Phylogram representation of trees. More...

#include <Bpp/Phyl/Graphics/PhylogramPlot.h>

Inheritance diagram for bpp::PhylogramPlot:

Collaboration diagram for bpp::PhylogramPlot:

Public Member Functions
	PhylogramPlot ()

virtual	~PhylogramPlot ()

PhylogramPlot *	clone () const override

std::string	getName () const override

void	setTree (const Tree &tree) override

double	getWidth () const override

double	getHeight () const override

void	treeHasChanged () override
	Method to implement to deal with redrawing when the underlying tree has been modified. More...

void	setHorizontalOrientation (short orientation)

void	setVerticalOrientation (short orientation)

short	getHorizontalOrientation () const

short	getVerticalOrientation () const

void	plot (GraphicDevice &gDevice) const
	Plot the tree onto the specified device. More...

bool	hasTree () const override

const Tree &	tree () const override

const TreeTemplate< INode > &	treeTemplate () const

Point2D< double >	getNodePosition (int nodeId) const override
	Get the position of a node. More...

int	getNodeAt (const Point2D< double > &position) const override
	Get the node corresponding to a position on the device. More...

bool	belongsTo (const Point2D< double > &p1, const Point2D< double > &p2) const
	Utilitary function, telling if a point belongs to a specified area. More...

virtual void	drawAtNode (GraphicDevice &gDevice, const INode &node, const std::string &text, double xOffset=0, double yOffset=0, short hpos=GraphicDevice::TEXT_HORIZONTAL_LEFT, short vpos=GraphicDevice::TEXT_VERTICAL_CENTER, double angle=0) const
	Draw some text at a particular node position. More...

virtual void	drawAtBranch (GraphicDevice &gDevice, const INode &node, const std::string &text, double xOffset=0, double yOffset=0, short hpos=GraphicDevice::TEXT_HORIZONTAL_LEFT, short vpos=GraphicDevice::TEXT_VERTICAL_CENTER, double angle=0) const
	Draw some text at a particular branch position. More...

void	setDisplaySettings (std::shared_ptr< const TreeDrawingSettings > tds) override
	Global drawing settings. More...

const TreeDrawingSettings &	displaySettings () const override

double	getXUnit () const override

double	getYUnit () const override

void	setXUnit (double xu) override
	Set the 'horizontal' expansion unit. More...

void	setYUnit (double yu) override
	Set the 'vertical' expansion unit. More...

void	collapseNode (int nodeId, bool yn) override
	Properties to draw. More...

bool	isNodeCollapsed (int nodeId) const override

void	addTreeDrawingListener (TreeDrawingListener *listener) override
	Add a drawing listener to this instance. More...

void	removeTreeDrawingListener (TreeDrawingListener *listener) override
	Remove a drawing listener from this instance. More...

Static Public Attributes
static short	ORIENTATION_LEFT_TO_RIGHT = 1

static short	ORIENTATION_RIGHT_TO_LEFT = 2

static short	ORIENTATION_TOP_TO_BOTTOM = 3

static short	ORIENTATION_BOTTOM_TO_TOP = 4

static std::shared_ptr< const TreeDrawingSettings >	DEFAULT_SETTINGS = std::make_shared<const TreeDrawingSettings>()

Protected Member Functions
void	fireBeforeTreeEvent_ (const DrawTreeEvent &event) const

void	fireAfterTreeEvent_ (const DrawTreeEvent &event) const

void	fireBeforeNodeEvent_ (const DrawINodeEvent &event) const

void	fireAfterNodeEvent_ (const DrawINodeEvent &event) const

void	fireBeforeBranchEvent_ (const DrawIBranchEvent &event) const

void	fireAfterBranchEvent_ (const DrawIBranchEvent &event) const

Protected Attributes
std::unique_ptr< TreeTemplate< INode > >	tree_

double	xUnit_

double	yUnit_

std::shared_ptr< const TreeDrawingSettings >	settings_

std::vector< TreeDrawingListener * >	listeners_

Private Member Functions
void	drawDendrogram_ (GraphicDevice &gDevice) const override

void	recursivePlot_ (GraphicDevice &gDevice, INode &node, double x, double &y, double hDirection, double vDirection, unsigned int &tipCounter) const

Private Attributes
double	totalDepth_

double	numberOfLeaves_

short	horOrientation_

short	verOrientation_

Detailed Description

Phylogram representation of trees.

