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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/tree_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/cobalt/tree.cpp Source File

50  for

(

i

= 0;

i

< level;

i

++)

54  if

(

tree

->IsLeaf() &&

tree

->GetValue().GetId() >= 0)

55

printf(

"query %d "

,

tree

->GetValue().GetId());

56  if

(

tree

->GetValue().IsSetDist())

57

printf(

"distance %lf"

,

tree

->GetValue().GetDist());

66  while

(child !=

tree

->SubNodeEnd()) {

67  for

(

i

= 0;

i

< level;

i

++)

80

vector<STreeEdge>& edge_list,

int

max_id)

86  if

(max_id >= 0 && node->

GetValue

().GetId() >= max_id) {

99

vector<STreeLeaf>& node_list,

118  double

new_dist = curr_dist;

125  _ASSERT

((*child)->GetValue().GetDist() >= -1e-6 || (*child)->IsLeaf());

126  if

((*child)->GetValue().GetDist() > 0) {

127

new_dist += (*child)->GetValue().GetDist();

static TTree * RerootTree(TTree *tree, TTree *node=NULL)

Reroot tree, new root is placed in the middle of the edge specified by node.

static TTree * NjTree(const TMatrix &dist_mat, const vector< string > &labels=vector< string >())

Compute a tree by neighbor joining; as per Hillis et al.

static TTree * FastMeTree(const TMatrix &dist_mat, const vector< string > &labels=vector< string >(), EFastMePar btype=eOls, EFastMePar wtype=eOls, EFastMePar ntype=eBalanced)

Compute a tree using the fast minimum evolution algorithm.

definition of a Culling tree

static void ListTreeEdges(const TPhyTreeNode *node, vector< STreeEdge > &edge_list, int max_id=-1)

Traverse a tree below a given starting point, listing all edges encountered along the way.

static void PrintTree(const TPhyTreeNode *node, int level=0)

Debug routine to recursively print out a tree.

void ComputeTree(const CDistMethods::TMatrix &distances, bool use_fastme=false)

Compute a new tree.

static void ListTreeLeaves(const TPhyTreeNode *node, vector< STreeLeaf > &node_list, double curr_dist=0)

Traverse a tree below a given starting point, listing all leaves encountered along the way.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

TNodeList_CI SubNodeBegin(void) const

Return first const iterator on subnode list.

TNodeList::const_iterator TNodeList_CI

bool IsLeaf() const

Report whether this is a leaf node.

TNodeList_CI SubNodeEnd(void) const

Return last const iterator on subnode list.

const TValue & GetValue(void) const

Return node's value.

const TTreeType * GetParent(void) const

Get node's parent.

Structure for listing tree edges.

Structure for listing tree leaves.

Interface for CTree class.

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