Tree subclass also has functions and data needed for rendering and selection. More...

#include <gui/widgets/phylo_tree/phylo_tree.hpp>

Inheritance diagram for CPhyloTree:

Collaboration diagram for CPhyloTree:

Public Types
typedef CPhyloNodeData::TClusterID	TClusterID

typedef CPhyloNodeData::TID	TID

typedef pair< TTreeIdx, CPhyloNodeData::TSelectedState >	TSelStateValue

typedef vector< TSelStateValue >	TSelState

Public Types inherited from CTreeModel< CPhyloTreeNode >
typedef CPhyloTreeNode	TNodeType

typedef std::vector< TNodeType >	TNodeVecType

typedef TNode::TValueType	TValueType

typedef TNode::TTreeIdx	TTreeIdx

typedef TNodeType::TNodeList	TNodeList

typedef TNodeType::TNodeList_I	TNodeList_I

typedef TNodeType::TNodeList_CI	TNodeList_CI

typedef TNodeType::TNodeList_RI	TNodeList_RI

typedef TNodeType::TNodeList_CRI	TNodeList_CRI

Public Types inherited from CObject
enum	EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern }
	Control filling of newly allocated memory. More...

typedef CObjectCounterLocker	TLockerType
	Default locker type for CRef. More...

typedef atomic< Uint8 >	TCounter
	Counter type is CAtomiCounter. More...

typedef Uint8	TCount
	Alias for value type of counter. More...

Public Member Functions
	CPhyloTree ()
	ctor - need to add nodes to make tree valid More...

void	Clear ()
	Clear the tree nodes, graphics model and selected nodes. More...

CTreeGraphicsModel &	GetGraphicsModel ()
	Get model for rendering. More...

void	SetGraphicsModelRef (CRef< CTreeGraphicsModel > gm)
	Set graphics model - may be needed if we want to render to different graphics contexts since graphics model has context-specific data (e.g. More...

CRef< CTreeGraphicsModel >	GetGraphicsModelRef ()

CRgbaGradColorTable *	GetColorTable ()

void	Sort (TTreeIdx idx, bool order)
	Sort the children of a node based on the number of children they have. More...

void	SortSubtreeDist (TTreeIdx idx, const vector< float > &distances, bool order)
	Sort the children of a node based on length of longest subtree. More...

void	SortLabel (TTreeIdx idx, bool order)
	Sort the children of a node based on label comparison (alphabetical order) More...

void	SortLabelRange (TTreeIdx idx, const vector< pair< string, string > > &subtree_labels, bool order)
	Sort the children of a node based on the alphanumeric range of their child nodes. More...

void	SetSelection (TTreeIdx idx, bool sel, bool sel_children=true, bool sel_parents=true)
	Select or deselect the node at the specified index and, optionally, its parents and children as well. More...

void	GetSelState (TSelState &sel_state, TTreeIdx idx, bool sel_children=true, bool sel_parents=true) const
	Given the selection of node 'idx', store the selection state (selected, traced, shared) of that node and its parents. More...

void	ClearSelection ()
	Sets selection state of all nodes to eNotSelected and clears m_Selected. More...

void	GetSelected (vector< TTreeIdx > &sel) const
	Returns indices of selected nodes. More...

void	GetSelectedIDs (vector< TID > &sel) const
	Returns the node ids of selected nodes. More...

size_t	GetNumSelected () const
	Returns the number of selected nodes. More...

void	GetExplicitlySelected (vector< TTreeIdx > &esel) const
	Returns only indices of nodes explicitly selected, not their parents or children, i.e. More...

void	GetExplicitlySelectedAndNotCollapsed (vector< TTreeIdx > &esel) const
	Returns only indices of nodes explicitly selected, but when a node is underneath a collapsed node, the collapsed parent is returned. More...

void	GetExplicitlySelectedIDs (vector< TID > &esel) const
	Returns only ids of nodes explicitly selected, not their parents or children, i.e. More...

void	SetExplicitlySelected (const vector< TID > &esel)
	Reset explicitly selected nodes to those currently selected nodes that are also found in the vector 'esel'. More...

void	SetLeavesExplicitlySelected ()
	Set the nodes used for iteration to default to the leaf nodes. More...

void	SetSelection (const vector< TTreeIdx > &sel, bool sel_children=true, bool sel_parents=true)
	Select a set of nodes - equivalent to calling SetSelection(idx, true, true, true) on each of the nodes. More...

void	SetSelectionIDs (const vector< TID > &ids, bool sel=true, bool sel_children=true)
	Select a set of nodes - equivalent to calling SetSelection(idx, true, true, true) on each of the nodes. More...

bool	HasSelection () const

bool	GetSelectedBoundary (CVect2< float > &ll, CVect2< float > &ur)
	Return bounding rectangle from lower-left to upper-right of selected nodes (eSelected) and false if no nodes are currently selected. More...

bool	SelectByPoint (const CVect2< float > &pt, bool sel, bool toggle, bool labels_visible, bool rotated_labels=false)
	Determine if the point pt is close enough to a node to select or deselect it. More...

bool	SelectByRect (const CVect2< float > &ll, const CVect2< float > &ur, bool toggle)
	Select or deselect all nodes in the rectangle bounded by ll and ur. More...

vector< TTreeIdx >	GetAllCollapsed () const
	Returns indices of nodes thate are currently collapsed. More...

TTreeIdx	GetCollapsedParentIdx (TTreeIdx node_idx) const
	Return the index of the given node (node_idx) if none of its parent nodes up to the root are collapsed, otherwise return the node index of the collapsed parent node closest to the root. More...

void	SetCurrentNode (TTreeIdx node_idx)
	Set the index of the currently active node. More...

bool	SetCurrentNode (const CVect2< float > &pt, bool labels_visible, bool rotated_labels, bool unselect=true)
	If a node is close enough to the given position, set it to be the currently active node. More...

TTreeIdx	GetCurrentNodeIdx () const
	Return the index of the currently active node (may be Null()). More...

CPhyloTreeNode &	GetCurrentNode ()
	Get reference to currently active node. Throws exception if it's Null() More...

bool	HasCurrentNode () const
	Return true if the currently active node is not Null() More...

void	SetCurrentEdge (TTreeIdx child_idx, TTreeIdx parent_idx)
	Set/Get the edge between the two specified nodes as current. More...

void	GetCurrentEdge (TTreeIdx &child_idx, TTreeIdx &parent_idx) const

bool	HasCurrentEdge () const

TTreeIdx	TestForNode (const CVect2< float > &pt, bool labels_visible, bool rotated_labels=false)
	Search nodes to find and return closest node to 'pt' that is within the max. More...

bool	IsVisible (TTreeIdx node_idx)
	Determine if the node at node_idx is within a collapsed subtree or not. More...

TTreeIdx	FindNodeById (TID id) const
	Return index of the node with the given id or Null(). More...

bool	IsUnused (TTreeIdx idx) const
	Return true if the given position in the array is not currently included as a node in the tree. More...

