CPhyloTreeDataSource Class Reference

Search Toolkit Book for CPhyloTreeDataSource

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

Inheritance diagram for CPhyloTreeDataSource:

Collaboration diagram for CPhyloTreeDataSource:

Classes
class	visitor_read_properties

Public Types
typedef CAppJobDispatcher::TJobID	TJobID
typedef CPhyloTree	TTreeType
typedef CPhyloTree::TTreeIdx	TTreeIdx
typedef CPhyloTree::TNodeType	TNodeType
typedef CPhyloTree::TClusterID	TClusterID
typedef std::map< int, size_t >	TClusterToColorMap
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 Types inherited from IQueryDataSource
typedef vector< pair< string, string > >	TNamedQueries

Public Member Functions
	CPhyloTreeDataSource (const objects::CBioTreeContainer &tree, objects::CScope &scope, bool expand_all=false)
	Throws exception if tree is empty - at least 1 node is required. More...
	~CPhyloTreeDataSource ()
void	Init (const objects::CBioTreeContainer &tree, objects::CScope &scope, bool expand_all=false)
	Throws exception if tree is empty - at least 1 node is required. More...
void	Clear ()
void	SetColorIndices (CPhyloTreeScheme *scheme)
string	GenerateTooltipFormat ()
void	ComputeLengthsFromRoot ()
	Create sorted array of distances of nodes from the parent (the m_LenDistribution array) More...
float	GetClosestLen (float pct) const
	Look in vector of sorted distances of nodes from the root and given a pct (0..1), return the distance closest to that value. More...
bool	HasLenDistribution () const
	Return true if data is available (for trees without distances, may not be) More...
void	MeasureTree (TTreeIdx node)
void	MeasureTree ()
void	ApplyAttributes (CBioTreeAttrReader::TAttrTable &attrs, CPhyloTreeScheme *scheme, const string &labelfmt="")
bool	HasClusters ()
void	Clusterize (CPhyloTreeScheme *scheme)
void	ReRoot (TTreeIdx root_idx)
	Set the root node of the tree to the node at root_idx. More...
void	ReRootEdge (TTreeIdx edge_child_node)
	Re-root on the edge between the selected node and its parent. More...
void	ReRootMidpoint ()
	Re-root tree using midpoint-method. More...
set< CPhyloNodeData::TID >	CollapseByDistance (int leaf_count_target, SCollapsable *collapse_func)
	Collapse, based on distance, enough nodes in the tree to get the total number of leaves down to the requested number. More...
void	Relabel (CPhyloTreeScheme *scheme, string labelFmt)
void	Sort (bool ascending)
void	SortDist (bool ascending)
void	SortLabel (bool ascending)
void	SortLabelRange (bool ascending)
TModelRect	GetBoundRect ()
void	Clean ()
void	Filter ()
void	FilterDistances (double x_dist)
CPhyloTree *	GetTree ()
const CPhyloTree *	GetTree () const
void	SetTreeLabel (const CTreeLabel &l)
	Label for tree (optional element of biotreecontainer) More...
CTreeLabel	GetTreeLabel () const
CTreeGraphicsModel &	GetModel ()
	Get model for rendering. More...
const CBioTreeFeatureDictionary &	GetDictionary () const
unsigned int	GetNumNodes (void)
unsigned int	GetVisibleNodes (void)
unsigned int	GetNumEdges (void)
int	GetWidth (void)
int	GetSize (void)
int	GetMaxLabelLen (void)
double	GetNormDistance (void)
double	GetMinDistance (void)
TClusterID	GetMaxClusterID ()
vector< TTreeIdx >	FindNodes (const string &query, size_t &num_queried, CStringMatching::EStringMatching string_matching, NStr::ECase use_case) const
	search for nodes via the specified text matching algorithm More...
const vector< CPhyloTree::TID > &	GetStringQueryIDs () const
	Get IDs selected by most recent call to FindNodes. More...
TTreeIdx	IterateOverSelNodes (int direction, bool highlight)
TTreeIdx	GetCurrentSearchNode () const
void	SetCurrentSearchNode (TTreeIdx node_idx)
CPhyloSelectionSetMgr &	GetSelectionSets ()
void	UpdateSelectionSets (CPhyloTreeScheme *scheme)
const TClusterToColorMap &	GetClusterToColorMap () const
	Get map that translates cluster-ids to color indices. More...
void	Cut ()
void	Paste ()
TTreeIdx	NewNode (bool after=true)
void	Remove (bool subtree=true)
void	RemoveSelected ()
void	MoveNode (bool up)
bool	ClipboardEmpty () const
void	SetCollapsedLabel (CPhyloTree::TTreeIdx idx)
	Collapse single node, do any relabeling if needed. More...
void	SetCollapsedLabels (const vector< CPhyloNodeData::TID > &node_ids)
	Collapse all nodes in node_ids, doing relabeling if needed. More...
void	CollapseSelected ()
IQueryDataSource interface implementation
virtual string	GetColumnLabel (size_t col) const
	get number and names of columns in data source More...
virtual size_t	GetColsCount () const
virtual CMacroQueryExec *	GetQueryExec (bool casesensitive, CStringMatching::EStringMatching matching)
	Create an appropriate instance of a subclass of CQueryExec for that will be used to execute a query on the data source. More...
virtual void	SetQueryResults (CMacroQueryExec *q)
	Set selection results to be whatever elements are selected in 'q'. More...
virtual void	ClearQueryResults ()
	Clear any current results from previous queries. More...
virtual CRef< objects::CScope >	GetScope ()
	Return a scope for the data source, if available. More...
virtual void	ExecuteStringQuery (const string &query, size_t &num_selected, size_t &num_queried, CStringMatching::EStringMatching string_matching=CStringMatching::ePlainSearch, NStr::ECase use_case=NStr::eCase)
	Execute a string-matching query on the underlying data. 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
Public Member Functions inherited from IQueryDataSource
virtual	~IQueryDataSource ()
	dtor More...

Protected Attributes
CRef< CPhyloTree >	m_TreeModel
CTreeLabel	m_TreeLabel
CPhyloTreeCalculator *	m_Calc
CRef< objects::CScope >	m_Scope
TTreeIdx	m_SearchCurrentNode
TClusterToColorMap	m_ClusterToColorMap
std::vector< float >	m_LenDistribution
vector< CPhyloTree::TID >	m_StringQueryIDs
	Temporary storage for string query results to get ID's back to caller. More...

Static Protected Attributes
static CPhyloTree	m_sTreeClipboard
	static (to allow copying between trees) More...

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

Detailed Description

Definition at line 231 of file phylo_tree_ds.hpp.

Member Typedef Documentation

TClusterID

typedef CPhyloTree::TClusterID CPhyloTreeDataSource::TClusterID

Definition at line 240 of file phylo_tree_ds.hpp.

TClusterToColorMap

typedef std::map<int, size_t> CPhyloTreeDataSource::TClusterToColorMap

Definition at line 241 of file phylo_tree_ds.hpp.

TJobID

typedef CAppJobDispatcher::TJobID CPhyloTreeDataSource::TJobID

Definition at line 236 of file phylo_tree_ds.hpp.

TNodeType

typedef CPhyloTree::TNodeType CPhyloTreeDataSource::TNodeType

Definition at line 239 of file phylo_tree_ds.hpp.

TTreeIdx

typedef CPhyloTree::TTreeIdx CPhyloTreeDataSource::TTreeIdx

Definition at line 238 of file phylo_tree_ds.hpp.

