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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 ()
 
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_entryentry (size_t pos) const
 
size_t opposite_position (size_t pos) const
 
BI_PAIR_TYPE pairtype (size_t pos) const
 
const charhelixNr (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

charpairs [HELIX_MAX]
 
charchar_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 321 of file BI_helix.cxx.

References pairs.

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

static GB_ERROR BI_helix::get_error ( )
inlinestatic

Definition at line 77 of file BI_helix.hxx.

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

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

Definition at line 292 of file BI_helix.cxx.

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

GB_ERROR BI_helix::init ( GBDATA gb_helix_nr,
GBDATA gb_helix,
size_t  size 
)

Definition at line 254 of file BI_helix.cxx.

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

GB_ERROR BI_helix::initFromData ( const char helix_nr,
const char helix,
size_t  size 
)
int BI_helix::check_pair ( char  left,
char  right,
BI_PAIR_TYPE  pair_type 
)
size_t BI_helix::size ( ) const
inline
bool BI_helix::has_entries ( ) const
inline

Definition at line 90 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 91 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
BI_PAIR_TYPE BI_helix::pairtype ( size_t  pos) const
inline
const char* BI_helix::helixNr ( size_t  pos) const
inline
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().

long BI_helix::next_pair_position ( size_t  pos) const
long BI_helix::first_position ( const char helixNr) const
long BI_helix::last_position ( const char helixNr) const

Member Data Documentation

char* BI_helix::pairs[HELIX_MAX]
protected

Definition at line 70 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 71 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: