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NCBI C++ ToolKit: include/algo/phy_tree/bio_tree.hpp Source File

GetFeatureValue(

);

HasFeature(

& feature_name)

;

<

TBioNode>

btr->SetParentTree(*subnode);

&

(

& feature_name)

.features[fid];

& feature_value)

btr->

(

, feature_name, feature_value);

&

(

& feature_name)

& feature_value);

& feature_name,

& feature_value);

(tree_node.GetValue().GetId() ==

) {

tree_node.SetParentTree(

);

<

TBioNode>

<

TBioNode>

: m_FeatureDict(btr.m_FeatureDict),

m_NodeIdCounter(btr.m_NodeIdCounter),

<

TBioNode>

<

TBioNode>

(tree_node == 0) {

<

TBioNode>

& feature_value)

id_found = m_FeatureDict.HasFeature(feature_id);

node->

().features.SetFeature(feature_id, feature_value);

<

TBioNode>

& feature_name,

& feature_value)

= m_FeatureDict.GetId(feature_name);

feature_id = m_FeatureDict.Register(feature_name);

AddFeature(node, feature_id, feature_value);

<

TBioNode>

<

TBioNode>

m_TreeNode.reset(node);

<

TBioNode>

ret = parent_node->

(node_value);

<

TBioNode>

ret = parent_node->

(node_value);

<

TBioNode>

m_FeatureDict.Clear();

Basic data contained in every bio-tree node.

Features storage for the bio tree node.

Find node by UID functor.

Basic tree structure for biological applications.

definition of a Culling tree

Interface to obtain custom labels for nodes.

Include a standard set of the NCBI C++ Toolkit most basic headers.

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

TNodeList::iterator TNodeList_I

CBioTreeFeaturePair(TBioTreeFeatureId fid, const string &fvalue)

void SetParentTree(CBioNode &node, CBioTree *tr)

Recursively set parent tree for the node.

TTreeType * DetachNode(TTreeType *subnode)

Remove the subtree from the tree without destroying it.

const TBioTreeNode * GetNode() const

void AddNode(TTreeType *subnode)

Node is added as a subnode the this node.

virtual TBioTreeNodeId GetNodeId(const TBioTreeNode &)

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

const string & GetFeature(const string &feature_name) const

Get dynamic feature by name.

CBioTree(const CBioTree< TBioNode > &btr)

void SetNodeId(TBioTreeNode *node)

Assign new unique node id to the node.

map< string, TBioTreeFeatureId > TFeatureNameIdx

Feature reverse index (feature name -> id)

TFeatureDict m_Dict

id -> feature name map

void 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 dictiona...

CTreeNode< TBioNode > TParent

void Clear()

Clear the bio tree.

void SetParentTree(CBioNode &node)

Recursively set this tree as parent tree for the node.

CTreeNode & operator=(const TTreeType &tree)

Fun TreeDepthFirstTraverse(TTreeNode &tree_node, Fun func)

Depth-first tree traversal algorithm.

ETreeTraverseCode

Tree traverse code returned by the traverse predicate function.

unsigned int TBioTreeNodeId

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

TBioTree * GetParentTree()

Return pointer on the hosting tree (can be NULL)

void PrintNode(CNcbiOstream &os, const CBioTreeDynamic &tree, const CBioTreeDynamic::TBioTreeNode &node, const IBioTreeDynamicLabelFormatter *label_fmt=nullptr)

Newick but without the terminal ';'.

void WriteNewickTree(CNcbiOstream &os, const CBioTreeDynamic &tree, const IBioTreeDynamicLabelFormatter *label_fmt=nullptr)

Newick format output.

void 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 dictiona...

CBioNode & operator=(const CBioNode &tree)

Recursive assignment.

const TBioTreeNode * FindNode(TBioTreeNodeId node_id) const

Finds node by id.

CBioTreeFeatureDictionary & GetFeatureDict()

Return feature dictionary.

unsigned int TBioTreeFeatureId

Feature Id.

CFindUidFunc(TBioTreeNodeId uid)

TFeatureNameIdx m_Name2Id

id -> feature name map

CBioTreeFeatureDictionary m_FeatureDict

unique_ptr< TBioTreeNode > m_TreeNode

Top level node.

const CBioTreeFeatureDictionary & GetFeatureDict() const

Return feature dictionary.

virtual string GetLabelForNode(const CBioTreeDynamic::TBioTreeNode &node) const =0

TBioTreeNode * AddNode(const TBioNodeType &node_value, TBioTreeNodeId parent_id)

Add node to the tree (node location is defined by the parent id.

TNodeFeatures TNodeFeaturesType

TFeatureList m_FeatureList

TBioTreeFeatureId GetId(const string &feature_name) const

If feature is already registered returns its id by name.

virtual TBioTreeNodeId GetNodeId()

Get new unique node id.

const TFeatureList & GetFeatureList() const

Return reference on the internal container.

TBioTreeNode * GetTreeNodeNonConst()

CBioNode(const TBioNode &value=TBioNode())

Construct tree node with specified value.

const string & operator[](TBioTreeFeatureId id) const

Get feature value by id (operator semantics)

BioTreeBaseNode(TBioTreeNodeId uid_value=0)

bool operator<(const CBioTreeFeaturePair &rhs) const

virtual ~IBioTreeDynamicLabelFormatter()

CBioTreeFeaturePair(void)

CBioTree< TBioNode > TBioTree

void SetParentTree(TBioTree *pt)

Associate node with the hosting class (non-recursive)

void AddNode(TTreeType *subnode)

Add new subnode.

map< TBioTreeFeatureId, string > TFeatureDict

Feature dictionary (feature id -> feature name map)

CBioNode TBioTreeNode

Biotree node (forms the tree hierarchy)

TTreeType * DetachNode(typename TParent::TNodeList_I it)

Node is detached from the tree (Parent becomes 0)

unsigned int m_IdCounter

Feature id counter.

void SetId(TBioTreeNodeId id)

TNodeFeatures features

list of node features

TBioTreeNode * m_Node

Search result.

ETreeTraverseCode operator()(TBioTreeNode &tree_node, int delta)

CBioTree< BioTreeBaseNode< CBioTreeEmptyNodeData, CBioTreeFeatureList > > CBioTreeDynamic

Bio tree without static elements.

const TBioTreeNode * GetTreeNode() const

TBioTreeNodeId m_Uid

Node uid to search for.

TBioTreeNodeId m_NodeIdCounter

const TBioNode & GetValue(void) const

Return node's value.

TNodeData data

additional node info

CBioNode * AddNode(const TBioNode &val=TBioNode())

Add a subnode to this node based on value.

const TFeatureDict & GetFeatureDict() const

Get reference on the internal map.

TBioTreeNode * AddNode(const TBioNodeType &node_value, TBioTreeNode *parent_node)

Add a node to the tree when you have already looked up the parent node (faster)

ETreeTraverseCode operator()(TBioTreeNode &tree_node, int delta)

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).

vector< CBioTreeFeaturePair > TFeatureList

CAssignTreeFunc(CBioTree *tree)

TBioTreeNodeId GetId() const

const TBioTree * GetParentTree() const

Return pointer on the hosting tree (can be NULL)

void SetTreeNode(TBioTreeNode *node)

Assign new top level tree node.

const string & operator[](const string &feature_name) const

CBioNode(const CBioNode &bn)

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

TBioTreeNodeId uid

Unique node Id.

TBioTree * m_ParentTree

Pointer on the hosting class.

void SetFeature(const string &feature_name, const string &feature_value)

const TTreeType * GetParent(void) const

Get node's parent.

CNcbiOstream & operator<<(CNcbiOstream &os, const CBioTreeDynamic &tree)

Newick format output.

CBioTreeFeaturePair(TBioTreeFeatureId fid)

CBioTree< TBioNode > & operator=(const CBioTree< TBioNode > &btr)

TTreeType * DetachNode(TTreeType *subnode)

@ eTreeTraverseStop

Stop traversal (return form algorithm)

@ eTreeTraverse

Keep traversal.

#define NCBI_XALGOPHYTREE_EXPORT

const GenericPointer< typename T::ValueType > T2 value

Int4 delta(size_t dimension_, const Int4 *score_)

Basic node data structure used by BioTreeBaseNode.

Tree node feature pair (id to string)

Functor to reset tree pointer in all nodes.

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