CBioTreeFeatureDictionary &	GetFeatureDict ()
	Return feature dictionary. More...

const CBioTreeFeatureDictionary &	GetFeatureDict () const

CPhyloSelectionSetMgr &	GetSelectionSets ()

const CPhyloSelectionSetMgr &	GetSelectionSets () const

void	UpdateNodesMapping ()

Public Member Functions inherited from CTreeModel< CPhyloTreeNode >
	CTreeModel ()
	Create empty tree. Tree is not valid at this point (no nodes) More...

virtual	~CTreeModel ()

void	Clear ()
	Remove all nodes (empty array) and set root index to Null. More...

TNodeType &	GetNode (TTreeIdx idx)
	Return a reference to the node at the given index. More...

const CPhyloTreeNode &	GetNode (TTreeIdx idx) const

TNodeType &	operator[] (TTreeIdx idx)
	Use operator[] to return a reference to the node at 'idx'. More...

const CPhyloTreeNode &	operator[] (TTreeIdx idx) const

size_t	GetSize () const
	Get the number of nodes currently in the array. More...

size_t	GetNumNodes () const
	Get the number of displayed nodes in current tree layout. More...

void	SetNumNodes (int count)
	Set the number of displayed nodes in current tree layout. More...

TNodeType &	GetParent (TNodeType &node)
	Return a reference to the parent node of the given node. More...

const TNodeType &	GetParent (TNodeType &node) const

TValueType &	GetNodeValue (TTreeIdx idx)
	Return a reference to the 'value' object of a node. More...

const TValueType &	GetNodeValue (TTreeIdx idx) const

TNodeType &	GetRoot ()
	Return a reference to the root node of the tree. More...

const CPhyloTreeNode &	GetRoot () const

void	SetRootIdx (TTreeIdx idx)
	Set the index of the root node of the tree. More...

TTreeIdx	GetRootIdx () const
	Return the index of the root node. More...

void	RemoveChild (TTreeIdx parent_idx, TTreeIdx child_idx)
	Remove the node at 'child_idx' from its parent 'parent_idx' Nothing is done if the node 'child_idx' is not a child of that parent. More...

void	AddChild (TTreeIdx parent_idx, TTreeIdx child_idx)
	Add the node at 'child_idx' to the children 'parent_idx'. More...

void	ReRoot (TTreeIdx idx)
	Sets the root idx to be 'idx' and updates the tree so that all nodes above the new root become children of that node. More...

TTreeIdx	AddNode ()
	Add a new default node to the tree and return its index. More...

TTreeIdx	AddNode (const CPhyloTreeNode &node)
	Add a copy of node 'node' to the tree and return its index. More...

void	Reserve (size_t target_size)
	Allocate the memory in advance, if you know how big the tree will be. More...

Public Member Functions inherited from CObject
	CObject (void)
	Constructor. More...

	CObject (const CObject &src)
	Copy constructor. More...

virtual	~CObject (void)
	Destructor. More...

CObject &	operator= (const CObject &src) THROWS_NONE
	Assignment operator. More...

bool	CanBeDeleted (void) const THROWS_NONE
	Check if object can be deleted. More...

bool	IsAllocatedInPool (void) const THROWS_NONE
	Check if object is allocated in memory pool (not system heap) More...

bool	Referenced (void) const THROWS_NONE
	Check if object is referenced. More...

bool	ReferencedOnlyOnce (void) const THROWS_NONE
	Check if object is referenced only once. More...

void	AddReference (void) const
	Add reference to object. More...

void	RemoveReference (void) const
	Remove reference to object. More...

void	ReleaseReference (void) const
	Remove reference without deleting object. More...

virtual void	DoNotDeleteThisObject (void)
	Mark this object as not allocated in heap – do not delete this object. More...

virtual void	DoDeleteThisObject (void)
	Mark this object as allocated in heap – object can be deleted. More...

void *	operator new (size_t size)
	Define new operator for memory allocation. More...

void *	operator new[] (size_t size)
	Define new[] operator for 'array' memory allocation. More...

void	operator delete (void *ptr)
	Define delete operator for memory deallocation. More...

void	operator delete[] (void *ptr)
	Define delete[] operator for memory deallocation. More...

void *	operator new (size_t size, void *place)
	Define new operator. More...

void	operator delete (void ptr, void place)
	Define delete operator. More...

void *	operator new (size_t size, CObjectMemoryPool *place)
	Define new operator using memory pool. More...

void	operator delete (void ptr, CObjectMemoryPool place)
	Define delete operator. More...

virtual void	DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information. More...

Public Member Functions inherited from CDebugDumpable
	CDebugDumpable (void)

virtual	~CDebugDumpable (void)

void	DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const

void	DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const

void	DumpToConsole (void) const

Protected Types
typedef set< TTreeIdx >	TTreeIdxSet
	Indices of all the nodes with selection state eSelected. More...

typedef map< TID, TTreeIdx >	TTIDPhyloTreeNodeMap
	Node ID to tree index map. More...

Protected Member Functions
void	x_SetSelState (TTreeIdx idx, CPhyloNodeData::TSelectedState state, bool override_explicit=true)
	Set selected state of anode and add/remove it from m_Selected as needed. More...

void	x_SelectChildren (CPhyloTreeNode &node, bool sel)
	Propogate selection operation (selecte/deselect) to a nodes children. More...

void	x_SelectParents (CPhyloTreeNode &node, bool sel, bool children_selected=true)
	Propogate selection (eTraced) to a nodes parents and if children aren't be selected, don't override explicit parent selection. More...

TTreeIdx	x_CommonNodeSearch (TTreeIdx idx)
	Check recursively parents of node and set selection state to eShared if all of their children are selected. More...

void	x_PropagateCommonState (CPhyloTreeNode &node)

void	x_GetParentState (TSelState &sel_state, TTreeIdx idx) const
	Get (and return) selection state for parents of a given node. More...

void	x_GetChildState (TSelState &sel_state, TTreeIdx idx) const
	Get (and return) selection state for children of a given node. More...

virtual void	x_ConvertUpstream (TTreeIdx node_idx)
	Convert parents of node_idx to be its children. More...

Protected Member Functions inherited from CTreeModel< CPhyloTreeNode >
virtual void	x_ConvertUpstream (TTreeIdx node_idx)
	Convert parents of node_idx to be its children. More...

Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Protected Attributes
TTreeIdxSet	m_Selected

TTreeIdxSet	m_ExplicitlySelected
	Often when you select a node, it's children or parents may also join the selection set. More...

TTIDPhyloTreeNodeMap	m_NodesMap

TTreeIdx	m_CurrentNode
	Currently active node (for operations like edit), or Null() More...

TTreeIdx	m_CurrentEdgeChild
	Currently active edge (to allow re-rooting by edge). More...

TTreeIdx	m_CurrentEdgeParent

CRef< CTreeGraphicsModel >	m_GraphicsModel
	Model for rendering (updated from current tree state) More...

CRef< CRgbaGradColorTable >	m_ColorTable
	Color table to store colors by index. More...

CBioTreeFeatureDictionary	m_FeatureDict
	Feature dictionary. More...

CPhyloSelectionSetMgr	m_SelectionSets
	Selection sets - sets of selected nodes, which are saved in the biotreecontainer in user data (visualized kind of like clusters) More...

