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NCBI C++ ToolKit: Tree Templates

struct   CBioTreeFeaturePair   Tree node feature pair (id to string) More...
  class   CBioTreeFeatureList   Features storage for the bio tree node. More...
  struct   CBioTreeEmptyNodeData   Basic node data structure used by BioTreeBaseNode. More...
  class   BioTreeBaseNode< TNodeData, TNodeFeatures >   Basic data contained in every bio-tree node. More...
  class   CBioTreeFeatureDictionary   Feature dictionary. More...
  class   CBioTree< TBioNode >   Basic tree structure for biological applications. More...
  class   CBioTree< TBioNode >::CBioNode   class   CBioTree< TBioNode >::CFindUidFunc   Find node by UID functor. More...
  struct   CBioTree< TBioNode >::CAssignTreeFunc   Functor to reset tree pointer in all nodes. More...
  class   IBioTreeDynamicLabelFormatter   Interface to obtain custom labels for nodes. More...
  class   CTree2TreeFunc< TDstTreeNode, TSrcTreeNode, TNodeConvFunc >   Visitor functor to convert one tree to another. More...
  class   CBioTreeConvert2ContainerFunc< TBioTreeContainer, TDynamicTree >   Visitor functor to convert dynamic tree nodes to ASN.1 BioTree container. More...
  class   CTaxon1NodeConvertVisitor< TITaxon4Each, TITaxon1Node, TITreeIterator, TBioTreeContainer >   Taxon1 tree visitor functor. More...
  class   CTaxon1ConvertToBioTreeContainer< TBioTreeContainer, TTaxon1, TITaxon1Node, TITreeIterator >   class   CTreeParentTraceFunc< TTreeNode, TTraceContainer >   Functor to trace node pointers to root (TreeForEachParent) More...
  class   CTreePrintFunc< TTreeNode, TConverter >   Tree print functor used as a tree traversal payload. More...
  class   CTreeIdToSetFunc< TTreeNode, TBackInsert >   Functor to trace node pointers to root and create set of parents (TreeForEachParent) More...
  class   CTreeSet2NodeListFunc< TTreeNode, TSet, TNodeList >   Functor to convert tree to a nodelist by the set pattern. More...
  class   CTreeNonRedundantSet< TNode, TSet, TNodeList >   Class-algorithm to compute Non Redundant Set. More...
  class   CTreeMinimalSet< TNode, TSet, TNodeList >   Functor takes a single nodelist as an argument and tries to push that nodelist as high as it can. More...
  class   CNodesToBitset< TNode, TSet, TNodeList >   Utility to join to node lists according to a set of ids. More...
  class   CTreeNodesAnd< TNode, TSet, TNodeList >   Node list AND (set intersection) More...
  class   CTreeNodesOr< TNode, TSet, TNodeList >   Node list OR (set union) More...
  class   CDefaultNodeKeyGetter< TValue, TKeyEqualP >   Bi-directionaly linked N way tree. More...
  struct   CTreeNode< TValue, TKeyGetterP >   definition of a Culling tree More...
  class   CTreeNode< TValue, TKeyGetterP >::CSorter< TNodeComparator >   class   CPairNodeKeyGetter< TNode, TKeyEqualP >   Default key getter for pair-node (id + value) More...
  struct   CTreePair< TId, TValue, TIdEqual >   Node data template for id-value trees. More...
  class   CCompareByLeafCount< TValue, TKeyGetter >   typedef unsigned int  TBioTreeFeatureId   Feature Id. More...
  typedef unsigned int  TBioTreeNodeId   Tree node id. Every node has its unique id in the tree. More...
  typedef vector< CBioTreeFeaturePair >  CBioTreeFeatureList::TFeatureList   typedef TNodeData  BioTreeBaseNode< TNodeData, TNodeFeatures >::TNodeDataType   typedef TNodeFeatures  BioTreeBaseNode< TNodeData, TNodeFeatures >::TNodeFeaturesType   typedef map< TBioTreeFeatureId, string >  CBioTreeFeatureDictionary::TFeatureDict   Feature dictionary (feature id -> feature name map) More...
  typedef map< string, TBioTreeFeatureId >  CBioTreeFeatureDictionary::TFeatureNameIdx   Feature reverse index (feature name -> id) More...
  typedef CBioTree< TBioNode >  CBioTree< TBioNode >::TBioTree   typedef CTreeNode< TBioNode >  CBioTree< TBioNode >::CBioNode::TParent   typedef CBioNode  CBioTree< TBioNode >::CBioNode::TTreeType   typedef CBioNode  CBioTree< TBioNode >::TBioTreeNode   Biotree node (forms the tree hierarchy) More...
  typedef TBioNode  CBioTree< TBioNode >::TBioNodeType   typedef CBioTree< BioTreeBaseNode< CBioTreeEmptyNodeData, CBioTreeFeatureList > >  CBioTreeDynamic   Bio tree without static elements. More...
  typedef TDstTreeNode  CTree2TreeFunc< TDstTreeNode, TSrcTreeNode, TNodeConvFunc >::TDstTreeNodeType   typedef TSrcTreeNode  CTree2TreeFunc< TDstTreeNode, TSrcTreeNode, TNodeConvFunc >::TSrcTreeNodeType   typedef TDynamicTree::TBioTreeNode  CBioTreeConvert2ContainerFunc< TBioTreeContainer, TDynamicTree >::TDynamicNodeType   typedef TDynamicNodeType::TValueType  CBioTreeConvert2ContainerFunc< TBioTreeContainer, TDynamicTree >::TDynamicNodeValueType   typedef TBioTreeContainer::TNodes  CBioTreeConvert2ContainerFunc< TBioTreeContainer, TDynamicTree >::TCNodeSet   typedef TCNodeSet::Tdata  CBioTreeConvert2ContainerFunc< TBioTreeContainer, TDynamicTree >::TNodeList   typedef TNodeList::value_type::element_type  CBioTreeConvert2ContainerFunc< TBioTreeContainer, TDynamicTree >::TCNode   typedef TCNode::TFeatures  CBioTreeConvert2ContainerFunc< TBioTreeContainer, TDynamicTree >::TCNodeFeatureSet   typedef TCNodeFeatureSet::Tdata  CBioTreeConvert2ContainerFunc< TBioTreeContainer, TDynamicTree >::TNodeFeatureList   typedef TNodeFeatureList::value_type::element_type  CBioTreeConvert2ContainerFunc< TBioTreeContainer, TDynamicTree >::TCNodeFeature   typedef TITreeIterator::EAction  CTaxon1NodeConvertVisitor< TITaxon4Each, TITaxon1Node, TITreeIterator, TBioTreeContainer >::EAction   typedef TBioTreeContainer::TNodes  CTaxon1NodeConvertVisitor< TITaxon4Each, TITaxon1Node, TITreeIterator, TBioTreeContainer >::TCNodeSet   typedef TCNodeSet::Tdata  CTaxon1NodeConvertVisitor< TITaxon4Each, TITaxon1Node, TITreeIterator, TBioTreeContainer >::TNodeList   typedef TNodeList::value_type::element_type  CTaxon1NodeConvertVisitor< TITaxon4Each, TITaxon1Node, TITreeIterator, TBioTreeContainer >::TCNode   typedef TCNode::TFeatures  CTaxon1NodeConvertVisitor< TITaxon4Each, TITaxon1Node, TITreeIterator, TBioTreeContainer >::TCNodeFeatureSet   typedef TCNodeFeatureSet::Tdata  CTaxon1NodeConvertVisitor< TITaxon4Each, TITaxon1Node, TITreeIterator, TBioTreeContainer >::TNodeFeatureList   typedef TNodeFeatureList::value_type::element_type  CTaxon1NodeConvertVisitor< TITaxon4Each, TITaxon1Node, TITreeIterator, TBioTreeContainer >::TCNodeFeature   typedef TITreeIterator::I4Each  CTaxon1ConvertToBioTreeContainer< TBioTreeContainer, TTaxon1, TITaxon1Node, TITreeIterator >::T4Each   typedef CTaxon1NodeConvertVisitor< T4Each, TITaxon1Node, TITreeIterator, TBioTreeContainer >  CTaxon1ConvertToBioTreeContainer< TBioTreeContainer, TTaxon1, TITaxon1Node, TITreeIterator >::TTaxon1Visitor   typedef TValue  CDefaultNodeKeyGetter< TValue, TKeyEqualP >::TNodeType   same as CTreeNode template argument More...
  typedef TValue  CDefaultNodeKeyGetter< TValue, TKeyEqualP >::TValueType   node's value More...
  typedef TValue  CDefaultNodeKeyGetter< TValue, TKeyEqualP >::TKeyType   node's key More...
  typedef TKeyEqualP  CDefaultNodeKeyGetter< TValue, TKeyEqualP >::TKeyEqual   key equal comparator More...
  typedef TValue  CTreeNode< TValue, TKeyGetterP >::TValueType   typedef TKeyGetterP  CTreeNode< TValue, TKeyGetterP >::TKeyGetter   typedef TKeyGetter::TKeyType  CTreeNode< TValue, TKeyGetterP >::TKeyType   typedef TKeyGetter::TKeyEqual  CTreeNode< TValue, TKeyGetterP >::TKeyEqual   typedef CTreeNode< TValue, TKeyGetter >  CTreeNode< TValue, TKeyGetterP >::TTreeType   typedef list< TTreeType * >  CTreeNode< TValue, TKeyGetterP >::TNodeList   typedef list< const TTreeType * >  CTreeNode< TValue, TKeyGetterP >::TConstNodeList   typedef TNodeList::iterator  CTreeNode< TValue, TKeyGetterP >::TNodeList_I   typedef TNodeList::const_iterator  CTreeNode< TValue, TKeyGetterP >::TNodeList_CI   typedef TNodeList::reverse_iterator  CTreeNode< TValue, TKeyGetterP >::TNodeList_RI   typedef TNodeList::const_reverse_iterator  CTreeNode< TValue, TKeyGetterP >::TNodeList_CRI   typedef list< TKeyType >  CTreeNode< TValue, TKeyGetterP >::TKeyList   typedef int  CTreeNode< TValue, TKeyGetterP >::TNodeSearchMode   Bitwise mask of ENodeSearchType. More...
  typedef int  CTreeNode< TValue, TKeyGetterP >::TCountNodes   Bitwise mask of ECountNodes. More...
  typedef TNode  CPairNodeKeyGetter< TNode, TKeyEqualP >::TNodeType   typedef TNode::TValueType  CPairNodeKeyGetter< TNode, TKeyEqualP >::TValueType   typedef TNode::TIdType  CPairNodeKeyGetter< TNode, TKeyEqualP >::TKeyType   typedef TKeyEqualP  CPairNodeKeyGetter< TNode, TKeyEqualP >::TKeyEqual   typedef TId  CTreePair< TId, TValue, TIdEqual >::TIdType   typedef TValue  CTreePair< TId, TValue, TIdEqual >::TValueType   typedef CTreePair< TId, TValue, TIdEqual >  CTreePair< TId, TValue, TIdEqual >::TTreePair   Node data type. More...
  typedef CPairNodeKeyGetter< TTreePair, TIdEqual >  CTreePair< TId, TValue, TIdEqual >::TPairKeyGetter   Key getter for CTreeNode. More...
  typedef CTreeNode< TTreePair, TPairKeyGetter >  CTreePair< TId, TValue, TIdEqual >::TPairTreeNode   Tree node type. More...
  typedef CTreeNode< TValue, TKeyGetter >  CCompareByLeafCount< TValue, TKeyGetter >::TNodeType   enum   ETaxon1ConvFeatures {
  eTaxTree_Name = 1 , eTaxTree_BlastName = 2 , eTaxTree_Rank = 3 , eTaxTree_Division = 4 ,
  eTaxTree_GC = 5 , eTaxTree_MGC = 6 , eTaxTree_IsUncultured = 7 , eTaxTree_TaxId = 8 ,
  eTaxTree_SeqId = 9 , eTaxTree_Label = 10
}   Feature ids for Bio-Tree. More...
  enum   ETreeTraverseCode { eTreeTraverse , eTreeTraverseStop , eTreeTraverseStepOver }   Tree traverse code returned by the traverse predicate function. More...
  enum   CTreeNode< TValue, TKeyGetterP >::EDeletePolicy { CTreeNode< TValue, TKeyGetterP >::eDelete , CTreeNode< TValue, TKeyGetterP >::eNoDelete }   Whether to destroy the sub-nodes when bulk-cleaning the node. More...
  enum   CTreeNode< TValue, TKeyGetterP >::ENodeSearchType { CTreeNode< TValue, TKeyGetterP >::eImmediateSubNodes = (1 << 0) , CTreeNode< TValue, TKeyGetterP >::eTopLevelNodes = (1 << 1) , CTreeNode< TValue, TKeyGetterP >::eAllUpperSubNodes = (1 << 2) , CTreeNode< TValue, TKeyGetterP >::eImmediateAndTop = (eImmediateSubNodes | eTopLevelNodes) }   Parameters for node search by key. More...
  enum   CTreeNode< TValue, TKeyGetterP >::ECountNodes { CTreeNode< TValue, TKeyGetterP >::fOnlyLeafs = (1 << 0) , CTreeNode< TValue, TKeyGetterP >::fCumulative = (1 << 1) }   How to count nodes in the tree of which this node is a root. More...
    CBioTreeFeaturePair::CBioTreeFeaturePair (TBioTreeFeatureId fid, const string &fvalue)     CBioTreeFeaturePair::CBioTreeFeaturePair (TBioTreeFeatureId fid)     CBioTreeFeaturePair::CBioTreeFeaturePair (void)   bool  CBioTreeFeaturePair::operator< (const CBioTreeFeaturePair &rhs) const     CBioTreeFeatureList::CBioTreeFeatureList ()     CBioTreeFeatureList::CBioTreeFeatureList (const CBioTreeFeatureList &flist)   CBioTreeFeatureList &  CBioTreeFeatureList::operator= (const CBioTreeFeatureList &flist)   void  CBioTreeFeatureList::SetFeature (TBioTreeFeatureId id, const string &value)   Set feature value, feature if exists replaced, if not added. More...
  const string &  CBioTreeFeatureList::GetFeatureValue (TBioTreeFeatureId id) const   Get feature value by id. More...
  bool  CBioTreeFeatureList::GetFeatureValue (TBioTreeFeatureId id, string &result) const   Place feature value in 'result', if available. More...
  void  CBioTreeFeatureList::RemoveFeature (TBioTreeFeatureId id)   Remove feature from the list. More...
  const string &  CBioTreeFeatureList::operator[] (TBioTreeFeatureId id) const   Get feature value by id (operator semantics) More...
  const TFeatureList &  CBioTreeFeatureList::GetFeatureList () const   Return reference on the internal container. More...
    BioTreeBaseNode< TNodeData, TNodeFeatures >::BioTreeBaseNode (TBioTreeNodeId uid_value=0)   TBioTreeNodeId  BioTreeBaseNode< TNodeData, TNodeFeatures >::GetId () const   void  BioTreeBaseNode< TNodeData, TNodeFeatures >::SetId (TBioTreeNodeId id)     CBioTreeFeatureDictionary::CBioTreeFeatureDictionary ()     CBioTreeFeatureDictionary::CBioTreeFeatureDictionary (const CBioTreeFeatureDictionary &btr)   CBioTreeFeatureDictionary &  CBioTreeFeatureDictionary::operator= (const CBioTreeFeatureDictionary &btr)   bool  CBioTreeFeatureDictionary::HasFeature (const string &feature_name) const   Check if feature is listed in the dictionary. More...
  bool  CBioTreeFeatureDictionary::HasFeature (TBioTreeFeatureId id) const   Check if feature is listed in the dictionary. More...
  TBioTreeFeatureId  CBioTreeFeatureDictionary::Register (const string &feature_name)   Register new feature, return its id. More...
  void  CBioTreeFeatureDictionary::Register (TBioTreeFeatureId id, const string &feature_name)   Register new feature. More...
  void  CBioTreeFeatureDictionary::Unregister (TBioTreeFeatureId id)   TBioTreeFeatureId  CBioTreeFeatureDictionary::GetId (const string &feature_name) const   If feature is already registered returns its id by name. More...
  string  CBioTreeFeatureDictionary::GetName (TBioTreeFeatureId id) const   Return the featue name given the id, or "" if not found. More...
  void  CBioTreeFeatureDictionary::Clear ()   Clear the dictionary. More...
  const TFeatureDict &  CBioTreeFeatureDictionary::GetFeatureDict () const   Get reference on the internal map. More...
    CBioTree< TBioNode >::CBioNode::CBioNode (const TBioNode &value=TBioNode())   Construct tree node with specified value. More...
    CBioTree< TBioNode >::CBioNode::CBioNode (const CBioNode &bn)   Construct tree node based on source tree node (recursive copy) More...
  CBioNode &  CBioTree< TBioNode >::CBioNode::operator= (const CBioNode &tree)   Recursive assignment. More...
  void  CBioTree< TBioNode >::CBioNode::SetParentTree (TBioTree *pt)   Associate node with the hosting class (non-recursive) More...
  const TBioTree *  CBioTree< TBioNode >::CBioNode::GetParentTree () const   Return pointer on the hosting tree (can be NULL) More...
  TBioTree *  CBioTree< TBioNode >::CBioNode::GetParentTree ()   Return pointer on the hosting tree (can be NULL) More...
  TTreeType *  CBioTree< TBioNode >::CBioNode::DetachNode (TTreeType *subnode)   TTreeType *  CBioTree< TBioNode >::CBioNode::DetachNode (typename TParent::TNodeList_I it)   Node is detached from the tree (Parent becomes 0) More...
  void  CBioTree< TBioNode >::CBioNode::AddNode (TTreeType *subnode)   Node is added as a subnode the this node. More...
  CBioNode *  CBioTree< TBioNode >::CBioNode::AddNode (const TBioNode &val=TBioNode())   Add a subnode to this node based on value. More...
  const string &  CBioTree< TBioNode >::CBioNode::GetFeature (const string &feature_name) const   Get dynamic feature by name. More...
  void  CBioTree< TBioNode >::CBioNode::SetFeature (const string &feature_name, const string &feature_value)   const string &  CBioTree< TBioNode >::CBioNode::operator[] (const string &feature_name) const     CBioTree< TBioNode >::CBioTree ()   virtual  CBioTree< TBioNode >::~CBioTree ()     CBioTree< TBioNode >::CBioTree (const CBioTree< TBioNode > &btr)   CBioTree< TBioNode > &  CBioTree< TBioNode >::operator= (const CBioTree< TBioNode > &btr)   const TBioTreeNode *  CBioTree< TBioNode >::FindNode (TBioTreeNodeId node_id) const   Finds node by id. More...
  void  CBioTree< TBioNode >::AddFeature (TBioTreeNode *node, TBioTreeFeatureId feature_id, const string &feature_value)   Add feature to the tree node Function controls that the feature is registered in the feature dictionary of this tree. More...
  void  CBioTree< TBioNode >::AddFeature (TBioTreeNode *node, const string &feature_name, const string &feature_value)   Add feature to the tree node Function controls that the feature is registered in the feature dictionary of this tree. More...
  virtual TBioTreeNodeId  CBioTree< TBioNode >::GetNodeId ()   Get new unique node id. More...
  virtual TBioTreeNodeId  CBioTree< TBioNode >::GetNodeId (const TBioTreeNode &)   Get new unique node id (for cases when node id depends on the node's content. More...
  void  CBioTree< TBioNode >::SetNodeId (TBioTreeNode *node)   Assign new unique node id to the node. More...
  void  CBioTree< TBioNode >::SetTreeNode (TBioTreeNode *node)   Assign new top level tree node. More...
  const TBioTreeNode *  CBioTree< TBioNode >::GetTreeNode () const   TBioTreeNode *  CBioTree< TBioNode >::GetTreeNodeNonConst ()   void  CBioTree< TBioNode >::DetachTreeNode ()   TBioTreeNode *  CBioTree< TBioNode >::AddNode (const TBioNodeType &node_value, TBioTreeNodeId parent_id)   Add node to the tree (node location is defined by the parent id. More...
  TBioTreeNode *  CBioTree< TBioNode >::AddNode (const TBioNodeType &node_value, TBioTreeNode *parent_node)   Add a node to the tree when you have already looked up the parent node (faster) More...
  void  CBioTree< TBioNode >::SetParentTree (CBioNode &node)   Recursively set this tree as parent tree for the node. More...
  void  CBioTree< TBioNode >::SetParentTree (CBioNode &node, CBioTree *tr)   Recursively set parent tree for the node. More...
  void  CBioTree< TBioNode >::Clear ()   Clear the bio tree. More...
  CBioTreeFeatureDictionary &  CBioTree< TBioNode >::GetFeatureDict ()   Return feature dictionary. More...
  const CBioTreeFeatureDictionary &  CBioTree< TBioNode >::GetFeatureDict () const   Return feature dictionary. More...
    CBioTree< TBioNode >::CFindUidFunc::CFindUidFunc (TBioTreeNodeId uid)   ETreeTraverseCode  CBioTree< TBioNode >::CFindUidFunc::operator() (TBioTreeNode &tree_node, int delta)   const TBioTreeNode *  CBioTree< TBioNode >::CFindUidFunc::GetNode () const     CBioTree< TBioNode >::CAssignTreeFunc::CAssignTreeFunc (CBioTree *tree)   ETreeTraverseCode  CBioTree< TBioNode >::CAssignTreeFunc::operator() (TBioTreeNode &tree_node, int delta)   virtual string  IBioTreeDynamicLabelFormatter::GetLabelForNode (const CBioTreeDynamic::TBioTreeNode &node) const =0   virtual  IBioTreeDynamicLabelFormatter::~IBioTreeDynamicLabelFormatter ()   CNcbiOstream &  operator<< (CNcbiOstream &os, const CBioTreeDynamic &tree)   Newick format output. More...
  void  WriteNewickTree (CNcbiOstream &os, const CBioTreeDynamic &tree, const IBioTreeDynamicLabelFormatter *label_fmt=nullptr)   Newick format output. More...
  void  WriteNexusTree (CNcbiOstream &os, const CBioTreeDynamic &tree, const string &tree_name="the_tree", const IBioTreeDynamicLabelFormatter *label_fmt=nullptr)   Nexus format output (Newick with some stuff around it). More...
  void  PrintNode (CNcbiOstream &os, const CBioTreeDynamic &tree, const CBioTreeDynamic::TBioTreeNode &node, const IBioTreeDynamicLabelFormatter *label_fmt=nullptr)   Newick but without the terminal ';'. More...
    CTree2TreeFunc< TDstTreeNode, TSrcTreeNode, TNodeConvFunc >::CTree2TreeFunc (TNodeConvFunc &func)   ETreeTraverseCode  CTree2TreeFunc< TDstTreeNode, TSrcTreeNode, TNodeConvFunc >::operator() (const TSrcTreeNodeType &node, int delta_level)   TDstTreeNodeType *  CTree2TreeFunc< TDstTreeNode, TSrcTreeNode, TNodeConvFunc >::GetTreeNode ()   TDstTreeNodeType *  CTree2TreeFunc< TDstTreeNode, TSrcTreeNode, TNodeConvFunc >::MakeNewTreeNode (const TSrcTreeNodeType &src_node)   template<class TDynamicTree , class TSrcBioTree , class TNodeConvFunc > void  BioTreeConvert2Dynamic (TDynamicTree &dyn_tree, const TSrcBioTree &bio_tree, TNodeConvFunc node_conv)   Convert biotree to dynamic tree using a node converter. More...
  template<class TDynamicTree , class TTreeNode , class TNodeConvFunc > void  TreeConvert2Dynamic (TDynamicTree &dyn_tree, const TTreeNode *src_tree, TNodeConvFunc node_conv)   Convert CTreeNode<> to dynamic tree using a node converter. More...
  template<class TDynamicTree , class TTreeNode , class TNodeConvFunc > TTreeNode *  DynamicConvert2Tree (TDynamicTree &dyn_tree, TNodeConvFunc node_conv, TTreeNode *&dst_node)   Convert dynamic tree to CTreeNode<>, returned CTReeNode<> to be deleted by caller. More...
    CBioTreeConvert2ContainerFunc< TBioTreeContainer, TDynamicTree >::CBioTreeConvert2ContainerFunc (TBioTreeContainer *tree_container)   ETreeTraverseCode  CBioTreeConvert2ContainerFunc< TBioTreeContainer, TDynamicTree >::operator() (const TDynamicNodeType &node, int delta_level)   template<class TBioTreeContainer , class TDynamicTree > void  BioTreeConvert2Container (TBioTreeContainer &tree_container, const TDynamicTree &dyn_tree)   Convert Dynamic tree to ASN.1 BioTree container. More...
  template<class TBioTreeContainer , class TDynamicTree > void  BioTreeConvertContainer2Dynamic (TDynamicTree &dyn_tree, const TBioTreeContainer &tree_container, bool preserve_node_ids=false)   Convert ASN.1 BioTree container to dynamic tree. More...
  template<class TBioTreeContainer , class TDynamicForest > void  BioTreeForestConvert2Container (TBioTreeContainer &tree_container, const TDynamicForest &dyn_forest)   Convert forest of Dynamic trees to ASN.1 BioTree container. More...
  template<class TBioTreeContainer , class TDynamicForest > void  BioTreeConvertContainer2DynamicForest (TDynamicForest &dyn_forest, const TBioTreeContainer &tree_container)   Convert ASN.1 BioTree container to forest of dynamic trees. More...
    CTaxon1NodeConvertVisitor< TITaxon4Each, TITaxon1Node, TITreeIterator, TBioTreeContainer >::CTaxon1NodeConvertVisitor (TBioTreeContainer *tree_container)   virtual  CTaxon1NodeConvertVisitor< TITaxon4Each, TITaxon1Node, TITreeIterator, TBioTreeContainer >::~CTaxon1NodeConvertVisitor ()   virtual EAction  CTaxon1NodeConvertVisitor< TITaxon4Each, TITaxon1Node, TITreeIterator, TBioTreeContainer >::Execute (const TITaxon1Node *pNode)   virtual EAction  CTaxon1NodeConvertVisitor< TITaxon4Each, TITaxon1Node, TITreeIterator, TBioTreeContainer >::LevelBegin (const TITaxon1Node *pParent)   virtual EAction  CTaxon1NodeConvertVisitor< TITaxon4Each, TITaxon1Node, TITreeIterator, TBioTreeContainer >::LevelEnd (const TITaxon1Node *)   int  CTaxon1NodeConvertVisitor< TITaxon4Each, TITaxon1Node, TITreeIterator, TBioTreeContainer >::GetMaxNodeId () const   template<class TBioTreeContainer > void  BioTreeAddFeatureToDictionary (TBioTreeContainer &tree_container, unsigned int feature_id, const string &feature_name)     CTaxon1ConvertToBioTreeContainer< TBioTreeContainer, TTaxon1, TITaxon1Node, TITreeIterator >::CTaxon1ConvertToBioTreeContainer ()   void  CTaxon1ConvertToBioTreeContainer< TBioTreeContainer, TTaxon1, TITaxon1Node, TITreeIterator >::operator() (TBioTreeContainer &tree_container, TTaxon1 &tax, TTaxId tax_id)   void  CTaxon1ConvertToBioTreeContainer< TBioTreeContainer, TTaxon1, TITaxon1Node, TITreeIterator >::operator() (TBioTreeContainer &tree_container, CRef< TITreeIterator > tax_tree_iter)   int  CTaxon1ConvertToBioTreeContainer< TBioTreeContainer, TTaxon1, TITaxon1Node, TITreeIterator >::GetMaxNodeId () const   Get max node id (available after conversion) More...
  void  CTaxon1ConvertToBioTreeContainer< TBioTreeContainer, TTaxon1, TITaxon1Node, TITreeIterator >::SetupFeatureDictionary (TBioTreeContainer &tree_container)   Add elements to the feature dictionary. More...
  template<class TBioTreeContainer > bool  BioTreeContainerIsForest (const TBioTreeContainer &tree_container)   Function to determine tree if a given biotree container is a single tree or a forest. More...
  template<class TTreeNode , class TCompFun > bool  TreeCompare (const TTreeNode &tree1, const TTreeNode &tree2, TCompFun func)   Compare two trees using comparison functor where order of children matters. More...
  template<class TTreeNode , class TFunc > TFunc  TreeForEachParent (const TTreeNode &tree_node, TFunc func, bool skip_self=false)   Visit every parent of the specified node. More...
    CTreeParentTraceFunc< TTreeNode, TTraceContainer >::CTreeParentTraceFunc (TTraceContainer *trace)   void  CTreeParentTraceFunc< TTreeNode, TTraceContainer >::operator() (const TTreeNode &node)   template<class TTreeNode , class TTraceContainer > void  TreeTraceToRoot (const TTreeNode &tree_node, TTraceContainer &trace)   Trace from the specified node to to the tree root. More...
  template<class TTreeNode > void  TreeReRoot (TTreeNode &new_root_node)   Change tree root (tree rotation) More...
  template<class TTreeNode > const TTreeNode *  TreeFindCommonParent (const TTreeNode &tree_node_a, const TTreeNode &tree_node_b)   Check if two nodes have the same common root. More...
    CTreePrintFunc< TTreeNode, TConverter >::CTreePrintFunc (CNcbiOstream &os, TConverter &conv, bool print_ptr)   ETreeTraverseCode  CTreePrintFunc< TTreeNode, TConverter >::operator() (const TTreeNode &tr, int delta)   void  CTreePrintFunc< TTreeNode, TConverter >::PrintLevelMargin ()   template<class TTreeNode , class TConverter > void  TreePrint (CNcbiOstream &os, const TTreeNode &tree_node, TConverter conv, bool print_ptr=false)   Tree printing (use for debugging purposes) More...
  template<class TPairTree , class TValue > const TPairTree *  PairTreeBackTraceNode (const TPairTree &tr, const TValue &search_id)   Algorithm to to search for a node with specified id. More...
  template<class TPairTree , class TPathList > const TPairTree *  PairTreeTraceNode (const TPairTree &tr, const TPathList &node_path)   Algorithm to trace the pair tree and find specified leaf along the node path. More...
  template<class TNodeListIt , class TBackInsert > void  TreeListToSet (TNodeListIt node_list_first, TNodeListIt node_list_last, TBackInsert back_ins)   Convert list of node pointers to set of ids Input set is represented by input forward iterators Output set is a back insert iterator. More...
  template<class TNodeList , class TBackInsert > void  TreeListToSet (const TNodeList &node_list, TBackInsert back_ins)   Convert list of node pointers to set of ids. More...
    CTreeIdToSetFunc< TTreeNode, TBackInsert >::CTreeIdToSetFunc (TBackInsert back_ins)   ETreeTraverseCode  CTreeIdToSetFunc< TTreeNode, TBackInsert >::operator() (const TTreeNode &node, int delta_level=0)   template<class TNode , class TBackInsert > void  TreeMakeParentsSet (const TNode &tree_node, TBackInsert back_ins)   Traverses all ancestors and add their ids to a set. More...
  template<class TNode , class TBackInsert > void  TreeMakeSet (const TNode &tree_node, TBackInsert back_ins)   Create set of all sub-nodes (recursively) More...
  template<class TNode , class TBackInsert > void  TreeMakeSubNodesSet (const TNode &tree_node, TBackInsert back_ins)   Create set of all immediate sub-nodes (one level down from the root) More...
    CTreeSet2NodeListFunc< TTreeNode, TSet, TNodeList >::CTreeSet2NodeListFunc (const TSet &node_set, TNodeList *node_list)   ETreeTraverseCode  CTreeSet2NodeListFunc< TTreeNode, TSet, TNodeList >::operator() (const TTreeNode &node, int delta_level=0)   template<class TNode , class TSet , class TNodeList > void  TreeSetToNodeList (const TNode &tree_node, const TSet &node_set, TNodeList &nlist)   Convert set of node ids to list of nodes. More...
  void  CTreeNonRedundantSet< TNode, TSet, TNodeList >::operator() (const TNodeList &src_nlist, TNodeList &dst_nlist)   void  CTreeMinimalSet< TNode, TSet, TNodeList >::operator() (const TNodeList &src_nlist, TNodeList &dst_nlist, const TSet *ignore_set=0)   Compute minimal set. More...
  void  CTreeMinimalSet< TNode, TSet, TNodeList >::MinimalSet (const TNodeList &src_nlist, TNodeList &dst_nlist, const TSet *ignore_set=0)   bool  CTreeMinimalSet< TNode, TSet, TNodeList >::CheckNodeList (const TNodeList &nlist, TNodeList &dst_nlist, TSet &src_set, TSet &tmp_set, TSet &child_set, const TSet *ignore_set)   void  CNodesToBitset< TNode, TSet, TNodeList >::JoinNodeList (const TNodeList &src_nlist_a, const TNodeList &src_nlist_b, const TSet &mask_set, TNodeList &dst_list, TSet &dst_set)   Join two node lists. More...
  void  CNodesToBitset< TNode, TSet, TNodeList >::MaskCopyNodes (const TNodeList &src_nlist, const TSet &mask_set, TNodeList &dst_list, TSet &dst_set)   Copy nodes from the source node list to destination if nodes are in the mask set and not yet in the destination set. More...
  void  CTreeNodesAnd< TNode, TSet, TNodeList >::operator() (const TNodeList &src_nlist_a, const TNodeList &src_nlist_b, TNodeList &dst_nlist)   void  CTreeNodesAnd< TNode, TSet, TNodeList >::operator() (const TNodeList &src_nlist_a, const TNodeList &src_nlist_b, TNodeList &dst_nlist, TSet &dst_set)   void  CTreeNodesOr< TNode, TSet, TNodeList >::operator() (const TNodeList &src_nlist_a, const TNodeList &src_nlist_b, TNodeList &dst_nlist)   void  CTreeNodesOr< TNode, TSet, TNodeList >::operator() (const TNodeList &src_nlist_a, const TNodeList &src_nlist_b, TNodeList &dst_nlist, TSet &dst_set)     CDefaultNodeKeyGetter< TValue, TKeyEqualP >::CDefaultNodeKeyGetter (const TKeyEqual &key_equal=TKeyEqual())   const TKeyEqual &  CDefaultNodeKeyGetter< TValue, TKeyEqualP >::GetKeyEqual () const   Get key comparator. More...
  const TValueType &  CDefaultNodeKeyGetter< TValue, TKeyEqualP >::GetValue (const TNodeType &node) const   Get value of a node. More...
  TValueType &  CDefaultNodeKeyGetter< TValue, TKeyEqualP >::GetValueNC (TNodeType &node) const   Get non-const value of a node. More...
  const TKeyType &  CDefaultNodeKeyGetter< TValue, TKeyEqualP >::GetKey (const TNodeType &node) const   Get key of a node. More...
  TKeyType &  CDefaultNodeKeyGetter< TValue, TKeyEqualP >::GetKeyNC (TNodeType &node) const   Get non-const key. More...
  bool  CDefaultNodeKeyGetter< TValue, TKeyEqualP >::KeyEqual (const TKeyType &key1, const TKeyType &key2) const   Check if the two keys are equal. More...
  bool  CDefaultNodeKeyGetter< TValue, TKeyEqualP >::KeyCompare (const TKeyType &key1, const TKeyType &key2) const   Check if the two keys are equal. More...
    CTreeNode< TValue, TKeyGetterP >::CTreeNode (const TValue &value=TValue())   Tree node construction. More...
    CTreeNode< TValue, TKeyGetterP >::CTreeNode (const TKeyGetter &getter, const TValue &value=TValue())   virtual  CTreeNode< TValue, TKeyGetterP >::~CTreeNode ()     CTreeNode< TValue, TKeyGetterP >::CTreeNode (const TTreeType &tree)   CTreeNode &  CTreeNode< TValue, TKeyGetterP >::operator= (const TTreeType &tree)   const TKeyGetter &  CTreeNode< TValue, TKeyGetterP >::GetKeyGetter (void) const   Get key getter. More...
  const TTreeType *  CTreeNode< TValue, TKeyGetterP >::GetParent (void) const   Get node's parent. More...
  TTreeType *  CTreeNode< TValue, TKeyGetterP >::GetParent (void)   Get node's parent. More...
  const TTreeType *  CTreeNode< TValue, TKeyGetterP >::GetRoot (void) const   Get the topmost node. More...
  TTreeType *  CTreeNode< TValue, TKeyGetterP >::GetRoot (void)   Get the topmost node. More...
  TNodeList_CI  CTreeNode< TValue, TKeyGetterP >::SubNodeBegin (void) const   Return first const iterator on subnode list. More...
  TNodeList_I  CTreeNode< TValue, TKeyGetterP >::SubNodeBegin (void)   Return first iterator on subnode list. More...
  TNodeList_CI  CTreeNode< TValue, TKeyGetterP >::SubNodeEnd (void) const   Return last const iterator on subnode list. More...
  TNodeList_I  CTreeNode< TValue, TKeyGetterP >::SubNodeEnd (void)   Return last iterator on subnode list. More...
  TNodeList_CRI  CTreeNode< TValue, TKeyGetterP >::SubNodeRBegin (void) const   Return first const reverse iterator on subnode list. More...
  TNodeList_RI  CTreeNode< TValue, TKeyGetterP >::SubNodeRBegin (void)   Return first reverse iterator on subnode list. More...
  TNodeList_CRI  CTreeNode< TValue, TKeyGetterP >::SubNodeREnd (void) const   Return last const reverse iterator on subnode list. More...
  TNodeList_RI  CTreeNode< TValue, TKeyGetterP >::SubNodeREnd (void)   Return last reverse iterator on subnode list. More...
  const TValue &  CTreeNode< TValue, TKeyGetterP >::GetValue (void) const   Return node's value. More...
  TValue &  CTreeNode< TValue, TKeyGetterP >::GetValue (void)   Return node's value. More...
  void  CTreeNode< TValue, TKeyGetterP >::SetValue (const TValue &value)   Set value for the node. More...
  const TValue &  CTreeNode< TValue, TKeyGetterP >::operator* (void) const   TValue &  CTreeNode< TValue, TKeyGetterP >::operator* (void)   const TValue *  CTreeNode< TValue, TKeyGetterP >::operator-> (void) const   TValue *  CTreeNode< TValue, TKeyGetterP >::operator-> (void)   const TKeyType &  CTreeNode< TValue, TKeyGetterP >::GetKey (void) const   TKeyType &  CTreeNode< TValue, TKeyGetterP >::GetKey (void)   const TKeyEqual &  CTreeNode< TValue, TKeyGetterP >::GetKeyEqual () const   Return key equal predicate. More...
  bool  CTreeNode< TValue, TKeyGetterP >::KeyEqual (const TKeyType &key) const   Check if the node's key is equal to the argument. More...
  void  CTreeNode< TValue, TKeyGetterP >::RemoveNode (TTreeType *subnode)   Remove subnode of the current node. More...
  void  CTreeNode< TValue, TKeyGetterP >::RemoveNode (TNodeList_I it)   Remove subnode of the current node. More...
  void  CTreeNode< TValue, TKeyGetterP >::RemoveAllSubNodes (EDeletePolicy del=eDelete)   Remove all immediate subnodes. More...
  TTreeType *  CTreeNode< TValue, TKeyGetterP >::DetachNode (TTreeType *subnode)   Remove the subtree from the tree without destroying it. More...
  TTreeType *  CTreeNode< TValue, TKeyGetterP >::DetachNode (TNodeList_I it)   Remove the subtree from the tree without destroying it. More...
  void  CTreeNode< TValue, TKeyGetterP >::AddNode (TTreeType *subnode)   Add new subnode. More...
  TTreeType *  CTreeNode< TValue, TKeyGetterP >::AddNode (const TValue &val=TValue())   Add new subnode whose value is (a copy of) val. More...
  void  CTreeNode< TValue, TKeyGetterP >::MoveSubnodes (TTreeType *src_tree_node)   Remove all subnodes from the source node and attach them to the current tree (node). More...
  void  CTreeNode< TValue, TKeyGetterP >::InsertNode (TNodeList_I it, TTreeType *subnode)   Insert new subnode before the specified location in the subnode list. More...
  bool  CTreeNode< TValue, TKeyGetterP >::IsLeaf () const   Report whether this is a leaf node. More...
  bool  CTreeNode< TValue, TKeyGetterP >::IsParent (const TTreeType &tree_node) const   Check if node is a direct or indirect parent of this node. More...
  void  CTreeNode< TValue, TKeyGetterP >::FindNodes (const TKeyList &node_path, TNodeList *res)   Find tree nodes corresponding to the path from the top. More...
  TTreeType *  CTreeNode< TValue, TKeyGetterP >::FindOrCreateNode (const TKeyList &node_path)   Find or create tree node corresponding to the path from the top. More...
  void  CTreeNode< TValue, TKeyGetterP >::FindNodes (const TKeyList &node_path, TConstNodeList *res) const   Find tree nodes corresponding to the path from the top. More...
  const TTreeType *  CTreeNode< TValue, TKeyGetterP >::FindSubNode (const TKeyType &key) const   Non recursive linear scan of all subnodes, with key comparison. More...
  TTreeType *  CTreeNode< TValue, TKeyGetterP >::FindSubNode (const TKeyType &key)   Non recursive linear scan of all subnodes, with key comparison. More...
  const TTreeType *  CTreeNode< TValue, TKeyGetterP >::FindNode (const TKeyType &key, TNodeSearchMode sflag=eImmediateAndTop) const   Search for node. More...
  unsigned int  CTreeNode< TValue, TKeyGetterP >::CountNodes (unsigned int depth=1, TCountNodes how=0) const   Count nodes of the tree of which this node is a root. More...
  template<class TNodeComparator > void  CTreeNode< TValue, TKeyGetterP >::SortChildren (const TNodeComparator &compare)     CTreeNode< TValue, TKeyGetterP >::CSorter< TNodeComparator >::CSorter (const TNodeComparator &compare)   ETreeTraverseCode  CTreeNode< TValue, TKeyGetterP >::CSorter< TNodeComparator >::operator() (TTreeType &node, int delta_level)   void  CTreeNode< TValue, TKeyGetterP >::CopyFrom (const TTreeType &tree)   void  CTreeNode< TValue, TKeyGetterP >::SetParent (TTreeType *parent_node)   const TNodeList &  CTreeNode< TValue, TKeyGetterP >::GetSubNodes () const     CPairNodeKeyGetter< TNode, TKeyEqualP >::CPairNodeKeyGetter (const TKeyEqual &key_equal=TKeyEqual())   const TKeyEqual &  CPairNodeKeyGetter< TNode, TKeyEqualP >::GetKeyEqual () const   Get key comparator. More...
  const TValueType &  CPairNodeKeyGetter< TNode, TKeyEqualP >::GetValue (const TNodeType &node) const   TValueType &  CPairNodeKeyGetter< TNode, TKeyEqualP >::GetValueNC (TNodeType &node) const   const TKeyType &  CPairNodeKeyGetter< TNode, TKeyEqualP >::GetKey (const TNodeType &node) const   TKeyType &  CPairNodeKeyGetter< TNode, TKeyEqualP >::GetKeyNC (TNodeType &node) const   bool  CPairNodeKeyGetter< TNode, TKeyEqualP >::KeyEqual (const TKeyType &key1, const TKeyType &key2) const   bool  CPairNodeKeyGetter< TNode, TKeyEqualP >::KeyCompare (const TKeyType &key1, const TKeyType &key2) const     CTreePair< TId, TValue, TIdEqual >::CTreePair ()     CTreePair< TId, TValue, TIdEqual >::CTreePair (const TId &aid, const TValue &avalue=TValue())   template<class TTreeNode , class Fun > Fun  TreeDepthFirstTraverse (TTreeNode &tree_node, Fun func)   Depth-first tree traversal algorithm. More...
  template<class TTreeNode , class Fun > Fun  TreeBreadthFirstTraverse (TTreeNode &tree_node, Fun func)   Breadth-first tree traversal algorithm. More...
  template<class TValue , class TNodeComparator > void  SortTree (CTreeNode< TValue > &root, const TNodeComparator &compare)     CCompareByLeafCount< TValue, TKeyGetter >::CCompareByLeafCount (bool ascending=false)   bool  CCompareByLeafCount< TValue, TKeyGetter >::operator() (const TNodeType *node1, const TNodeType *node2) const   TBioTreeFeatureId  CBioTreeFeaturePair::id   string  CBioTreeFeaturePair::value   TFeatureList  CBioTreeFeatureList::m_FeatureList   TBioTreeNodeId  BioTreeBaseNode< TNodeData, TNodeFeatures >::uid   Unique node Id. More...
  TNodeData  BioTreeBaseNode< TNodeData, TNodeFeatures >::data   additional node info More...
  TNodeFeatures  BioTreeBaseNode< TNodeData, TNodeFeatures >::features   list of node features More...
  TFeatureDict  CBioTreeFeatureDictionary::m_Dict   id -> feature name map More...
  TFeatureNameIdx  CBioTreeFeatureDictionary::m_Name2Id   id -> feature name map More...
  unsigned int  CBioTreeFeatureDictionary::m_IdCounter   Feature id counter. More...
  TBioTree *  CBioTree< TBioNode >::CBioNode::m_ParentTree   Pointer on the hosting class. More...
  TBioTreeNodeId  CBioTree< TBioNode >::CFindUidFunc::m_Uid   Node uid to search for. More...
  TBioTreeNode *  CBioTree< TBioNode >::CFindUidFunc::m_Node   Search result. More...
  CBioTree *  CBioTree< TBioNode >::CAssignTreeFunc::m_Tree   CBioTreeFeatureDictionary  CBioTree< TBioNode >::m_FeatureDict   TBioTreeNodeId  CBioTree< TBioNode >::m_NodeIdCounter   unique_ptr< TBioTreeNode >  CBioTree< TBioNode >::m_TreeNode   Top level node. More...
  TDstTreeNodeType *  CTree2TreeFunc< TDstTreeNode, TSrcTreeNode, TNodeConvFunc >::m_DstTree   TNodeConvFunc &  CTree2TreeFunc< TDstTreeNode, TSrcTreeNode, TNodeConvFunc >::m_ConvFunc   vector< TDstTreeNodeType * >  CTree2TreeFunc< TDstTreeNode, TSrcTreeNode, TNodeConvFunc >::m_TreeStack   TBioTreeContainer *  CBioTreeConvert2ContainerFunc< TBioTreeContainer, TDynamicTree >::m_Container   TNodeList *  CBioTreeConvert2ContainerFunc< TBioTreeContainer, TDynamicTree >::m_NodeList   TBioTreeContainer *  CTaxon1NodeConvertVisitor< TITaxon4Each, TITaxon1Node, TITreeIterator, TBioTreeContainer >::m_TreeContainer   TNodeList *  CTaxon1NodeConvertVisitor< TITaxon4Each, TITaxon1Node, TITreeIterator, TBioTreeContainer >::m_NodeList   vector< TTaxId >  CTaxon1NodeConvertVisitor< TITaxon4Each, TITaxon1Node, TITreeIterator, TBioTreeContainer >::m_Parents   int  CTaxon1NodeConvertVisitor< TITaxon4Each, TITaxon1Node, TITreeIterator, TBioTreeContainer >::m_MaxUID   int  CTaxon1ConvertToBioTreeContainer< TBioTreeContainer, TTaxon1, TITaxon1Node, TITreeIterator >::m_MaxNodeId   TTraceContainer *  CTreeParentTraceFunc< TTreeNode, TTraceContainer >::m_Trace   CNcbiOstream &  CTreePrintFunc< TTreeNode, TConverter >::m_OStream   TConverter &  CTreePrintFunc< TTreeNode, TConverter >::m_Conv   int  CTreePrintFunc< TTreeNode, TConverter >::m_Level   bool  CTreePrintFunc< TTreeNode, TConverter >::m_PrintPtr   TBackInsert  CTreeIdToSetFunc< TTreeNode, TBackInsert >::m_BackIns   const TSet &  CTreeSet2NodeListFunc< TTreeNode, TSet, TNodeList >::m_NodeSet   TNodeList *  CTreeSet2NodeListFunc< TTreeNode, TSet, TNodeList >::m_NodeList   const TNodeComparator &  CTreeNode< TValue, TKeyGetterP >::CSorter< TNodeComparator >::m_Compare   pair_base_member< TKeyGetter, TTreeType * >  CTreeNode< TValue, TKeyGetterP >::m_GetterAndParent   Key getter and pointer to the parent node. More...
  TNodeList  CTreeNode< TValue, TKeyGetterP >::m_Nodes   List of dependent nodes. More...
  TValue  CTreeNode< TValue, TKeyGetterP >::m_Value   Node value. More...
  TId  CTreePair< TId, TValue, TIdEqual >::id   TValue  CTreePair< TId, TValue, TIdEqual >::value   bool  CCompareByLeafCount< TValue, TKeyGetter >::m_Ascending   ◆ CBioTreeDynamic

Bio tree without static elements.

Everything is stored as features.

Definition at line 493 of file bio_tree.hpp.

◆ EAction

template<class TITaxon4Each , class TITaxon1Node , class TITreeIterator , class TBioTreeContainer >

Definition at line 583 of file bio_tree_conv.hpp.

◆ T4Each

template<class TBioTreeContainer , class TTaxon1 , class TITaxon1Node , class TITreeIterator >

Definition at line 773 of file bio_tree_conv.hpp.

◆ TBioNodeType ◆ TBioTree ◆ TBioTreeFeatureId

Feature Id.

All bio tree dynamic features are encoded by feature ids. Ids are shared among the tree nodes. Feature id to feature name map is supported by the tree.

Definition at line 60 of file bio_tree.hpp.

◆ TBioTreeNode

template<class TBioNode >

Biotree node (forms the tree hierarchy)

Definition at line 358 of file bio_tree.hpp.

◆ TBioTreeNodeId

Tree node id. Every node has its unique id in the tree.

Definition at line 63 of file bio_tree.hpp.

◆ TCNode [1/2]

template<class TBioTreeContainer , class TDynamicTree >

Definition at line 219 of file bio_tree_conv.hpp.

◆ TCNode [2/2]

template<class TITaxon4Each , class TITaxon1Node , class TITreeIterator , class TBioTreeContainer >

Definition at line 587 of file bio_tree_conv.hpp.

◆ TCNodeFeature [1/2]

template<class TBioTreeContainer , class TDynamicTree >

Definition at line 223 of file bio_tree_conv.hpp.

◆ TCNodeFeature [2/2]

template<class TITaxon4Each , class TITaxon1Node , class TITreeIterator , class TBioTreeContainer >

Definition at line 591 of file bio_tree_conv.hpp.

◆ TCNodeFeatureSet [1/2]

template<class TBioTreeContainer , class TDynamicTree >

Definition at line 220 of file bio_tree_conv.hpp.

◆ TCNodeFeatureSet [2/2]

template<class TITaxon4Each , class TITaxon1Node , class TITreeIterator , class TBioTreeContainer >

Definition at line 588 of file bio_tree_conv.hpp.

◆ TCNodeSet [1/2]

template<class TBioTreeContainer , class TDynamicTree >

Definition at line 217 of file bio_tree_conv.hpp.

◆ TCNodeSet [2/2]

template<class TITaxon4Each , class TITaxon1Node , class TITreeIterator , class TBioTreeContainer >

Definition at line 585 of file bio_tree_conv.hpp.

◆ TConstNodeList

template<class TValue , class TKeyGetterP = CDefaultNodeKeyGetter<TValue>>

Definition at line 108 of file ncbi_tree.hpp.

◆ TCountNodes

template<class TValue , class TKeyGetterP = CDefaultNodeKeyGetter<TValue>>

◆ TDstTreeNodeType

template<class TDstTreeNode , class TSrcTreeNode , class TNodeConvFunc >

Definition at line 59 of file bio_tree_conv.hpp.

◆ TDynamicNodeType

template<class TBioTreeContainer , class TDynamicTree >

Definition at line 214 of file bio_tree_conv.hpp.

◆ TDynamicNodeValueType

template<class TBioTreeContainer , class TDynamicTree >

Definition at line 215 of file bio_tree_conv.hpp.

◆ TFeatureDict

Feature dictionary (feature id -> feature name map)

Definition at line 179 of file bio_tree.hpp.

◆ TFeatureList ◆ TFeatureNameIdx

Feature reverse index (feature name -> id)

Definition at line 182 of file bio_tree.hpp.

◆ TIdType

template<class TId , class TValue , class TIdEqual = std::equal_to<TId>>

Definition at line 455 of file ncbi_tree.hpp.

◆ TKeyEqual [1/3]

template<class TValue , class TKeyEqualP = std::equal_to<TValue>>

◆ TKeyEqual [2/3]

template<class TValue , class TKeyGetterP = CDefaultNodeKeyGetter<TValue>>

Definition at line 105 of file ncbi_tree.hpp.

◆ TKeyEqual [3/3]

template<class TNode , class TKeyEqualP = std::equal_to<typename TNode::TIdType>>

Definition at line 425 of file ncbi_tree.hpp.

◆ TKeyGetter

template<class TValue , class TKeyGetterP = CDefaultNodeKeyGetter<TValue>>

Definition at line 103 of file ncbi_tree.hpp.

◆ TKeyList

template<class TValue , class TKeyGetterP = CDefaultNodeKeyGetter<TValue>>

Definition at line 113 of file ncbi_tree.hpp.

◆ TKeyType [1/3]

template<class TValue , class TKeyEqualP = std::equal_to<TValue>>

◆ TKeyType [2/3]

template<class TValue , class TKeyGetterP = CDefaultNodeKeyGetter<TValue>>

Definition at line 104 of file ncbi_tree.hpp.

◆ TKeyType [3/3]

template<class TNode , class TKeyEqualP = std::equal_to<typename TNode::TIdType>>

Definition at line 424 of file ncbi_tree.hpp.

◆ TNodeDataType

template<class TNodeData = CBioTreeEmptyNodeData, class TNodeFeatures = CBioTreeFeatureList>

Definition at line 154 of file bio_tree.hpp.

◆ TNodeFeatureList [1/2]

template<class TBioTreeContainer , class TDynamicTree >

Definition at line 221 of file bio_tree_conv.hpp.

◆ TNodeFeatureList [2/2]

template<class TITaxon4Each , class TITaxon1Node , class TITreeIterator , class TBioTreeContainer >

Definition at line 589 of file bio_tree_conv.hpp.

◆ TNodeFeaturesType

template<class TNodeData = CBioTreeEmptyNodeData, class TNodeFeatures = CBioTreeFeatureList>

Definition at line 155 of file bio_tree.hpp.

◆ TNodeList [1/3]

template<class TBioTreeContainer , class TDynamicTree >

Definition at line 218 of file bio_tree_conv.hpp.

◆ TNodeList [2/3]

template<class TITaxon4Each , class TITaxon1Node , class TITreeIterator , class TBioTreeContainer >

Definition at line 586 of file bio_tree_conv.hpp.

◆ TNodeList [3/3]

template<class TValue , class TKeyGetterP = CDefaultNodeKeyGetter<TValue>>

Definition at line 107 of file ncbi_tree.hpp.

◆ TNodeList_CI

template<class TValue , class TKeyGetterP = CDefaultNodeKeyGetter<TValue>>

Definition at line 110 of file ncbi_tree.hpp.

◆ TNodeList_CRI

template<class TValue , class TKeyGetterP = CDefaultNodeKeyGetter<TValue>>

Definition at line 112 of file ncbi_tree.hpp.

◆ TNodeList_I

template<class TValue , class TKeyGetterP = CDefaultNodeKeyGetter<TValue>>

Definition at line 109 of file ncbi_tree.hpp.

◆ TNodeList_RI

template<class TValue , class TKeyGetterP = CDefaultNodeKeyGetter<TValue>>

Definition at line 111 of file ncbi_tree.hpp.

◆ TNodeSearchMode

template<class TValue , class TKeyGetterP = CDefaultNodeKeyGetter<TValue>>

◆ TNodeType [1/3]

template<class TValue , class TKeyEqualP = std::equal_to<TValue>>

◆ TNodeType [2/3]

template<class TNode , class TKeyEqualP = std::equal_to<typename TNode::TIdType>>

Definition at line 422 of file ncbi_tree.hpp.

◆ TNodeType [3/3]

template<class TValue , class TKeyGetter = CDefaultNodeKeyGetter<TValue>>

Definition at line 1045 of file ncbi_tree.hpp.

◆ TPairKeyGetter

template<class TId , class TValue , class TIdEqual = std::equal_to<TId>>

◆ TPairTreeNode

template<class TId , class TValue , class TIdEqual = std::equal_to<TId>>

◆ TParent ◆ TSrcTreeNodeType

template<class TDstTreeNode , class TSrcTreeNode , class TNodeConvFunc >

Definition at line 60 of file bio_tree_conv.hpp.

◆ TTaxon1Visitor

template<class TBioTreeContainer , class TTaxon1 , class TITaxon1Node , class TITreeIterator >

Definition at line 776 of file bio_tree_conv.hpp.

◆ TTreePair

template<class TId , class TValue , class TIdEqual = std::equal_to<TId>>

◆ TTreeType [1/2] ◆ TTreeType [2/2]

template<class TValue , class TKeyGetterP = CDefaultNodeKeyGetter<TValue>>

Definition at line 106 of file ncbi_tree.hpp.

◆ TValueType [1/4]

template<class TValue , class TKeyEqualP = std::equal_to<TValue>>

◆ TValueType [2/4]

template<class TValue , class TKeyGetterP = CDefaultNodeKeyGetter<TValue>>

Definition at line 102 of file ncbi_tree.hpp.

◆ TValueType [3/4]

template<class TNode , class TKeyEqualP = std::equal_to<typename TNode::TIdType>>

Definition at line 423 of file ncbi_tree.hpp.

◆ TValueType [4/4]

template<class TId , class TValue , class TIdEqual = std::equal_to<TId>>

Definition at line 456 of file ncbi_tree.hpp.

◆ ECountNodes

template<class TValue , class TKeyGetterP = CDefaultNodeKeyGetter<TValue>>

How to count nodes in the tree of which this node is a root.

See also
CountNodes, TConstNodeList
Enumerator fOnlyLeafs 

Only "leaf" nodes.

fCumulative 

All nodes up to the specified depth.

Definition at line 367 of file ncbi_tree.hpp.

◆ EDeletePolicy

template<class TValue , class TKeyGetterP = CDefaultNodeKeyGetter<TValue>>

Whether to destroy the sub-nodes when bulk-cleaning the node.

See also
RemoveAllSubNodes
Enumerator eDelete 

Destroy the sub-nodes when bulk-cleaning the node.

eNoDelete 

Just exclude nodes from the tree, do not destroy them.

Definition at line 226 of file ncbi_tree.hpp.

◆ ENodeSearchType

template<class TValue , class TKeyGetterP = CDefaultNodeKeyGetter<TValue>>

Parameters for node search by key.

Enumerator eImmediateSubNodes 

Search direct subnodes.

eTopLevelNodes 

Search subnodes of the root.

eAllUpperSubNodes 

Search all subnodes on the way up.

eImmediateAndTop 

Definition at line 345 of file ncbi_tree.hpp.

◆ ETaxon1ConvFeatures

Feature ids for Bio-Tree.

Enumerator eTaxTree_Name  eTaxTree_BlastName  eTaxTree_Rank  eTaxTree_Division  eTaxTree_GC  eTaxTree_MGC  eTaxTree_IsUncultured  eTaxTree_TaxId  eTaxTree_SeqId  eTaxTree_Label 

Definition at line 559 of file bio_tree_conv.hpp.

◆ ETreeTraverseCode

Tree traverse code returned by the traverse predicate function.

Enumerator eTreeTraverse 

Keep traversal.

eTreeTraverseStop 

Stop traversal (return form algorithm)

eTreeTraverseStepOver 

Do not traverse current node (pick the next one)

Definition at line 50 of file ncbi_tree.hpp.

◆ AddFeature() [1/2]

template<class TBioNode >

Add feature to the tree node Function controls that the feature is registered in the feature dictionary of this tree.

If feature is not found it is added to the dictionary

Definition at line 589 of file bio_tree.hpp.

◆ AddFeature() [2/2]

template<class TBioNode >

◆ AddNode() [1/6]

template<class TBioNode >

Add a subnode to this node based on value.

Definition at line 316 of file bio_tree.hpp.

◆ AddNode() [2/6]

template<class TBioNode >

◆ AddNode() [3/6]

template<class TBioNode >

◆ AddNode() [4/6]

template<class TValue , class TKeyGetter >

Add new subnode whose value is (a copy of) val.

Parameters
Returns
pointer to new subtree

Definition at line 752 of file ncbi_tree.hpp.

References AddNode(), and val.

◆ AddNode() [5/6]

template<class TBioNode >

◆ AddNode() [6/6]

template<class TValue , class TKeyGetter >

Add new subnode.

Parameters

Definition at line 743 of file ncbi_tree.hpp.

References _ASSERT, and CTreeNode< TValue, TKeyGetterP >::SetParent().

Referenced by AddFunc_Arg(), AddIn_Arg(), CMenuItem::AddSubItem(), CClusterer::ComputeClusters(), CConfig::ConvertRegToTree(), CTreeFiller::Execute(), CTreeNode< TValue, TKeyGetterP >::FindOrCreateNode(), Flatten_ParseTree(), CGBDataLoader::GetParamsSubnode(), newickparse(), CDistMethods::NjTree(), QTreeAddNode(), CDistMethods::RerootTree(), s_AddFastMeSubtree(), s_AddOrReplaceSubNode(), s_IncludeNode(), s_MakeTwoLeafTree(), s_ParseSubNodes(), CMacroRep::SetAssignmentWhereClause(), CMacroRep::SetFunction(), CMacroRep::SetFunctionParameterAsBool(), CMacroRep::SetFunctionParameterAsFloat(), CMacroRep::SetFunctionParameterAsIdent(), CMacroRep::SetFunctionParameterAsInt(), CMacroRep::SetFunctionParameterAsString(), CGBDataLoader::SetParam(), SPluginParams::SetSubNode(), CMultiAligner::x_AttachClusterTrees(), CClusterer::x_JoinClustElem(), CClusterer::x_JoinClusters(), CClusterer::x_JoinElements(), CMacroParser::x_ParseDo(), CAlignFilter::x_ParseTree_Flatten(), and CMacroParser::x_SortParseTree().

◆ BioTreeAddFeatureToDictionary()

template<class TBioTreeContainer >

void BioTreeAddFeatureToDictionary ( TBioTreeContainer &  tree_container, unsigned int  feature_id, const string &  feature_name  ) ◆ BioTreeBaseNode()

template<class TNodeData = CBioTreeEmptyNodeData, class TNodeFeatures = CBioTreeFeatureList>

Definition at line 158 of file bio_tree.hpp.

◆ BioTreeContainerIsForest()

template<class TBioTreeContainer >

bool BioTreeContainerIsForest ( const TBioTreeContainer &  tree_container )

Function to determine tree if a given biotree container is a single tree or a forest.

Definition at line 844 of file bio_tree_conv.hpp.

References ITERATE.

◆ BioTreeConvert2Container()

template<class TBioTreeContainer , class TDynamicTree >

void BioTreeConvert2Container ( TBioTreeContainer &  tree_container, const TDynamicTree &  dyn_tree  ) ◆ BioTreeConvert2Dynamic()

template<class TDynamicTree , class TSrcBioTree , class TNodeConvFunc >

void BioTreeConvert2Dynamic ( TDynamicTree &  dyn_tree, const TSrcBioTree &  bio_tree, TNodeConvFunc  node_conv  ) ◆ BioTreeConvertContainer2Dynamic()

template<class TBioTreeContainer , class TDynamicTree >

void BioTreeConvertContainer2Dynamic ( TDynamicTree &  dyn_tree, const TBioTreeContainer &  tree_container, bool  preserve_node_ids = false  ) ◆ BioTreeConvertContainer2DynamicForest()

template<class TBioTreeContainer , class TDynamicForest >

void BioTreeConvertContainer2DynamicForest ( TDynamicForest &  dyn_forest, const TBioTreeContainer &  tree_container  ) ◆ BioTreeForestConvert2Container()

template<class TBioTreeContainer , class TDynamicForest >

void BioTreeForestConvert2Container ( TBioTreeContainer &  tree_container, const TDynamicForest &  dyn_forest  ) ◆ CAssignTreeFunc() ◆ CBioNode() [1/2]

template<class TBioNode >

Construct tree node based on source tree node (recursive copy)

Definition at line 253 of file bio_tree.hpp.

◆ CBioNode() [2/2]

template<class TBioNode >

CBioTree< TBioNode >::CBioNode::CBioNode ( const TBioNode &  value = TBioNode() ) inline ◆ CBioTree() [1/2] ◆ CBioTree() [2/2] ◆ CBioTreeConvert2ContainerFunc()

template<class TBioTreeContainer , class TDynamicTree >

◆ CBioTreeFeatureDictionary() [1/2] CBioTreeFeatureDictionary::CBioTreeFeatureDictionary ( )

Definition at line 106 of file bio_tree.cpp.

◆ CBioTreeFeatureDictionary() [2/2] ◆ CBioTreeFeatureList() [1/2] CBioTreeFeatureList::CBioTreeFeatureList ( )

Definition at line 40 of file bio_tree.cpp.

◆ CBioTreeFeatureList() [2/2] ◆ CBioTreeFeaturePair() [1/3] ◆ CBioTreeFeaturePair() [2/3] ◆ CBioTreeFeaturePair() [3/3] CBioTreeFeaturePair::CBioTreeFeaturePair ( void  ) inline

Definition at line 83 of file bio_tree.hpp.

◆ CCompareByLeafCount()

template<class TValue , class TKeyGetter = CDefaultNodeKeyGetter<TValue>>

Definition at line 1047 of file ncbi_tree.hpp.

◆ CDefaultNodeKeyGetter()

template<class TValue , class TKeyEqualP = std::equal_to<TValue>>

Definition at line 74 of file ncbi_tree.hpp.

◆ CFindUidFunc() ◆ CheckNodeList()

template<class TNode , class TSet , class TNodeList >

bool CTreeMinimalSet< TNode, TSet, TNodeList >::CheckNodeList ( const TNodeList &  nlist, TNodeList &  dst_nlist, TSet &  src_set, TSet &  tmp_set, TSet &  child_set, const TSet *  ignore_set  ) inlineprotected ◆ Clear() [1/2] void CBioTreeFeatureDictionary::Clear ( void  ) ◆ Clear() [2/2]

template<class TBioNode >

void CBioTree< TBioNode >::Clear ( void  ) ◆ CopyFrom()

template<class TValue , class TKeyGetter >

◆ CountNodes()

template<class TValue , class TKeyGetter >

◆ CPairNodeKeyGetter()

template<class TNode , class TKeyEqualP = std::equal_to<typename TNode::TIdType>>

Definition at line 427 of file ncbi_tree.hpp.

◆ CSorter()

template<class TValue , class TKeyGetterP = CDefaultNodeKeyGetter<TValue>>

template<class TNodeComparator >

Definition at line 388 of file ncbi_tree.hpp.

◆ CTaxon1ConvertToBioTreeContainer()

template<class TBioTreeContainer , class TTaxon1 , class TITaxon1Node , class TITreeIterator >

Definition at line 780 of file bio_tree_conv.hpp.

◆ CTaxon1NodeConvertVisitor()

template<class TITaxon4Each , class TITaxon1Node , class TITreeIterator , class TBioTreeContainer >

◆ CTree2TreeFunc()

template<class TDstTreeNode , class TSrcTreeNode , class TNodeConvFunc >

Definition at line 63 of file bio_tree_conv.hpp.

◆ CTreeIdToSetFunc()

template<class TTreeNode , class TBackInsert >

Definition at line 499 of file tree_algo.hpp.

◆ CTreeNode() [1/3]

template<class TValue , class TKeyGetter >

Definition at line 656 of file ncbi_tree.hpp.

◆ CTreeNode() [2/3]

template<class TValue , class TKeyGetter >

◆ CTreeNode() [3/3]

template<class TValue , class TKeyGetterP = CDefaultNodeKeyGetter<TValue>>

Tree node construction.

Parameters

Definition at line 119 of file ncbi_tree.hpp.

◆ CTreePair() [1/2]

template<class TId , class TValue , class TIdEqual = std::equal_to<TId>>

Definition at line 465 of file ncbi_tree.hpp.

◆ CTreePair() [2/2]

template<class TId , class TValue , class TIdEqual = std::equal_to<TId>>

Definition at line 466 of file ncbi_tree.hpp.

◆ CTreeParentTraceFunc()

template<class TTreeNode , class TTraceContainer >

Definition at line 178 of file tree_algo.hpp.

◆ CTreePrintFunc()

template<class TTreeNode , class TConverter >

Definition at line 293 of file tree_algo.hpp.

◆ CTreeSet2NodeListFunc()

template<class TTreeNode , class TSet , class TNodeList >

Definition at line 577 of file tree_algo.hpp.

◆ DetachNode() [1/4]

template<class TValue , class TKeyGetter >

Remove the subtree from the tree without destroying it.

If subnode is not connected directly with the current node the call has no effect. The caller is responsible for deletion of the returned subtree.

Parameters
subnode direct subnode pointer
Returns
subtree pointer or NULL if requested subnode does not exist

Definition at line 733 of file ncbi_tree.hpp.

References CTreeNode< TValue, TKeyGetterP >::SetParent().

◆ DetachNode() [2/4] ◆ DetachNode() [3/4]

template<class TValue , class TKeyGetter >

◆ DetachNode() [4/4]

template<class TBioNode >

Node is detached from the tree (Parent becomes 0)

Definition at line 292 of file bio_tree.hpp.

◆ DetachTreeNode()

template<class TBioNode >

void CBioTree< TBioNode >::DetachTreeNode ( ) inline

Definition at line 410 of file bio_tree.hpp.

◆ DynamicConvert2Tree()

template<class TDynamicTree , class TTreeNode , class TNodeConvFunc >

TTreeNode* DynamicConvert2Tree ( TDynamicTree &  dyn_tree, TNodeConvFunc  node_conv, TTreeNode *&  dst_node  ) ◆ Execute()

template<class TITaxon4Each , class TITaxon1Node , class TITreeIterator , class TBioTreeContainer >

Definition at line 604 of file bio_tree_conv.hpp.

References eTaxTree_BlastName, eTaxTree_Division, eTaxTree_GC, eTaxTree_IsUncultured, eTaxTree_Label, eTaxTree_MGC, eTaxTree_Name, eTaxTree_Rank, eTaxTree_TaxId, int, NStr::IntToString(), CTaxon1NodeConvertVisitor< TITaxon4Each, TITaxon1Node, TITreeIterator, TBioTreeContainer >::m_MaxUID, CTaxon1NodeConvertVisitor< TITaxon4Each, TITaxon1Node, TITreeIterator, TBioTreeContainer >::m_NodeList, CTaxon1NodeConvertVisitor< TITaxon4Each, TITaxon1Node, TITreeIterator, TBioTreeContainer >::m_Parents, and TAX_ID_TO.

◆ FindNode() [1/2]

template<class TValue , class TKeyGetter >

Search for node.

Parameters
key key to search for sflag ORed ENodeSearchType
Returns
node pointer or NULL

Definition at line 970 of file ncbi_tree.hpp.

References CTreeNode< TValue, TKeyGetterP >::FindSubNode(), CTreeNode< TValue, TKeyGetterP >::GetParent(), and ncbi::grid::netcache::search::fields::key.

Referenced by CDLPatcher_DataLoaderCF::CreateAndRegister(), CPluginManager< TClass >::CreateInstanceFromKey(), CPluginManager< TClass >::CreateInstanceFromList(), Get_I_DriverContext(), C_xDriverMgr::GetDriverContext(), CCacheReader::InitializeCache(), CCacheWriter::InitializeCache(), s_AddOrReplaceSubNode(), CBDB_Cache::SameCacheParams(), and CSQLITE3_Cache::SameCacheParams().

◆ FindNode() [2/2]

template<class TBioNode >

◆ FindNodes() [1/2]

template<class TValue , class TKeyGetter >

◆ FindNodes() [2/2]

template<class TValue , class TKeyGetter >

◆ FindOrCreateNode()

template<class TValue , class TKeyGetter >

◆ FindSubNode() [1/2]

template<class TValue , class TKeyGetter >

◆ FindSubNode() [2/2]

template<class TValue , class TKeyGetter >

Non recursive linear scan of all subnodes, with key comparison.

Parameters
Returns
SubNode pointer or NULL

Definition at line 940 of file ncbi_tree.hpp.

References ncbi::grid::netcache::search::fields::key.

Referenced by CID2SNPProcessor_Impl::CID2SNPProcessor_Impl(), CNetScheduleClientFactory::CreateInstance(), CBlobStorageFactory::CreateInstance(), CTreeNode< TValue, TKeyGetterP >::FindNode(), SPluginParams::FindSubNode(), CIncreasingTime::Init(), CCgiApplicationCached::Init(), NS_GetDataSize(), NS_ValidateDataSize(), s_FindSubNode(), s_IncludeNode(), CCDDDataLoader::SLoaderParams::SLoaderParams(), and SPubseqGatewaySettings::x_GetDataSize().

◆ GetFeature()

template<class TBioNode >

◆ GetFeatureDict() [1/3]

template<class TBioNode >

◆ GetFeatureDict() [2/3]

Get reference on the internal map.

Definition at line 219 of file bio_tree.hpp.

References CBioTreeFeatureDictionary::m_Dict.

Referenced by BioTreeConvert2Container(), BioTreeConvertContainer2Dynamic(), BioTreeConvertContainer2DynamicForest(), BioTreeConvertContainer2Tree(), BioTreeForestConvert2Container(), DictConvert2ContainerFeatureDict(), CPhyloTreeDataSource::GenerateTooltipFormat(), CPhyloTreeDataSource::GetColsCount(), CPhyloTreeDataSource::GetColumnLabel(), CTreeQueryExec::GetFeatureIdNoCase(), CPhyloTreeDataSource::NewNode(), CPhyloTreeWidget::OnExportSelection(), CChangePhyloPropertyCmd::PerformFeatureDictEdit(), CwxPhyloEditDlg::SetParams(), CwxPhyloSettingsDlg::SetParams(), TreeConvert2Container(), TreeConvert2ContainerPartial(), TreeConvertNonSingleChild2Container(), and TreeConvertSelected2Container().

◆ GetFeatureDict() [3/3]

template<class TBioNode >

◆ GetFeatureList() ◆ GetFeatureValue() [1/2]

Get feature value by id.

Returns
Feature value or empty string if feature does not exists

Definition at line 69 of file bio_tree.cpp.

References ITERATE, kEmptyStr, and CBioTreeFeatureList::m_FeatureList.

Referenced by CUpdatedFeature::FeatureUpdated(), CBioTreeFormatLabel::FormatLabel(), CPhyloNodeData::Init(), CPhyloNodeData::InitFeatures(), CPhyloTreeWidget::OnExportSelection(), CVisitorAccumulateProperty::operator()(), CBioTreeFeatureList::operator[](), CPhyloTreeDataSource::SetCollapsedLabel(), and CPhyloSelectionSetMgr::SetSelectionSetProperty().

◆ GetFeatureValue() [2/2] ◆ GetId() [1/2]

template<class TNodeData = CBioTreeEmptyNodeData, class TNodeFeatures = CBioTreeFeatureList>

◆ GetId() [2/2]

If feature is already registered returns its id by name.

If feature does not exist returns -1.

Definition at line 209 of file bio_tree.cpp.

References map_checker< Container >::end(), map_checker< Container >::find(), and CBioTreeFeatureDictionary::m_Name2Id.

Referenced by CBioTreeFormatLabel::CBioTreeFormatLabel(), CPhyloTreeWidget::EditLabel(), CBioTree< BioTreeBaseNode< CBioTreeEmptyNodeData, CBioTreeFeatureList > >::CBioNode::GetFeature(), CPhyTreeView::GetSelection(), CPhyloNodeData::Init(), CPhyloNodeData::InitFeatures(), CwxPhyloEditDlg::OnOkClick(), CPhyloNodeData::RemoveFeature(), CFeatureEdit::SeqIdEdited(), CPhyloTreeCalculator::SetAttrTable(), CPhyloTreeDataSource::SetCollapsedLabel(), CPhyloNodeData::SetFeature(), SPriorityCollapse::SPriorityCollapse(), and CPhyTreeView::x_OnSetSelection().

◆ GetKey() [1/4]

template<class TValue , class TKeyEqualP = std::equal_to<TValue>>

◆ GetKey() [2/4]

template<class TNode , class TKeyEqualP = std::equal_to<typename TNode::TIdType>>

Definition at line 439 of file ncbi_tree.hpp.

◆ GetKey() [3/4]

template<class TValue , class TKeyGetterP = CDefaultNodeKeyGetter<TValue>>

Definition at line 198 of file ncbi_tree.hpp.

◆ GetKey() [4/4]

template<class TValue , class TKeyGetterP = CDefaultNodeKeyGetter<TValue>>

◆ GetKeyEqual() [1/3]

template<class TValue , class TKeyEqualP = std::equal_to<TValue>>

◆ GetKeyEqual() [2/3]

template<class TValue , class TKeyGetterP = CDefaultNodeKeyGetter<TValue>>

◆ GetKeyEqual() [3/3]

template<class TNode , class TKeyEqualP = std::equal_to<typename TNode::TIdType>>

◆ GetKeyGetter()

template<class TValue , class TKeyGetterP = CDefaultNodeKeyGetter<TValue>>

◆ GetKeyNC() [1/2]

template<class TValue , class TKeyEqualP = std::equal_to<TValue>>

◆ GetKeyNC() [2/2]

template<class TNode , class TKeyEqualP = std::equal_to<typename TNode::TIdType>>

Definition at line 441 of file ncbi_tree.hpp.

◆ GetLabelForNode() ◆ GetMaxNodeId() [1/2]

template<class TITaxon4Each , class TITaxon1Node , class TITreeIterator , class TBioTreeContainer >

◆ GetMaxNodeId() [2/2]

template<class TBioTreeContainer , class TTaxon1 , class TITaxon1Node , class TITreeIterator >

◆ GetName() ◆ GetNode()

template<class TBioNode >

◆ GetNodeId() [1/2]

template<class TBioNode >

◆ GetNodeId() [2/2]

template<class TBioNode >

Get new unique node id (for cases when node id depends on the node's content.

Definition at line 397 of file bio_tree.hpp.

◆ GetParent() [1/2]

template<class TValue , class TKeyGetterP = CDefaultNodeKeyGetter<TValue>>

Get node's parent.

Returns
parent to the current node, NULL if it is a top of the tree

Definition at line 145 of file ncbi_tree.hpp.

◆ GetParent() [2/2]

template<class TValue , class TKeyGetterP = CDefaultNodeKeyGetter<TValue>>

Get node's parent.

Returns
parent to the current node, NULL if it is a top of the tree

Definition at line 139 of file ncbi_tree.hpp.

Referenced by CTreeQueryExec::CallFunction(), CMacroEngine::CallFunction(), CMacroResolver::CallFunction(), CConfig::ConvertRegToTree(), CMQueryFunctionValue::Evaluate(), CTreeNode< TValue, TKeyGetterP >::FindNode(), CMenuItem::GetParent(), CTreeNode< TValue, TKeyGetterP >::GetRoot(), CTreeNode< TValue, TKeyGetterP >::IsParent(), CTree::ListTreeEdges(), CAssignQueryTreeGetArgs::operator()(), CDoQueryTreeGetArgs::operator()(), CWhereQueryTreeGetArgs::operator()(), CScannerEvaluateFunc::operator()(), CQueryExecEvalFunc::operator()(), SNodeNameUpdater::operator()(), CDistMethods::RerootTree(), s_FindNodeDistance(), s_IsParentNode(), s_ScaleTreeEdges(), s_TestTree(), s_TraverseTree(), CMacroRep::SetAssignmentWhereClause(), and CBioTree< TBioNode >::SetTreeNode().

◆ GetParentTree() [1/2]

template<class TBioNode >

Return pointer on the hosting tree (can be NULL)

Definition at line 275 of file bio_tree.hpp.

◆ GetParentTree() [2/2]

template<class TBioNode >

◆ GetRoot() [1/2]

template<class TValue , class TKeyGetterP = CDefaultNodeKeyGetter<TValue>>

Get the topmost node.

Returns
global parent of the current node, this if it is a top of the tree
◆ GetRoot() [2/2]

template<class TValue , class TKeyGetter >

◆ GetSubNodes()

template<class TValue , class TKeyGetterP = CDefaultNodeKeyGetter<TValue>>

Definition at line 407 of file ncbi_tree.hpp.

◆ GetTreeNode() [1/2]

template<class TDstTreeNode , class TSrcTreeNode , class TNodeConvFunc >

◆ GetTreeNode() [2/2]

template<class TBioNode >

◆ GetTreeNodeNonConst()

template<class TBioNode >

◆ GetValue() [1/4]

template<class TValue , class TKeyEqualP = std::equal_to<TValue>>

◆ GetValue() [2/4]

template<class TNode , class TKeyEqualP = std::equal_to<typename TNode::TIdType>>

Definition at line 435 of file ncbi_tree.hpp.

◆ GetValue() [3/4]

template<class TValue , class TKeyGetterP = CDefaultNodeKeyGetter<TValue>>

TValue& CTreeNode< TValue, TKeyGetterP >::GetValue ( void  ) inline ◆ GetValue() [4/4]

template<class TValue , class TKeyGetterP = CDefaultNodeKeyGetter<TValue>>

const TValue& CTreeNode< TValue, TKeyGetterP >::GetValue ( void  ) const inline

Return node's value.

Definition at line 184 of file ncbi_tree.hpp.

Referenced by CBioTree< TBioNode >::AddFeature(), CTreeQueryExec::CallFunction(), CMacroEngine::CallFunction(), CMacroResolver::CallFunction(), CClusterer::ComputeClusters(), CTree::ComputeTree(), CBlobStorageFactory::CreateInstance(), CPluginManager< TClass >::CreateInstanceFromKey(), CScannerFunctorEQ::Eval(), CScannerFunctorGT::Eval(), CScannerFunctorGE::Eval(), CScannerFunctorLT::Eval(), CScannerFunctorLE::Eval(), CScannerFunctorAND::Eval(), CScannerFunctorOR::Eval(), CScannerFunctorNOT::Eval(), CTableQueryExec::EvalNext(), CTreeQueryExec::EvalNext(), CBDB_FileScanner::Evaluate(), CMQueryFunctionValue::Evaluate(), CMQueryFunctionRTVar::Evaluate(), CMQueryFunctionAssignment::Evaluate(), CMQueryFunctionFunction::Evaluate(), CMQueryFunctionDummy::Evaluate(), CQueryFuncAssignment::Evaluate(), CMQueryFunctionOps_BooleanBinary::Evaluate(), CMQueryFunctionOps_Comparison::Evaluate(), CQueryFuncRTVar::Evaluate(), CQueryFuncPromoteIdentifier::Evaluate(), CQueryFuncPromoteAndOr::Evaluate(), CQueryFuncPromoteLogic::Evaluate(), CQueryFuncPromoteEq::Evaluate(), CQueryFuncPromoteIn::Evaluate(), CQueryFuncLike::Evaluate(), CQueryFuncPromoteGtLt::Evaluate(), CQueryFuncPromoteBetween::Evaluate(), CQueryFunction_BV_In_Or< BV >::Evaluate(), CQueryFunction_BV_Base< BV >::GetContainer(), CGBDataLoader::GetParam(), CQueryFuncPromoteBase::GetQueryNodeValue(), CCgiApplicationCached::Init(), CCacheReader::InitializeCache(), CCacheWriter::InitializeCache(), IsDisabledCache(), CTree::ListTreeEdges(), CTree::ListTreeLeaves(), CQueryFunction_BV_Base< BV >::MakeContainer(), CQueryFuncPromoteBase::MakeQueryNodeValue(), newickparse(), CDistMethods::NjTree(), CQueryTreePrintFunc::operator()(), CQueryTreeListFunctions::operator()(), CAssignQueryTreeGetArgs::operator()(), CDoQueryTreeGetArgs::operator()(), CWhereQueryTreeGetArgs::operator()(), CQueryHighlightFunction::operator()(), SUidCollector::operator()(), SUidCounter::operator()(), CQueryTreeFieldResolveFunc::operator()(), CScannerEvaluateFunc::operator()(), CQueryExecPreProcessFunc::operator()(), CQueryExecEvalFunc::operator()(), CQueryTreeResetFunc::operator()(), SNodeNameUpdater::operator()(), STreeNodeMapper::operator()(), CQueryFuncPromoteBase::PreProcess(), PrintNode(), CDistMethods::RerootTree(), CQueryFuncPromoteBase::ResolveAndPromote(), s_AddFastMeSubtree(), s_AddNodeToBtc(), s_AddOrReplaceSubNode(), s_ConvertFastMeTree(), s_CreateTreeLeaf(), s_FindNodeDistance(), s_GetNewick(), s_MakeTwoLeafTree(), s_ResetQueryNode(), s_ScaleTreeEdges(), s_SetLeafIds(), s_TestTree(), s_TraverseTree(), CBDB_Cache::SameCacheParams(), CSQLITE3_Cache::SameCacheParams(), CMacroRep::SetAssignmentWhereClause(), SPluginParams::SetDefaultValue(), CMacroRep::SetFunction(), CMacroRep::SetFunctionParameterAsBool(), CMacroRep::SetFunctionParameterAsFloat(), CMacroRep::SetFunctionParameterAsIdent(), CMacroRep::SetFunctionParameterAsInt(), CMacroRep::SetFunctionParameterAsString(), CBioTree< TBioNode >::SetNodeId(), CGBDataLoader::SetParam(), ThrowCMacroExecException(), CMultiAligner::x_AlignClusterQueries(), CMultiAligner::x_AlignProgressive(), CMultiAligner::x_AttachClusterTrees(), CAlignFilter::x_Complexity(), CPhyTreeCalc::x_ComputeTree(), CPhyTreeCalc::x_CorrectBranchLengths(), CMacroExec::x_EvaluateQueryTree(), CQueryParsePanel::x_ExecuteQuery(), CDistMethods::x_FindLargestEdge(), CAlignFilter::x_FuncCall(), CTaxTreeBrowser::x_GetName(), CConfig::x_GetString(), CMacroExec::x_GetTopUserNodeValue(), CAssignQueryTreeGetArgs::x_IsDBLinkField(), CAssignQueryTreeGetArgs::x_IsStructCommField(), CQueryParsePanel::x_IsValidQuery(), CClusterer::x_JoinClustElem(), CClusterer::x_JoinClusters(), CClusterer::x_JoinElements(), CAlignFilter::x_Match(), CMacroParser::x_ParseDo(), CAssignQueryTreeGetArgs::x_ProcessFunction(), CWhereQueryTreeGetArgs::x_ProcessFunction(), CAlignFilter::x_Query_Op(), CMacroEngine::x_ResolveRTVar(), CMacroResolver::x_ResolveRTVar(), CAlignFilter::x_TermValue(), and CDistMethods::ZeroNegativeBranches().

◆ GetValueNC() [1/2]

template<class TValue , class TKeyEqualP = std::equal_to<TValue>>

Get non-const value of a node.

Definition at line 84 of file ncbi_tree.hpp.

◆ GetValueNC() [2/2]

template<class TNode , class TKeyEqualP = std::equal_to<typename TNode::TIdType>>

Definition at line 437 of file ncbi_tree.hpp.

◆ HasFeature() [1/2] bool CBioTreeFeatureDictionary::HasFeature ( const string &  feature_name ) const

Check if feature is listed in the dictionary.

Definition at line 146 of file bio_tree.cpp.

References map_checker< Container >::end(), map_checker< Container >::find(), and CBioTreeFeatureDictionary::m_Name2Id.

Referenced by CPhyloTreeDataSource::CollapseByDistance(), CPhyloTreeDataSource::ComputeLengthsFromRoot(), CPhyTreeLabelTracker::CPhyTreeLabelTracker(), CPhyTreeFormatter::CQueryNodeChecker::CQueryNodeChecker(), CPhyTreeFormatter::CSingleBlastNameExaminer::CSingleBlastNameExaminer(), CPhyTreeView::GetSelection(), CPhyTreeNodeGroupper::Init(), CPhyTreeNodeAnalyzer::Init(), CPhyTreeView::OnBioTreeChanged(), CwxPhyloEditDlg::OnOkClick(), CTreeConvert2ContainerPartialFunc< TBioTreeContainer, TTreeType >::operator()(), CPhyloNodeData::RemoveFeature(), CPhyloTreeDataSource::ReRootEdge(), CPhyloTreeDataSource::ReRootMidpoint(), CPhyloTreeCalculator::SetAttrTable(), CPhyloTreeDataSource::SetCollapsedLabel(), CPhyloNodeData::SetFeature(), CwxPhyloEditDlg::SetParams(), CPhyloTreeDataSource::SortDist(), and CPhyTreeView::x_OnSetSelection().

◆ HasFeature() [2/2] ◆ InsertNode()

template<class TValue , class TKeyGetter >

◆ IsLeaf()

template<class TValue , class TKeyGetterP = CDefaultNodeKeyGetter<TValue>>

Report whether this is a leaf node.

Returns
TRUE if this is a leaf node (has no children), false otherwise

Definition at line 296 of file ncbi_tree.hpp.

Referenced by CTree::ListTreeLeaves(), CQueryTreeFieldResolveFunc::operator()(), CScannerEvaluateFunc::operator()(), CMQueryNodePreprocessor::operator()(), CQueryExecPreProcessFunc::operator()(), CSGQueryNodePreprocessor::operator()(), CQueryExecEvalFunc::operator()(), PrintNode(), s_FindNodeDistance(), s_GetNewick(), s_ScaleTreeEdges(), s_SetLeafIds(), s_TestTree(), s_TraverseTree(), CMultiAligner::x_AlignClusterQueries(), CMultiAligner::x_AlignProgressive(), CMultiAligner::x_AttachClusterTrees(), CPhyTreeCalc::x_CorrectBranchLengths(), x_FillNewDistanceMatrix(), CDistMethods::x_FindLargestEdge(), and CDistMethods::ZeroNegativeBranches().

◆ IsParent()

template<class TValue , class TKeyGetter >

◆ JoinNodeList()

template<class TNode , class TSet , class TNodeList >

void CNodesToBitset< TNode, TSet, TNodeList >::JoinNodeList ( const TNodeList &  src_nlist_a, const TNodeList &  src_nlist_b, const TSet &  mask_set, TNodeList &  dst_list, TSet &  dst_set  ) inline ◆ KeyCompare() [1/2]

template<class TValue , class TKeyEqualP = std::equal_to<TValue>>

◆ KeyCompare() [2/2]

template<class TNode , class TKeyEqualP = std::equal_to<typename TNode::TIdType>>

◆ KeyEqual() [1/3]

template<class TValue , class TKeyGetterP = CDefaultNodeKeyGetter<TValue>>

◆ KeyEqual() [2/3]

template<class TValue , class TKeyEqualP = std::equal_to<TValue>>

◆ KeyEqual() [3/3]

template<class TNode , class TKeyEqualP = std::equal_to<typename TNode::TIdType>>

◆ LevelBegin()

template<class TITaxon4Each , class TITaxon1Node , class TITreeIterator , class TBioTreeContainer >

◆ LevelEnd()

template<class TITaxon4Each , class TITaxon1Node , class TITreeIterator , class TBioTreeContainer >

◆ MakeNewTreeNode()

template<class TDstTreeNode , class TSrcTreeNode , class TNodeConvFunc >

◆ MaskCopyNodes()

template<class TNode , class TSet , class TNodeList >

void CNodesToBitset< TNode, TSet, TNodeList >::MaskCopyNodes ( const TNodeList &  src_nlist, const TSet &  mask_set, TNodeList &  dst_list, TSet &  dst_set  ) inline ◆ MinimalSet()

template<class TNode , class TSet , class TNodeList >

void CTreeMinimalSet< TNode, TSet, TNodeList >::MinimalSet ( const TNodeList &  src_nlist, TNodeList &  dst_nlist, const TSet *  ignore_set = 0  ) inlineprotected ◆ MoveSubnodes()

template<class TValue , class TKeyGetter >

◆ operator()() [1/18]

template<class TBioTreeContainer , class TDynamicTree >

◆ operator()() [2/18]

template<class TNode , class TSet , class TNodeList >

◆ operator()() [3/18]

template<class TNode , class TSet , class TNodeList >

void CTreeMinimalSet< TNode, TSet, TNodeList >::operator() ( const TNodeList &  src_nlist, TNodeList &  dst_nlist, const TSet *  ignore_set = 0  ) inline ◆ operator()() [4/18]

template<class TNode , class TSet , class TNodeList >

void CTreeNodesAnd< TNode, TSet, TNodeList >::operator() ( const TNodeList &  src_nlist_a, const TNodeList &  src_nlist_b, TNodeList &  dst_nlist  ) inline

Definition at line 877 of file tree_algo.hpp.

◆ operator()() [5/18]

template<class TNode , class TSet , class TNodeList >

void CTreeNodesOr< TNode, TSet, TNodeList >::operator() ( const TNodeList &  src_nlist_a, const TNodeList &  src_nlist_b, TNodeList &  dst_nlist  ) inline

Definition at line 912 of file tree_algo.hpp.

◆ operator()() [6/18]

template<class TNode , class TSet , class TNodeList >

void CTreeNodesAnd< TNode, TSet, TNodeList >::operator() ( const TNodeList &  src_nlist_a, const TNodeList &  src_nlist_b, TNodeList &  dst_nlist, TSet &  dst_set  ) inline ◆ operator()() [7/18]

template<class TNode , class TSet , class TNodeList >

void CTreeNodesOr< TNode, TSet, TNodeList >::operator() ( const TNodeList &  src_nlist_a, const TNodeList &  src_nlist_b, TNodeList &  dst_nlist, TSet &  dst_set  ) inline ◆ operator()() [8/18]

template<class TValue , class TKeyGetter = CDefaultNodeKeyGetter<TValue>>

◆ operator()() [9/18]

template<class TDstTreeNode , class TSrcTreeNode , class TNodeConvFunc >

◆ operator()() [10/18]

template<class TTreeNode , class TTraceContainer >

◆ operator()() [11/18]

template<class TTreeNode , class TBackInsert >

◆ operator()() [12/18]

template<class TTreeNode , class TSet , class TNodeList >

◆ operator()() [13/18]

template<class TTreeNode , class TConverter >

Definition at line 301 of file tree_algo.hpp.

References delta(), eTreeTraverse, hex(), CTreePrintFunc< TTreeNode, TConverter >::m_Conv, CTreePrintFunc< TTreeNode, TConverter >::m_Level, CTreePrintFunc< TTreeNode, TConverter >::m_OStream, CTreePrintFunc< TTreeNode, TConverter >::m_PrintPtr, and CTreePrintFunc< TTreeNode, TConverter >::PrintLevelMargin().

◆ operator()() [14/18]

template<class TBioTreeContainer , class TTaxon1 , class TITaxon1Node , class TITreeIterator >

void CTaxon1ConvertToBioTreeContainer< TBioTreeContainer, TTaxon1, TITaxon1Node, TITreeIterator >::operator() ( TBioTreeContainer &  tree_container, CRef< TITreeIterator >  tax_tree_iter  ) inline

Definition at line 802 of file bio_tree_conv.hpp.

References CTaxon1NodeConvertVisitor< TITaxon4Each, TITaxon1Node, TITreeIterator, TBioTreeContainer >::GetMaxNodeId(), CTaxon1ConvertToBioTreeContainer< TBioTreeContainer, TTaxon1, TITaxon1Node, TITreeIterator >::m_MaxNodeId, and CTaxon1ConvertToBioTreeContainer< TBioTreeContainer, TTaxon1, TITaxon1Node, TITreeIterator >::SetupFeatureDictionary().

◆ operator()() [15/18]

template<class TBioTreeContainer , class TTaxon1 , class TITaxon1Node , class TITreeIterator >

Definition at line 784 of file bio_tree_conv.hpp.

References CTaxon1NodeConvertVisitor< TITaxon4Each, TITaxon1Node, TITreeIterator, TBioTreeContainer >::GetMaxNodeId(), CTaxon1ConvertToBioTreeContainer< TBioTreeContainer, TTaxon1, TITaxon1Node, TITreeIterator >::m_MaxNodeId, and CTaxon1ConvertToBioTreeContainer< TBioTreeContainer, TTaxon1, TITaxon1Node, TITreeIterator >::SetupFeatureDictionary().

◆ operator()() [16/18] ◆ operator()() [17/18] ◆ operator()() [18/18]

template<class TValue , class TKeyGetterP = CDefaultNodeKeyGetter<TValue>>

template<class TNodeComparator >

Definition at line 390 of file ncbi_tree.hpp.

◆ operator*() [1/2]

template<class TValue , class TKeyGetterP = CDefaultNodeKeyGetter<TValue>>

TValue& CTreeNode< TValue, TKeyGetterP >::operator* ( void  ) inline

Definition at line 193 of file ncbi_tree.hpp.

◆ operator*() [2/2]

template<class TValue , class TKeyGetterP = CDefaultNodeKeyGetter<TValue>>

const TValue& CTreeNode< TValue, TKeyGetterP >::operator* ( void  ) const inline

Definition at line 192 of file ncbi_tree.hpp.

◆ operator->() [1/2]

template<class TValue , class TKeyGetterP = CDefaultNodeKeyGetter<TValue>>

TValue* CTreeNode< TValue, TKeyGetterP >::operator-> ( void  ) inline

Definition at line 195 of file ncbi_tree.hpp.

◆ operator->() [2/2]

template<class TValue , class TKeyGetterP = CDefaultNodeKeyGetter<TValue>>

const TValue* CTreeNode< TValue, TKeyGetterP >::operator-> ( void  ) const inline

Definition at line 194 of file ncbi_tree.hpp.

◆ operator<() ◆ operator<<() ◆ operator=() [1/5]

template<class TBioNode >

◆ operator=() [2/5]

template<class TBioNode >

◆ operator=() [3/5] ◆ operator=() [4/5] ◆ operator=() [5/5]

template<class TValue , class TKeyGetter >

Definition at line 678 of file ncbi_tree.hpp.

◆ operator[]() [1/2] ◆ operator[]() [2/2] ◆ PairTreeBackTraceNode()

template<class TPairTree , class TValue >

const TPairTree* PairTreeBackTraceNode ( const TPairTree &  tr, const TValue &  search_id  )

Algorithm to to search for a node with specified id.

Tree is traversed back. When searching the upper(parent) level the algorithm never goes down the hierarchy but tries only immediate children.

Definition at line 375 of file tree_algo.hpp.

◆ PairTreeTraceNode()

template<class TPairTree , class TPathList >

const TPairTree* PairTreeTraceNode ( const TPairTree &  tr, const TPathList &  node_path  )

Algorithm to trace the pair tree and find specified leaf along the node path.

Algorithm always chooses the deepest leaf

Definition at line 412 of file tree_algo.hpp.

References _ASSERT, and ITERATE.

◆ PrintLevelMargin()

template<class TTreeNode , class TConverter >

◆ PrintNode() ◆ Register() [1/2]

Register new feature, return its id.

If feature is already registered just returns the id. Feature ids are auto incremented variable managed by the class.

Definition at line 160 of file bio_tree.cpp.

References map_checker< Container >::end(), map_checker< Container >::find(), CBioTreeFeatureDictionary::m_IdCounter, and CBioTreeFeatureDictionary::m_Name2Id.

Referenced by BioTreeConvertContainer2Dynamic(), BioTreeConvertContainer2DynamicForest(), BioTreeConvertContainer2Tree(), CwxPhyloEditDlg::OnOkClick(), visitor_paste_subtree::operator()(), CPhyloTreeWidget::SendEditEvent(), CPhyloNodeData::SetFeature(), CPhyloSelectionSetMgr::SetSelectionSetProperty(), and TreeConvert2ContainerPartial().

◆ Register() [2/2] ◆ RemoveAllSubNodes()

template<class TValue , class TKeyGetter >

◆ RemoveFeature() ◆ RemoveNode() [1/2]

template<class TValue , class TKeyGetter >

◆ RemoveNode() [2/2]

template<class TValue , class TKeyGetter >

◆ SetFeature() [1/2] ◆ SetFeature() [2/2] ◆ SetId()

template<class TNodeData = CBioTreeEmptyNodeData, class TNodeFeatures = CBioTreeFeatureList>

◆ SetNodeId()

template<class TBioNode >

◆ SetParent()

template<class TValue , class TKeyGetterP = CDefaultNodeKeyGetter<TValue>>

◆ SetParentTree() [1/3]

template<class TBioNode >

◆ SetParentTree() [2/3]

template<class TBioNode >

Recursively set parent tree for the node.

Definition at line 425 of file bio_tree.hpp.

◆ SetParentTree() [3/3]

template<class TBioNode >

◆ SetTreeNode()

template<class TBioNode >

◆ SetupFeatureDictionary()

template<class TBioTreeContainer , class TTaxon1 , class TITaxon1Node , class TITreeIterator >

void CTaxon1ConvertToBioTreeContainer< TBioTreeContainer, TTaxon1, TITaxon1Node, TITreeIterator >::SetupFeatureDictionary ( TBioTreeContainer &  tree_container ) inlineprotected

Add elements to the feature dictionary.

Definition at line 822 of file bio_tree_conv.hpp.

References BioTreeAddFeatureToDictionary(), eTaxTree_BlastName, eTaxTree_Division, eTaxTree_GC, eTaxTree_IsUncultured, eTaxTree_Label, eTaxTree_MGC, eTaxTree_Name, eTaxTree_Rank, eTaxTree_SeqId, and eTaxTree_TaxId.

Referenced by CTaxon1ConvertToBioTreeContainer< TBioTreeContainer, TTaxon1, TITaxon1Node, TITreeIterator >::operator()().

◆ SetValue()

template<class TValue , class TKeyGetterP = CDefaultNodeKeyGetter<TValue>>

void CTreeNode< TValue, TKeyGetterP >::SetValue ( const TValue &  value ) inline ◆ SortChildren()

template<class TValue , class TKeyGetterP = CDefaultNodeKeyGetter<TValue>>

template<class TNodeComparator >

void CTreeNode< TValue, TKeyGetterP >::SortChildren ( const TNodeComparator &  compare ) inline ◆ SortTree()

template<class TValue , class TNodeComparator >

void SortTree ( CTreeNode< TValue > &  root, const TNodeComparator &  compare  ) ◆ SubNodeBegin() [1/2]

template<class TValue , class TKeyGetterP = CDefaultNodeKeyGetter<TValue>>

Return first iterator on subnode list.

Definition at line 163 of file ncbi_tree.hpp.

◆ SubNodeBegin() [2/2]

template<class TValue , class TKeyGetterP = CDefaultNodeKeyGetter<TValue>>

Return first const iterator on subnode list.

Definition at line 160 of file ncbi_tree.hpp.

Referenced by CDbapiCtlibCFBase::CreateInstance(), CDbapiOdbcCFBase::CreateInstance(), CMenuItem::DestroyAllSubNodes(), CTreeNode< TValue, TKeyGetterP >::FindNodes(), CTreeNode< TValue, TKeyGetterP >::FindOrCreateNode(), Flatten_ParseTree(), CQueryFunctionBase::GetArg0(), CScannerFunctorArgN::GetArguments(), CMenuItem::IsSubmenuEmpty(), CTree::ListTreeEdges(), CTree::ListTreeLeaves(), CQueryFunctionBase::MakeArgVector(), ncbi_q_parse(), CAssignQueryTreeGetArgs::operator()(), CDoQueryTreeGetArgs::operator()(), CWhereQueryTreeGetArgs::operator()(), CSGQueryNodePreprocessor::operator()(), PrintNode(), s_AddNodeToBtc(), s_ExpandSubNodes(), s_FindNodeDistance(), s_GetNewick(), s_IncludeNode(), s_ScaleTreeEdges(), s_SetLeafIds(), s_TestTree(), s_TraverseTree(), CMenuItem::SubItemsBegin(), CMultiAligner::x_AlignClusterQueries(), CMultiAligner::x_AttachClusterTrees(), CAlignFilter::x_Complexity(), CPhyTreeCalc::x_ComputeTree(), CPhyTreeCalc::x_CorrectBranchLengths(), CMacroExec::x_EvaluateQueryTree(), x_FillNewDistanceMatrix(), CDistMethods::x_FindLargestEdge(), CAlignFilter::x_FuncCall(), CAssignQueryTreeGetArgs::x_IsDBLinkField(), CAssignQueryTreeGetArgs::x_IsStructCommField(), CAlignFilter::x_Match(), CAlignFilter::x_ParseTree_Flatten(), CAssignQueryTreeGetArgs::x_ProcessFunction(), CWhereQueryTreeGetArgs::x_ProcessFunction(), ITreeMacroFunction::x_SetUserObjects(), IEditMacroFunction::x_SetUserObjects(), CMacroParser::x_SortParseTree(), and CDistMethods::ZeroNegativeBranches().

◆ SubNodeEnd() [1/2]

template<class TValue , class TKeyGetterP = CDefaultNodeKeyGetter<TValue>>

Return last iterator on subnode list.

Definition at line 169 of file ncbi_tree.hpp.

◆ SubNodeEnd() [2/2]

template<class TValue , class TKeyGetterP = CDefaultNodeKeyGetter<TValue>>

Return last const iterator on subnode list.

Definition at line 166 of file ncbi_tree.hpp.

Referenced by CDbapiCtlibCFBase::CreateInstance(), CDbapiOdbcCFBase::CreateInstance(), CMenuItem::DestroyAllSubNodes(), CTreeNode< TValue, TKeyGetterP >::FindNodes(), CTreeNode< TValue, TKeyGetterP >::FindOrCreateNode(), Flatten_ParseTree(), CQueryFunctionBase::GetArg0(), CScannerFunctorArgN::GetArguments(), CMenuItem::IsSubmenuEmpty(), CTree::ListTreeEdges(), CTree::ListTreeLeaves(), CQueryFunctionBase::MakeArgVector(), CDoQueryTreeGetArgs::operator()(), CWhereQueryTreeGetArgs::operator()(), CSGQueryNodePreprocessor::operator()(), PrintNode(), s_AddNodeToBtc(), s_ExpandSubNodes(), s_FindNodeDistance(), s_GetNewick(), s_IncludeNode(), s_ScaleTreeEdges(), s_SetLeafIds(), s_TestTree(), s_TraverseTree(), CMenuItem::SubItemsEnd(), CMultiAligner::x_AlignClusterQueries(), CMultiAligner::x_AttachClusterTrees(), CAlignFilter::x_Complexity(), CPhyTreeCalc::x_ComputeTree(), CPhyTreeCalc::x_CorrectBranchLengths(), CMacroExec::x_EvaluateQueryTree(), x_FillNewDistanceMatrix(), CDistMethods::x_FindLargestEdge(), CAlignFilter::x_FuncCall(), CAssignQueryTreeGetArgs::x_IsStructCommField(), CAlignFilter::x_Match(), CAlignFilter::x_ParseTree_Flatten(), CAssignQueryTreeGetArgs::x_ProcessFunction(), CWhereQueryTreeGetArgs::x_ProcessFunction(), ITreeMacroFunction::x_SetUserObjects(), IEditMacroFunction::x_SetUserObjects(), CMacroParser::x_SortParseTree(), and CDistMethods::ZeroNegativeBranches().

◆ SubNodeRBegin() [1/2]

template<class TValue , class TKeyGetterP = CDefaultNodeKeyGetter<TValue>>

Return first reverse iterator on subnode list.

Definition at line 175 of file ncbi_tree.hpp.

◆ SubNodeRBegin() [2/2]

template<class TValue , class TKeyGetterP = CDefaultNodeKeyGetter<TValue>>

◆ SubNodeREnd() [1/2]

template<class TValue , class TKeyGetterP = CDefaultNodeKeyGetter<TValue>>

Return last reverse iterator on subnode list.

Definition at line 181 of file ncbi_tree.hpp.

◆ SubNodeREnd() [2/2]

template<class TValue , class TKeyGetterP = CDefaultNodeKeyGetter<TValue>>

◆ TreeBreadthFirstTraverse()

template<class TTreeNode , class Fun >

Fun TreeBreadthFirstTraverse ( TTreeNode &  tree_node, Fun  func  ) ◆ TreeCompare()

template<class TTreeNode , class TCompFun >

bool TreeCompare ( const TTreeNode &  tree1, const TTreeNode &  tree2, TCompFun  func  )

Compare two trees using comparison functor where order of children matters.

Parameters
tree1 First tree tree2 Second tree func Comparison functor (operates on 2 node-value types and returns bool)

Definition at line 62 of file tree_algo.hpp.

◆ TreeConvert2Dynamic()

template<class TDynamicTree , class TTreeNode , class TNodeConvFunc >

void TreeConvert2Dynamic ( TDynamicTree &  dyn_tree, const TTreeNode *  src_tree, TNodeConvFunc  node_conv  ) ◆ TreeDepthFirstTraverse()

template<class TTreeNode , class Fun >

Fun TreeDepthFirstTraverse ( TTreeNode &  tree_node, Fun  func  )

Depth-first tree traversal algorithm.

Takes tree and visitor function and calls function for every node in the tree.

Functor should have the next prototype: ETreeTraverseCode Func(TreeNode& node, int delta_level) where node is a reference to the visited node and delta_level reflects the current traverse direction(depth wise) in the tree, 0 - algorithm stays is on the same level 1 - we are going one level deep into the tree (from the root) -1 - we are traveling back by one level (getting close to the root)

The specificts of the algorithm is that it calls visitor both on the way from the root to leafs and on the way back Using this template we can implement both variants of tree traversal (pre-order and post-order) Visitor controls the traversal by returning ETreeTraverseCode

See also
ETreeTraverseCode

Definition at line 504 of file ncbi_tree.hpp.

References eTreeTraverse, eTreeTraverseStepOver, and eTreeTraverseStop.

Referenced by CBioTreeForest< BioTree >::AddNode(), BDB_PrintQueryTree(), BioTreeConvert2Container(), BioTreeConvert2Dynamic(), BioTreeForestConvert2Container(), CPhyTreeFormatter::CollapseToViewPort(), CConfig::ConvertRegToTree(), CBDB_QueryParserEnvironment::DetachQueryClause(), CQueryParserEnv::DetachQueryTree(), DynamicConvert2Tree(), CBDB_FileScanner::Evaluate(), CQueryExec::Evaluate(), CQueryFuncPromoteAndOr::Evaluate(), CPhyTreeFormatter::ExpandCollapseSubtree(), CBioTree< TBioNode >::FindNode(), CQueryParserEnv::Free(), CPhyTreeFormatter::FullyExpand(), NMFncParse::GetDoFunctionsWithArgs(), CTaxTreeBrowser::GetSelectedUids(), NMFncParse::GetWhereFunctionsWithArgs(), CFeatureFilter::Init(), CPhyTreeFormatter::IsSingleBlastName(), CDoQueryTreeGetArgs::operator()(), CQueryParseTree::Print(), CBDB_Query::ResetQueryClause(), CQueryParseTree::ResetUserObjects(), CBDB_FileScanner::ResolveFields(), CBioTree< BioTreeBaseNode< CBioTreeEmptyNodeData, CBioTreeFeatureList > >::SetParentTree(), CBioTree< TBioNode >::SetTreeNode(), CPhyTreeFormatter::SimplifyTree(), SortTree(), TreeConvert2Dynamic(), TreeMakeSet(), TreePrint(), TreeSetToNodeList(), CPhyTreeFormatter::x_AddFeaturesForInnerNodes(), CMSAToolJob::x_AddTreeProjectItem(), CPhyTreeFormatter::x_CollapseSubtrees(), CTaxTreeBrowser::x_CountNodes(), CPhyTreeFormatter::x_GetBioNode(), CMacroExec::x_Init(), CQueryParsePanel::x_IsValidQuery(), CQueryParsePanel::x_StartQueryJob(), and CBDB_QueryParserEnvironment::~CBDB_QueryParserEnvironment().

◆ TreeFindCommonParent()

template<class TTreeNode >

const TTreeNode* TreeFindCommonParent ( const TTreeNode &  tree_node_a, const TTreeNode &  tree_node_b  )

Check if two nodes have the same common root.

Algorithm finds first common ancestor (farthest from the root)

Parameters
tree_node_a Node A tree_node_b Node B
Returns
Nearest common root or NULL if there is no common parent

Definition at line 244 of file tree_algo.hpp.

References TreeTraceToRoot().

◆ TreeForEachParent()

template<class TTreeNode , class TFunc >

Visit every parent of the specified node.

Parameters
tree_node Starting node func Visiting functor skip_self Flag to skip the first node (tree_node itself) When TRUE visits only true ancestors

Definition at line 156 of file tree_algo.hpp.

Referenced by TreeMakeParentsSet(), and TreeTraceToRoot().

◆ TreeListToSet() [1/2]

template<class TNodeList , class TBackInsert >

void TreeListToSet ( const TNodeList &  node_list, TBackInsert  back_ins  )

Convert list of node pointers to set of ids.

Parameters
node_list node list container (must support const_iterator) back_ins back insert iterator for the set container

Definition at line 482 of file tree_algo.hpp.

References TreeListToSet().

◆ TreeListToSet() [2/2]

template<class TNodeListIt , class TBackInsert >

void TreeListToSet ( TNodeListIt  node_list_first, TNodeListIt  node_list_last, TBackInsert  back_ins  )

Convert list of node pointers to set of ids Input set is represented by input forward iterators Output set is a back insert iterator.

Definition at line 464 of file tree_algo.hpp.

Referenced by CTreeMinimalSet< TNode, TSet, TNodeList >::MinimalSet(), CTreeNonRedundantSet< TNode, TSet, TNodeList >::operator()(), CTreeNodesAnd< TNode, TSet, TNodeList >::operator()(), CTreeNodesOr< TNode, TSet, TNodeList >::operator()(), and TreeListToSet().

◆ TreeMakeParentsSet()

template<class TNode , class TBackInsert >

void TreeMakeParentsSet ( const TNode &  tree_node, TBackInsert  back_ins  ) ◆ TreeMakeSet()

template<class TNode , class TBackInsert >

void TreeMakeSet ( const TNode &  tree_node, TBackInsert  back_ins  ) ◆ TreeMakeSubNodesSet()

template<class TNode , class TBackInsert >

void TreeMakeSubNodesSet ( const TNode &  tree_node, TBackInsert  back_ins  ) ◆ TreePrint()

template<class TTreeNode , class TConverter >

Tree printing (use for debugging purposes)

Parameters
os Stream to print the tree tree_node Tree node to print (top or sub-tree) conv Converter of node value to string (string Conv(node_value) ) print_ptr When TRUE function prints all internal pointers (debugging)

Definition at line 348 of file tree_algo.hpp.

References conv, and TreeDepthFirstTraverse().

◆ TreeReRoot()

template<class TTreeNode >

void TreeReRoot ( TTreeNode &  new_root_node ) ◆ TreeSetToNodeList()

template<class TNode , class TSet , class TNodeList >

void TreeSetToNodeList ( const TNode &  tree_node, const TSet &  node_set, TNodeList &  nlist  ) ◆ TreeTraceToRoot()

template<class TTreeNode , class TTraceContainer >

void TreeTraceToRoot ( const TTreeNode &  tree_node, TTraceContainer &  trace  )

Trace from the specified node to to the tree root.

Trace path is a container of node const node pointers (The only requirement is push_back method) The input node becomes first element, then comes its parent. If the node is a tree top its pointer is the only element of the trace vector

Parameters
tree_node Starting node (added to the trace first) trace Trace container (vector<const TTreeNode*> or similar)

Definition at line 205 of file tree_algo.hpp.

References trace, and TreeForEachParent().

Referenced by TreeFindCommonParent(), and TreeReRoot().

◆ Unregister() ◆ WriteNewickTree() ◆ WriteNexusTree() ◆ ~CBioTree() ◆ ~CTaxon1NodeConvertVisitor()

template<class TITaxon4Each , class TITaxon1Node , class TITreeIterator , class TBioTreeContainer >

Definition at line 601 of file bio_tree_conv.hpp.

◆ ~CTreeNode()

template<class TValue , class TKeyGetter >

◆ ~IBioTreeDynamicLabelFormatter() virtual IBioTreeDynamicLabelFormatter::~IBioTreeDynamicLabelFormatter ( ) inlinevirtual

Definition at line 500 of file bio_tree.hpp.

◆ data

template<class TNodeData = CBioTreeEmptyNodeData, class TNodeFeatures = CBioTreeFeatureList>

◆ features

template<class TNodeData = CBioTreeEmptyNodeData, class TNodeFeatures = CBioTreeFeatureList>

◆ id [1/2] ◆ id [2/2]

template<class TId , class TValue , class TIdEqual = std::equal_to<TId>>

Definition at line 471 of file ncbi_tree.hpp.

◆ m_Ascending

template<class TValue , class TKeyGetter = CDefaultNodeKeyGetter<TValue>>

◆ m_BackIns

template<class TTreeNode , class TBackInsert >

◆ m_Compare

template<class TValue , class TKeyGetterP = CDefaultNodeKeyGetter<TValue>>

template<class TNodeComparator >

◆ m_Container

template<class TBioTreeContainer , class TDynamicTree >

Definition at line 279 of file bio_tree_conv.hpp.

◆ m_Conv

template<class TTreeNode , class TConverter >

◆ m_ConvFunc

template<class TDstTreeNode , class TSrcTreeNode , class TNodeConvFunc >

TNodeConvFunc& CTree2TreeFunc< TDstTreeNode, TSrcTreeNode, TNodeConvFunc >::m_ConvFunc private ◆ m_Dict ◆ m_DstTree

template<class TDstTreeNode , class TSrcTreeNode , class TNodeConvFunc >

◆ m_FeatureDict

template<class TBioNode >

◆ m_FeatureList ◆ m_GetterAndParent

template<class TValue , class TKeyGetterP = CDefaultNodeKeyGetter<TValue>>

◆ m_IdCounter unsigned int CBioTreeFeatureDictionary::m_IdCounter protected ◆ m_Level

template<class TTreeNode , class TConverter >

◆ m_MaxNodeId

template<class TBioTreeContainer , class TTaxon1 , class TITaxon1Node , class TITreeIterator >

◆ m_MaxUID

template<class TITaxon4Each , class TITaxon1Node , class TITreeIterator , class TBioTreeContainer >

◆ m_Name2Id ◆ m_Node

template<class TBioNode >

◆ m_NodeIdCounter

template<class TBioNode >

◆ m_NodeList [1/3]

template<class TBioTreeContainer , class TDynamicTree >

◆ m_NodeList [2/3]

template<class TITaxon4Each , class TITaxon1Node , class TITreeIterator , class TBioTreeContainer >

◆ m_NodeList [3/3]

template<class TTreeNode , class TSet , class TNodeList >

◆ m_Nodes

template<class TValue , class TKeyGetterP = CDefaultNodeKeyGetter<TValue>>

◆ m_NodeSet

template<class TTreeNode , class TSet , class TNodeList >

◆ m_OStream

template<class TTreeNode , class TConverter >

◆ m_Parents

template<class TITaxon4Each , class TITaxon1Node , class TITreeIterator , class TBioTreeContainer >

Definition at line 737 of file bio_tree_conv.hpp.

Referenced by CTaxon1NodeConvertVisitor< TITaxon4Each, TITaxon1Node, TITreeIterator, TBioTreeContainer >::Execute(), CTaxon1NodeConvertVisitor< TITaxon4Each, TITaxon1Node, TITreeIterator, TBioTreeContainer >::LevelBegin(), and CTaxon1NodeConvertVisitor< TITaxon4Each, TITaxon1Node, TITreeIterator, TBioTreeContainer >::LevelEnd().

◆ m_ParentTree

template<class TBioNode >

◆ m_PrintPtr

template<class TTreeNode , class TConverter >

◆ m_Trace

template<class TTreeNode , class TTraceContainer >

◆ m_Tree

template<class TBioNode >

◆ m_TreeContainer

template<class TITaxon4Each , class TITaxon1Node , class TITreeIterator , class TBioTreeContainer >

TBioTreeContainer* CTaxon1NodeConvertVisitor< TITaxon4Each, TITaxon1Node, TITreeIterator, TBioTreeContainer >::m_TreeContainer private

Definition at line 735 of file bio_tree_conv.hpp.

◆ m_TreeNode

template<class TBioNode >

◆ m_TreeStack

template<class TDstTreeNode , class TSrcTreeNode , class TNodeConvFunc >

◆ m_Uid

template<class TBioNode >

◆ m_Value

template<class TValue , class TKeyGetterP = CDefaultNodeKeyGetter<TValue>>

TValue CTreeNode< TValue, TKeyGetterP >::m_Value protected ◆ uid

template<class TNodeData = CBioTreeEmptyNodeData, class TNodeFeatures = CBioTreeFeatureList>

◆ value [1/2] ◆ value [2/2]

template<class TId , class TValue , class TIdEqual = std::equal_to<TId>>

TValue CTreePair< TId, TValue, TIdEqual >::value

Definition at line 472 of file ncbi_tree.hpp.

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