TTreeType

typedef CPhyloTree CPhyloTreeDataSource::TTreeType

Definition at line 237 of file phylo_tree_ds.hpp.

Constructor & Destructor Documentation

CPhyloTreeDataSource()

CPhyloTreeDataSource::CPhyloTreeDataSource	(	const objects::CBioTreeContainer &	tree,
		objects::CScope &	scope,
		bool	expand_all = false
	)

Throws exception if tree is empty - at least 1 node is required.

Definition at line 165 of file phylo_tree_ds.cpp.

References Init().

~CPhyloTreeDataSource()

CPhyloTreeDataSource::~CPhyloTreeDataSource

(

)

Definition at line 173 of file phylo_tree_ds.cpp.

References m_Calc, and NULL.

Member Function Documentation

ApplyAttributes()

void CPhyloTreeDataSource::ApplyAttributes	(	CBioTreeAttrReader::TAttrTable &	attrs,
		CPhyloTreeScheme *	scheme,
		const string &	labelfmt = ""
	)

Definition at line 302 of file phylo_tree_ds.cpp.

References CPhyloTreeCalculator::ClearAttrTable(), CRgbaGradColorTable::ClearColors(), Clusterize(), CPhyloTree::GetColorTable(), CRef< C, Locker >::GetNCObject(), CTreeModel< TNode >::GetRootIdx(), CPhyloTreeCalculator::Init(), m_Calc, m_TreeModel, CPhyloTreeCalculator::SetAttrTable(), CPhyloTreeCalculator::SetLabelFormat(), and TreeDepthFirst().

Referenced by CPhyloTreeWidget::OnLoadAttributes().

Clean()

void CPhyloTreeDataSource::Clean

(

)

Definition at line 811 of file phylo_tree_ds.cpp.

References CSpatialHash2D< T >::Clear(), CTreeGraphicsModel::GetCollisionData(), GetModel(), GetTree(), Init(), m_Scope, TreeConvert2Container(), and TreeConvertNonSingleChild2Container().

Referenced by CPhyloTreeWidget::OnClean().

Clear()

void CPhyloTreeDataSource::Clear

(

void

)

Definition at line 214 of file phylo_tree_ds.cpp.

References CPhyloTree::Clear(), m_SearchCurrentNode, m_TreeModel, and CTreeModel< CPhyloTreeNode >::Null().

Referenced by CPhyTreeView::OnBioTreeChanged(), and CPhyloTreeWidget::RemoveCurrentDataSource().

ClearQueryResults()

void CPhyloTreeDataSource::ClearQueryResults ( )

virtual

Clear any current results from previous queries.

Implements IQueryDataSource.

Definition at line 946 of file phylo_tree_ds.cpp.

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

Referenced by CPhyloTreeWidget::OnUpdateSelChanged(), and SetQueryResults().

ClipboardEmpty()

bool CPhyloTreeDataSource::ClipboardEmpty ( ) const

inline

Definition at line 377 of file phylo_tree_ds.hpp.

References CTreeModel< TNode >::GetRootIdx(), m_sTreeClipboard, and CTreeModelNode< CPhyloNodeData >::Null().

Referenced by CPhyloTreeWidget::OnUpdateEdit().

Clusterize()

void CPhyloTreeDataSource::Clusterize

(

CPhyloTreeScheme *

scheme

)

Definition at line 332 of file phylo_tree_ds.cpp.

References CRgbaGradColorTable::AddColor(), color, CRgbaColor::ColorDistance(), CRgbaColor::Darken(), CPhyloTreeScheme::eClusters, map_checker< Container >::end(), map_checker< Container >::find(), CRgbaGradColorTable::FindClosestColor(), CRgbaGradColorTable::FindColor(), CPhyloTreeCalculator::GetClusters(), CPhyloSelectionSetMgr::GetClusterToSelectionMap(), CRgbaGradColorTable::GetColor(), CPhyloTreeScheme::GetColoration(), CPhyloTree::GetColorTable(), CTreeModel< TNode >::GetParent(), CPhyloTree::GetSelectionSets(), CPhyloSelectionSetMgr::GetSets(), CPhyloTreeCalculator::GetWidth(), CTreeModelNode< TData >::IsLeaf(), ITERATE, m_Calc, m_ClusterToColorMap, m_TreeModel, CRgbaColor::RotateColor(), SetColorIndices(), and map_checker< Container >::size().

Referenced by ApplyAttributes(), CPhyloTreeWidget::RedrawDataSource(), Relabel(), and UpdateSelectionSets().

CollapseByDistance()

set< CPhyloNodeData::TID > CPhyloTreeDataSource::CollapseByDistance	(	int	leaf_count_target,
		SCollapsable *	collapse_func
	)

Collapse, based on distance, enough nodes in the tree to get the total number of leaves down to the requested number.

(or just over if exact match is not possible)

(or just over if exact match is not possible). We do not expand nodes that may already be collapsed.

Definition at line 656 of file phylo_tree_ds.cpp.

References CPhyloNodeData::eHideChildren, set< Key, Compare >::end(), set< Key, Compare >::erase(), set< Key, Compare >::find(), CPhyloTreeMaxDirectChildDist::GetDistances(), CPhyloTree::GetFeatureDict(), CRef< C, Locker >::GetNCObject(), CRef< C, Locker >::GetNCPointer(), CTreeModel< TNode >::GetNode(), CTreeModel< TNode >::GetRoot(), CTreeModel< TNode >::GetRootIdx(), CBioTreeFeatureDictionary::HasFeature(), i, set< Key, Compare >::insert(), CPhyloTreeNode::IsLeafEx(), m_TreeModel, n, ncbi::grid::netcache::search::fields::size, ct::sort(), and TreeDepthFirst().

Referenced by CPhyloTreeWidget::OnCollapseToViewport().

CollapseSelected()

void CPhyloTreeDataSource::CollapseSelected

(

)

Definition at line 1549 of file phylo_tree_ds.cpp.

References _TRACE, CPhyloTreeNode::CanExpandCollapse(), CPhyloNodeData::eHideChildren, CPhyloTreeNode::ExpandCollapse(), CPhyloTree::GetExplicitlySelected(), CPhyloTree::GetFeatureDict(), CTreeModel< TNode >::GetNode(), CTreeModelNode< TData >::GetParent(), CTreeModel< TNode >::GetRootIdx(), i, m_TreeModel, MeasureTree(), and SetCollapsedLabel().

Referenced by CPhyloTreeWidget::OnCollapseSelected().

ComputeLengthsFromRoot()

void CPhyloTreeDataSource::ComputeLengthsFromRoot

(

)

Create sorted array of distances of nodes from the parent (the m_LenDistribution array)

Definition at line 247 of file phylo_tree_ds.cpp.

References CPhyloTreeMaxChildDist::GetDistances(), CPhyloTree::GetFeatureDict(), CPhyloTreeMaxChildDist::GetMaxDist(), CPhyloTreeMaxChildDist::GetMinDist(), CRef< C, Locker >::GetNCObject(), CRef< C, Locker >::GetNCPointer(), CTreeModel< TNode >::GetNode(), CTreeModel< TNode >::GetRootIdx(), CBioTreeFeatureDictionary::HasFeature(), i, m_LenDistribution, m_TreeModel, ct::sort(), and TreeDepthFirst().

Referenced by IPhyloTreeRender::x_ComputeEdgeHighlight().

