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

(label_obj.HasField(

) &&

label_obj.GetField(

).GetData().IsStr()) {

= label_obj.GetField(

).GetData().GetStr();

(label_obj.HasField(

) &&

label_obj.GetField(

).GetData().IsStr()) {

= label_obj.GetField(

).GetData().GetStr();

(label_obj.HasField(

) &&

label_obj.GetField(

).GetData().IsInt()) {

= label_obj.GetField(

).GetData().GetInt();

(label_obj.HasField(

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= label_obj.GetField(

).GetData().GetInt();

(label_obj.HasField(

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).GetData().IsInt()) {

= label_obj.GetField(

).GetData().GetInt();

(label_obj.HasField(

) &&

label_obj.GetField(

).GetData().IsStr()) {

uo_id->

(

);

label_object.

(label_uo);

uo.

(

, *label_uo);

(label_object->HasField(

) &&

label_object->GetField(

).GetData().IsStr()) {

label_object->SetField(

).SetData().SetStr(

);

label_object->AddField(

,

);

(label_object->HasField(

) &&

label_object->GetField(

).GetData().IsStr()) {

label_object->SetField(

).SetData().SetStr(

);

label_object->AddField(

,

);

(label_object->HasField(

) &&

label_object->GetField(

).GetData().IsInt()) {

label_object->SetField(

).SetData().SetInt(

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label_object->AddField(

,

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(label_object->HasField(

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label_object->GetField(

).GetData().IsInt()) {

label_object->SetField(

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label_object->AddField(

,

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(label_object->HasField(

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label_object->GetField(

).GetData().IsInt()) {

label_object->SetField(

).SetData().SetInt(

);

label_object->AddField(

,

);

(label_object->HasField(

) &&

label_object->GetField(

).GetData().IsStr()) {

label_object->SetField(

).SetData().SetStr(

.

());

objects::CScope& scope,

objects::CScope& scope,

(

.GetNodeCount() == 0 ) {

(

.IsSetUser()) {

dist_scaler = 1.0f / (max_dist - min_dist);

sName = it->second;

sKey =

+ it->second +

;

ttf += ttf.empty()?

:

;

ttf += (sName +

+ sKey);

ttf.empty()?

:ttf;

& labelfmt)

(!labelfmt.empty())

colorStep = nmbClusters? (180.0 / nmbClusters): 0;

narrow_angle = colorStep < 5.0;

cluster_id = cl->first;

(cluster_id_to_selection_map.

(cluster_id) != cluster_id_to_selection_map.

()) {

select_set_idx = cluster_id_to_selection_map[cluster_id];

(c_dist < 0.2f) {

cluster_color.

(0.15f);

color_idx = closest_idx;

rotate_angle = colorStep + (narrow_angle ? 90.0 : 180.0);

(vector<TTreeIdx>, node_iter, cl->second) {

((*parent).IDX().first < minX) {

minX = (*parent).IDX().first;

selection_cluster = (cluster_id_to_selection_map.

(cl->first) != cluster_id_to_selection_map.

());

(selection_cluster)

(vector<TTreeIdx>, node_iter, cl->second) {

(; (*m_TreeModel)[parent_idx].HasParent();

parent_idx = (*m_TreeModel)[parent_idx].GetParent()) {

((*cursor).IDX().first > minX) {

primary_cluster_id = (*cursor).GetPrimaryCluster();

(parent_idx == *node_iter) {

(primary_cluster_id == cl->first) {

(*cursor).SetClusterColorIdx(color_idx);

(cursor.

() && (*cursor).GetNumClusters() > 1) {

(selection_cluster) {

(*cursor).SetMarkerSize(2.0f);

(*cursor).GetMarkerColors().push_back(

(*cursor).SetClusterColorIdx(color_idx);

std::vector<CPhyloTree::TTreeIdx> path;

midpoint = dist / 2.0f;

(path.size() > 1) {

dist_from_parent = 0.0f;

dist_from_child = 0.0f;

(

=0;

< path.size(); ++

) {

midpoint_child = path[

];

midpoint_parent = path[

+ 1];

dist_from_parent = d - midpoint;

dist_from_child = midpoint - base_distance;

(next_node.