This representation is for trees with branch lengths.

Definition at line 32 of file PhylogramPlot.h.

Constructor & Destructor Documentation

◆ PhylogramPlot()

bpp::PhylogramPlot::PhylogramPlot ( )

inline

Definition at line 40 of file PhylogramPlot.h.

Referenced by clone().

◆ ~PhylogramPlot()

virtual bpp::PhylogramPlot::~PhylogramPlot ( )

inlinevirtual

Definition at line 44 of file PhylogramPlot.h.

Member Function Documentation

◆ addTreeDrawingListener()

void bpp::AbstractTreeDrawing::addTreeDrawingListener ( TreeDrawingListener * listener )

inlineoverridevirtualinherited

Add a drawing listener to this instance.

Parameters

listener a pointer toward an object implementing the TreeDrawingListener interface. This object will then be owned by the class and copied and deleted if/when needed, unless it is autonomous.

See also: TreeDrawingListener

Implements bpp::TreeDrawing.

Definition at line 281 of file AbstractTreeDrawing.h.

References bpp::AbstractTreeDrawing::listeners_.

◆ belongsTo()

bool AbstractTreeDrawing::belongsTo	(	const Point2D< double > &	p1,
		const Point2D< double > &	p2
	)		const

inherited

Utilitary function, telling if a point belongs to a specified area.

This method is used internally to get a node coordinates.

Parameters

p1	Point to look for.
p2	Second point defining the center of the area.

Returns: True if p1 belongs to the area defined by p2.

Definition at line 47 of file AbstractTreeDrawing.cpp.

References bpp::Point2D< class >::getX(), bpp::Point2D< class >::getY(), and bpp::AbstractTreeDrawing::settings_.

Referenced by bpp::AbstractTreeDrawing::getNodeAt().

◆ clone()

PhylogramPlot * bpp::PhylogramPlot::clone ( ) const

inlineoverridevirtual

Implements bpp::TreeDrawing.

Definition at line 46 of file PhylogramPlot.h.

References PhylogramPlot().

◆ collapseNode()

void bpp::AbstractTreeDrawing::collapseNode	(	int	nodeId,
		bool	yn
	)

inlineoverridevirtualinherited

Properties to draw.

Collapsing nodes

Implements bpp::TreeDrawing.

Definition at line 269 of file AbstractTreeDrawing.h.

References bpp::AbstractTreeDrawing::tree_.

◆ displaySettings()

const TreeDrawingSettings & bpp::AbstractTreeDrawing::displaySettings ( ) const

inlineoverridevirtualinherited

Implements bpp::TreeDrawing.

Definition at line 259 of file AbstractTreeDrawing.h.

References bpp::AbstractTreeDrawing::settings_.

Referenced by bpp::AbstractDendrogramPlot::plot().

◆ drawAtBranch()

void AbstractTreeDrawing::drawAtBranch	(	GraphicDevice &	gDevice,
		const INode &	node,
		const std::string &	text,
		double	xOffset = `0`,
		double	yOffset = `0`,
		short	hpos = `GraphicDevice::TEXT_HORIZONTAL_LEFT`,
		short	vpos = `GraphicDevice::TEXT_VERTICAL_CENTER`,
		double	angle = `0`
	)		const

virtualinherited

Draw some text at a particular branch position.

Parameters

gDevice	The GraphicDevice object on which to draw.
node	The node of interest.
text	The text to draw.
xOffset	Horizontal offset.
yOffset	Vertical offset.
hpos	The way the text should be aligned horizontally (see GraphicDevice).
vpos	The way the text should be aligned vertically (see GraphicDevice).
angle	The rotation value of the text.

