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NCBI C++ ToolKit: include/gui/widgets/phylo_tree/phylo_tree_algorithm.hpp Source File

(

&

,

idx)

vector<float>& distances,

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

(vector<TTreeIdx>& path,

& length);

vector<float>& distances,

vector<pair<string,string> >& label_ranges,

(node.GetChildren().size() == 1 && node.GetParent() !=

()) {

child_idx = node.GetChildren()[0];

,

((float)x_dist) {}

((*node).GetDistance() >

);

((*node).IDX().first <=

);

<

TPhyloTree>

vector<CPhyloTree::TID>& node_ids,

pair<TTreeIdx, float> TNodeDist;

vector<TNodeDist> node_distances;

(

= 0;

< node_ids.size(); ++

) {

node_idx = phylo_tree.FindNodeById(node_ids[

]);

node_distances.push_back(TNodeDist(node_idx, 0.0f));

visited_nodes.

(node_idx);

(!phylo_tree.GetFeatureDict().HasFeature(

) || d <= 0.0f)

(node_distances.size() > 0) {

vector<TNodeDist> prev_node_distances = node_distances;

node_distances.clear();

(

= 0;

< prev_node_distances.size(); ++

) {

TNodeType&

= phylo_tree.GetNode(prev_node_distances[

].

);

accumulated_dist = prev_node_distances[

].second;

(

.HasParent()) {

parent_dist =

.GetValue().GetDistance();

(accumulated_dist + parent_dist <= d && visited_nodes.

(parent_idx) == visited_nodes.

()) {

node_distances.push_back(TNodeDist(parent_idx, accumulated_dist + parent_dist));

TNodeType::TNodeList_I child_iter =

.GetChildren().begin();

(; child_iter !=

.GetChildren().end(); ++child_iter) {

child_dist = phylo_tree.GetNode(child_idx).GetValue().GetDistance();

(accumulated_dist + child_dist <= d && visited_nodes.

(child_idx) == visited_nodes.

()) {

node_distances.push_back(TNodeDist(child_idx, accumulated_dist + child_dist));

visited_nodes.

(prev_node_distances[

].

);

<

TBioTreeContainer,

TPhyloTree>

TBioTreeContainer& tree_container,

preserve_node_ids =

,

expand_all =

)

TBioTreeContainer::TFdict TContainerDict;

TContainerDict& fd = tree_container.GetFdict();

TContainerDict::Tdata& feat_list = fd.Get();

(

TContainerDict::Tdata, it, feat_list) {

& fvalue = (*it)->GetName();

(fvalue ==

)

expand_collapse_id = fid;

TBioTreeContainer::TNodes TCNodeSet;

TCNodeSet::Tdata TNodeList;

TNodeList::value_type::element_type TCNode;

TNodeList node_list = tree_container.GetNodes().Get();

std::map<TBioTreeNodeId, typename TPhyloTree::TTreeIdx> pmap;

phylo_tree.Reserve(node_list.size());

(

TNodeList, it, node_list) {

TPhyloTree::TNodeType TNodeType;

TNodeType::TValueType TNodeValueType;

(preserve_node_ids) {

TCNode::TFeatures TCNodeFeatureSet;

(cnode->CanGetFeatures()) {

TCNodeFeatureSet& fset = cnode->GetFeatures();

TCNodeFeatureSet::Tdata& flist = fset.Get();

(

TCNodeFeatureSet::Tdata, fit, flist) {

fid = (*fit)->GetFeatureid();

& fvalue = (*fit)->GetValue();

(expand_all && fid == expand_collapse_id) {

v.GetBioTreeFeatureList().SetFeature(fid,

);

v.GetBioTreeFeatureList().SetFeature(fid, fvalue);

(cnode->CanGetParent()) {

(parent_node_idx != TPhyloTree::Null()) {

node_idx = phylo_tree.AddNode();

phylo_tree[node_idx].SetValue(v);

phylo_tree.AddChild(parent_node_idx, node_idx);

(!preserve_node_ids) {

phylo_tree[node_idx].GetValue().SetId(++node_id);

pmap[uid] = node_idx;

phylo_tree[node_idx].SetValue(v);

phylo_tree.SetRootIdx(node_idx);

(!preserve_node_ids) {

phylo_tree[node_idx].GetValue().SetId(++node_id);

pmap[uid] = node_idx;