Protected Attributes inherited from CTreeModel< CPhyloTreeNode >
TNodeVecType	m_Nodes
	The list of nodes in the tree. More...

int	m_NumNodes
	Number of nodes in tree (not including collapsed/hidden nodes) More...

TTreeIdx	m_RootIdx
	The index of the root node within the tree. More...

Private Member Functions
	CPhyloTree (const CPhyloTree &)
	Disable copy. More...

CPhyloTree &	operator= (const CPhyloTree &)

Additional Inherited Members
Static Public Member Functions inherited from CTreeModel< CPhyloTreeNode >
static TTreeIdx	Null ()
	Return the index value that represents a NULL node. More...

Static Public Member Functions inherited from CObject
static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (void)
	Define method to throw null pointer exception. More...

static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (const type_info &type)

static EAllocFillMode	GetAllocFillMode (void)

static void	SetAllocFillMode (EAllocFillMode mode)

static void	SetAllocFillMode (const string &value)
	Set mode from configuration parameter value. More...

Static Public Member Functions inherited from CDebugDumpable
static void	EnableDebugDump (bool on)

Static Public Attributes inherited from CObject
static const TCount	eCounterBitsCanBeDeleted = 1 << 0
	Define possible object states. More...

static const TCount	eCounterBitsInPlainHeap = 1 << 1
	Heap signature was found. More...

static const TCount	eCounterBitsPlaceMask
	Mask for 'in heap' state flags. More...

static const int	eCounterStep = 1 << 2
	Skip over the "in heap" bits. More...

static const TCount	eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2)
	Minimal value for valid objects (reference counter is zero) Must be a single bit value. More...

static const TCount	eCounterStateMask
	Valid object, and object in heap. More...

Detailed Description

Tree subclass also has functions and data needed for rendering and selection.

Definition at line 51 of file phylo_tree.hpp.

Member Typedef Documentation

◆ TClusterID

typedef CPhyloNodeData::TClusterID CPhyloTree::TClusterID

Definition at line 54 of file phylo_tree.hpp.

◆ TID

typedef CPhyloNodeData::TID CPhyloTree::TID

Definition at line 55 of file phylo_tree.hpp.

◆ TSelState

typedef vector<TSelStateValue> CPhyloTree::TSelState

Definition at line 57 of file phylo_tree.hpp.

◆ TSelStateValue

typedef pair<TTreeIdx, CPhyloNodeData::TSelectedState> CPhyloTree::TSelStateValue

Definition at line 56 of file phylo_tree.hpp.

◆ TTIDPhyloTreeNodeMap

typedef map<TID, TTreeIdx> CPhyloTree::TTIDPhyloTreeNodeMap

protected

Node ID to tree index map.

Definition at line 370 of file phylo_tree.hpp.

◆ TTreeIdxSet

typedef set<TTreeIdx> CPhyloTree::TTreeIdxSet

protected

Indices of all the nodes with selection state eSelected.

Definition at line 360 of file phylo_tree.hpp.

Constructor & Destructor Documentation

◆ CPhyloTree() [1/2]

CPhyloTree::CPhyloTree ( )

ctor - need to add nodes to make tree valid

Definition at line 42 of file phylo_tree.cpp.

References Clear().

◆ CPhyloTree() [2/2]

CPhyloTree::CPhyloTree ( const CPhyloTree & )

private

Disable copy.

Member Function Documentation

◆ Clear()

void CPhyloTree::Clear ( void )

Clear the tree nodes, graphics model and selected nodes.

Definition at line 48 of file phylo_tree.cpp.

References CTreeModel< TNode >::Clear(), CGlModel2D::ClearAll(), ClearSelection(), CTreeGraphicsModel::Init(), CRef< C, Locker >::IsNull(), and m_GraphicsModel.

Referenced by CPhyloTreeDataSource::Clear(), CPhyloTree(), CPhyloTreeDataSource::Cut(), and CPhyloTreeDataSource::Init().

◆ ClearSelection()

void CPhyloTree::ClearSelection ( )

Sets selection state of all nodes to eNotSelected and clears m_Selected.

Definition at line 242 of file phylo_tree.cpp.

References set< Key, Compare >::clear(), CPhyloNodeData::eNotSelected, m_CurrentEdgeChild, m_CurrentEdgeParent, m_CurrentNode, m_ExplicitlySelected, CTreeModel< CPhyloTreeNode >::m_Nodes, m_Selected, and CTreeModel< CPhyloTreeNode >::Null().

Referenced by Clear(), CPhyloTreeDataSource::Cut(), CPhyloTreeDataSource::ExecuteStringQuery(), CPhyloTreeWidget::OnClearSelection(), CPhyloTreeWidget::OnRerootTree(), CPhyloTreeWidget::OnRerootTreeAtEdge(), CPhyloTreeWidget::OnSetMidpointRoot(), IPhyloTreeRender::OnTimerLeftUp(), CPhyloTreeWidget::OnZoomToSubtree(), CPhyloTreeWidget::QueryEnd(), CPhyloTreeDataSource::Remove(), CPhyloTreeDataSource::RemoveSelected(), SelectByPoint(), CPhyloTreeDataSource::SetQueryResults(), CPhyloSaveSelectiondlg::SetSelections(), and CPhyTreeView::x_OnSetSelection().

◆ FindNodeById()

TTreeIdx CPhyloTree::FindNodeById ( TID id ) const

inline

Return index of the node with the given id or Null().

ID's are unique.

Parameters

id	- the id to search for

Returns: - the node with the given ID or Null().

Definition at line 307 of file phylo_tree.hpp.

References map_checker< Container >::end(), map_checker< Container >::find(), m_NodesMap, and CTreeModel< CPhyloTreeNode >::Null().

Referenced by CPhyloTreeWidget::OnInfoTip(), CPhyloTreeWidget::OnSearchTip(), CPhyloTreeWidget::OnZoomTip(), visitor_copy_subtree::operator()(), visitor_paste_subtree::operator()(), CChangePhyloPropertyCmd::PerformEdit(), CChangePhyloExpandCollapseCmd::PerformEdit(), IPhyloTreeRender::PointToNode(), CPhyloTreeDataSource::RemoveSelected(), IPhyloTreeRender::SetActiveTooltipNode(), CPhyloTreeDataSource::SetCollapsedLabels(), SetExplicitlySelected(), SetSelectionIDs(), CPhyloSelectionSetMgr::SetSelectionSetProperty(), CTreeQueryExec::x_EvalAdvance(), and CPhyloSelectionSetMgr::x_SyncSelectionSets().

◆ GetAllCollapsed()

vector< CPhyloTree::TTreeIdx > CPhyloTree::GetAllCollapsed ( ) const

Returns indices of nodes thate are currently collapsed.

Returns: - vector of all collapsed nodes

Definition at line 368 of file phylo_tree.cpp.

References CPhyloNodeData::eHideChildren, i, IsUnused(), and CTreeModel< CPhyloTreeNode >::m_Nodes.

Referenced by CPhyloTreeWidget::OnShowAll().