Definition at line 58 of file AbstractTreeDrawing.cpp.

References bpp::GraphicDevice::drawText(), bpp::NodeTemplate< NodeInfos >::getFather(), bpp::NodeTemplate< NodeInfos >::getInfos(), bpp::Node::hasFather(), bpp::AbstractTreeDrawing::xUnit_, and bpp::AbstractTreeDrawing::yUnit_.

◆ drawAtNode()

void AbstractTreeDrawing::drawAtNode	(	GraphicDevice &	gDevice,
		const INode &	node,
		const std::string &	text,
		double	xOffset = `0`,
		double	yOffset = `0`,
		short	hpos = `GraphicDevice::TEXT_HORIZONTAL_LEFT`,
		short	vpos = `GraphicDevice::TEXT_VERTICAL_CENTER`,
		double	angle = `0`
	)		const

virtualinherited

Draw some text at a particular node position.

Parameters

gDevice	The GraphicDevice object on which to draw.
node	The node of interest.
text	The text to draw.
xOffset	Horizontal offset.
yOffset	Vertical offset.
hpos	The way the text should be aligned horizontally (see GraphicDevice).
vpos	The way the text should be aligned vertically (see GraphicDevice).
angle	The rotation value of the text.

Definition at line 53 of file AbstractTreeDrawing.cpp.

References bpp::GraphicDevice::drawText(), bpp::NodeTemplate< NodeInfos >::getInfos(), bpp::AbstractTreeDrawing::xUnit_, and bpp::AbstractTreeDrawing::yUnit_.

◆ drawDendrogram_()

void PhylogramPlot::drawDendrogram_ ( GraphicDevice & gDevice ) const

overrideprivatevirtual

Implements bpp::AbstractDendrogramPlot.

Definition at line 37 of file PhylogramPlot.cpp.

References bpp::AbstractTreeDrawing::fireAfterTreeEvent_(), bpp::AbstractTreeDrawing::fireBeforeTreeEvent_(), bpp::AbstractDendrogramPlot::getHorizontalOrientation(), bpp::AbstractDendrogramPlot::getVerticalOrientation(), getWidth(), bpp::AbstractTreeDrawing::getXUnit(), bpp::AbstractTreeDrawing::hasTree(), bpp::AbstractDendrogramPlot::ORIENTATION_LEFT_TO_RIGHT, bpp::AbstractDendrogramPlot::ORIENTATION_TOP_TO_BOTTOM, recursivePlot_(), and bpp::AbstractTreeDrawing::tree_.

◆ fireAfterBranchEvent_()

void bpp::AbstractTreeDrawing::fireAfterBranchEvent_ ( const DrawIBranchEvent & event ) const

inlineprotectedinherited

Definition at line 349 of file AbstractTreeDrawing.h.

References bpp::AbstractTreeDrawing::listeners_.

Referenced by bpp::CladogramPlot::recursivePlot_(), and recursivePlot_().

◆ fireAfterNodeEvent_()

void bpp::AbstractTreeDrawing::fireAfterNodeEvent_ ( const DrawINodeEvent & event ) const

inlineprotectedinherited

Definition at line 331 of file AbstractTreeDrawing.h.

References bpp::AbstractTreeDrawing::listeners_.

Referenced by bpp::CladogramPlot::recursivePlot_(), and recursivePlot_().

◆ fireAfterTreeEvent_()

void bpp::AbstractTreeDrawing::fireAfterTreeEvent_ ( const DrawTreeEvent & event ) const

inlineprotectedinherited

Definition at line 313 of file AbstractTreeDrawing.h.

References bpp::AbstractTreeDrawing::listeners_.

Referenced by bpp::CladogramPlot::drawDendrogram_(), and drawDendrogram_().