() == path[

]) {

midpoint_parent = path[

];

midpoint_child = path[

+ 1];

dist_from_parent = midpoint - base_distance;

dist_from_child = d - midpoint;

= (dist/float(path.size() - 1))/100.0f;

(dist_from_parent <=

)

close_idx = midpoint_parent;

(dist_from_child <=

)

close_idx = midpoint_child;

(

<<

);

collapsed_nodes;

vector<SChildMaxDist> distances = child_dist.

();

(distances.begin(), distances.end());

(current_leaf_count > leaf_count_target) {

vector<SChildMaxDist>::reverse_iterator riter = distances.rbegin();

(; riter != distances.rend(); ++riter) {

has_subtree =

;

(

= 0;

<

.GetChildren().

(); ++

) {

(collapsed_nodes.

(child_node->GetId()) == collapsed_nodes.

()) {

(riter == distances.rend())

(

= 0;

<

.GetChildren().

(); ++

) {

iter = collapsed_nodes.

(child_node->GetId());

(iter != collapsed_nodes.

()) {

collapsed_nodes.

(iter);

collapsed_nodes.

(

->GetId());

current_leaf_count -=

.GetChildren().size() - 1;

distances.erase(--riter.base());

collapsed_nodes;

(new_container->IsSetUser()) {

btc->SetUser().Assign(new_container->GetUser());

(fiter=fdict.

(); fiter != fdict.

(); ++fiter, ++

) {

(*fiter).second;

& num_selected,

& num_queried,

vector<TTreeIdx> sel =

(

, num_queried, string_matching, use_case);

num_selected = sel.size();

(

iter=sel.begin(); iter!=sel.end(); ++iter) {

(

<<

<<

<<

<< sel.size());

[node]->GetBioTreeFeatureList().GetFeatureList();

vector<CPhyloTree::TTreeIdx>

vector<TTreeIdx> selNodes;

vector<TTreeIdx> search_cache;

(search_cache.empty())

(direction>0) {

vector<TTreeIdx>::iterator itt =

(itt == search_cache.end()) {

(itt != search_cache.end())

vector<TTreeIdx>::iterator itt =

(itt == search_cache.end()) {

(itt != search_cache.begin())

[source_id] = target_id;

new_node->SetId(target_id);

node->GetBioTreeFeatureList().GetFeatureList()) {

(

<<

);

(

);

(

);

(

);

(

);

(

);

(

);

new_node->SetId(next_id.

() + 1);

new_node_idx;

(

);

(

);

vector<CPhyloNodeData::TID> sel;

(sel.size() == 0) {

(

);

(

= 0;

< sel.size(); ++

) {

(

);

(

= 0;

< sel.size(); ++

)

priority_label = priority_node_features.

(label_feat_id);

current->

(priority_label);

features.

(label_feat_id, priority_label);

(

= 0;

< node_ids.size(); ++

) {

vector<TTreeIdx> sel;

(sel.size() == 0) {

(

);

(

= 0;

< sel.size(); ++

)

collapse_node =

;

(parent_node_idx != root_idx) {

collapse_node =

;

(std::find(sel.begin(), sel.end(), parent_node_idx) != sel.end()) {

collapse_node =

;

(collapse_node) {

(

);

(

);

(*it == current_node_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.

Features storage for the bio tree node.

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

void Sync(CBioTreeFeatureDictionary &dict)

void SetDistance(TDistance x_dist)

CBioTreeFeatureList & GetBioTreeFeatureList()

TDistance GetDistance() const

void SetFeature(CBioTreeFeatureDictionary &dict, const string &name, const string &value)

void InitFromUserObject(CPhyloTree *tree_model, const objects::CBioTreeContainer_Base::TUser &uo)

vector< CPhyloSelectionSet > & GetSets()

void SetSelectionSetProperty(CPhyloTree *tree_model)

void RenumberClusterIDs(int start_id)

Update all cluster ids using the starting-id as the lowest value.

map< int, size_t > GetClusterToSelectionMap()

void SetLabelFormat(string labelFmt)

void SetAttrTable(const TAttrTable &attr)

const TClusterHash & GetClusters()

void Init(CRgbaGradColorTable *ct)

void SortDist(bool ascending)

vector< CPhyloTree::TID > m_StringQueryIDs

Temporary storage for string query results to get ID's back to caller.

virtual string GetColumnLabel(size_t col) const

get number and names of columns in data source

void Init(const objects::CBioTreeContainer &tree, objects::CScope &scope, bool expand_all=false)

Throws exception if tree is empty - at least 1 node is required.

void ReRootMidpoint()

Re-root tree using midpoint-method.

TTreeIdx IterateOverSelNodes(int direction, bool highlight)

virtual CMacroQueryExec * GetQueryExec(bool casesensitive, CStringMatching::EStringMatching matching)

Create an appropriate instance of a subclass of CQueryExec for that will be used to execute a query o...

void FilterDistances(double x_dist)

void Clusterize(CPhyloTreeScheme *scheme)

void ComputeLengthsFromRoot()

Create sorted array of distances of nodes from the parent (the m_LenDistribution array)

void SortLabel(bool ascending)

CRef< objects::CScope > m_Scope

void UpdateSelectionSets(CPhyloTreeScheme *scheme)

virtual void ClearQueryResults()

Clear any current results from previous queries.

TTreeIdx m_SearchCurrentNode

void ApplyAttributes(CBioTreeAttrReader::TAttrTable &attrs, CPhyloTreeScheme *scheme, const string &labelfmt="")

CPhyloTree::TClusterID TClusterID

virtual void ExecuteStringQuery(const string &query, size_t &num_selected, size_t &num_queried, CStringMatching::EStringMatching string_matching=CStringMatching::ePlainSearch, NStr::ECase use_case=NStr::eCase)

Execute a string-matching query on the underlying data.

virtual void SetQueryResults(CMacroQueryExec *q)

Set selection results to be whatever elements are selected in 'q'.

TClusterID GetMaxClusterID()

void ReRootEdge(TTreeIdx edge_child_node)

Re-root on the edge between the selected node and its parent.

void Relabel(CPhyloTreeScheme *scheme, string labelFmt)

void ReRoot(TTreeIdx root_idx)

Set the root node of the tree to the node at root_idx.

TTreeIdx NewNode(bool after=true)

vector< TTreeIdx > FindNodes(const string &query, size_t &num_queried, CStringMatching::EStringMatching string_matching, NStr::ECase use_case) const

search for nodes via the specified text matching algorithm

CRef< CPhyloTree > m_TreeModel

void Remove(bool subtree=true)

void Sort(bool ascending)

CPhyloSelectionSetMgr & GetSelectionSets()

static CPhyloTree m_sTreeClipboard

static (to allow copying between trees)

float GetClosestLen(float pct) const

Look in vector of sorted distances of nodes from the root and given a pct (0..1), return the distance...

CPhyloTreeCalculator * m_Calc

CPhyloTree::TTreeIdx TTreeIdx

void SetColorIndices(CPhyloTreeScheme *scheme)

virtual size_t GetColsCount() const

set< CPhyloNodeData::TID > CollapseByDistance(int leaf_count_target, SCollapsable *collapse_func)

Collapse, based on distance, enough nodes in the tree to get the total number of leaves down to the r...

void SetCollapsedLabels(const vector< CPhyloNodeData::TID > &node_ids)

Collapse all nodes in node_ids, doing relabeling if needed.

std::vector< float > m_LenDistribution

CPhyloTreeDataSource(const objects::CBioTreeContainer &tree, objects::CScope &scope, bool expand_all=false)

Throws exception if tree is empty - at least 1 node is required.

void SortLabelRange(bool ascending)

const CBioTreeFeatureDictionary & GetDictionary() const

CTreeGraphicsModel & GetModel()

Get model for rendering.

string GenerateTooltipFormat()

TModelRect GetBoundRect()

TClusterToColorMap m_ClusterToColorMap

void SetCollapsedLabel(CPhyloTree::TTreeIdx idx)

Collapse single node, do any relabeling if needed.

vector< float > & GetDistances()

TTreeIdx GetMaxDistNode() const

vector< pair< string, string > > & GetLabelRanges()

For each node, this returns the maximum distances of any of its children (recursively searched) from ...

vector< float > & GetDistances()

For each node this finds the maximum distance of any of its immediate (not recursively searched) chil...

vector< SChildMaxDist > & GetDistances()

CPhyloNodeData::TID GetMaxId() const

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

void ExpandCollapse(CBioTreeFeatureDictionary &dict, CPhyloNodeData::TDisplayChildren chds)

Set this node to be expanded/collapsed.

bool CanExpandCollapse(CPhyloNodeData::TDisplayChildren chds)

Return true if node can have its expand/collapsed state changed to chds.

void SetLabel(CBioTreeFeatureDictionary &dict, const string &label)

Set label string and synch value to the feature list for this ndoe.

bool IsLeafEx() const

Return true if node is a leaf or is collapsed.

TTreeIdx GetMaxPriorityNode() const

const TModelRect & GetRect() const

void SetMaxBranchDist(GLdouble bd)

void SetMaxNumChildren(GLdouble max_num_children)

void UpdateColorTable(CRgbaGradColorTable *color_table)

Make sure all current colors used by the scheme are in 'color_table' and add the ones that are not.

const TColoration & GetColoration(void) const

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

void ClearSelection()

Sets selection state of all nodes to eNotSelected and clears m_Selected.

void Clear()

Clear the tree nodes, graphics model and selected nodes.

void UpdateNodesMapping()

CPhyloNodeData::TClusterID TClusterID

CPhyloSelectionSetMgr & GetSelectionSets()

void SetCurrentNode(TTreeIdx node_idx)

Set the index of the currently active node.

void SetSelection(TTreeIdx idx, bool sel, bool sel_children=true, bool sel_parents=true)

Select or deselect the node at the specified index and, optionally, its parents and children as well.

TTreeIdx GetCurrentNodeIdx() const

Return the index of the currently active node (may be Null()).

void GetExplicitlySelectedAndNotCollapsed(vector< TTreeIdx > &esel) const

Returns only indices of nodes explicitly selected, but when a node is underneath a collapsed node,...

CPhyloTreeNode & GetCurrentNode()

Get reference to currently active node. Throws exception if it's Null()

CRgbaGradColorTable * GetColorTable()

void GetExplicitlySelectedIDs(vector< TID > &esel) const

Returns only ids of nodes explicitly selected, not their parents or children, i.e.

TTreeIdx FindNodeById(TID id) const

Return index of the node with the given id or Null().

void GetExplicitlySelected(vector< TTreeIdx > &esel) const

Returns only indices of nodes explicitly selected, not their parents or children, i....

CBioTreeFeatureDictionary & GetFeatureDict()

Return feature dictionary.

Query execution function for assignment operator.

Query execution function for run-time variables.

class CRgbaColor provides a simple abstraction for managing colors.

EStringMatching

String matching algorithms.

bool MatchString(const CTempString &str)

Matches a string to a pattern, using the specified string matching algorithm.

CTreeCollisionModel2D & GetCollisionData()

void InitializeFromUserObject(const CBioTreeContainer_Base::TUser &uo)

void SaveToUserObject(CBioTreeContainer_Base::TUser &uo)

TTreeIdx GetParent() const

Get node's parent.

void ClearConnections()

Remove connections to parent and children of this node.

TNodeList_CI SubNodeEnd() const

Return const iterator to end of subnode list.

TNodeList & GetChildren()

Return the indices of this node's child nodes.

TNodeList::iterator TNodeList_I

void SetParent(TTreeIdx parent_idx)

Set index of nodes parent.

TData & GetValue()

Return the value object for the node.

bool HasParent() const

Check if the node has a parent.

bool IsLeaf() const

Report whether this is a leaf node.

static TTreeIdx Null()

Static function that returns the null value.

TNodeList_CI SubNodeBegin() const

Return const iterator to first subnode index.

void ReRoot(TTreeIdx idx)

Sets the root idx to be 'idx' and updates the tree so that all nodes above the new root become childr...

TNodeType & GetParent(TNodeType &node)

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

static TTreeIdx Null()

Return the index value that represents a NULL node.

void SetNumNodes(int count)

Set the number of displayed nodes in current tree layout.

TNodeType & GetNode(TTreeIdx idx)

Return a reference to the node at the given index.

TNodeType & GetRoot()

Return a reference to the root node of the tree.

void AddChild(TTreeIdx parent_idx, TTreeIdx child_idx)

Add the node at 'child_idx' to the children 'parent_idx'.

TTreeIdx GetRootIdx() const

Return the index of the root node.

TTreeIdx AddNode()

Add a new default node to the tree and return its index.

void RemoveChild(TTreeIdx parent_idx, TTreeIdx child_idx)

Remove the node at 'child_idx' from its parent 'parent_idx' Nothing is done if the node 'child_idx' i...

void SetRootIdx(TTreeIdx idx)

Set the index of the root node of the tree.

void SetTree(CPhyloTree *t)

Set current node for query execution.

std::vector< TTreeIdx > GetTreeSelected() const

bool HasField(const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const

Verify that a named field exists.

CUser_object & AddField(const string &label, const string &value, EParseField parse=eParse_String)

add a data field to the user object that holds a given value

CUser_field & SetField(const string &str, const string &delim=".", const string &obj_subtype=kEmptyStr, NStr::ECase use_case=NStr::eCase)

Access a named field in this user object.

const CUser_field & GetField(const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const

Access a named field in this user object.

container_type::const_iterator const_iterator

const_iterator begin() const

const_iterator end() const

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

parent_type::iterator iterator

const_iterator find(const key_type &key) const

const_iterator end() const

visitor_copy_subtree(CPhyloTree &tree, CPhyloTree &target)

CPhyloTree::TNodeType TNodeType

ETreeTraverseCode operator()(CPhyloTree &tree, CPhyloTree::TTreeIdx node_idx, int delta)

CPhyloTree::TTreeIdx TTreeIdx

ETreeTraverseCode operator()(CPhyloTree &tree, CPhyloTree::TTreeIdx node, int delta)

CPhyloTree::TTreeIdx TTreeIdx

map< CPhyloNodeData::TID, CPhyloNodeData::TID > m_IdMap

mapping from Ids in source tree to target tree

CPhyloTree::TNodeType TNodeType

CPhyloNodeData::TID m_TargetMaxId

visitor_paste_subtree(CPhyloTree &source, CPhyloTree &target, TTreeIdx target_idx)

ETreeTraverseCode operator()(CPhyloTree &tree, CPhyloTree::TTreeIdx node_idx, int delta)

visitor_stringmatch_query(CStringMatching &stringMatching, vector< TTreeIdx > &selNodes, size_t &numQueried)

ETreeTraverseCode operator()(CPhyloTree &tree, TTreeIdx node, int delta)

vector< TTreeIdx > & m_SelNodes

CPhyloTree::TTreeIdx TTreeIdx

CStringMatching & m_StringMatching

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

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

void swap(NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair1, NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair2)

#define LOG_POST(message)

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

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

void Info(CExceptionArgs_Base &args)

size_t AddColor(const CRgbaColor &c)

Add a single color to the table.

float FindClosestColor(const CRgbaColor &c, size_t &idx) const

Return index of color with minimum color disance (as defined in CRgbaColor) from c.

bool FindColor(const CRgbaColor &c, size_t &idx) const

On exact match, returns true with index in idx, false otherwise.

void LoadTexture(int alpha_levels=8)

OpenGL parameters and operations to allow color table to (also) be stored as a 1D texture.

void ClearColors()

Empty color table.

