SEC_root Class Reference

#include <SEC_root.hxx>

Inheritance diagram for SEC_root:

Collaboration diagram for SEC_root:

Public Member Functions
	SEC_root ()
	~SEC_root ()
void	init (SEC_graphic *gfx, AWT_canvas *scr, ED4_plugin_host &host)
bool	under_construction () const
void	set_under_construction (bool construct)
const SEC_db_interface *	get_db () const
const ED4_plugin_host &	host () const
bool	canDisplay () const
const BI_helix *	get_helixDef () const
bool	is_pairpos (int abspos) const
const char *	helixNrAt (int abspos) const
const size_t *	getHelixPositions (const char *helixNr) const
const double &	get_char_radius (int gc) const
void	reread_display_params (AW_root *aw_root, const ED4_plugin_host &Host)
const SEC_displayParams &	display_params () const
bool	has_xString () const
const XString &	get_xString () const
void	paintBackgroundColor (AW_device *device, SEC_bgpaint_mode mode, const Position &p1, int color1, int gc1, const Position &p2, int color2, int gc2, int skel_gc)
void	paintSearchPatternStrings (AW_device *device, int clickedPos, AW_pos xPos, AW_pos yPos)
char *	buildStructureString ()
GB_ERROR	read_data (const char *input_string, const char *x_string_in)
void	add_autoscroll (const Vector &scroll)
void	nail_position (size_t absPos)
void	nail_cursor ()
void	position_cursor (bool toCenter, bool evenIfVisible)
void	set_cursor (int abspos)
bool	perform_autoscroll ()
void	recalc ()
void	relayout ()
GB_ERROR	split_loop (int start1, int end1, int start2, int end2)
GB_ERROR	paint (AW_device *device)
GB_ERROR	unsplit_loop (SEC_helix_strand *delete_strand)
void	set_root (SEC_loop *loop)
void	create_default_bone ()
void	generate_x_string ()
void	update_shown_positions ()
bool	shallDisplayPosition (int abspos) const
void	invalidate_base_positions ()
int	getBackgroundColor (int abspos)
const Vector &	get_center_char_vector (int gc)
size_t	max_index ()
int	get_cursor () const
SEC_loop *	get_root_loop () const
void	set_root_loop (SEC_loop *loop)
SEC_BASE_TYPE	get_show_constraints ()
void	set_show_constraints (SEC_BASE_TYPE show)
void	set_last_drawed_cursor_position (const LineVector &line)
const LineVector &	get_last_drawed_cursor_position () const
void	clear_last_drawed_cursor_position ()
SEC_base_part *	find (int pos)
void	announce_base_position (int base_pos, const Position &draw_pos)
void	clear_announced_positions ()
const AW_font_group &	get_font_group () const
void	paintAnnotation (AW_device *device, int gc, const Position &annotate, const Position &left, const Position &right, double noteDistance, const char *text, bool lineToAnnotated, bool linesToLeftRight, bool boxText)
void	paintPosAnnotation (AW_device *device, int gc, size_t absPos, const char *text, bool lineToBase, bool boxText)
double	get_bondThickWorld () const

Detailed Description

Definition at line 679 of file SEC_root.hxx.

Constructor & Destructor Documentation

SEC_root::SEC_root

(

)

Definition at line 63 of file SEC_structure.cxx.

References SEC_GC_DATA_COUNT.

SEC_root::~SEC_root

(

)

Definition at line 168 of file SEC_structure.cxx.

Member Function Documentation

void SEC_root::init	(	SEC_graphic *	gfx,
		AWT_canvas *	scr,
		ED4_plugin_host &	host
	)

Definition at line 82 of file SEC_structure.cxx.

Referenced by start_SECEDIT_plugin().

bool SEC_root::under_construction ( ) const

inline

Definition at line 744 of file SEC_root.hxx.

void SEC_root::set_under_construction ( bool  construct )

inline

Definition at line 745 of file SEC_root.hxx.

Referenced by create_default_bone().

const SEC_db_interface* SEC_root::get_db ( ) const

inline

Definition at line 747 of file SEC_root.hxx.

Referenced by SEC_region::read(), sec_mode_event(), and start_SECEDIT_plugin().

const ED4_plugin_host& SEC_root::host ( ) const

inline

Definition at line 748 of file SEC_root.hxx.

References SEC_db_interface::host().

bool SEC_root::canDisplay ( ) const

inline

Definition at line 749 of file SEC_root.hxx.