<

TBioTreeContainer,

TTreeType>

TNodeList::value_type::element_type

;

= &(tree_container->SetNodes().Set());

(delta_level < 0) {

(node_idx !=

&& node.HasParent()) {

cnode->SetParent(node_parent.GetValue().GetId());

TNodeValueType::TNodeFeaturesType::TFeatureList TFList;

TFList& flist = v.GetBioTreeFeatureList().GetFeatureList();

(!flist.empty()) {

(

TFList, it, flist) {

fvalue = it->value;

cfeat->SetFeatureid(fid);

cfeat->SetValue(fvalue);

fset.Set().push_back(cfeat);

<

TBioTreeContainer,

TTreeType>

TNodeList::value_type::element_type

;

= &(tree_container->SetNodes().Set());

(delta_level < 0) {

(node_idx !=

&& node.HasParent()) {

cnode->SetParent(node_parent.GetValue().GetId());

TNodeValueType::TNodeFeaturesType::TFeatureList TFList;

TFList& flist = v.GetBioTreeFeatureList().GetFeatureList();

(!flist.empty()) {

(

TFList, it, flist) {

fvalue = it->value;

cfeat->SetFeatureid(fid);

cfeat->SetValue(fvalue);

fset.Set().push_back(cfeat);

<

TBioTreeContainer,

TTreeType>

TNodeList::value_type::element_type

;

TBioTreeContainer* tree_container,

= &(tree_container->SetNodes().Set());

(

.GetFeatureDict().HasFeature(

)) {

(delta_level < 0) {

(node.GetChildren().size() == 1) {

(node_idx !=

&& node.HasParent()) {

cnode->SetParent(node_parent.GetValue().GetId());

TNodeValueType::TNodeFeaturesType::TFeatureList TFList;

TFList& flist = v.GetBioTreeFeatureList().GetFeatureList();

(!flist.empty()) {

(

TFList, it, flist) {

fvalue = it->value;

(!fvalue.empty()) {

(std::exception&) {}

cfeat->SetFeatureid(fid);

cfeat->SetValue(fvalue);

fset.Set().push_back(cfeat);

<

TBioTreeContainer,

TPhyloTree>

TPhyloTree& phylo_tree,

TBioTreeContainer::TFdict TContainerDict;

TContainerDict& fd = tree_container.SetFdict();

TContainerDict::Tdata& feat_list = fd.Set();

TContainerDict::Tdata::value_type::element_type TCFeatureDescr;

& fvalue = it->second;

feat_list.push_back(d);

func(&tree_container, node_idx);

(node_idx==TPhyloTree::Null())

<

TBioTreeContainer,

TPhyloTree>

TPhyloTree& phylo_tree,

TBioTreeContainer::TFdict TContainerDict;

TContainerDict& fd = tree_container.SetFdict();

TContainerDict::Tdata& feat_list = fd.Set();

TContainerDict::Tdata::value_type::element_type TCFeatureDescr;

& fvalue = it->second;

feat_list.push_back(d);

func(&tree_container, node_idx);

(node_idx == TPhyloTree::Null())

<

TBioTreeContainer,

TPhyloTree>

TPhyloTree& phylo_tree,

TBioTreeContainer::TFdict TContainerDict;

TContainerDict& fd = tree_container.SetFdict();

TContainerDict::Tdata& feat_list = fd.Set();

TContainerDict::Tdata::value_type::element_type TCFeatureDescr;

& fvalue = it->second;

feat_list.push_back(d);

func(phylo_tree, &tree_container, node_idx);

(node_idx == TPhyloTree::Null())

<

TBioTreeContainer,

TTreeType>

TNodeList::value_type::element_type

;

= &(tree_container->SetNodes().Set());

(delta_level < 0) {

(node_idx !=

&& node.HasParent()) {

cnode->SetParent(node_parent.GetValue().GetId());

TNodeValueType::TNodeFeaturesType::TFeatureList TFList;

TFList& flist = v.GetBioTreeFeatureList().GetFeatureList();

(!flist.empty()) {

(

TFList, it, flist) {

fvalue = it->value;

cfeat->SetFeatureid(fid);

cfeat->SetValue(fvalue);

fset.Set().push_back(cfeat);

<

TBioTreeContainer,

TPhyloTree>

TPhyloTree& phylo_tree,

TBioTreeContainer::TFdict TContainerDict;

TContainerDict& fd = tree_container.SetFdict();

TContainerDict::Tdata& feat_list = fd.Set();

TContainerDict::Tdata::value_type::element_type TCFeatureDescr;

& fvalue = it->second;

(features.