CRgbaColor & GetColor(size_t i)

static CRgbaColor RotateColor(const CRgbaColor &c, float degrees)

Rotate the hue of the color by degrees.

string ToString(bool printAlpha=true, bool uchars=true) const

Return a string representation of the current color.

static float ColorDistance(const CRgbaColor &c1, const CRgbaColor &c2)

returns the distance in the RGB color cube between the two colors, scaled to a range [0,...

void FromString(const string &str)

Assign color values encoded in a string.

TObjectType * GetNCPointer(void) const THROWS_NONE

Get pointer,.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

bool IsNull(void) const THROWS_NONE

Check if pointer is null – same effect as Empty().

TObjectType & GetObject(void)

Get object.

TObjectType & GetNCObject(void) const

Get object.

void AddFunc(CQueryParseNode::EType func_type, CQueryFunctionBase *func)

Register function implementation.

@ eIdentifier

Identifier like db.field (Org, Fld12, etc.)

@ eFloatConst

Floating point const.

@ eIntConst

Integer const.

@ eBoolConst

Boolean (TRUE or FALSE)

@ eString

String ("free text")

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static string DoubleToString(double value, int precision=-1, TNumToStringFlags flags=0)

Convert double to string.

ECase

Which type of string comparison.

@ eNocase

Case insensitive compare.

@ eCase

Case sensitive compare.

string GetName(TBioTreeFeatureId id) const

Return the featue name given the id, or "" if not found.

ETreeTraverseCode

Tree traverse code returned by the traverse predicate function.

unsigned int TBioTreeFeatureId

Feature Id.

void SetFeature(TBioTreeFeatureId id, const string &value)

Set feature value, feature if exists replaced, if not added.

TBioTreeFeatureId GetId(const string &feature_name) const

If feature is already registered returns its id by name.

TBioTreeFeatureId Register(const string &feature_name)

Register new feature, return its id.

const string & GetFeatureValue(TBioTreeFeatureId id) const

Get feature value by id.

bool HasFeature(const string &feature_name) const

Check if feature is listed in the dictionary.

const TFeatureDict & GetFeatureDict() const

Get reference on the internal map.

vector< CBioTreeFeaturePair > TFeatureList

@ eTreeTraverse

Keep traversal.

const TData & GetData(void) const

Get the Data member data.

TStr & SetStr(void)

Select the variant.

const TObject & GetObject(void) const

Get the variant data.

void SetType(TType &value)

Assign a value to Type data member.

void SetData(TData &value)

Assign a value to Data data member.

bool IsObject(void) const

Check if variant Object is selected.

constexpr auto sort(_Init &&init)

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

const CharType(& source)[N]

Int4 delta(size_t dimension_, const Int4 *score_)

void TreeConvertNonSingleChild2Container(TBioTreeContainer &tree_container, TPhyloTree &phylo_tree, typename TPhyloTree::TTreeIdx node_idx=TPhyloTree::Null())

Convert selected nodes from tree to ASN.1 BioTree container.

void TreeConvert2Container(TBioTreeContainer &tree_container, TPhyloTree &phylo_tree, typename TPhyloTree::TTreeIdx node_idx=TPhyloTree::Null())

Convert tree to ASN.1 BioTree container.

void BioTreeConvertContainer2Tree(TPhyloTree &phylo_tree, const TBioTreeContainer &tree_container, CBioTreeFeatureDictionary *dictionary, bool preserve_node_ids=true, bool expand_all=false)

Convert ASN.1 BioTree container to phylo tree.

bool operator()(CPhyloTree::TTreeIdx lhs, CPhyloTree::TTreeIdx rhs) const

const CPhyloTree & m_Tree

NodeIdxSort(const CPhyloTree &t)

Fun TreeDepthFirst(TTreeModel &tree_model, typename TTreeModel::TTreeIdx node_idx, Fun func)

Depth-first tree traversal algorithm.

Fun TreeDepthFirstInvarient(TTreeModel &tree_model, typename TTreeModel::TTreeIdx node_idx, Fun func)

C++ wrappers for the Perl-compatible regular expression (PCRE) library.

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