◆ GetCollapsedParentIdx()

TTreeIdx CPhyloTree::GetCollapsedParentIdx ( TTreeIdx node_idx ) const

Return the index of the given node (node_idx) if none of its parent nodes up to the root are collapsed, otherwise return the node index of the collapsed parent node closest to the root.

Parameters

node_idx - the node to check

Returns: - Index of the node itself or of the collapsed parent node, if any, closest to the root.

Definition at line 382 of file phylo_tree.cpp.

References CTreeModel< CPhyloTreeNode >::GetNode(), CTreeModelNode< TData >::GetParent(), CTreeModelNode< CPhyloNodeData >::Null(), and result.

◆ GetColorTable()

CRgbaGradColorTable * CPhyloTree::GetColorTable ( )

Definition at line 64 of file phylo_tree.cpp.

References CRef< C, Locker >::GetPointer(), CRef< C, Locker >::IsNull(), m_ColorTable, and CRef< C, Locker >::Reset().

Referenced by CPhyloTreeDataSource::ApplyAttributes(), CPhyloTreeDataSource::Clusterize(), CPhyloTreeDataSource::Init(), CPhyloTreeDataSource::MeasureTree(), CPhyloTreeDataSource::NewNode(), CPhyloTreeDataSource::Relabel(), and CPhyloTreeDataSource::SetColorIndices().

◆ GetCurrentEdge()

void CPhyloTree::GetCurrentEdge	(	TTreeIdx &	child_idx,
		TTreeIdx &	parent_idx
	)		const

Definition at line 448 of file phylo_tree.cpp.

References m_CurrentEdgeChild, and m_CurrentEdgeParent.

Referenced by CPhyloTreeWidget::OnRerootTreeAtEdge().

◆ GetCurrentNode()

CPhyloTreeNode & CPhyloTree::GetCurrentNode ( )

Get reference to currently active node. Throws exception if it's Null()

Definition at line 434 of file phylo_tree.cpp.

References eUnknown, HasCurrentNode(), m_CurrentNode, CTreeModel< CPhyloTreeNode >::m_Nodes, and NCBI_THROW.

Referenced by CPhyloTreeDataSource::Cut(), CPhyloTreeWidget::EditLabel(), CPhyloTreeDataSource::NewNode(), CPhyloTreeWidget::OnEditNode(), CPhyloTreeWidget::OnUpdateEdit(), and CPhyloTreeWidget::SendEditEvent().

◆ GetCurrentNodeIdx()

TTreeIdx CPhyloTree::GetCurrentNodeIdx ( ) const

inline

Return the index of the currently active node (may be Null()).

Definition at line 268 of file phylo_tree.hpp.

References m_CurrentNode.

◆ GetExplicitlySelected()

void CPhyloTree::GetExplicitlySelected ( vector< TTreeIdx > & esel ) const

Returns only indices of nodes explicitly selected, not their parents or children, i.e.

nodes passed as first parameter to SetSelection(...)

Returns: - vector of all explicitly selected nodes

Definition at line 273 of file phylo_tree.cpp.

References set< Key, Compare >::begin(), copy(), set< Key, Compare >::end(), m_ExplicitlySelected, and set< Key, Compare >::size().

Referenced by CPhyloTreeDataSource::CollapseSelected(), and CPhyloSaveSelectiondlg::SetSelections().

◆ GetExplicitlySelectedAndNotCollapsed()

void CPhyloTree::GetExplicitlySelectedAndNotCollapsed ( vector< TTreeIdx > & esel ) const

Returns only indices of nodes explicitly selected, but when a node is underneath a collapsed node, the collapsed parent is returned.

Returns: - vector of all explicitly selected nodes

Definition at line 279 of file phylo_tree.cpp.

References set< Key, Compare >::begin(), set< Key, Compare >::end(), CPhyloTreeNode::Expanded(), CTreeModelNode< TData >::GetParent(), m_ExplicitlySelected, CTreeModel< CPhyloTreeNode >::m_Nodes, n, CTreeModelNode< CPhyloNodeData >::Null(), and set< Key, Compare >::size().

Referenced by CPhyloTreeDataSource::IterateOverSelNodes(), and CPhyloTreeWidget::OnUpdateSelChanged().

◆ GetExplicitlySelectedIDs()

void CPhyloTree::GetExplicitlySelectedIDs ( vector< TID > & esel ) const

Returns only ids of nodes explicitly selected, not their parents or children, i.e.

nodes passed as first parameter to SetSelection(...)

Returns: - vector of ids of all explictly selected nodes

Definition at line 313 of file phylo_tree.cpp.

References GetId(), ITERATE, m_ExplicitlySelected, CTreeModel< CPhyloTreeNode >::m_Nodes, and set< Key, Compare >::size().

Referenced by CPhyTreeView::GetSelection(), and CPhyloTreeDataSource::RemoveSelected().

◆ GetFeatureDict() [1/2]

CBioTreeFeatureDictionary& CPhyloTree::GetFeatureDict ( )

inline

Return feature dictionary.

Definition at line 323 of file phylo_tree.hpp.

References m_FeatureDict.

◆ GetFeatureDict() [2/2]

const CBioTreeFeatureDictionary& CPhyloTree::GetFeatureDict ( ) const

inline

Definition at line 324 of file phylo_tree.hpp.

References m_FeatureDict.

◆ GetGraphicsModel()

CTreeGraphicsModel & CPhyloTree::GetGraphicsModel ( )

Get model for rendering.

Definition at line 74 of file phylo_tree.cpp.

References CRef< C, Locker >::GetObject(), CTreeGraphicsModel::Init(), CRef< C, Locker >::IsNull(), m_GraphicsModel, and CRef< C, Locker >::Reset().

Referenced by CPhyloTreeDataSource::GetModel(), CPhyloTreePane::RenderPdf(), SelectByRect(), and TestForNode().

◆ GetGraphicsModelRef()

CRef<CTreeGraphicsModel> CPhyloTree::GetGraphicsModelRef ( )

inline

Definition at line 74 of file phylo_tree.hpp.

References m_GraphicsModel.

◆ GetNumSelected()

size_t CPhyloTree::GetNumSelected ( ) const

inline

Returns the number of selected nodes.

Returns: - number of selected nodes with state eSelected

Definition at line 151 of file phylo_tree.hpp.

References m_Selected, and set< Key, Compare >::size().

Referenced by CPhyTreeView::OnCreateSelectedSubtree(), and CPhyloTreeWidget::OnUpdateSubtreeFromSelection().

◆ GetSelected()

void CPhyloTree::GetSelected ( vector< TTreeIdx > & sel ) const

Returns indices of selected nodes.

Returns: - vector of all nodes with state eSelected

Definition at line 259 of file phylo_tree.cpp.

References set< Key, Compare >::begin(), copy(), set< Key, Compare >::end(), m_Selected, and set< Key, Compare >::size().

Referenced by CPhyTreeView::GetSelection(), CPhyloTreeWidget::OnUpdateCollapseSelected(), and CPhyloSaveSelectiondlg::SetSelections().