References SEC_db_interface::canDisplay().

const BI_helix* SEC_root::get_helixDef ( ) const

inline

Definition at line 750 of file SEC_root.hxx.

References SEC_db_interface::helix(), and sec_assert.

Referenced by SEC_region::align_helix_strands(), create_default_bone(), export_structure_to_file(), and import_structure_from_file().

bool SEC_root::is_pairpos ( int  abspos ) const

inline

Definition at line 751 of file SEC_root.hxx.

References BI_helix::is_pairpos().

const char* SEC_root::helixNrAt ( int  abspos ) const

inline

Definition at line 755 of file SEC_root.hxx.

const size_t * SEC_root::getHelixPositions

(

const char *

helixNr

)

const

Definition at line 19 of file SEC_helix.cxx.

References BI_helix::first_position(), BI_helix::last_position(), NULp, BI_helix::opposite_position(), and sec_assert.

const double& SEC_root::get_char_radius ( int  gc ) const

inline

Definition at line 758 of file SEC_root.hxx.

void SEC_root::reread_display_params ( AW_root *  aw_root, const ED4_plugin_host &  Host  )

inline

Definition at line 760 of file SEC_root.hxx.

References SEC_displayParams::reread().

const SEC_displayParams& SEC_root::display_params ( ) const

inline

Definition at line 761 of file SEC_root.hxx.

bool SEC_root::has_xString ( ) const

inline

Definition at line 763 of file SEC_root.hxx.

Referenced by import_structure_from_file().

const XString& SEC_root::get_xString ( ) const

inline

Definition at line 764 of file SEC_root.hxx.

References sec_assert.

Referenced by export_structure_to_file(), import_structure_from_file(), and SEC_region::read().

void SEC_root::paintBackgroundColor	(	AW_device *	device,
		SEC_bgpaint_mode	mode,
		const Position &	p1,
		int	color1,
		int	gc1,
		const Position &	p2,
		int	color2,
		int	gc2,
		int	skel_gc
	)

Definition at line 400 of file SEC_paint.cxx.

References AW_SOLID, BG_PAINT_FIRST, BG_PAINT_SECOND, AW_device::circle(), PaintData::convert_BackgroundGC(), PaintData::get_linePropertyGC(), AW::Vector::length(), AW_device::line(), sec_assert, AW_stylable::set_line_attributes(), AW::FillStyle::SOLID, arb_test::space(), and valid_cb_params().

void SEC_root::paintSearchPatternStrings	(	AW_device *	device,
		int	clickedPos,
		AW_pos	xPos,
		AW_pos	yPos
	)

Definition at line 463 of file SEC_paint.cxx.

References aw_message(), AW_SCREEN, SEC_GC_SBACK_0, SEC_GC_SBACK_8, and AW_device::text().

char * SEC_root::buildStructureString

(

)

Definition at line 108 of file SEC_io.cxx.

References DATA_VERSION, NULp, and result.

Referenced by export_structure_to_file().

GB_ERROR SEC_root::read_data	(	const char *	input_string,
		const char *	x_string_in
	)

Definition at line 367 of file SEC_read.cxx.

References DATA_VERSION, error(), GBS_global_string(), XString::getLength(), M_PI, NULp, sec_assert, sec_expect_keyword_and_doubles(), sec_expect_keyword_and_ints(), and sec_read_line().

void SEC_root::add_autoscroll

(

const Vector &

scroll

)

Definition at line 69 of file SEC_main.cxx.

Referenced by perform_autoscroll().

void SEC_root::nail_position

(

size_t

absPos

)

Definition at line 52 of file SEC_main.cxx.

References SEC_drawn_positions::drawn_at().

void SEC_root::nail_cursor

(

)

Definition at line 59 of file SEC_main.cxx.

References abs, SEC_drawn_positions::drawn_after(), and SEC_drawn_positions::empty().

void SEC_root::position_cursor	(	bool	toCenter,
		bool	evenIfVisible
	)

Definition at line 140 of file SEC_main.cxx.

References AW_MIDDLE_AREA, SEC_db_interface::canvas(), AW_device::get_area_size(), get_last_drawed_cursor_position(), AW::INCLUSIVE_OUTLINE, perform_autoscroll(), sec_assert, AW_zoomable::transform(), and AW::LineVector::valid().

Referenced by SEC_center_cb().

void SEC_root::set_cursor

(

int

abspos

)

Definition at line 227 of file SEC_db.cxx.

bool SEC_root::perform_autoscroll

(

)

Definition at line 74 of file SEC_main.cxx.