(fvalue) != features.

()) {

return_dict.

(fid, fvalue);

feat_list.push_back(d);

func(&tree_container, node_idx, return_dict);

(node_idx == TPhyloTree::Null())

<

TContainerDict>

TContainerDict::Tdata& feat_list = fd.Set();

TContainerDict::Tdata::value_type::element_type TCFeatureDescr;

& fvalue = it->second;

feat_list.push_back(d);

Things for representing and manipulating bio trees.

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

CRgbaGradColorTable * m_ColorTable

void x_UpdateProperties(TNodeType &node, int row_idx)

Updates node properties using values from m_AttrTable.

void SetClusters(const TClusterHash &clst)

virtual ETreeTraverseCode x_OnStepDown(TTreeIdx x_node)

CPhyloTreeNode::TTreeIdx m_CollapsedParentIdx

CPhyloTreeCalculator(TTreeType *tree, CRgbaGradColorTable *color_table)

map< TClusterID, vector< TTreeIdx > > TClusterHash

virtual ETreeTraverseCode x_OnStep(TTreeIdx x_node, int delta)

void SetLabelFormat(string labelFmt)

void SetAttrTable(const TAttrTable &attr)

TClusterID m_MaxClusterID

virtual ETreeTraverseCode x_OnStepRight(TTreeIdx x_node)

TBioTreeFeatureId m_AttrKeyId

const TClusterHash & GetClusters()

string m_LabelFormat

label calculation

const TAttrTable * m_AttrTable

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

CPhyloTree::TClusterID TClusterID

virtual ~CPhyloTreeCalculator()

TClusterID GetMaxClusterID() const

CNcbiTable< string, unsigned, string > TAttrTable

void Init(CRgbaGradColorTable *ct)

unsigned GetVisibleNodes()

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.

vector< float > & GetDistances()

virtual ETreeTraverseCode x_OnStep(TTreeIdx node_idx, int delta)

CPhyloTreeDistFromRoot(TTreeType *tree)

TTreeIdx GetMaxDistNode() const

vector< float > m_Distances

Distance of each node from root.

virtual bool x_Allowed(TNodeType &node)

CPhyloTreeFilter_Depth(TTreeType *tree, int x_depth)

virtual bool x_Allowed(TNodeType &node)

CPhyloTreeFilter_Distance(TTreeType *tree, float x_dist)

CPhyloTreeFilter_Export(TTreeType *tree)

virtual bool x_Allowed(TNodeType &node)

virtual bool x_Allowed(TNodeType &node)

CPhyloTreeFilter_Selector(TTreeType *tree)

CPhyloTreeLabelRange(TTreeType *tree, bool x_order)

virtual ETreeTraverseCode x_OnStep(TTreeIdx node_idx, int delta)

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

vector< pair< string, string > > m_LabelRanges

Min and max label values (according to lexicographic.

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

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)

vector< float > & GetDistances()

CPhyloTreeMaxChildDist(TTreeType *tree)

float m_MaxDist

Keep track of overall max and min distances.

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

CPhyloTreeMaxDirectChildDist(TTreeType *tree, SCollapsable *collapsable_func=new SCollapsable())

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.

vector< SChildMaxDist > & GetDistances()

virtual ~CPhyloTreeMaxIdCalculator()

virtual ETreeTraverseCode x_OnStep(TTreeIdx node_idx, int delta)

CPhyloNodeData::TID GetMaxId() const

CPhyloTreeMaxIdCalculator(TTreeType *tree)

CPhyloTreeMidpointDist(TTreeType *tree, vector< float > &distances, TTreeIdx max_dist_node_idx)

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.

float m_LeafMidpoint

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

TTreeIdx m_PriorityLeafIdx

Leaf with highest priority number.

TTreeIdx GetMaxPriorityNode() const

virtual ~CPhyloTreePriorityNode()

virtual ETreeTraverseCode x_OnStep(TTreeIdx node_idx, int delta)

size_t m_MaxPriorityLeafNum

Leaf index of node with m_MaxPriority.

