ARB: BI_helix Class Reference

ARB

#include <BI_helix.hxx>

Inheritance diagram for BI_helix:

Inheritance graph

Collaboration diagram for BI_helix:

Collaboration graph

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	initFromData (const char helix_nr, const char helix, size_t size)

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

bool	is_pairpos (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 ()

Detailed Description

Definition at line 85 of file BI_helix.hxx.

Constructor & Destructor Documentation

BI_helix::BI_helix ( )

Definition at line 122 of file BI_helix.cxx.

References NULp.

BI_helix::~BI_helix ( )

Definition at line 127 of file BI_helix.cxx.

Member Function Documentation

static GB_ERROR BI_helix::get_error ( )

inlinestatic

Definition at line 96 of file BI_helix.hxx.

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

GB_ERROR BI_helix::init ( GBDATA * gb_main )

Definition at line 327 of file BI_helix.cxx.

References alignment_name, GB_await_error(), GBT_get_default_alignment(), get_error(), and ta.

Referenced by ARB_main(), ColumnStat::calculate(), ED4_alignment_length_changed(), and reload_helix_cb().

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

Definition at line 292 of file BI_helix.cxx.

References GB_await_error(), GB_read_char_pntr(), GBS_global_string(), GBT_find_SAI_rel_SAI_data(), GBT_find_sequence(), GBT_get_alignment_len(), GBT_get_default_helix(), GBT_get_default_helix_nr(), GBT_get_SAI_data(), get_error(), initFromData(), NULp, and ta.

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

Definition at line 158 of file BI_helix.cxx.

References BI_helix_entry::allocated, ARB_alloc(), arb_assert, 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(), BI_helix_entry::helix_nr, BI_helix_entry::is_pairpos, LEFT_HELIX, helix_stack::next, NULp, BI_helix_entry::pair_pos, helix_stack::pos, and RIGHT_HELIX.

Referenced by init().

size_t BI_helix::size ( ) const

inline

Definition at line 105 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 106 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 107 of file BI_helix.hxx.

References bi_assert.

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

size_t BI_helix::opposite_position ( size_t pos ) const

inline

Definition at line 113 of file BI_helix.hxx.

References bi_assert, entry(), is_pairpos(), and BI_helix_entry::pair_pos.

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().

bool BI_helix::is_pairpos ( size_t pos ) const

inline

Definition at line 117 of file BI_helix.hxx.

References entry(), and BI_helix_entry::is_pairpos.

Referenced by SEC_region::align_helix_strands(), ColumnStat::calculate(), ED4_helix_jump_opposite(), ED4_show_helix_on_device(), helixNr(), SEC_root::is_pairpos(), next_pair_position(), old_decode_xstring_rel_helix(), opposite_position(), 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 118 of file BI_helix.hxx.

References entry(), BI_helix_entry::helix_nr, is_pairpos(), and NULp.

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 342 of file BI_helix.cxx.

References BI_helix_entry::is_pairpos, and next_pair_position().

Referenced by findLongestHelix(), and first_position().

long BI_helix::next_pair_position ( size_t pos ) const

Definition at line 346 of file BI_helix.cxx.

References bi_assert, is_pairpos(), 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 369 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 377 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().

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

SL/HELIX/BI_helix.hxx
SL/HELIX/BI_helix.cxx