References add_autoscroll(), AW_MIDDLE_AREA, AWT_canvas::aww, SEC_db_interface::canvas(), AW_device::clear(), SEC_drawn_positions::drawn_at(), AWT_graphic::exports, AW_window::get_device(), AWT_graphic_exports::get_modifying_flag_ref(), AWT_canvas::gfx, AWT_canvas::init_device(), NULp, AWT_canvas::scroll(), AW_zoomable::transform(), AWT_graphic_exports::update_display_as_requested(), AW::Vector::x(), AW::Position::xpos(), AW::Vector::y(), and AW::Position::ypos().

Referenced by position_cursor().

void SEC_root::recalc ( )

inline

Definition at line 803 of file SEC_root.hxx.

void SEC_root::relayout ( )

inline

Definition at line 806 of file SEC_root.hxx.

Referenced by create_default_bone().

GB_ERROR SEC_root::split_loop	(	int	start1,
		int	end1,
		int	start2,
		int	end2
	)

Definition at line 212 of file SEC_split.cxx.

References are_adjacent_regions(), BUFFER_CENTER_RELATIVE, error(), findSegmentContaining(), GBS_global_string(), NULp, AngleBuffer::restoreAll(), s, sec_assert, AngleBuffer::set_angle(), AngleBuffer::storeAllHelices(), and swap().

GB_ERROR SEC_root::paint

(

AW_device *

device

)

Definition at line 971 of file SEC_paint.cxx.

References BasePosition::abs_2_rel(), AW_ALL_DEVICES_UNSCALED, AW_DASHED, AW_PRINTER, AW_PRINTER_EXT, AW_SOLID, AW_device::box(), AW::centroid(), SEC_db_interface::ecoli(), AW::FillStyle::EMPTY, error(), GBS_global_string(), BI_helix::get_error(), AW_device::get_filter(), AW::LineVector::head(), AW::hypotenuse(), info2bio(), AW::Vector::length(), AW_device::line(), max, mid(), SEC_structure_toggler::name(), pos1, pos2, AW::Vector::rotate270deg(), AW::Vector::rotate90deg(), AW_zoomable::rtransform(), AW_zoomable::rtransform_size(), sec_assert, SEC_GC_BONDS, SEC_GC_CURSOR, SEC_GC_DEFAULT, SEC_GC_ECOLI, SEC_GC_FIRST_DATA, SEC_GC_FIRST_FONT, SEC_GC_LAST_DATA, SEC_GC_LAST_FONT, SEC_SKELE_HELIX, SEC_SKELE_LOOP, SEC_SKELE_NHELIX, AW_stylable::set_line_attributes(), SHOW_ABS_CURPOS, SHOW_BASE_CURPOS, SHOW_ECOLI_CURPOS, SHOW_NO_CURPOS, SEC_db_interface::structure(), AW_device::text(), AW_zoomable::transform(), AW::Position::xpos(), and AW::Position::ypos().

GB_ERROR SEC_root::unsplit_loop

(

SEC_helix_strand *

delete_strand

)

Definition at line 370 of file SEC_split.cxx.

References after(), before(), BUFFER_CENTER_RELATIVE, error(), NULp, AngleBuffer::restoreAll(), s, sec_assert, and AngleBuffer::storeAllHelices().

void SEC_root::set_root

(

SEC_loop *

loop

)

Definition at line 124 of file SEC_split.cxx.

void SEC_root::create_default_bone

(

)

Definition at line 482 of file SEC_structure.cxx.

References findLongestHelix(), generate_x_string(), get_helixDef(), NULp, AW::Origin, relayout(), set_root_loop(), and set_under_construction().

Referenced by SEC_new_structure().

void SEC_root::generate_x_string

(

)

Definition at line 23 of file SEC_io.cxx.

References XString::initialize(), and sec_assert.

Referenced by create_default_bone().

void SEC_root::update_shown_positions

(

)

Definition at line 479 of file SEC_db.cxx.

References SEC_db_interface::update_shown_positions().

bool SEC_root::shallDisplayPosition ( int  abspos ) const

inline

Definition at line 821 of file SEC_root.hxx.

References SEC_db_interface::shallDisplayPosition().

void SEC_root::invalidate_base_positions

(

)

Definition at line 36 of file SEC_main.cxx.

