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NCBI C++ ToolKit: src/gui/widgets/phylo_tree/phylo_tree_algorithm.cpp Source File

(

);

key_x = 0;

(id_str.empty())

;

(attr_name ==

) {

(*node).SetLabel(attr_value);

max_branch_dist = 0.0f;

(

iter = node.GetChildren().begin(); iter != node.GetChildren().end(); ++iter) {

max_branch_dist =

(max_branch_dist, (*

)[*iter]->GetDistance() + (*

)[*iter]->GetMaxChildDistance());

node->SetMaxChildDistance(max_branch_dist);

(

==0 && node.HasParent()) {

node.GetValue().GetDistance();

key_x = -1;

node_has_key =

;

((*node).GetSeqID().IsNull()) {

node_has_key =

;

comp_key.

= (*node).GetSeqID()->GetSeqIdString();

node_has_key =

;

std::vector<AttrKey>::iterator iter;

(comp_key.

== (*iter).m_IDStr) {

objects::CSeq_id sid((*iter).m_IDStr);

((*node).GetSeqID()->Match(sid))

(seqid_str.empty())

;

objects::CSeq_id sid(seqid_str);

((*node).GetSeqID()->Match(sid)) {

(...){

;}

(node.HasParent()) {

(*node).SetNumLeaves(0);

(*node).SetNumLeavesEx(0);

(!(node).IsLeaf()) {

(*node).SetPamlCounter(

++);

(*node).SetDisplayLabel(

);

(node.IsLeaf() && ((*node).GetLabel().length() >

)) {

clusterID = (*node).GetClusterID();

(clusterID != -1) {

((*node).HasSelClusters()) {

vector<int> selection_clusters = (*node).GetSelClusters();

(

=0;

<selection_clusters.size(); ++

) {

[selection_clusters[

]].push_back(x_node);

(*node).GetMarkerColors().

();

(*node).SetClusterColorIdx(-1);

node->SetMaxChildDistance(0.0f);

traverse_code;

(*node).IDX().first =

;

(*node).IDX().second =

;

(*node).IDX().first =

;

(*node).IDX().second =

;

it != node.SubNodeEnd();

(node.Expanded()){

(*node).SetNumLeavesEx((*node).GetNumLeavesEx() + 1);

(*node).SetNumLeavesEx((*node).GetNumLeavesEx() + (*nn).GetNumLeavesEx());

(*node).SetNumLeaves((*node).GetNumLeaves() + 1);

(*node).SetNumLeaves((*node).GetNumLeaves() + (*nn).GetNumLeaves());

.

(xy.

()-1e-04, xy.

()-1e-04, xy.

()+1e-04, xy.

()+1e-04);

priority_str = (*node).GetBioTreeFeatureList().GetFeatureValue(

);

(priority_str !=

) {

num_leaves = (*m_Tree)[node_idx].GetValue().GetNumLeaves();

= (*m_Tree).GetFeatureDict().GetId(

);

max_child_dist = 0.0f;

do_not_collapse =

;

child_dist =

(0.0f, child_node->GetDistance());

do_not_collapse =

;

max_child_dist = 0.0f;

[node_idx].m_MaxChildDist = max_child_dist;

sprintf(

,

, max_child_dist);

traverse_code;

max_branch_dist = 0.0f;

traverse_code;

traverse_code;

vector<TTreeIdx> path;

parent_idx = (*m_Tree)[idx].GetParent();

leaf_dist += (*m_Tree)[idx].GetValue().GetDistance();

traverse_code;

(node->GetLabel() !=

) {

traverse_code;

& parent = (*m_Tree)[parent_idx];

& parent = (*m_Tree)[parent_idx];

& parent = (*m_Tree)[parent_idx];

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

Things for representing and manipulating bio trees.

Template class to create a table with custom row-column access.

const TColumn & Column(unsigned int idx) const

Get column name.

unsigned int ColumnIdx(const TColumn &col) const

Get column index.

const TValueType & GetCell(unsigned int row_idx, unsigned int col_idx) const

Access table element by index.

unsigned int Rows() const

Number of rows.

unsigned int Cols() const

Number of column.

