ARB: SEC_region Class Reference

ARB

#include <SEC_root.hxx>

Inheritance diagram for SEC_region:

Inheritance graph

Collaboration diagram for SEC_region:

Collaboration graph

Public Member Functions
	SEC_region (int start, int end)

virtual	~SEC_region ()

void	save (std::ostream &out, int indent, const XString &x_string)

GB_ERROR	read (std::istream &in, SEC_root *root, int version)

void	update_base_count (SEC_root *root)

void	invalidate_base_count ()

int	get_sequence_start () const

int	get_sequence_end () const

int	get_base_count () const

bool	contains_seq_position (int pos) const

void	set_sequence_portion (int start, int end)

void	generate_x_string (XString &x_string)

void	align_helix_strands (SEC_root root, SEC_region other_region)

int	getBasePos (int basenr) const

Detailed Description

Definition at line 73 of file SEC_root.hxx.

Constructor & Destructor Documentation

SEC_region::SEC_region	(	int	start,
		int	end
	)

Definition at line 89 of file SEC_structure.cxx.

References sec_assert.

SEC_region::~SEC_region ( )

virtual

Definition at line 101 of file SEC_structure.cxx.

References invalidate_base_count().

Member Function Documentation

void SEC_region::save	(	std::ostream &	out,
		int	indent,
		const XString &	x_string
	)

Definition at line 73 of file SEC_io.cxx.

References do_indent(), and XString::getXleftOf().

GB_ERROR SEC_region::read	(	std::istream &	in,
		SEC_root *	root,
		int	version
	)

Definition at line 125 of file SEC_read.cxx.

References SEC_db_interface::canDisplay(), error(), GBS_global_string(), SEC_root::get_db(), SEC_root::get_xString(), XString::getAbsPos(), XString::getXcount(), sec_assert, sec_expect_keyword_and_ints(), and sec_read_line().

void SEC_region::update_base_count ( SEC_root * root )

inline

Definition at line 103 of file SEC_root.hxx.

References count_bases().

void SEC_region::invalidate_base_count ( )

Definition at line 266 of file SEC_layout.cxx.

References NULp.

Referenced by SEC_root::invalidate_base_positions(), and ~SEC_region().

int SEC_region::get_sequence_start ( ) const

inline

Definition at line 107 of file SEC_root.hxx.

Referenced by are_adjacent_regions(), SEC_root::find(), and SEC_base_part::getNextAbspos().

int SEC_region::get_sequence_end ( ) const

inline

Definition at line 108 of file SEC_root.hxx.

Referenced by are_adjacent_regions(), SEC_root::find(), and SEC_base_part::getNextAbspos().

int SEC_region::get_base_count ( ) const

inline

Definition at line 110 of file SEC_root.hxx.

References sec_assert.

Referenced by FINAL_TYPE< SEQTYPE >::rightAttachAbspos().

bool SEC_region::contains_seq_position ( int pos ) const

inline

Definition at line 112 of file SEC_root.hxx.

Referenced by SEC_root::find().

void SEC_region::set_sequence_portion	(	int	start,
		int	end
	)

inline

Definition at line 119 of file SEC_root.hxx.

References start.

void SEC_region::generate_x_string ( XString & x_string )

Definition at line 19 of file SEC_io.cxx.

References XString::addXpair().

void SEC_region::align_helix_strands	(	SEC_root *	root,
		SEC_region *	other_region
	)

Definition at line 1125 of file SEC_paint.cxx.

References aw_message(), error(), GBS_global_string(), BI_helix::get_error(), SEC_root::get_helixDef(), BI_helix::helixNr(), BI_helix::is_pairpos(), NULp, BI_helix::opposite_position(), sec_assert, and swap().

int SEC_region::getBasePos ( int basenr ) const

inline

Definition at line 127 of file SEC_root.hxx.

References sec_assert.

Referenced by FINAL_TYPE< SEQTYPE >::rightAttachAbspos().

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

SECEDIT/SEC_root.hxx
SECEDIT/SEC_io.cxx
SECEDIT/SEC_layout.cxx
SECEDIT/SEC_paint.cxx
SECEDIT/SEC_read.cxx
SECEDIT/SEC_structure.cxx