◆ fireBeforeBranchEvent_()

void bpp::AbstractTreeDrawing::fireBeforeBranchEvent_ ( const DrawIBranchEvent & event ) const

inlineprotectedinherited

Definition at line 340 of file AbstractTreeDrawing.h.

References bpp::AbstractTreeDrawing::listeners_.

Referenced by bpp::CladogramPlot::recursivePlot_(), and recursivePlot_().

◆ fireBeforeNodeEvent_()

void bpp::AbstractTreeDrawing::fireBeforeNodeEvent_ ( const DrawINodeEvent & event ) const

inlineprotectedinherited

Definition at line 322 of file AbstractTreeDrawing.h.

References bpp::AbstractTreeDrawing::listeners_.

Referenced by bpp::CladogramPlot::recursivePlot_(), and recursivePlot_().

◆ fireBeforeTreeEvent_()

void bpp::AbstractTreeDrawing::fireBeforeTreeEvent_ ( const DrawTreeEvent & event ) const

inlineprotectedinherited

Definition at line 304 of file AbstractTreeDrawing.h.

References bpp::AbstractTreeDrawing::listeners_.

Referenced by bpp::CladogramPlot::drawDendrogram_(), and drawDendrogram_().

◆ getHeight()

double bpp::PhylogramPlot::getHeight ( ) const

inlineoverridevirtual

Returns: The total height of the drawing, in Y units.

Implements bpp::TreeDrawing.

Definition at line 54 of file PhylogramPlot.h.

References numberOfLeaves_.

Referenced by recursivePlot_().

◆ getHorizontalOrientation()

short bpp::AbstractDendrogramPlot::getHorizontalOrientation ( ) const

inlineinherited

Definition at line 37 of file AbstractDendrogramPlot.h.

References bpp::AbstractDendrogramPlot::horOrientation_.

Referenced by bpp::CladogramPlot::drawDendrogram_(), drawDendrogram_(), bpp::CladogramPlot::recursivePlot_(), and recursivePlot_().

◆ getName()

std::string bpp::PhylogramPlot::getName ( ) const

inlineoverridevirtual

Returns: A string describing this drawing algorithm.

Implements bpp::TreeDrawing.

Definition at line 49 of file PhylogramPlot.h.

◆ getNodeAt()

int AbstractTreeDrawing::getNodeAt ( const Point2D< double > & position ) const

overridevirtualinherited

Get the node corresponding to a position on the device.

Parameters

position A position in the coordinates system of the last GraphicDevice used.

Returns: The corresponding node identifier if available.

Exceptions

NodeNotFoundException If the node does not correspond to a node in the tree.

Implements bpp::TreeDrawing.

Definition at line 33 of file AbstractTreeDrawing.cpp.

References bpp::AbstractTreeDrawing::belongsTo(), and bpp::AbstractTreeDrawing::tree_.

◆ getNodePosition()

Point2D< double > AbstractTreeDrawing::getNodePosition ( int nodeId ) const

overridevirtualinherited

Get the position of a node.

Parameters

nodeId The identifier of the node.

Returns: The localization of the node using the coordinate system of the last GraphicDevice used.

Exceptions

NodeNotFoundException If the node does not correspond to a node in the tree.

Implements bpp::TreeDrawing.

Definition at line 20 of file AbstractTreeDrawing.cpp.

References bpp::TextTools::toString(), and bpp::AbstractTreeDrawing::tree_.

◆ getVerticalOrientation()

short bpp::AbstractDendrogramPlot::getVerticalOrientation ( ) const

inlineinherited

Definition at line 38 of file AbstractDendrogramPlot.h.

References bpp::AbstractDendrogramPlot::verOrientation_.

Referenced by bpp::CladogramPlot::drawDendrogram_(), drawDendrogram_(), bpp::CladogramPlot::recursivePlot_(), and recursivePlot_().

◆ getWidth()

double bpp::PhylogramPlot::getWidth ( ) const

inlineoverridevirtual

Returns: The total width of the drawing, in X units.