References SEC_base_part::get_region(), SEC_region::invalidate_base_count(), and SEC_base_part::next().

int SEC_root::getBackgroundColor ( int  abspos )

inline

Definition at line 824 of file SEC_root.hxx.

const Vector& SEC_root::get_center_char_vector ( int  gc )

inline

Definition at line 825 of file SEC_root.hxx.

References sec_assert, SEC_GC_FIRST_FONT, and SEC_GC_LAST_FONT.

size_t SEC_root::max_index ( )

inline

Definition at line 830 of file SEC_root.hxx.

References SEC_db_interface::length(), and sec_assert.

int SEC_root::get_cursor ( ) const

inline

Definition at line 836 of file SEC_root.hxx.

SEC_loop* SEC_root::get_root_loop ( ) const

inline

Definition at line 838 of file SEC_root.hxx.

Referenced by export_structure_to_file().

void SEC_root::set_root_loop ( SEC_loop *  loop )

inline

Definition at line 839 of file SEC_root.hxx.

Referenced by create_default_bone().

SEC_BASE_TYPE SEC_root::get_show_constraints ( )

inline

Definition at line 841 of file SEC_root.hxx.

void SEC_root::set_show_constraints ( SEC_BASE_TYPE  show )

inline

Definition at line 842 of file SEC_root.hxx.

Referenced by sec_mode_event().

void SEC_root::set_last_drawed_cursor_position ( const LineVector &  line )

inline

Definition at line 844 of file SEC_root.hxx.

References line.

const LineVector& SEC_root::get_last_drawed_cursor_position ( ) const

inline

Definition at line 845 of file SEC_root.hxx.

Referenced by position_cursor().

void SEC_root::clear_last_drawed_cursor_position ( )

inline

Definition at line 846 of file SEC_root.hxx.

SEC_base_part * SEC_root::find

(

int

pos

)

Definition at line 138 of file SEC_split.cxx.

References SEC_region::contains_seq_position(), SEC_region::get_sequence_end(), SEC_region::get_sequence_start(), and NULp.

Referenced by findSegmentContaining().

void SEC_root::announce_base_position	(	int	base_pos,
		const Position &	draw_pos
	)

Definition at line 318 of file SEC_paint.cxx.

void SEC_root::clear_announced_positions

(

)

Definition at line 321 of file SEC_paint.cxx.

References SEC_drawn_positions::clear().

const AW_font_group& SEC_root::get_font_group ( ) const

inline

Definition at line 853 of file SEC_root.hxx.

void SEC_root::paintAnnotation	(	AW_device *	device,
		int	gc,
		const Position &	annotate,
		const Position &	left,
		const Position &	right,
		double	noteDistance,
		const char *	text,
		bool	lineToAnnotated,
		bool	linesToLeftRight,
		bool	boxText
	)

Definition at line 127 of file SEC_paint.cxx.

References AW_ALL_DEVICES_SCALED, AW_PRINTER, AW_SOLID, AW_device::box(), AW_device::clear_part(), AW::FillStyle::EMPTY, AW_device::get_filter(), AW_stylable::get_string_size(), AW::Vector::length(), AW_device::line(), max, AW::Angle::normal(), AW::Vector::rotate270deg(), AW::Angle::rotate270deg(), AW::Vector::rotate90deg(), AW_zoomable::rtransform_size(), sec_assert, SEC_GC_DEFAULT, SEC_GC_LAST_FONT, AW::Vector::set_length(), AW_stylable::set_line_attributes(), AW_device::text(), and valid_cb_params().

void SEC_root::paintPosAnnotation	(	AW_device *	device,
		int	gc,
		size_t	absPos,
		const char *	text,
		bool	lineToBase,
		bool	boxText
	)

Definition at line 223 of file SEC_paint.cxx.

References AW::LineVector::centroid(), GBS_global_string(), AW::LineVector::length(), pos1, and pos2.

double SEC_root::get_bondThickWorld ( ) const

inline

Definition at line 865 of file SEC_root.hxx.

---

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

• SECEDIT/SEC_root.hxx
• SECEDIT/SEC_db.cxx
• SECEDIT/SEC_helix.cxx
• SECEDIT/SEC_io.cxx
• SECEDIT/SEC_layout.cxx
• SECEDIT/SEC_main.cxx
• SECEDIT/SEC_paint.cxx
• SECEDIT/SEC_read.cxx
• SECEDIT/SEC_split.cxx
• SECEDIT/SEC_structure.cxx