(), init, and ta.

const char * BI_helix::init ( GBDATA *  gb_helix_nr,
GBDATA *  gb_helix,
size_t  size 
)

Definition at line 249 of file BI_helix.cxx.

References clear_error(), GB_read_char_pntr(), get_error(), initFromData(), set_error(), and ta.

const char * BI_helix::initFromData ( const char *  helix_nr,
const char *  helix,
size_t  size 
)

Definition at line 115 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, clear_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 322 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().

size_t BI_helix::size ( ) const
inline

Definition at line 88 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().

bool BI_helix::has_entries ( ) const
inline

Definition at line 89 of file BI_helix.hxx.

Referenced by ED4_set_helixnr(), and SQ_helix::SQ_calc_helix_layout().

const BI_helix_entry& BI_helix::entry ( size_t  pos) const
inline

Definition at line 90 of file BI_helix.hxx.

References bi_assert.

Referenced by helixNr(), opposite_position(), and pairtype().

size_t BI_helix::opposite_position ( size_t  pos) const
inline

Definition at line 96 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().

BI_PAIR_TYPE BI_helix::pairtype ( size_t  pos) const
inline

Definition at line 101 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().

const char* BI_helix::helixNr ( size_t  pos) const
inline

Definition at line 102 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 348 of file BI_helix.cxx.

References HELIX_NONE, next_pair_position(), and BI_helix_entry::pair_type.

Referenced by findLongestHelix(), and first_position().

long BI_helix::next_pair_position ( size_t  pos) const

Definition at line 352 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().

long BI_helix::first_position ( const char *  helixNr) const

Definition at line 375 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().

long BI_helix::last_position ( const char *  helixNr) const

Definition at line 383 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().

Member Data Documentation

char* BI_helix::pairs[HELIX_MAX]
protected

Definition at line 67 of file BI_helix.hxx.

Referenced by AW_helix::AW_helix(), is_pairtype(), and ~BI_helix().

char* BI_helix::char_bind[HELIX_MAX]
protected

Definition at line 68 of file BI_helix.hxx.

Referenced by AW_helix::AW_helix(), AW_helix::get_symbol(), and ~BI_helix().

The documentation for this class was generated from the following files:
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