A RetroSearch Logo

Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Search Query:

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/classCPhyloTreeDataSource.html below:

NCBI C++ ToolKit: CPhyloTreeDataSource Class Reference

Search Toolkit Book for CPhyloTreeDataSource

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

  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 ()   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...
    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...
    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   virtual  ~IQueryDataSource ()   dtor More...
 

Definition at line 231 of file phylo_tree_ds.hpp.

◆ TClusterID ◆ TClusterToColorMap ◆ TJobID ◆ TNodeType ◆ TTreeIdx ◆ TTreeType ◆ 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 ( ) ◆ ApplyAttributes()

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 ( ) ◆ Clear() void CPhyloTreeDataSource::Clear ( void  ) ◆ ClearQueryResults() void CPhyloTreeDataSource::ClearQueryResults ( ) virtual ◆ ClipboardEmpty() bool CPhyloTreeDataSource::ClipboardEmpty ( ) const inline ◆ Clusterize()

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()

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()

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 ( ) ◆ FilterDistances() void CPhyloTreeDataSource::FilterDistances ( double  x_dist ) ◆ FindNodes() ◆ GenerateTooltipFormat() string CPhyloTreeDataSource::GenerateTooltipFormat ( ) ◆ 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 ◆ GetClusterToColorMap() ◆ GetColsCount() size_t CPhyloTreeDataSource::GetColsCount ( ) const virtual ◆ GetColumnLabel() string CPhyloTreeDataSource::GetColumnLabel ( size_t  col ) const virtual ◆ GetCurrentSearchNode() TTreeIdx CPhyloTreeDataSource::GetCurrentSearchNode ( ) const inline ◆ GetDictionary()

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 ◆ GetMaxLabelLen() int CPhyloTreeDataSource::GetMaxLabelLen ( void  ) inline ◆ GetMinDistance() double CPhyloTreeDataSource::GetMinDistance ( void  ) inline ◆ GetModel()

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 ◆ GetNumNodes() unsigned int CPhyloTreeDataSource::GetNumNodes ( void  ) inline ◆ GetQueryExec()

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 ◆ GetSelectionSets()

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() ◆ 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] ◆ GetTreeLabel() CTreeLabel CPhyloTreeDataSource::GetTreeLabel ( ) const inline ◆ GetVisibleNodes() unsigned int CPhyloTreeDataSource::GetVisibleNodes ( void  ) inline ◆ GetWidth() int CPhyloTreeDataSource::GetWidth ( void  ) inline ◆ HasClusters() bool CPhyloTreeDataSource::HasClusters ( ) ◆ HasLenDistribution() bool CPhyloTreeDataSource::HasLenDistribution ( ) const inline ◆ 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()

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 ) ◆ MoveNode() void CPhyloTreeDataSource::MoveNode ( bool  up ) ◆ NewNode()

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()

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()

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() ◆ SetColorIndices() ◆ SetCurrentSearchNode() void CPhyloTreeDataSource::SetCurrentSearchNode ( TTreeIdx  node_idx ) inline ◆ SetQueryResults() ◆ SetTreeLabel() ◆ Sort() void CPhyloTreeDataSource::Sort ( bool  ascending ) ◆ 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 ) ◆ SortLabelRange() void CPhyloTreeDataSource::SortLabelRange ( bool  ascending ) ◆ UpdateSelectionSets()

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().

◆ m_Calc

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 ◆ m_LenDistribution std::vector<float> CPhyloTreeDataSource::m_LenDistribution protected ◆ m_Scope CRef<objects::CScope> CPhyloTreeDataSource::m_Scope protected ◆ m_SearchCurrentNode TTreeIdx CPhyloTreeDataSource::m_SearchCurrentNode protected ◆ m_sTreeClipboard ◆ m_StringQueryIDs ◆ m_TreeLabel ◆ m_TreeModel

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:

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4