TDistance GetDistance() const

CRgbaGradColorTable * m_ColorTable

void x_UpdateProperties(TNodeType &node, int row_idx)

Updates node properties using values from m_AttrTable.

virtual ETreeTraverseCode x_OnStepDown(TTreeIdx x_node)

CPhyloTreeNode::TTreeIdx m_CollapsedParentIdx

CPhyloTreeCalculator(TTreeType *tree, CRgbaGradColorTable *color_table)

virtual ETreeTraverseCode x_OnStep(TTreeIdx x_node, int delta)

void SetAttrTable(const TAttrTable &attr)

TClusterID m_MaxClusterID

virtual ETreeTraverseCode x_OnStepRight(TTreeIdx x_node)

TBioTreeFeatureId m_AttrKeyId

string m_LabelFormat

label calculation

const TAttrTable * m_AttrTable

Attributes with seq-ids optionally provided to update tree properties.

CPhyloTree::TClusterID TClusterID

void Init(CRgbaGradColorTable *ct)

vector< AttrKey > m_AttrKeys

Mapping for efficient lookup of seq-ids in m_AttrTable.

virtual ETreeTraverseCode x_OnStepLeft(TTreeIdx x_node)

TTreeIdx m_MaxDistNode

Index of node that is furthest from the root.

virtual ETreeTraverseCode x_OnStep(TTreeIdx node_idx, int delta)

vector< float > m_Distances

Distance of each node from root.

virtual ETreeTraverseCode x_OnStep(TTreeIdx node_idx, int delta)

vector< pair< string, string > > m_LabelRanges

Min and max label values (according to lexicographic.

string GetLabelForNode(const CPhyloTree &tree, const CPhyloTreeNode &node, const string &format)

vector< float > m_Distances

Max distace of any child of a node from the root, saved in same order as node array in tree.

virtual ETreeTraverseCode x_OnStep(TTreeIdx node_idx, int delta)

float m_MaxDist

Keep track of overall max and min distances.

virtual ETreeTraverseCode x_OnStep(TTreeIdx node_idx, int delta)

CRef< SCollapsable > m_CheckCollapseFunc

vector< SChildMaxDist > m_Distances

Max distace of any direct child of a node from the root, saved in same order as node array in tree.

virtual ETreeTraverseCode x_OnStep(TTreeIdx node_idx, int delta)

virtual ETreeTraverseCode x_OnStep(TTreeIdx node_idx, int delta)

float m_MaxDist

Total distance along m_MaxPath.

vector< TTreeIdx > m_MaxDistPathToRoot

vector< TTreeIdx > m_SortedMaxDistPathToRoot

vector< float > m_Distances

Distance of each node from root node.

void GetLongest(vector< TTreeIdx > &path, float &length)

TTreeIdx m_MaxDistNode

Node at greatest distance from root, its distance and vector of nodes from root to m_MaxDistNode (sor...

vector< TTreeIdx > m_MaxPath

Path (set of nodes) that is the longest path in the tree.

bool Expanded() const

Return true if node is currently not collapsed.

TNodeList_I SubNodeEndEx()

TNodeList_I SubNodeBeginEx()

Return the child nodes only if visible.

float m_LeafMidpoint

Index of leaf at center of subtree (leaves in subtree/2)

TTreeIdx m_PriorityLeafIdx

Leaf with highest priority number.

virtual ETreeTraverseCode x_OnStep(TTreeIdx node_idx, int delta)

size_t m_MaxPriorityLeafNum

Leaf index of node with m_MaxPriority.

void Init(TTreeIdx node_idx)

int m_MaxPriority

Max priority value found in priority field in subtree.