Cut()

void CPhyloTreeDataSource::Cut

(

)

Definition at line 1310 of file phylo_tree_ds.cpp.

References _TRACE, CPhyloTree::Clear(), CPhyloTree::ClearSelection(), CPhyloTree::GetCurrentNode(), CPhyloTree::GetCurrentNodeIdx(), CRef< C, Locker >::GetNCObject(), CTreeModel< TNode >::GetRootIdx(), m_sTreeClipboard, m_TreeModel, MeasureTree(), n, CTreeModel< CPhyloTreeNode >::Null(), CTreeModel< TNode >::RemoveChild(), CPhyloTree::SetSelection(), TreeDepthFirst(), and CPhyloTree::UpdateNodesMapping().

Referenced by CPhyloTreeWidget::OnEdit().

ExecuteStringQuery()

void CPhyloTreeDataSource::ExecuteStringQuery ( const string &  query, size_t &  num_selected, size_t &  num_queried, CStringMatching::EStringMatching  string_matching = CStringMatching::ePlainSearch, NStr::ECase  use_case = NStr::eCase  )

virtual

Execute a string-matching query on the underlying data.

Parameters

[in]	query	Reference to a pattern to search for.
[out]	num_selected	Number of matching rows.
[out]	num_queried	Total rows queried.
[in]	string_matching	String matching algorithm to use.
[in]	use_case	Whether to do a case sensitive compare (default), or not.

Implements IQueryDataSource.

Definition at line 951 of file phylo_tree_ds.cpp.

References CPhyloTree::ClearSelection(), FindNodes(), CPhyloNodeData::GetId(), CTreeModel< TNode >::GetNode(), CTreeModelNode< TData >::GetValue(), Info(), LOG_POST, m_SearchCurrentNode, m_StringQueryIDs, m_TreeModel, CTreeModel< CPhyloTreeNode >::Null(), query, and CPhyloTree::SetSelection().

Filter()

void CPhyloTreeDataSource::Filter

(

)

Definition at line 832 of file phylo_tree_ds.cpp.

References CRef< C, Locker >::GetNCObject(), CRef< C, Locker >::GetNCPointer(), CTreeModel< TNode >::GetRootIdx(), m_TreeModel, MeasureTree(), and TreeDepthFirstInvarient().

Referenced by CPhyloTreeWidget::OnFilter().

FilterDistances()

void CPhyloTreeDataSource::FilterDistances

(

double

x_dist

)

Definition at line 842 of file phylo_tree_ds.cpp.

References CRef< C, Locker >::GetNCObject(), CRef< C, Locker >::GetNCPointer(), CTreeModel< TNode >::GetRootIdx(), m_TreeModel, MeasureTree(), and TreeDepthFirstInvarient().

FindNodes()

vector< CPhyloTree::TTreeIdx > CPhyloTreeDataSource::FindNodes	(	const string &	query,
		size_t &	num_queried,
		CStringMatching::EStringMatching	string_matching,
		NStr::ECase	use_case
	)		const

search for nodes via the specified text matching algorithm

Definition at line 1022 of file phylo_tree_ds.cpp.

References CRef< C, Locker >::GetNCObject(), m_TreeModel, query, and TreeDepthFirst().

Referenced by ExecuteStringQuery().

GenerateTooltipFormat()

string CPhyloTreeDataSource::GenerateTooltipFormat

(

)

Definition at line 282 of file phylo_tree_ds.cpp.

References CPhyloTree::GetFeatureDict(), CBioTreeFeatureDictionary::GetFeatureDict(), CRef< C, Locker >::IsNull(), ITERATE, and m_TreeModel.

Referenced by CPhyTreeView::OnBioTreeChanged(), CPhyloTreeWidget::OnEditNode(), CPhyloTreeWidget::OnInfoTip(), CPhyloTreeWidget::OnOpenPropertiesDlg(), and CPhyTreeView::OnProjectChanged().

GetBoundRect()

TModelRect CPhyloTreeDataSource::GetBoundRect

(

void

)

Definition at line 802 of file phylo_tree_ds.cpp.

References CRef< C, Locker >::GetNCObject(), CPhyloTreeRectCalculator::GetRect(), CTreeModel< TNode >::GetRootIdx(), CPhyloTreeRectCalculator::Init(), m_TreeModel, and TreeDepthFirst().

Referenced by CPhyloCircularCladogram::x_Layout(), CPhyloForce::x_Layout(), CPhyloRadial::x_Layout(), CPhyloRectCladogram::x_Layout(), and CPhyloSlantedCladogram::x_Layout().

GetClosestLen()

float CPhyloTreeDataSource::GetClosestLen

(

float

pct

)

const

Look in vector of sorted distances of nodes from the root and given a pct (0..1), return the distance closest to that value.

Definition at line 229 of file phylo_tree_ds.cpp.

References m_LenDistribution, and min().

Referenced by IPhyloTreeRender::GetEdgeColor().

GetClusterToColorMap()

const TClusterToColorMap& CPhyloTreeDataSource::GetClusterToColorMap ( ) const

inline

Get map that translates cluster-ids to color indices.

Definition at line 368 of file phylo_tree_ds.hpp.

References m_ClusterToColorMap.

Referenced by CPhyloSaveSelectiondlg::SetSelections().

GetColsCount()

size_t CPhyloTreeDataSource::GetColsCount ( ) const

virtual

Implements IQueryDataSource.

Definition at line 869 of file phylo_tree_ds.cpp.

References CPhyloTree::GetFeatureDict(), CBioTreeFeatureDictionary::GetFeatureDict(), m_TreeModel, and map_checker< Container >::size().

GetColumnLabel()

string CPhyloTreeDataSource::GetColumnLabel ( size_t  col ) const

virtual

get number and names of columns in data source

Implements IQueryDataSource.

Definition at line 853 of file phylo_tree_ds.cpp.

References map_checker< Container >::begin(), count, map_checker< Container >::end(), CPhyloTree::GetFeatureDict(), CBioTreeFeatureDictionary::GetFeatureDict(), and m_TreeModel.

GetCurrentSearchNode()

TTreeIdx CPhyloTreeDataSource::GetCurrentSearchNode ( ) const

inline

Definition at line 360 of file phylo_tree_ds.hpp.

References m_SearchCurrentNode.

Referenced by CPhyloTreeWidget::OnUpdateSelChanged().

GetDictionary()

const CBioTreeFeatureDictionary& CPhyloTreeDataSource::GetDictionary ( void  ) const

inline

Definition at line 321 of file phylo_tree_ds.hpp.

References CPhyloTree::GetFeatureDict(), and m_TreeModel.

Referenced by CPhyloTreeWidget::EditLabel(), GetQueryExec(), CPhyTreeView::GetSelection(), CPhyloTreeWidget::OnEditNode(), CPhyloTreeWidget::OnExportSelection(), CPhyloTreeWidget::OnInfoTip(), CPhyloTreeWidget::QueryEnd(), CPhyloTreeWidget::SendEditEvent(), CwxPhyloSettingsDlg::SetParams(), and CPhyTreeView::x_OnSetSelection().

GetMaxClusterID()

TClusterID CPhyloTreeDataSource::GetMaxClusterID ( )

inline

Definition at line 332 of file phylo_tree_ds.hpp.

References CPhyloTreeCalculator::GetMaxClusterID(), and m_Calc.

Referenced by CChangePhyloSelectionSetCmd::PerformEdit(), and UpdateSelectionSets().

GetMaxLabelLen()

int CPhyloTreeDataSource::GetMaxLabelLen ( void  )

inline

Definition at line 329 of file phylo_tree_ds.hpp.

References CPhyloTreeCalculator::GetMaxLabelLen(), and m_Calc.

GetMinDistance()

double CPhyloTreeDataSource::GetMinDistance ( void  )

inline

Definition at line 331 of file phylo_tree_ds.hpp.

References CPhyloTreeCalculator::GetMinDistance(), and m_Calc.

GetModel()

CTreeGraphicsModel& CPhyloTreeDataSource::GetModel ( )

inline

Get model for rendering.

Definition at line 318 of file phylo_tree_ds.hpp.

References CPhyloTree::GetGraphicsModel(), and m_TreeModel.

Referenced by IPhyloTreeRender::BufferedRender(), Clean(), IPhyloTreeRender::GetEdgeColor(), IPhyloTreeRender::InitCollisionInfo(), CPhyloTreeWidget::IterateSelection(), CChangePhyloPropertyCmd::PerformEdit(), IPhyloTreeRender::Render(), IPhyloTreeRender::RenderPdf(), CPhyloTreeWidget::SetScheme(), CPhyloSaveSelectiondlg::SetSelections(), IPhyloTreeRender::x_AddCollapsedGeomNode(), IPhyloTreeRender::x_AddCollapsedTextureNode(), IPhyloTreeRender::x_ComputeEdgeHighlight(), CPhyloCircularCladogram::x_DrawTree(), CPhyloForce::x_Layout(), CPhyloTreePane::x_Render(), IPhyloTreeRender::x_RenderNodeVbo(), CPhyloCircularCladogram::x_RenderVbo(), CPhyloRadial::x_RenderVbo(), CPhyloRectCladogram::x_RenderVbo(), CPhyloSlantedCladogram::x_RenderVbo(), CPhyloRectCladogram::x_RenderVboPseudoSplines(), CPhyloRectCladogram::x_RenderVboSplines(), CPhyloRectCladogram::x_SetElementVisibility(), IPhyloTreeRender::x_SetElementVisibility(), CPhyloCircularCladogram::x_SetGlRenderOptions(), CPhyloRadial::x_SetGlRenderOptions(), CPhyloRectCladogram::x_SetGlRenderOptions(), and CPhyloSlantedCladogram::x_SetGlRenderOptions().

GetNormDistance()

double CPhyloTreeDataSource::GetNormDistance ( void  )

inline

Definition at line 330 of file phylo_tree_ds.hpp.

References CPhyloTreeCalculator::GetMaxDistance(), and m_Calc.

Referenced by CCalcCircularTree::CCalcCircularTree(), CCalcRadialTree::CCalcRadialTree(), CCalcRectangularTree::CCalcRectangularTree(), CDrawCircularTreeVbo::CDrawCircularTreeVbo(), CPhyloCircularCladogram::ComputeDistFromPixels(), IPhyloTreeRender::ComputeDistFromPixels(), CPhyloCircularCladogram::x_Layout(), CPhyloForce::x_Layout(), CPhyloRadial::x_Layout(), CPhyloRectCladogram::x_Layout(), and CPhyloSlantedCladogram::x_Layout().

GetNumEdges()

unsigned int CPhyloTreeDataSource::GetNumEdges ( void  )

inline

Definition at line 325 of file phylo_tree_ds.hpp.

References CPhyloTreeCalculator::GetNumEdges(), and m_Calc.

Referenced by CPhyloCircularCladogram::x_RenderVbo(), CPhyloRadial::x_RenderVbo(), CPhyloSlantedCladogram::x_RenderVbo(), CPhyloRectCladogram::x_RenderVboPseudoSplines(), and CPhyloRectCladogram::x_RenderVboSplines().

GetNumNodes()

unsigned int CPhyloTreeDataSource::GetNumNodes ( void  )

inline

Definition at line 323 of file phylo_tree_ds.hpp.

References CPhyloTreeCalculator::GetNumNodes(), and m_Calc.

Referenced by CPhyloTreeWidget::SetDataSource(), CPhyloTreeWidget::SetDataSourceNoUpdate(), CPhyloTreeWidget::SetPortLimits(), CPhyloCircularCladogram::x_RenderVbo(), CPhyloRadial::x_RenderVbo(), CPhyloRectCladogram::x_RenderVbo(), CPhyloSlantedCladogram::x_RenderVbo(), CPhyloRectCladogram::x_RenderVboPseudoSplines(), and CPhyloRectCladogram::x_RenderVboSplines().

GetQueryExec()

CMacroQueryExec * CPhyloTreeDataSource::GetQueryExec ( bool  casesensitive, CStringMatching::EStringMatching  matching  )

virtual

Create an appropriate instance of a subclass of CQueryExec for that will be used to execute a query on the data source.

Implements IQueryDataSource.

Definition at line 874 of file phylo_tree_ds.cpp.

References CQueryExec::AddFunc(), CQueryParseNode::eAnd, CQueryParseNode::eBetween, CQueryParseNode::eBoolConst, NStr::eCase, CQueryParseNode::eEQ, CQueryParseNode::eFloatConst, CQueryParseNode::eFrom, CQueryParseNode::eFunction, CQueryParseNode::eGE, CQueryParseNode::eGT, CQueryParseNode::eIdentifier, CQueryParseNode::eIn, CQueryParseNode::eIntConst, CQueryParseNode::eLE, CQueryParseNode::eLike, CQueryParseNode::eLT, NStr::eNocase, CQueryParseNode::eNot, CQueryParseNode::eOr, CQueryParseNode::eSelect, CQueryParseNode::eString, CQueryParseNode::eSub, CQueryParseNode::eXor, GetDictionary(), GetTree(), and CTreeQueryExec::SetTree().

GetScope()

virtual CRef<objects::CScope> CPhyloTreeDataSource::GetScope ( void  )

inlinevirtual

Return a scope for the data source, if available.

Reimplemented from IQueryDataSource.

Definition at line 344 of file phylo_tree_ds.hpp.

References m_Scope.

GetSelectionSets()

CPhyloSelectionSetMgr& CPhyloTreeDataSource::GetSelectionSets ( )

inline

Definition at line 363 of file phylo_tree_ds.hpp.

References CPhyloTree::GetSelectionSets(), and m_TreeModel.

Referenced by CPhyloSaveSelectiondlg::OnAddCurrentSelBtnClick(), CPhyloTreeWidget::OnAddSelectionSet(), CPhyloSaveSelectiondlg::OnBitmapbuttonDownClick(), CPhyloSaveSelectiondlg::OnBitmapbuttonUpClick(), CPhyloSaveSelectiondlg::OnDeleteSelBtnClick(), CPhyloSaveSelectiondlg::OnLeftDown(), CPhyloSaveSelectiondlg::OnSelColorPickerColourPickerChanged(), CPhyloSaveSelectiondlg::OnSelectionTextUpdated(), CPhyloSaveSelectiondlg::OnSelListctrlSelected(), CChangePhyloSelectionSetCmd::PerformEdit(), CPhyloSaveSelectiondlg::SetSelections(), CPhyloSaveSelectiondlg::UpdateSelections(), and UpdateSelectionSets().

GetSize()

int CPhyloTreeDataSource::GetSize ( void  )

inline

Definition at line 328 of file phylo_tree_ds.hpp.

References CPhyloTreeCalculator::GetHeight(), and m_Calc.

Referenced by CCalcRadialTree::CCalcRadialTree(), CCalcRectangularTree::CCalcRectangularTree(), CDrawCircularTreeVbo::CDrawCircularTreeVbo(), IPhyloTreeRender::InitCollisionInfo(), CPhyloTreeWidget::OnZoomTip(), IPhyloTreeRender::x_ComputeEdgeHighlight(), IPhyloTreeRender::x_FindBestSize(), CPhyloCircularCladogram::x_Layout(), CPhyloForce::x_Layout(), CPhyloRadial::x_Layout(), CPhyloRectCladogram::x_Layout(), and CPhyloSlantedCladogram::x_Layout().

GetStringQueryIDs()

const vector<CPhyloTree::TID>& CPhyloTreeDataSource::GetStringQueryIDs ( ) const

inline

Get IDs selected by most recent call to FindNodes.

Definition at line 356 of file phylo_tree_ds.hpp.

References m_StringQueryIDs.

GetTree() [1/2]

CPhyloTree* CPhyloTreeDataSource::GetTree ( void  )

inline

Definition at line 310 of file phylo_tree_ds.hpp.

References CRef< C, Locker >::GetPointerOrNull(), and m_TreeModel.

Referenced by IPhyloTreeRender::BufferedRender(), CCalcCircularTree::CCalcCircularTree(), CCalcRadialTree::CCalcRadialTree(), CCalcSlantedTree::CCalcSlantedTree(), CChangePhyloPropertyCmd::CChangePhyloPropertyCmd(), CDrawCircularTreeVbo::CDrawCircularTreeVbo(), Clean(), CPhyloTreeWidget::EditLabel(), CChangePhyloSelectionSetCmd::Execute(), CChangePhyloPropertyCmd::Execute(), IPhyloTreeRender::GetHoverNode(), IPhyloTreeRender::GetHoverNodeIdx(), GetQueryExec(), CwxPhyloSettingsDlg::GetRandomNode(), CPhyTreeView::GetSelection(), CPhyloTreePS::Init(), CPhyloTreeWidget::IterateSelection(), CPhyloSaveSelectiondlg::OnAddCurrentSelBtnClick(), CPhyloTreeWidget::OnAddSelectionSet(), CPhyTreeView::OnBioTreeChanged(), CPhyloTreeWidget::OnClearSelection(), CPhyloTreeWidget::OnCollapseChildren(), CPhyloTreeWidget::OnCollapseToViewport(), CPhyTreeView::OnCreateSelectedSubtree(), CPhyloTreeWidget::OnEditNode(), CPhyloTreeWidget::OnExpandChildren(), CPhyloTreeWidget::OnExportSelection(), CPhyTreeView::OnExportTree(), CPhyloTreeWidget::OnInfoTip(), IPhyloTreeRender::OnLeftDblClick(), IPhyloTreeRender::OnLeftDown(), CPhyloTreeWidget::OnRerootTree(), CPhyloTreeWidget::OnRerootTreeAtEdge(), IPhyloTreeRender::OnRightDown(), CPhyloTreeWidget::OnSearchTip(), CPhyloTreeWidget::OnSelectAll(), CPhyloTreeWidget::OnSetMidpointRoot(), CPhyloTreeWidget::OnShowAll(), CPhyTreeView::OnSomethingEdited(), IPhyloTreeRender::OnTimerLeftUp(), CPhyloTreeWidget::OnUpdateCollapseChildren(), CPhyloTreeWidget::OnUpdateCollapseSelected(), CPhyloTreeWidget::OnUpdateEdit(), CPhyloTreeWidget::OnUpdateEditLabel(), CPhyloTreeWidget::OnUpdateEditNode(), CPhyloTreeWidget::OnUpdateExpandChildren(), CPhyloTreeWidget::OnUpdateRerootTree(), CPhyloTreeWidget::OnUpdateRerootTreeAtEdge(), CPhyloTreeWidget::OnUpdateSelChanged(), CPhyloTreeWidget::OnUpdateSetMidpointRoot(), CPhyloTreeWidget::OnUpdateSubtreeFromSelection(), CPhyloTreeWidget::OnUpdateZoomSel(), CPhyloTreeWidget::OnUpdateZoomToSubtree(), CPhyloTreeWidget::OnZoomTip(), CPhyloTreeWidget::OnZoomToSelection(), CPhyloTreeWidget::OnZoomToSubtree(), CChangePhyloSelectionSetCmd::PerformEdit(), CChangePhyloPropertyCmd::PerformEdit(), CChangePhyloExpandCollapseCmd::PerformEdit(), IPhyloTreeRender::PointToNode(), CPhyloTreeWidget::QueryEnd(), CPhyTreeView::RebuildObjectIndex(), CPhyloTreeWidget::RedrawDataSource(), CPhyloTreePane::RenderPdf(), CPhyloTreeWidget::SendEditEvent(), IPhyloTreeRender::SetActiveTooltipNode(), IPhyloTreeRender::SetScheme(), CPhyloSaveSelectiondlg::SetSelections(), IPhyloTreeRender::TTHH_GetTooltip(), CChangePhyloSelectionSetCmd::Unexecute(), CChangePhyloPropertyCmd::Unexecute(), CPhyloTreePane::Update(), CwxPhyloSettingsDlg::UpdateSample(), CPhyloForce::x_CalculateBoundary(), CPhyloRectCladogram::x_DrawPseudoSplineTree(), CPhyloRectCladogram::x_DrawSplineTree(), CPhyloCircularCladogram::x_DrawTree(), CPhyloCircularCladogram::x_Layout(), CPhyloForce::x_Layout(), CPhyloRadial::x_Layout(), CPhyloRectCladogram::x_Layout(), CPhyloSlantedCladogram::x_Layout(), CPhyTreeView::x_OnSetSelection(), CPhyloTreePane::x_Render(), IPhyloTreeRender::x_RenderCircularVbo(), IPhyloTreeRender::x_RenderLineVbo(), IPhyloTreeRender::x_RenderNodeHighlight(), IPhyloTreeRender::x_RenderPseudoSplineVbo(), IPhyloTreeRender::x_RenderSelection(), IPhyloTreeRender::x_RenderSplineVbo(), IPhyloTreeRender::x_RenderTooltipHints(), CPhyloCircularCladogram::x_RenderVbo(), CPhyloRadial::x_RenderVbo(), CPhyloSlantedCladogram::x_RenderVbo(), CPhyloRectCladogram::x_RenderVboPseudoSplines(), CPhyloRectCladogram::x_RenderVboSplines(), IPhyloTreeRender::x_SelectByRect(), and CPhyloSaveSelectiondlg::x_SetClusterIds().

GetTree() [2/2]

const CPhyloTree* CPhyloTreeDataSource::GetTree ( void  ) const

inline

Definition at line 311 of file phylo_tree_ds.hpp.

References CRef< C, Locker >::GetPointerOrNull(), and m_TreeModel.

GetTreeLabel()

CTreeLabel CPhyloTreeDataSource::GetTreeLabel ( ) const

inline

Definition at line 315 of file phylo_tree_ds.hpp.

References m_TreeLabel.

Referenced by CPhyTreeView::OnSomethingEdited(), CwxTreeLabelEdit::SetParams(), and IPhyloTreeRender::x_RenderTreeLabel().

GetVisibleNodes()

unsigned int CPhyloTreeDataSource::GetVisibleNodes ( void  )

inline

Definition at line 324 of file phylo_tree_ds.hpp.

References CPhyloTreeCalculator::GetVisibleNodes(), and m_Calc.

Referenced by IPhyloTreeRender::ComputeViewingLimits().

GetWidth()

int CPhyloTreeDataSource::GetWidth ( void  )

inline

Definition at line 327 of file phylo_tree_ds.hpp.

References CPhyloTreeCalculator::GetWidth(), and m_Calc.

Referenced by CCalcRadialTree::CCalcRadialTree(), CCalcRectangularTree::CCalcRectangularTree(), IPhyloTreeRender::GetMinDimensions(), CCalcCircularTree::operator()(), CPhyloCircularCladogram::x_Layout(), CPhyloForce::x_Layout(), CPhyloRadial::x_Layout(), CPhyloRectCladogram::x_Layout(), and CPhyloSlantedCladogram::x_Layout().

HasClusters()

bool CPhyloTreeDataSource::HasClusters

(

)

Definition at line 325 of file phylo_tree_ds.cpp.

References map_checker< Container >::empty(), CPhyloTreeCalculator::GetClusters(), m_Calc, and NULL.

HasLenDistribution()

bool CPhyloTreeDataSource::HasLenDistribution ( ) const

inline

Return true if data is available (for trees without distances, may not be)

Definition at line 268 of file phylo_tree_ds.hpp.

References m_LenDistribution.

Referenced by IPhyloTreeRender::GetEdgeColor().

Init()

void CPhyloTreeDataSource::Init	(	const objects::CBioTreeContainer &	tree,
		objects::CScope &	scope,
		bool	expand_all = false
	)

Throws exception if tree is empty - at least 1 node is required.

Definition at line 179 of file phylo_tree_ds.cpp.

References BioTreeConvertContainer2Tree(), CPhyloSelectionSetMgr::Clear(), CPhyloTree::Clear(), CPhyloTreeCalculator::DumpStats(), eUnknown, CPhyloTree::GetColorTable(), CPhyloTree::GetFeatureDict(), CRef< C, Locker >::GetNCObject(), CRef< C, Locker >::GetPointer(), CPhyloTree::GetSelectionSets(), CPhyloSelectionSetMgr::InitFromUserObject(), CTreeLabel::InitializeFromUserObject(), CRef< C, Locker >::IsNull(), m_Calc, m_Scope, m_TreeLabel, m_TreeModel, MeasureTree(), NCBI_THROW, CRef< C, Locker >::Reset(), TreeDepthFirst(), and CPhyloTree::UpdateNodesMapping().

Referenced by Clean(), CPhyloTreeDataSource(), and CPhyTreeView::OnBioTreeChanged().

IterateOverSelNodes()

CPhyloTree::TTreeIdx CPhyloTreeDataSource::IterateOverSelNodes	(	int	direction,
		bool	highlight
	)

Definition at line 1055 of file phylo_tree_ds.cpp.

References CPhyloTree::GetExplicitlySelectedAndNotCollapsed(), CRef< C, Locker >::GetObject(), CTreeModel< TNode >::GetRootIdx(), m_SearchCurrentNode, m_TreeModel, CTreeModel< CPhyloTreeNode >::Null(), CPhyloTree::SetCurrentNode(), and ct::sort().

Referenced by CPhyloTreeWidget::IterateSelection(), CPhyloTreeWidget::QueryEnd(), and CPhyloTreeWidget::SetSelectAll().

MeasureTree() [1/2]

void CPhyloTreeDataSource::MeasureTree

(

)

Definition at line 277 of file phylo_tree_ds.cpp.

References CTreeModel< TNode >::GetRootIdx(), and m_TreeModel.

Referenced by CollapseSelected(), Cut(), Filter(), FilterDistances(), Init(), NewNode(), Paste(), Remove(), RemoveSelected(), Sort(), SortDist(), SortLabel(), SortLabelRange(), and UpdateSelectionSets().

MeasureTree() [2/2]

void CPhyloTreeDataSource::MeasureTree

(

TTreeIdx

node

)

Definition at line 235 of file phylo_tree_ds.cpp.

References CPhyloTree::GetColorTable(), CRef< C, Locker >::GetNCObject(), CRef< C, Locker >::GetPointer(), CPhyloTreeCalculator::Init(), m_Calc, m_LenDistribution, m_TreeModel, and TreeDepthFirst().

Referenced by CPhyloTreeWidget::RedrawDataSource().

MoveNode()

void CPhyloTreeDataSource::MoveNode

(

bool

up

)

Definition at line 1598 of file phylo_tree_ds.cpp.

References _TRACE, CPhyloTree::GetCurrentNodeIdx(), CTreeModel< TNode >::GetNode(), CTreeModelNode< TData >::GetParent(), last(), m_TreeModel, CTreeModel< CPhyloTreeNode >::Null(), CTreeModelNode< TData >::SubNodeBegin(), CTreeModelNode< TData >::SubNodeEnd(), and swap().

Referenced by CPhyloTreeWidget::OnEdit().

NewNode()

TTreeIdx CPhyloTreeDataSource::NewNode

(

bool

after = true

)

Definition at line 1361 of file phylo_tree_ds.cpp.

References _TRACE, CTreeModel< TNode >::AddChild(), CTreeModel< TNode >::AddNode(), CTreeModelNode< TData >::GetChildren(), CPhyloTree::GetColorTable(), CPhyloTree::GetCurrentNode(), CPhyloTree::GetCurrentNodeIdx(), CPhyloTree::GetFeatureDict(), CBioTreeFeatureDictionary::GetFeatureDict(), CPhyloTreeMaxIdCalculator::GetMaxId(), CRef< C, Locker >::GetNCObject(), CTreeModel< TNode >::GetNode(), CTreeModelNode< TData >::GetParent(), CTreeModelNode< TData >::GetValue(), ITERATE, m_TreeModel, MeasureTree(), CTreeModel< CPhyloTreeNode >::Null(), CTreeModel< TNode >::RemoveChild(), CPhyloNodeData::SetFeature(), CTreeModelNode< TData >::SetParent(), CTreeModelNode< TData >::SubNodeBegin(), TreeDepthFirst(), and CPhyloTree::UpdateNodesMapping().

Referenced by CPhyloTreeWidget::OnEdit(), ReRootEdge(), and ReRootMidpoint().

Paste()

void CPhyloTreeDataSource::Paste

(

void

)

Definition at line 1340 of file phylo_tree_ds.cpp.

References _TRACE, CPhyloTree::GetCurrentNodeIdx(), CRef< C, Locker >::GetNCObject(), CTreeModel< TNode >::GetRootIdx(), m_sTreeClipboard, m_TreeModel, MeasureTree(), CTreeModelNode< CPhyloNodeData >::Null(), CTreeModel< CPhyloTreeNode >::Null(), TreeDepthFirst(), and CPhyloTree::UpdateNodesMapping().

Referenced by CPhyloTreeWidget::OnEdit().

Relabel()

void CPhyloTreeDataSource::Relabel	(	CPhyloTreeScheme *	scheme,
		string	labelFmt
	)

Definition at line 738 of file phylo_tree_ds.cpp.