Implements bpp::TreeDrawing.

Definition at line 53 of file PhylogramPlot.h.

References totalDepth_.

Referenced by drawDendrogram_().

◆ getXUnit()

double bpp::AbstractTreeDrawing::getXUnit ( ) const

inlineoverridevirtualinherited

Returns: The horizontal unit length.

Implements bpp::TreeDrawing.

Definition at line 261 of file AbstractTreeDrawing.h.

References bpp::AbstractTreeDrawing::xUnit_.

Referenced by bpp::CladogramPlot::drawDendrogram_(), drawDendrogram_(), bpp::CladogramPlot::recursivePlot_(), and recursivePlot_().

◆ getYUnit()

double bpp::AbstractTreeDrawing::getYUnit ( ) const

inlineoverridevirtualinherited

Returns: The vertical unit length.

Implements bpp::TreeDrawing.

Definition at line 263 of file AbstractTreeDrawing.h.

References bpp::AbstractTreeDrawing::yUnit_.

Referenced by bpp::CladogramPlot::recursivePlot_(), and recursivePlot_().

◆ hasTree()

bool bpp::AbstractTreeDrawing::hasTree ( ) const

inlineoverridevirtualinherited

Returns: 'True' if a tree is attached to this instance.

Implements bpp::TreeDrawing.

Definition at line 172 of file AbstractTreeDrawing.h.

References bpp::AbstractTreeDrawing::tree_.

Referenced by bpp::CladogramPlot::drawDendrogram_(), drawDendrogram_(), bpp::CladogramPlot::setTree(), bpp::AbstractTreeDrawing::tree(), bpp::CladogramPlot::treeHasChanged(), treeHasChanged(), and bpp::AbstractTreeDrawing::treeTemplate().

◆ isNodeCollapsed()

bool bpp::AbstractTreeDrawing::isNodeCollapsed ( int nodeId ) const

inlineoverridevirtualinherited

Implements bpp::TreeDrawing.

Definition at line 275 of file AbstractTreeDrawing.h.

References bpp::AbstractTreeDrawing::tree_.

◆ plot()

void AbstractDendrogramPlot::plot ( GraphicDevice & gDevice ) const

virtualinherited

Plot the tree onto the specified device.

Parameters

gDevice An object implementing the GraphicDevice interface.

Implements bpp::TreeDrawing.

Definition at line 15 of file AbstractDendrogramPlot.cpp.

References bpp::AbstractTreeDrawing::displaySettings(), bpp::AbstractDendrogramPlot::drawDendrogram_(), and bpp::GraphicDevice::setCurrentPointSize().

◆ recursivePlot_()

void PhylogramPlot::recursivePlot_	(	GraphicDevice &	gDevice,
		INode &	node,
		double	x,
		double &	y,
		double	hDirection,
		double	vDirection,
		unsigned int &	tipCounter
	)		const

private

Definition at line 55 of file PhylogramPlot.cpp.

References bpp::GraphicDevice::drawLine(), bpp::AbstractTreeDrawing::fireAfterBranchEvent_(), bpp::AbstractTreeDrawing::fireAfterNodeEvent_(), bpp::AbstractTreeDrawing::fireBeforeBranchEvent_(), bpp::AbstractTreeDrawing::fireBeforeNodeEvent_(), bpp::Node::getDistanceToFather(), getHeight(), bpp::AbstractDendrogramPlot::getHorizontalOrientation(), bpp::NodeTemplate< NodeInfos >::getInfos(), bpp::Node::getNumberOfSons(), bpp::NodeTemplate< NodeInfos >::getSon(), bpp::AbstractDendrogramPlot::getVerticalOrientation(), bpp::AbstractTreeDrawing::getXUnit(), bpp::AbstractTreeDrawing::getYUnit(), bpp::Node::hasDistanceToFather(), bpp::Node::isLeaf(), bpp::AbstractDendrogramPlot::ORIENTATION_LEFT_TO_RIGHT, bpp::AbstractDendrogramPlot::ORIENTATION_TOP_TO_BOTTOM, recursivePlot_(), bpp::GraphicDevice::TEXT_HORIZONTAL_LEFT, and bpp::GraphicDevice::TEXT_HORIZONTAL_RIGHT.