TBioTreeFeatureId m_PriorityId

Id of priority feature in tree.

size_t m_LeafCount

Current leaf count (as we iterate over the subtree)

virtual ETreeTraverseCode x_OnStep(TTreeIdx node_idx, int delta)

virtual ETreeTraverseCode x_OnStep(TTreeIdx node_idx, int delta)

const vector< pair< string, string > > & m_LabelRanges

virtual ETreeTraverseCode x_OnStep(TTreeIdx node_idx, int delta)

virtual ETreeTraverseCode x_OnStep(TTreeIdx node_idx, int delta)

const vector< float > & m_Distances

virtual ETreeTraverseCode x_OnStep(TTreeIdx node_idx, int delta)

Tree subclass also has functions and data needed for rendering and selection.

void SortSubtreeDist(TTreeIdx idx, const vector< float > &distances, bool order)

Sort the children of a node based on length of longest subtree.

CBioTreeFeatureDictionary & GetFeatureDict()

Return feature dictionary.

void SortLabel(TTreeIdx idx, bool order)

Sort the children of a node based on label comparison (alphabetical order)

void SortLabelRange(TTreeIdx idx, const vector< pair< string, string > > &subtree_labels, bool order)

Sort the children of a node based on the alphanumeric range of their child nodes.

void Sort(TTreeIdx idx, bool order)

Sort the children of a node based on the number of children they have.

CRgbaGradColorTable Provides a storage for colors (to eliminate color creation overhead) and Function...

void RemoveChild(TTreeIdx child_idx)

Remove child node if it is a child of this node.

TNodeList & GetChildren()

Return the indices of this node's child nodes.

void SetParent(TTreeIdx parent_idx)

Set index of nodes parent.

bool HasChild(TTreeIdx child_idx) const

Check if another node is a child of this node.

TData & GetValue()

Return the value object for the node.

bool HasParent() const

Check if the node has a parent.

TNodeList::const_iterator TNodeList_CI

bool IsLeaf() const

Report whether this is a leaf node.

static TTreeIdx Null()

Static function that returns the null value.

void AddChild(TTreeIdx child_idx)

Add a child node.

TNodeType & GetParent(TNodeType &node)

Return a reference to the parent node of the given node.

TNodeType::TNodeList_I TNodeList_I

static TTreeIdx Null()

Return the index value that represents a NULL node.

void SetRootIdx(TTreeIdx idx)

Set the index of the root node of the tree.

virtual bool x_Allowed(TNodeType &)

virtual ETreeTraverseCode x_OnStep(TTreeIdx x_node, int delta)

vector< TTreeIdx > m_TreeStack

virtual ETreeTraverseCode x_OnStepDown(TTreeIdx x_node)

ETreeTraverseCode operator()(TTreeType &tree, TTreeIdx tree_node, int delta)

virtual ETreeTraverseCode x_OnStep(TTreeIdx x_node, int delta)

virtual ETreeTraverseCode x_OnStepRight(TTreeIdx x_node)

CPhyloTree::TTreeIdx TTreeIdx

CPhyloTree::TNodeType TNodeType

virtual ETreeTraverseCode x_OnStepLeft(TTreeIdx x_node)

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

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

void Error(CExceptionArgs_Base &args)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

ETreeTraverseCode

Tree traverse code returned by the traverse predicate function.

TBioTreeFeatureId GetId(const string &feature_name) const

If feature is already registered returns its id by name.

bool HasFeature(const string &feature_name) const

Check if feature is listed in the dictionary.

@ eTreeTraverseStop

Stop traversal (return form algorithm)

@ eTreeTraverse

Keep traversal.

@ eTreeTraverseStepOver

Do not traverse current node (pick the next one)

constexpr auto sort(_Init &&init)

const struct ncbi::grid::netcache::search::fields::SIZE size

Compressed bitset (entry point to bm.h)

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

Int4 delta(size_t dimension_, const Int4 *score_)

Structure allows us to more efficiently store and look up keys (usually seq-ids) in m_AttrTable.

size_t TTreeIdx

Bi-directionaly linked N way tree allocated in a contiguous memory block.

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