◆ GetSelectedBoundary()

bool CPhyloTree::GetSelectedBoundary	(	CVect2< float > &	ll,
		CVect2< float > &	ur
	)

Return bounding rectangle from lower-left to upper-right of selected nodes (eSelected) and false if no nodes are currently selected.

Parameters

ll	- min x and y coordinates for selected set ur - max x and y coordinates for selected set

Returns: - true if one or more nodes are selected, false otherwise

Definition at line 397 of file phylo_tree.cpp.

References ITERATE, CTreeModel< CPhyloTreeNode >::m_Nodes, m_Selected, max(), min(), set< Key, Compare >::size(), CVect2< T >::X(), and CVect2< T >::Y().

Referenced by CPhyloTreeWidget::OnZoomToSelection().

◆ GetSelectedIDs()

void CPhyloTree::GetSelectedIDs ( vector< TID > & sel ) const

Returns the node ids of selected nodes.

Returns: - vector of all nodes with state eSelected

Definition at line 265 of file phylo_tree.cpp.

References GetId(), ITERATE, CTreeModel< CPhyloTreeNode >::m_Nodes, m_Selected, and set< Key, Compare >::size().

Referenced by CPhyTreeView::GetSelection(), CPhyloSaveSelectiondlg::OnAddCurrentSelBtnClick(), and CPhyloSaveSelectiondlg::SetSelections().

◆ GetSelectionSets() [1/2]

CPhyloSelectionSetMgr& CPhyloTree::GetSelectionSets ( )

inline

Definition at line 326 of file phylo_tree.hpp.

References m_SelectionSets.

Referenced by CPhyloTreeDataSource::Clusterize(), CTreeQueryExec::EvalStart(), CChangePhyloSelectionSetCmd::Execute(), CPhyloTreeDataSource::GetSelectionSets(), CPhyloTreeDataSource::Init(), CPhyloTreeWidget::OnAddSelectionSet(), CChangePhyloSelectionSetCmd::PerformEdit(), CPhyloTreeWidget::QueryEnd(), CChangePhyloSelectionSetCmd::Unexecute(), and CPhyloTreeDataSource::UpdateSelectionSets().

◆ GetSelectionSets() [2/2]

const CPhyloSelectionSetMgr& CPhyloTree::GetSelectionSets ( ) const

inline

Definition at line 327 of file phylo_tree.hpp.

References m_SelectionSets.

◆ GetSelState()

void CPhyloTree::GetSelState	(	TSelState &	sel_state,
		TTreeIdx	idx,
		bool	sel_children = `true`,
		bool	sel_parents = `true`
	)		const

Given the selection of node 'idx', store the selection state (selected, traced, shared) of that node and its parents.

This function does Not update selection state of the actual nodes.

Parameters

sel_state - vector to return the selection info idx - the node whose selection state we are retrieving sel_children - if true, all chidren recursively are added to sel state sel_parents - if true all ancestors are added to sel state

Definition at line 613 of file phylo_tree.cpp.

References set< Key, Compare >::end(), CPhyloNodeData::eSelected, set< Key, Compare >::find(), CTreeModelNode< TData >::GetParent(), CTreeModelNode< TData >::HasParent(), CTreeModelNode< TData >::IsLeaf(), m_ExplicitlySelected, CTreeModel< CPhyloTreeNode >::m_Nodes, x_GetChildState(), and x_GetParentState().

Referenced by IPhyloTreeRender::BufferedRender().

◆ HasCurrentEdge()

bool CPhyloTree::HasCurrentEdge ( ) const

Definition at line 454 of file phylo_tree.cpp.

References m_CurrentEdgeChild, m_CurrentEdgeParent, and CTreeModel< CPhyloTreeNode >::Null().

Referenced by CPhyloTreeWidget::OnRerootTreeAtEdge(), and CPhyloTreeWidget::OnUpdateRerootTreeAtEdge().

◆ HasCurrentNode()

bool CPhyloTree::HasCurrentNode ( ) const

inline

Return true if the currently active node is not Null()

Definition at line 274 of file phylo_tree.hpp.

References m_CurrentNode, and CTreeModel< CPhyloTreeNode >::Null().

Referenced by CPhyloTreeWidget::EditLabel(), GetCurrentNode(), CPhyTreeView::GetSelection(), CPhyloTreeWidget::OnEditNode(), CPhyloTreeWidget::OnUpdateEdit(), CPhyloTreeWidget::OnUpdateEditLabel(), CPhyloTreeWidget::OnUpdateEditNode(), and CPhyloTreeWidget::SendEditEvent().

◆ HasSelection()

bool CPhyloTree::HasSelection ( ) const

inline

Definition at line 201 of file phylo_tree.hpp.

References m_Selected, and set< Key, Compare >::size().

Referenced by CPhyloTreeWidget::OnUpdateEdit(), CPhyloTreeWidget::OnUpdateSelChanged(), and CPhyloTreeWidget::OnUpdateZoomSel().

◆ IsUnused()

bool CPhyloTree::IsUnused ( TTreeIdx idx ) const

inline

Return true if the given position in the array is not currently included as a node in the tree.

Can happen if nodes are deleted, for example

Parameters

idx	- the index to check

Returns: - true if the position is empty

Definition at line 320 of file phylo_tree.hpp.

References CTreeModel< CPhyloTreeNode >::m_Nodes.

Referenced by GetAllCollapsed().

◆ IsVisible()

bool CPhyloTree::IsVisible ( TTreeIdx node_idx )

Determine if the node at node_idx is within a collapsed subtree or not.

Parameters

node_idx - the node to check

Returns: - true if no parents (recursively) of node_idx are collapsed

Definition at line 469 of file phylo_tree.cpp.

References CPhyloNodeData::eHideChildren, CTreeModelNode< TData >::GetParent(), CTreeModel< CPhyloTreeNode >::m_Nodes, NULL, and CTreeModelNode< CPhyloNodeData >::Null().

◆ operator=()

CPhyloTree& CPhyloTree::operator= ( const CPhyloTree & )

private

◆ SelectByPoint()

bool CPhyloTree::SelectByPoint	(	const CVect2< float > &	pt,
		bool	sel,
		bool	toggle,
		bool	labels_visible,
		bool	rotated_labels = `false`
	)

Determine if the point pt is close enough to a node to select or deselect it.

If it is, select or deselect according to sel and toggle

Parameters

pt	- the selection position sel - if true we are doing normal (vs. incremental) selection toggle - if true we should toggle node's selection state

Returns: - true if a node's selections state was updated

Definition at line 486 of file phylo_tree.cpp.

References ClearSelection(), CPhyloNodeData::eSelected, m_CurrentNode, CTreeModel< CPhyloTreeNode >::m_Nodes, CTreeModel< CPhyloTreeNode >::Null(), SetSelection(), and TestForNode().

Referenced by IPhyloTreeRender::OnTimerLeftUp().

◆ SelectByRect()

bool CPhyloTree::SelectByRect	(	const CVect2< float > &	ll,
		const CVect2< float > &	ur,
		bool	toggle
	)

Select or deselect all nodes in the rectangle bounded by ll and ur.