Referenced by drawDendrogram_(), and recursivePlot_().

◆ removeTreeDrawingListener()

void bpp::AbstractTreeDrawing::removeTreeDrawingListener ( TreeDrawingListener * listener )

inlineoverridevirtualinherited

Remove a drawing listener from this instance.

Parameters

listener a pointer toward an object implementing the TreeDrawingListener interface. If the listener is autonomous, it will be deleted.

Implements bpp::TreeDrawing.

Definition at line 288 of file AbstractTreeDrawing.h.

References bpp::TreeDrawingListener::isAutonomous(), and bpp::AbstractTreeDrawing::listeners_.

◆ setDisplaySettings()

void bpp::AbstractTreeDrawing::setDisplaySettings ( std::shared_ptr< const TreeDrawingSettings > tds )

inlineoverridevirtualinherited

Global drawing settings.

Implements bpp::TreeDrawing.

Definition at line 253 of file AbstractTreeDrawing.h.

References bpp::AbstractTreeDrawing::settings_.

◆ setHorizontalOrientation()

void bpp::AbstractDendrogramPlot::setHorizontalOrientation ( short orientation )

inlineinherited

Definition at line 34 of file AbstractDendrogramPlot.h.

References bpp::AbstractDendrogramPlot::horOrientation_.

◆ setTree()

void PhylogramPlot::setTree ( const Tree & tree )

overridevirtual

Parameters

tree	A tree to associate with this drawing. The object will be copied.

Reimplemented from bpp::AbstractTreeDrawing.

Definition at line 31 of file PhylogramPlot.cpp.

References bpp::AbstractTreeDrawing::setTree(), bpp::AbstractTreeDrawing::tree(), and bpp::AbstractTreeDrawing::tree_.

◆ setVerticalOrientation()

void bpp::AbstractDendrogramPlot::setVerticalOrientation ( short orientation )

inlineinherited

Definition at line 35 of file AbstractDendrogramPlot.h.

References bpp::AbstractDendrogramPlot::verOrientation_.

◆ setXUnit()

void bpp::AbstractTreeDrawing::setXUnit ( double xu )

inlineoverridevirtualinherited

Set the 'horizontal' expansion unit.

The effect of this expansion factor depends on the implementation of the interface.

Parameters

xu	The horizontal unit length.

Implements bpp::TreeDrawing.

Definition at line 265 of file AbstractTreeDrawing.h.

References bpp::AbstractTreeDrawing::xUnit_.

◆ setYUnit()

void bpp::AbstractTreeDrawing::setYUnit ( double yu )

inlineoverridevirtualinherited

Set the 'vertical' expansion unit.

The effect of this expansion factor depends on the implementation of the interface.

Parameters

yu	The vertical unit length.

Implements bpp::TreeDrawing.

Definition at line 267 of file AbstractTreeDrawing.h.

References bpp::AbstractTreeDrawing::yUnit_.

◆ tree()

const Tree & bpp::AbstractTreeDrawing::tree ( ) const

inlineoverridevirtualinherited

Returns: A pointer toward the tree associated to this drawing.

Implements bpp::TreeDrawing.

Definition at line 178 of file AbstractTreeDrawing.h.

References bpp::AbstractTreeDrawing::hasTree(), and bpp::AbstractTreeDrawing::tree_.

Referenced by bpp::AbstractTreeDrawing::setTree(), bpp::CladogramPlot::setTree(), and setTree().

◆ treeHasChanged()

void bpp::PhylogramPlot::treeHasChanged ( )

inlineoverridevirtual

Method to implement to deal with redrawing when the underlying tree has been modified.

Implements bpp::AbstractTreeDrawing.