References Clusterize(), CPhyloTree::GetColorTable(), CPhyloTreeCalculator::GetHeight(), CPhyloTreeCalculator::GetMaxDistance(), CRef< C, Locker >::GetNCObject(), CPhyloTreeCalculator::GetNumNodes(), CTreeModel< TNode >::GetRootIdx(), CPhyloTreeCalculator::Init(), m_Calc, m_TreeModel, max(), CPhyloTreeCalculator::SetLabelFormat(), CPhyloTreeScheme::SetMaxBranchDist(), CPhyloTreeScheme::SetMaxNumChildren(), CTreeModel< TNode >::SetNumNodes(), and TreeDepthFirst().

Referenced by CPhyTreeView::OnBioTreeChanged(), CPhyloTreeWidget::OnClean(), CPhyloTreeWidget::OnOpenPropertiesDlg(), CPhyloTreeWidget::OnRerootTree(), CPhyloTreeWidget::OnRerootTreeAtEdge(), CPhyloTreeWidget::OnSetMidpointRoot(), CPhyloTreeWidget::QueryEnd(), and IPhyloTreeRender::RenderPdf().

Remove()

void CPhyloTreeDataSource::Remove

(

bool

subtree = true

)

Definition at line 1413 of file phylo_tree_ds.cpp.

References _TRACE, CTreeModel< TNode >::AddChild(), CTreeModelNode< TData >::ClearConnections(), CPhyloTree::ClearSelection(), CPhyloTree::GetCurrentNodeIdx(), CRef< C, Locker >::GetNCObject(), CTreeModel< TNode >::GetNode(), CTreeModelNode< TData >::GetParent(), CTreeModelNode< TData >::GetValue(), m_TreeModel, MeasureTree(), CTreeModel< CPhyloTreeNode >::Null(), CTreeModel< TNode >::RemoveChild(), CPhyloNodeData::SetId(), CTreeModelNode< TData >::SubNodeBegin(), CTreeModelNode< TData >::SubNodeEnd(), TreeDepthFirst(), and CPhyloTree::UpdateNodesMapping().

Referenced by CPhyloTreeWidget::OnEdit().

RemoveSelected()

void CPhyloTreeDataSource::RemoveSelected

(

)

Definition at line 1452 of file phylo_tree_ds.cpp.

References _TRACE, CPhyloTree::ClearSelection(), CPhyloTree::FindNodeById(), CPhyloTree::GetExplicitlySelectedIDs(), CRef< C, Locker >::GetNCObject(), CTreeModel< TNode >::GetNode(), CTreeModelNode< TData >::GetParent(), i, m_TreeModel, MeasureTree(), CTreeModel< CPhyloTreeNode >::Null(), CTreeModel< TNode >::RemoveChild(), TreeDepthFirst(), and CPhyloTree::UpdateNodesMapping().

Referenced by CPhyloTreeWidget::OnEdit().

ReRoot()

void CPhyloTreeDataSource::ReRoot

(

TTreeIdx

root_idx

)

Set the root node of the tree to the node at root_idx.

Definition at line 477 of file phylo_tree_ds.cpp.

References CPhyloTree::GetFeatureDict(), CTreeModel< TNode >::GetNode(), CTreeModelNode< TData >::GetValue(), m_TreeModel, CTreeModel< CPhyloTreeNode >::Null(), CTreeModel< TNode >::ReRoot(), CPhyloNodeData::SetDistance(), CTreeModelNode< TData >::SetParent(), and CPhyloNodeData::Sync().

Referenced by CPhyloTreeWidget::OnRerootTree(), CPhyloTreeWidget::OnZoomToSubtree(), ReRootEdge(), and ReRootMidpoint().

ReRootEdge()

void CPhyloTreeDataSource::ReRootEdge

(

TTreeIdx

edge_child_node

)

Re-root on the edge between the selected node and its parent.

Definition at line 488 of file phylo_tree_ds.cpp.

References CPhyloNodeData::GetDistance(), CPhyloTree::GetFeatureDict(), CTreeModel< TNode >::GetNode(), CTreeModelNode< TData >::GetValue(), CBioTreeFeatureDictionary::HasFeature(), m_TreeModel, NewNode(), CTreeModel< CPhyloTreeNode >::Null(), ReRoot(), CPhyloTree::SetCurrentNode(), CPhyloNodeData::SetDistance(), and CPhyloNodeData::Sync().

Referenced by CPhyloTreeWidget::OnRerootTreeAtEdge().

ReRootMidpoint()

void CPhyloTreeDataSource::ReRootMidpoint

(

)

Re-root tree using midpoint-method.

Definition at line 513 of file phylo_tree_ds.cpp.

References _ASSERT, close(), NStr::DoubleToString(), CPhyloNodeData::GetDistance(), CPhyloTreeDistFromRoot::GetDistances(), CPhyloTree::GetFeatureDict(), CPhyloTreeMidpointDist::GetLongest(), CPhyloTreeDistFromRoot::GetMaxDistNode(), CRef< C, Locker >::GetNCObject(), CRef< C, Locker >::GetNCPointer(), CTreeModel< TNode >::GetNode(), CTreeModelNode< TData >::GetParent(), CTreeModel< TNode >::GetRootIdx(), CTreeModelNode< TData >::GetValue(), CBioTreeFeatureDictionary::HasFeature(), CTreeModelNode< TData >::HasParent(), i, Info(), LOG_POST, m_TreeModel, NewNode(), CTreeModel< CPhyloTreeNode >::Null(), ReRoot(), CPhyloTree::SetCurrentNode(), CPhyloNodeData::SetDistance(), CPhyloNodeData::SetFeature(), CPhyloNodeData::Sync(), and TreeDepthFirst().

Referenced by CPhyloTreeWidget::OnSetMidpointRoot().

SetCollapsedLabel()

void CPhyloTreeDataSource::SetCollapsedLabel

(

CPhyloTree::TTreeIdx

idx

)

Collapse single node, do any relabeling if needed.

Definition at line 1493 of file phylo_tree_ds.cpp.

References CPhyloTreeNode::CanExpandCollapse(), CPhyloNodeData::eHideChildren, CPhyloTree::GetFeatureDict(), CBioTreeFeatureList::GetFeatureValue(), CBioTreeFeatureDictionary::GetId(), CPhyloTreePriorityNode::GetMaxPriorityNode(), CTreeModel< TNode >::GetNode(), CBioTreeFeatureDictionary::HasFeature(), m_TreeModel, CTreeModel< CPhyloTreeNode >::Null(), CBioTreeFeatureList::SetFeature(), CPhyloTreeNode::SetLabel(), and TreeDepthFirst().

Referenced by CollapseSelected(), CPhyloTreeWidget::OnCollapseChildren(), IPhyloTreeRender::OnLeftDblClick(), and SetCollapsedLabels().

SetCollapsedLabels()

void CPhyloTreeDataSource::SetCollapsedLabels

(

const vector< CPhyloNodeData::TID > &

node_ids

)

Collapse all nodes in node_ids, doing relabeling if needed.

Definition at line 1534 of file phylo_tree_ds.cpp.

References CPhyloTreeNode::CanExpandCollapse(), CPhyloNodeData::eHideChildren, CPhyloTree::FindNodeById(), CTreeModel< TNode >::GetNode(), i, m_TreeModel, CTreeModel< CPhyloTreeNode >::Null(), and SetCollapsedLabel().

Referenced by CPhyloTreeWidget::OnCollapseToViewport().

SetColorIndices()

void CPhyloTreeDataSource::SetColorIndices

(

CPhyloTreeScheme *

scheme

)

Definition at line 221 of file phylo_tree_ds.cpp.