Parameters

ll	- lower left corner of selection rectangle ur - upper right corner of selection rectangle toggle - if true we should toggle node's selection state

Returns: - true if one or more node's selection state was updated

Definition at line 512 of file phylo_tree.cpp.

References CPhyloNodeData::eSelected, CTreeGraphicsModel::GetCollisionData(), GetGraphicsModel(), i, CTreeModel< CPhyloTreeNode >::m_Nodes, CTreeCollisionModel2D::SelectNodes(), SetSelection(), CVect2< T >::X(), and CVect2< T >::Y().

Referenced by IPhyloTreeRender::x_SelectByRect().

◆ SetCurrentEdge()

void CPhyloTree::SetCurrentEdge	(	TTreeIdx	child_idx,
		TTreeIdx	parent_idx
	)

Set/Get the edge between the two specified nodes as current.

May be Null (but if one value is null, both are)

Parameters

child_idx - index of the child node of the edge (may be Null()) parent_idx - index of the parent node of the edge (may be NULL())

Definition at line 442 of file phylo_tree.cpp.

References m_CurrentEdgeChild, and m_CurrentEdgeParent.

Referenced by IPhyloTreeRender::BufferedRender(), IPhyloTreeRender::x_RenderCircularVbo(), IPhyloTreeRender::x_RenderLineVbo(), IPhyloTreeRender::x_RenderPseudoSplineVbo(), and IPhyloTreeRender::x_RenderSplineVbo().

◆ SetCurrentNode() [1/2]

bool CPhyloTree::SetCurrentNode	(	const CVect2< float > &	pt,
		bool	labels_visible,
		bool	rotated_labels,
		bool	unselect = `true`
	)

If a node is close enough to the given position, set it to be the currently active node.

Parameters

node_idx - index of the active node within the tree (may be Null())

Returns: -true if a node was selected (even if it was already current)

Definition at line 420 of file phylo_tree.cpp.

References m_CurrentNode, CTreeModel< CPhyloTreeNode >::Null(), and TestForNode().

◆ SetCurrentNode() [2/2]

void CPhyloTree::SetCurrentNode ( TTreeIdx node_idx )

Set the index of the currently active node.

Active nodes may have edits or property updates applied to them.

Parameters

node_idx - index of the active node within the tree (may be Null())

Definition at line 415 of file phylo_tree.cpp.

References m_CurrentNode.

Referenced by CPhyloTreeDataSource::IterateOverSelNodes(), IPhyloTreeRender::OnLeftDblClick(), IPhyloTreeRender::OnLeftDown(), IPhyloTreeRender::OnRightDown(), CPhyloTreeDataSource::ReRootEdge(), and CPhyloTreeDataSource::ReRootMidpoint().

◆ SetExplicitlySelected()

void CPhyloTree::SetExplicitlySelected ( const vector< TID > & esel )

Reset explicitly selected nodes to those currently selected nodes that are also found in the vector 'esel'.

Parameters

esel	- vector of node indices which, if they are Also in the current selection set, will marked as explicitly selected.

Definition at line 321 of file phylo_tree.cpp.

References set< Key, Compare >::clear(), set< Key, Compare >::end(), set< Key, Compare >::find(), FindNodeById(), set< Key, Compare >::insert(), ITERATE, m_ExplicitlySelected, and m_Selected.

Referenced by CPhyTreeView::x_OnSetSelection().

◆ SetGraphicsModelRef()

void CPhyloTree::SetGraphicsModelRef ( CRef< CTreeGraphicsModel > gm )

inline

Set graphics model - may be needed if we want to render to different graphics contexts since graphics model has context-specific data (e.g.

OpenGL buffer Ids)

Definition at line 73 of file phylo_tree.hpp.

References m_GraphicsModel.

◆ SetLeavesExplicitlySelected()

void CPhyloTree::SetLeavesExplicitlySelected ( )

Set the nodes used for iteration to default to the leaf nodes.

This is used when we set the selection via broadcasting from another tree such that we don't know which nodes were explicitly selected in the other tree.

Definition at line 337 of file phylo_tree.cpp.

References set< Key, Compare >::clear(), set< Key, Compare >::insert(), ITERATE, m_ExplicitlySelected, CTreeModel< CPhyloTreeNode >::m_Nodes, and m_Selected.

Referenced by CPhyTreeView::x_OnSetSelection().

◆ SetSelection() [1/2]

void CPhyloTree::SetSelection	(	const vector< TTreeIdx > &	sel,
		bool	sel_children = `true`,
		bool	sel_parents = `true`
	)

Select a set of nodes - equivalent to calling SetSelection(idx, true, true, true) on each of the nodes.

Parameters

sel	- the set of nodes to be selected

Definition at line 357 of file phylo_tree.cpp.

References SetSelection().

◆ SetSelection() [2/2]

void CPhyloTree::SetSelection	(	TTreeIdx	idx,
		bool	sel,
		bool	sel_children = `true`,
		bool	sel_parents = `true`
	)

Select or deselect the node at the specified index and, optionally, its parents and children as well.

Parent selection state is eTraced or eShared.

Parameters

idx	- the node to be selected or unselected (eSelected or eNotSelected) sel - if true the node should be selected, false - deselected sel_children - if true, all chidren recursively are selected/deselected sel_parents - if true all ancestors are selected/deselected

Definition at line 577 of file phylo_tree.cpp.

References set< Key, Compare >::end(), CPhyloNodeData::eNotSelected, set< Key, Compare >::erase(), CPhyloNodeData::eSelected, set< Key, Compare >::find(), set< Key, Compare >::insert(), m_ExplicitlySelected, CTreeModel< CPhyloTreeNode >::m_Nodes, CTreeModel< CPhyloTreeNode >::Null(), x_CommonNodeSearch(), x_PropagateCommonState(), x_SelectChildren(), x_SelectParents(), and x_SetSelState().

Referenced by CPhyloTreeDataSource::Cut(), CPhyloTreeDataSource::ExecuteStringQuery(), CPhyloTreeWidget::OnSelectAll(), SelectByPoint(), SelectByRect(), CPhyloTreeDataSource::SetQueryResults(), SetSelection(), SetSelectionIDs(), CPhyloSaveSelectiondlg::SetSelections(), and CPhyTreeView::x_OnSetSelection().

◆ SetSelectionIDs()

void CPhyloTree::SetSelectionIDs	(	const vector< TID > &	ids,
		bool	sel = `true`,
		bool	sel_children = `true`
	)

Select a set of nodes - equivalent to calling SetSelection(idx, true, true, true) on each of the nodes.

Parameters

sel	- the set of node IDs to be selected

Definition at line 346 of file phylo_tree.cpp.

References FindNodeById(), ITERATE, CTreeModel< CPhyloTreeNode >::Null(), and SetSelection().

Referenced by CPhyTreeView::x_OnSetSelection().

◆ Sort()

void CPhyloTree::Sort	(	TTreeIdx	idx,
		bool	order
	)

Sort the children of a node based on the number of children they have.

Parameters

idx	- index of the node whose children will be sorted order - if true order nodes in descending order of subtree size

Definition at line 208 of file phylo_tree.cpp.

References CTreeModel< CPhyloTreeNode >::m_Nodes, and ct::sort().