Definition at line 56 of file PhylogramPlot.h.

References bpp::TreeTemplateTools::getHeight(), bpp::AbstractTreeDrawing::hasTree(), numberOfLeaves_, totalDepth_, and bpp::AbstractTreeDrawing::tree_.

◆ treeTemplate()

const TreeTemplate< INode > & bpp::AbstractTreeDrawing::treeTemplate ( ) const

inlineinherited

Definition at line 190 of file AbstractTreeDrawing.h.

References bpp::AbstractTreeDrawing::hasTree(), and bpp::AbstractTreeDrawing::tree_.

Member Data Documentation

◆ DEFAULT_SETTINGS

shared_ptr< const TreeDrawingSettings > AbstractTreeDrawing::DEFAULT_SETTINGS = std::make_shared<const TreeDrawingSettings>()

staticinherited

Definition at line 359 of file AbstractTreeDrawing.h.

◆ horOrientation_

short bpp::AbstractDendrogramPlot::horOrientation_

privateinherited

Definition at line 25 of file AbstractDendrogramPlot.h.

Referenced by bpp::AbstractDendrogramPlot::getHorizontalOrientation(), and bpp::AbstractDendrogramPlot::setHorizontalOrientation().

◆ listeners_

std::vector<TreeDrawingListener*> bpp::AbstractTreeDrawing::listeners_

protectedinherited

Definition at line 122 of file AbstractTreeDrawing.h.

◆ numberOfLeaves_

double bpp::PhylogramPlot::numberOfLeaves_

private

Definition at line 37 of file PhylogramPlot.h.

Referenced by getHeight(), and treeHasChanged().

◆ ORIENTATION_BOTTOM_TO_TOP

short AbstractDendrogramPlot::ORIENTATION_BOTTOM_TO_TOP = 4

staticinherited

Definition at line 49 of file AbstractDendrogramPlot.h.

◆ ORIENTATION_LEFT_TO_RIGHT

short AbstractDendrogramPlot::ORIENTATION_LEFT_TO_RIGHT = 1

staticinherited

Definition at line 46 of file AbstractDendrogramPlot.h.

Referenced by bpp::CladogramDrawBranchEvent::CladogramDrawBranchEvent(), bpp::CladogramPlot::drawDendrogram_(), drawDendrogram_(), bpp::PhylogramDrawBranchEvent::PhylogramDrawBranchEvent(), bpp::CladogramPlot::recursivePlot_(), and recursivePlot_().

◆ ORIENTATION_RIGHT_TO_LEFT

short AbstractDendrogramPlot::ORIENTATION_RIGHT_TO_LEFT = 2

staticinherited

Definition at line 47 of file AbstractDendrogramPlot.h.

◆ ORIENTATION_TOP_TO_BOTTOM

short AbstractDendrogramPlot::ORIENTATION_TOP_TO_BOTTOM = 3

staticinherited

Definition at line 48 of file AbstractDendrogramPlot.h.

Referenced by bpp::CladogramPlot::drawDendrogram_(), drawDendrogram_(), bpp::CladogramPlot::recursivePlot_(), and recursivePlot_().

◆ settings_

std::shared_ptr<const TreeDrawingSettings> bpp::AbstractTreeDrawing::settings_

protectedinherited

Definition at line 121 of file AbstractTreeDrawing.h.

Referenced by bpp::AbstractTreeDrawing::belongsTo(), bpp::AbstractTreeDrawing::displaySettings(), bpp::AbstractTreeDrawing::operator=(), and bpp::AbstractTreeDrawing::setDisplaySettings().

◆ totalDepth_

double bpp::PhylogramPlot::totalDepth_

private

Definition at line 36 of file PhylogramPlot.h.

Referenced by getWidth(), and treeHasChanged().

◆ tree_

std::unique_ptr<TreeTemplate<INode> > bpp::AbstractTreeDrawing::tree_

protectedinherited

Definition at line 118 of file AbstractTreeDrawing.h.