References CPhyloTree::GetColorTable(), CRgbaGradColorTable::LoadTexture(), m_TreeModel, NULL, and CPhyloTreeScheme::UpdateColorTable().

Referenced by Clusterize().

SetCurrentSearchNode()

void CPhyloTreeDataSource::SetCurrentSearchNode ( TTreeIdx  node_idx )

inline

Definition at line 361 of file phylo_tree_ds.hpp.

References m_SearchCurrentNode.

SetQueryResults()

void CPhyloTreeDataSource::SetQueryResults ( CMacroQueryExec *  q )

virtual

Set selection results to be whatever elements are selected in 'q'.

Implements IQueryDataSource.

Definition at line 937 of file phylo_tree_ds.cpp.

References ClearQueryResults(), CPhyloTree::ClearSelection(), CTreeQueryExec::GetTreeSelected(), m_TreeModel, and CPhyloTree::SetSelection().

SetTreeLabel()

void CPhyloTreeDataSource::SetTreeLabel ( const CTreeLabel &  l )

inline

Label for tree (optional element of biotreecontainer)

Definition at line 314 of file phylo_tree_ds.hpp.

References l(), and m_TreeLabel.

Referenced by CwxTreeLabelEdit::OnOkClick().

Sort()

void CPhyloTreeDataSource::Sort

(

bool

ascending

)

Definition at line 753 of file phylo_tree_ds.cpp.

References CRef< C, Locker >::GetNCObject(), CRef< C, Locker >::GetPointer(), CTreeModel< TNode >::GetRootIdx(), m_TreeModel, MeasureTree(), and TreeDepthFirst().

Referenced by CPhyTreeView::OnBioTreeChanged(), and CPhyloTreeWidget::OnSort().

SortDist()

void CPhyloTreeDataSource::SortDist

(

bool

ascending

)

Definition at line 762 of file phylo_tree_ds.cpp.

References CPhyloTreeMaxChildDist::GetDistances(), CPhyloTree::GetFeatureDict(), CRef< C, Locker >::GetNCObject(), CRef< C, Locker >::GetNCPointer(), CTreeModel< TNode >::GetRootIdx(), CBioTreeFeatureDictionary::HasFeature(), m_TreeModel, MeasureTree(), and TreeDepthFirst().

Referenced by CPhyloTreeWidget::OnSort().

SortLabel()

void CPhyloTreeDataSource::SortLabel

(

bool

ascending

)

Definition at line 779 of file phylo_tree_ds.cpp.

References CRef< C, Locker >::GetNCObject(), CRef< C, Locker >::GetNCPointer(), CTreeModel< TNode >::GetRootIdx(), m_TreeModel, MeasureTree(), and TreeDepthFirst().

Referenced by CPhyloTreeWidget::OnSort().

SortLabelRange()

void CPhyloTreeDataSource::SortLabelRange

(

bool

ascending

)

Definition at line 788 of file phylo_tree_ds.cpp.

References CPhyloTreeLabelRange::GetLabelRanges(), CRef< C, Locker >::GetNCObject(), CRef< C, Locker >::GetNCPointer(), CTreeModel< TNode >::GetRootIdx(), m_TreeModel, MeasureTree(), and TreeDepthFirst().

Referenced by CPhyloTreeWidget::OnSort().

UpdateSelectionSets()

void CPhyloTreeDataSource::UpdateSelectionSets

(

CPhyloTreeScheme *

scheme

)

Definition at line 1131 of file phylo_tree_ds.cpp.

References Clusterize(), GetMaxClusterID(), CRef< C, Locker >::GetPointer(), CPhyloTree::GetSelectionSets(), GetSelectionSets(), CPhyloSelectionSetMgr::GetSets(), m_TreeModel, MeasureTree(), CPhyloSelectionSetMgr::RenumberClusterIDs(), and CPhyloSelectionSetMgr::SetSelectionSetProperty().

Referenced by CPhyloTreeWidget::OnAddSelectionSet().

Member Data Documentation

m_Calc

CPhyloTreeCalculator* CPhyloTreeDataSource::m_Calc

protected

Definition at line 395 of file phylo_tree_ds.hpp.

Referenced by ApplyAttributes(), Clusterize(), GetMaxClusterID(), GetMaxLabelLen(), GetMinDistance(), GetNormDistance(), GetNumEdges(), GetNumNodes(), GetSize(), GetVisibleNodes(), GetWidth(), HasClusters(), Init(), MeasureTree(), Relabel(), and ~CPhyloTreeDataSource().

m_ClusterToColorMap

TClusterToColorMap CPhyloTreeDataSource::m_ClusterToColorMap

protected

Definition at line 401 of file phylo_tree_ds.hpp.

Referenced by Clusterize(), and GetClusterToColorMap().

m_LenDistribution

std::vector<float> CPhyloTreeDataSource::m_LenDistribution

protected

Definition at line 406 of file phylo_tree_ds.hpp.

Referenced by ComputeLengthsFromRoot(), GetClosestLen(), HasLenDistribution(), and MeasureTree().

m_Scope

CRef<objects::CScope> CPhyloTreeDataSource::m_Scope

protected

Definition at line 397 of file phylo_tree_ds.hpp.

Referenced by Clean(), GetScope(), and Init().

m_SearchCurrentNode

TTreeIdx CPhyloTreeDataSource::m_SearchCurrentNode

protected

Definition at line 399 of file phylo_tree_ds.hpp.

Referenced by Clear(), ClearQueryResults(), ExecuteStringQuery(), GetCurrentSearchNode(), IterateOverSelNodes(), and SetCurrentSearchNode().

m_sTreeClipboard

CPhyloTree CPhyloTreeDataSource::m_sTreeClipboard

staticprotected

static (to allow copying between trees)

Definition at line 413 of file phylo_tree_ds.hpp.

Referenced by ClipboardEmpty(), Cut(), and Paste().

m_StringQueryIDs

vector<CPhyloTree::TID> CPhyloTreeDataSource::m_StringQueryIDs

protected

Temporary storage for string query results to get ID's back to caller.

Definition at line 409 of file phylo_tree_ds.hpp.

Referenced by ExecuteStringQuery(), and GetStringQueryIDs().

m_TreeLabel

CTreeLabel CPhyloTreeDataSource::m_TreeLabel

protected

Definition at line 392 of file phylo_tree_ds.hpp.

Referenced by GetTreeLabel(), Init(), and SetTreeLabel().

m_TreeModel

CRef<CPhyloTree> CPhyloTreeDataSource::m_TreeModel

protected

Definition at line 389 of file phylo_tree_ds.hpp.

Referenced by ApplyAttributes(), Clear(), Clusterize(), CollapseByDistance(), CollapseSelected(), ComputeLengthsFromRoot(), Cut(), ExecuteStringQuery(), Filter(), FilterDistances(), FindNodes(), GenerateTooltipFormat(), GetBoundRect(), GetColsCount(), GetColumnLabel(), GetDictionary(), GetModel(), GetSelectionSets(), GetTree(), Init(), IterateOverSelNodes(), MeasureTree(), MoveNode(), NewNode(), Paste(), Relabel(), Remove(), RemoveSelected(), ReRoot(), ReRootEdge(), ReRootMidpoint(), SetCollapsedLabel(), SetCollapsedLabels(), SetColorIndices(), SetQueryResults(), Sort(), SortDist(), SortLabel(), SortLabelRange(), and UpdateSelectionSets().

---

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

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