Referenced by CPhyloTreeSorter::x_OnStep().

◆ SortLabel()

void CPhyloTree::SortLabel	(	TTreeIdx	idx,
		bool	order
	)

Sort the children of a node based on label comparison (alphabetical order)

Parameters

idx	- index of the node whose children will be sorted order - if true order nodes in descending alphabetical order

Definition at line 224 of file phylo_tree.cpp.

References CTreeModel< CPhyloTreeNode >::m_Nodes, and ct::sort().

Referenced by CPhyloTreeSorterLabel::x_OnStep().

◆ SortLabelRange()

void CPhyloTree::SortLabelRange	(	TTreeIdx	idx,
		const vector< pair< string, string > > &	subtree_labels,
		bool	order
	)

Sort the children of a node based on the alphanumeric range of their child nodes.

Parameters

idx	- index of the node whose children will be sorted order - if true order nodes in descending alphabeitcal label range

Definition at line 232 of file phylo_tree.cpp.

References CTreeModel< CPhyloTreeNode >::m_Nodes, and ct::sort().

Referenced by CPhyloTreeSorterLabelRange::x_OnStep().

◆ SortSubtreeDist()

void CPhyloTree::SortSubtreeDist	(	TTreeIdx	idx,
		const vector< float > &	distances,
		bool	order
	)

Sort the children of a node based on length of longest subtree.

Parameters

idx	- index of the node whose children will be sorted order - if true order nodes in descending order of distance

Definition at line 216 of file phylo_tree.cpp.

References CTreeModel< CPhyloTreeNode >::m_Nodes, and ct::sort().

Referenced by CPhyloTreeSorterSubtreeDist::x_OnStep().

◆ TestForNode()

CPhyloTree::TTreeIdx CPhyloTree::TestForNode	(	const CVect2< float > &	pt,
		bool	labels_visible,
		bool	rotated_labels = `false`
	)

Search nodes to find and return closest node to 'pt' that is within the max.

selection distance (used for clicking on nodes)

Parameters

pt	- the position against which we are testing

Returns: - index of the closest node within selection distance or Null()

Definition at line 460 of file phylo_tree.cpp.

References CTreeGraphicsModel::GetCollisionData(), GetGraphicsModel(), CTreeModelNode< CPhyloNodeData >::Null(), CTreeCollisionModel2D::TestForNode(), CVect2< T >::X(), and CVect2< T >::Y().

Referenced by IPhyloTreeRender::GetHoverNode(), IPhyloTreeRender::GetHoverNodeIdx(), IPhyloTreeRender::OnLeftDown(), IPhyloTreeRender::OnTimerLeftUp(), SelectByPoint(), and SetCurrentNode().

◆ UpdateNodesMapping()

void CPhyloTree::UpdateNodesMapping ( )

Definition at line 535 of file phylo_tree.cpp.

References map_checker< Container >::clear(), ITERATE, CTreeModel< CPhyloTreeNode >::m_Nodes, and m_NodesMap.

Referenced by CPhyloTreeDataSource::Cut(), CPhyloTreeDataSource::Init(), CPhyloTreeDataSource::NewNode(), CPhyloTreeDataSource::Paste(), CPhyloTreeDataSource::Remove(), and CPhyloTreeDataSource::RemoveSelected().

◆ x_CommonNodeSearch()

CPhyloTree::TTreeIdx CPhyloTree::x_CommonNodeSearch ( TTreeIdx idx )

protected

Check recursively parents of node and set selection state to eShared if all of their children are selected.

Definition at line 689 of file phylo_tree.cpp.

References CPhyloNodeData::eNotSelected, CTreeModelNode< TData >::GetParent(), CTreeModel< CPhyloTreeNode >::m_Nodes, CTreeModel< CPhyloTreeNode >::Null(), CTreeModelNode< TData >::SubNodeBegin(), and CTreeModelNode< TData >::SubNodeEnd().

Referenced by SetSelection().

◆ x_ConvertUpstream()

void CPhyloTree::x_ConvertUpstream ( TTreeIdx node_idx )

protectedvirtual

Convert parents of node_idx to be its children.

Also moves edge data associated with node children to parents when parent/child role is reversed.

Definition at line 758 of file phylo_tree.cpp.

References CTreeModel< CPhyloTreeNode >::AddChild(), CTreeModel< CPhyloTreeNode >::GetNode(), CTreeModelNode< TData >::GetValue(), m_FeatureDict, CTreeModel< CPhyloTreeNode >::m_Nodes, CTreeModel< CPhyloTreeNode >::Null(), CTreeModel< CPhyloTreeNode >::RemoveChild(), CPhyloNodeData::SetDistance(), and CPhyloNodeData::Sync().

◆ x_GetChildState()

void CPhyloTree::x_GetChildState	(	TSelState &	sel_state,
		TTreeIdx	idx
	)		const

protected

Get (and return) selection state for children of a given node.

Definition at line 743 of file phylo_tree.cpp.

References CPhyloNodeData::eNotSelected, CTreeModel< CPhyloTreeNode >::m_Nodes, n, CTreeModelNode< TData >::SubNodeBegin(), and CTreeModelNode< TData >::SubNodeEnd().

Referenced by GetSelState().

◆ x_GetParentState()

void CPhyloTree::x_GetParentState	(	TSelState &	sel_state,
		TTreeIdx	idx
	)		const

protected

Get (and return) selection state for parents of a given node.

Definition at line 730 of file phylo_tree.cpp.

References CPhyloNodeData::eNotSelected, CTreeModelNode< TData >::GetParent(), CTreeModelNode< TData >::HasParent(), and CTreeModel< CPhyloTreeNode >::m_Nodes.

Referenced by GetSelState().

◆ x_PropagateCommonState()

void CPhyloTree::x_PropagateCommonState ( CPhyloTreeNode & node )

protected

Definition at line 718 of file phylo_tree.cpp.

References CPhyloNodeData::eShared, CPhyloNodeData::eTraced, CTreeModel< CPhyloTreeNode >::m_Nodes, CTreeModelNode< TData >::SubNodeBegin(), and CTreeModelNode< TData >::SubNodeEnd().

Referenced by SetSelection().

◆ x_SelectChildren()

void CPhyloTree::x_SelectChildren	(	CPhyloTreeNode &	node,
		bool	sel
	)

protected

Propogate selection operation (selecte/deselect) to a nodes children.

Definition at line 642 of file phylo_tree.cpp.

References CPhyloNodeData::eNotSelected, CPhyloNodeData::eSelected, CTreeModel< CPhyloTreeNode >::m_Nodes, CTreeModelNode< TData >::SubNodeBegin(), CTreeModelNode< TData >::SubNodeEnd(), and x_SetSelState().

Referenced by SetSelection().

◆ x_SelectParents()

void CPhyloTree::x_SelectParents	(	CPhyloTreeNode &	node,
		bool	sel,
		bool	children_selected = `true`
	)

protected

Propogate selection (eTraced) to a nodes parents and if children aren't be selected, don't override explicit parent selection.

Definition at line 655 of file phylo_tree.cpp.