Referenced by bpp::AbstractTreeDrawing::collapseNode(), bpp::CladogramPlot::drawDendrogram_(), drawDendrogram_(), bpp::AbstractTreeDrawing::getNodeAt(), bpp::AbstractTreeDrawing::getNodePosition(), bpp::AbstractTreeDrawing::hasTree(), bpp::AbstractTreeDrawing::isNodeCollapsed(), bpp::AbstractTreeDrawing::operator=(), bpp::AbstractTreeDrawing::setTree(), bpp::CladogramPlot::setTree(), setTree(), bpp::AbstractTreeDrawing::tree(), bpp::CladogramPlot::treeHasChanged(), treeHasChanged(), and bpp::AbstractTreeDrawing::treeTemplate().

◆ verOrientation_

short bpp::AbstractDendrogramPlot::verOrientation_

privateinherited

Definition at line 26 of file AbstractDendrogramPlot.h.

Referenced by bpp::AbstractDendrogramPlot::getVerticalOrientation(), and bpp::AbstractDendrogramPlot::setVerticalOrientation().

◆ xUnit_

double bpp::AbstractTreeDrawing::xUnit_

protectedinherited

Definition at line 119 of file AbstractTreeDrawing.h.

Referenced by bpp::AbstractTreeDrawing::drawAtBranch(), bpp::AbstractTreeDrawing::drawAtNode(), bpp::AbstractTreeDrawing::getXUnit(), bpp::AbstractTreeDrawing::operator=(), and bpp::AbstractTreeDrawing::setXUnit().

◆ yUnit_

double bpp::AbstractTreeDrawing::yUnit_

protectedinherited

Definition at line 120 of file AbstractTreeDrawing.h.

Referenced by bpp::AbstractTreeDrawing::drawAtBranch(), bpp::AbstractTreeDrawing::drawAtNode(), bpp::AbstractTreeDrawing::getYUnit(), bpp::AbstractTreeDrawing::operator=(), and bpp::AbstractTreeDrawing::setYUnit().

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

Bpp/Phyl/Graphics/PhylogramPlot.h
Bpp/Phyl/Graphics/PhylogramPlot.cpp

Public Member Functions

Static Public Attributes

Protected Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ PhylogramPlot()

◆ ~PhylogramPlot()

Member Function Documentation

◆ addTreeDrawingListener()

◆ belongsTo()

◆ clone()

◆ collapseNode()

◆ displaySettings()

◆ drawAtBranch()

◆ drawAtNode()

◆ drawDendrogram_()

◆ fireAfterBranchEvent_()

◆ fireAfterNodeEvent_()

◆ fireAfterTreeEvent_()

◆ fireBeforeBranchEvent_()

◆ fireBeforeNodeEvent_()

◆ fireBeforeTreeEvent_()

◆ getHeight()

◆ getHorizontalOrientation()

◆ getName()

◆ getNodeAt()

◆ getNodePosition()

◆ getVerticalOrientation()

◆ getWidth()

◆ getXUnit()

◆ getYUnit()

◆ hasTree()

◆ isNodeCollapsed()

◆ plot()

◆ recursivePlot_()

◆ removeTreeDrawingListener()

◆ setDisplaySettings()

◆ setHorizontalOrientation()

◆ setTree()

◆ setVerticalOrientation()

◆ setXUnit()

◆ setYUnit()

◆ tree()

◆ treeHasChanged()

◆ treeTemplate()

Member Data Documentation

◆ DEFAULT_SETTINGS

◆ horOrientation_

◆ listeners_

◆ numberOfLeaves_

◆ ORIENTATION_BOTTOM_TO_TOP

◆ ORIENTATION_LEFT_TO_RIGHT

◆ ORIENTATION_RIGHT_TO_LEFT

◆ ORIENTATION_TOP_TO_BOTTOM

◆ settings_

◆ totalDepth_

◆ tree_

◆ verOrientation_

◆ xUnit_

◆ yUnit_