References CPhyloNodeData::eNotSelected, CPhyloNodeData::eSelected, CPhyloNodeData::eTraced, CTreeModelNode< TData >::GetParent(), CTreeModelNode< TData >::HasParent(), CTreeModel< CPhyloTreeNode >::m_Nodes, CTreeModelNode< TData >::SubNodeBegin(), CTreeModelNode< TData >::SubNodeEnd(), and x_SetSelState().

Referenced by SetSelection().

◆ x_SetSelState()

void CPhyloTree::x_SetSelState	(	TTreeIdx	idx,
		CPhyloNodeData::TSelectedState	state,
		bool	override_explicit = `true`
	)

protected

Set selected state of anode and add/remove it from m_Selected as needed.

Definition at line 543 of file phylo_tree.cpp.

References set< Key, Compare >::end(), set< Key, Compare >::erase(), CPhyloNodeData::eSelected, set< Key, Compare >::find(), set< Key, Compare >::insert(), m_ExplicitlySelected, CTreeModel< CPhyloTreeNode >::m_Nodes, and m_Selected.

Referenced by SetSelection(), x_SelectChildren(), and x_SelectParents().

Member Data Documentation

◆ m_ColorTable

CRef<CRgbaGradColorTable> CPhyloTree::m_ColorTable

protected

Color table to store colors by index.

Definition at line 384 of file phylo_tree.hpp.

Referenced by GetColorTable().

◆ m_CurrentEdgeChild

TTreeIdx CPhyloTree::m_CurrentEdgeChild

protected

Currently active edge (to allow re-rooting by edge).

Since we do not explicitly store edges, save it as the edges parent and child nodes.

Definition at line 378 of file phylo_tree.hpp.

Referenced by ClearSelection(), GetCurrentEdge(), HasCurrentEdge(), and SetCurrentEdge().

◆ m_CurrentEdgeParent

TTreeIdx CPhyloTree::m_CurrentEdgeParent

protected

Definition at line 379 of file phylo_tree.hpp.

Referenced by ClearSelection(), GetCurrentEdge(), HasCurrentEdge(), and SetCurrentEdge().

◆ m_CurrentNode

TTreeIdx CPhyloTree::m_CurrentNode

protected

Currently active node (for operations like edit), or Null()

Definition at line 374 of file phylo_tree.hpp.

Referenced by ClearSelection(), GetCurrentNode(), GetCurrentNodeIdx(), HasCurrentNode(), SelectByPoint(), and SetCurrentNode().

◆ m_ExplicitlySelected

TTreeIdxSet CPhyloTree::m_ExplicitlySelected

protected

Often when you select a node, it's children or parents may also join the selection set.

But in case of queries, user may want to only see (or iterate over) nodes actually meeting query criteria or explictly clicked on.

Definition at line 367 of file phylo_tree.hpp.

Referenced by ClearSelection(), GetExplicitlySelected(), GetExplicitlySelectedAndNotCollapsed(), GetExplicitlySelectedIDs(), GetSelState(), SetExplicitlySelected(), SetLeavesExplicitlySelected(), SetSelection(), and x_SetSelState().

◆ m_FeatureDict

CBioTreeFeatureDictionary CPhyloTree::m_FeatureDict

protected

Feature dictionary.

Definition at line 387 of file phylo_tree.hpp.

Referenced by GetFeatureDict(), and x_ConvertUpstream().

◆ m_GraphicsModel

CRef<CTreeGraphicsModel> CPhyloTree::m_GraphicsModel

protected

Model for rendering (updated from current tree state)

Definition at line 382 of file phylo_tree.hpp.

Referenced by Clear(), GetGraphicsModel(), GetGraphicsModelRef(), and SetGraphicsModelRef().

◆ m_NodesMap

TTIDPhyloTreeNodeMap CPhyloTree::m_NodesMap

protected

Definition at line 371 of file phylo_tree.hpp.

Referenced by FindNodeById(), and UpdateNodesMapping().

◆ m_Selected

TTreeIdxSet CPhyloTree::m_Selected

protected

Definition at line 361 of file phylo_tree.hpp.

Referenced by ClearSelection(), GetNumSelected(), GetSelected(), GetSelectedBoundary(), GetSelectedIDs(), HasSelection(), SetExplicitlySelected(), SetLeavesExplicitlySelected(), and x_SetSelState().

◆ m_SelectionSets

CPhyloSelectionSetMgr CPhyloTree::m_SelectionSets

protected

Selection sets - sets of selected nodes, which are saved in the biotreecontainer in user data (visualized kind of like clusters)

Definition at line 391 of file phylo_tree.hpp.

Referenced by GetSelectionSets().

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

include/gui/widgets/phylo_tree/phylo_tree.hpp
src/gui/widgets/phylo_tree/phylo_tree.cpp

Public Types

Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Private Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ TClusterID

◆ TID

◆ TSelState

◆ TSelStateValue

◆ TTIDPhyloTreeNodeMap

◆ TTreeIdxSet

Constructor & Destructor Documentation

◆ CPhyloTree() [1/2]

◆ CPhyloTree() [2/2]

Member Function Documentation

◆ Clear()

◆ ClearSelection()

◆ FindNodeById()

◆ GetAllCollapsed()

◆ GetCollapsedParentIdx()

◆ GetColorTable()

◆ GetCurrentEdge()

◆ GetCurrentNode()

◆ GetCurrentNodeIdx()

◆ GetExplicitlySelected()

◆ GetExplicitlySelectedAndNotCollapsed()

◆ GetExplicitlySelectedIDs()

◆ GetFeatureDict() [1/2]

◆ GetFeatureDict() [2/2]

◆ GetGraphicsModel()

◆ GetGraphicsModelRef()

◆ GetNumSelected()

◆ GetSelected()

◆ GetSelectedBoundary()

◆ GetSelectedIDs()

◆ GetSelectionSets() [1/2]

◆ GetSelectionSets() [2/2]

◆ GetSelState()

◆ HasCurrentEdge()

◆ HasCurrentNode()

◆ HasSelection()

◆ IsUnused()

◆ IsVisible()

◆ operator=()

◆ SelectByPoint()

◆ SelectByRect()

◆ SetCurrentEdge()

◆ SetCurrentNode() [1/2]

◆ SetCurrentNode() [2/2]

◆ SetExplicitlySelected()

◆ SetGraphicsModelRef()

◆ SetLeavesExplicitlySelected()

◆ SetSelection() [1/2]

◆ SetSelection() [2/2]

◆ SetSelectionIDs()

◆ Sort()

◆ SortLabel()

◆ SortLabelRange()

◆ SortSubtreeDist()

◆ TestForNode()

◆ UpdateNodesMapping()

◆ x_CommonNodeSearch()

◆ x_ConvertUpstream()

◆ x_GetChildState()

◆ x_GetParentState()

◆ x_PropagateCommonState()

◆ x_SelectChildren()

◆ x_SelectParents()

◆ x_SetSelState()

Member Data Documentation

◆ m_ColorTable

◆ m_CurrentEdgeChild

◆ m_CurrentEdgeParent

◆ m_CurrentNode

◆ m_ExplicitlySelected

◆ m_FeatureDict