CPhyloTreePriorityNode(TTreeType *tree, TTreeIdx node_idx)

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)

const TModelRect & GetRect() const

virtual ETreeTraverseCode x_OnStep(TTreeIdx node_idx, int delta)

virtual ~CPhyloTreeRectCalculator()

CPhyloTreeRectCalculator(TTreeType *tree)

virtual ETreeTraverseCode x_OnStep(TTreeIdx node_idx, int delta)

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

CPhyloTreeSorterLabelRange(TTreeType *tree, const vector< pair< string, string > > &label_ranges, bool x_order)

CPhyloTreeSorterLabel(TTreeType *tree, bool x_order)

virtual ETreeTraverseCode x_OnStep(TTreeIdx node_idx, int delta)

CPhyloTreeSorterSubtreeDist(TTreeType *tree, const vector< float > &distances, bool x_order)

virtual ETreeTraverseCode x_OnStep(TTreeIdx node_idx, int delta)

const vector< float > & m_Distances

CPhyloTreeSorter(TTreeType *tree, bool x_order)

virtual ETreeTraverseCode x_OnStep(TTreeIdx node_idx, int delta)

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

CPhyloNodeData::TClusterID TClusterID

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

Visitor functor to convert phylo tree nodes to ASN.1 BioTree container.

ETreeTraverseCode operator()(TTreeType &tree, TTreeIdx node_idx, int delta_level)

TNodeFeatureList::value_type::element_type TCNodeFeature

TCNodeSet::Tdata TNodeList

TCNodeFeatureSet::Tdata TNodeFeatureList

TTreeType::TTreeIdx TTreeIdx

TCNode::TFeatures TCNodeFeatureSet

TTreeNodeType::TValueType TNodeValueType

TBioTreeContainer::TNodes TCNodeSet

CTreeConvert2ContainerFunc(TBioTreeContainer *tree_container, TTreeIdx root_idx)

TNodeList::value_type::element_type TCNode

TBioTreeContainer * m_Container

TTreeType::TNodeType TTreeNodeType

Visitor functor to convert phylo tree nodes to ASN.1 BioTree container not including all features.

TBioTreeContainer * m_Container

TNodeFeatureList::value_type::element_type TCNodeFeature

TTreeType::TTreeIdx TTreeIdx

ETreeTraverseCode operator()(TTreeType &tree, TTreeIdx node_idx, int delta_level)

const CBioTreeFeatureDictionary & m_ReturnDict

TCNodeFeatureSet::Tdata TNodeFeatureList

TTreeNodeType::TValueType TNodeValueType

TCNodeSet::Tdata TNodeList

TNodeList::value_type::element_type TCNode

TTreeType::TNodeType TTreeNodeType

TCNode::TFeatures TCNodeFeatureSet

CTreeConvert2ContainerPartialFunc(TBioTreeContainer *tree_container, TTreeIdx root_idx, const CBioTreeFeatureDictionary &return_dict)

TBioTreeContainer::TNodes TCNodeSet

TTreeType::TTreeIdx TTreeIdx

TBioTreeFeatureId m_DistFeatureId

TBioTreeContainer::TNodes TCNodeSet

TCNode::TFeatures TCNodeFeatureSet

TBioTreeContainer * m_Container

CTreeConvertNonSingleChild2ContainerFunc(TTreeType &tree, TBioTreeContainer *tree_container, TTreeIdx root_idx)

TNodeList::value_type::element_type TCNode

TCNodeFeatureSet::Tdata TNodeFeatureList

TCNodeSet::Tdata TNodeList

TTreeType::TNodeType TTreeNodeType

ETreeTraverseCode operator()(TTreeType &tree, TTreeIdx node_idx, int delta_level)

TBioTreeNodeId m_ParentID

TTreeNodeType::TValueType TNodeValueType

TNodeFeatureList::value_type::element_type TCNodeFeature

TCNode::TFeatures TCNodeFeatureSet

TNodeList::value_type::element_type TCNode

CTreeConvertSelected2ContainerFunc(TBioTreeContainer *tree_container, TTreeIdx root_idx)

TNodeFeatureList::value_type::element_type TCNodeFeature

TTreeType::TTreeIdx TTreeIdx

TTreeNodeType::TValueType TNodeValueType

TBioTreeContainer::TNodes TCNodeSet

TCNodeSet::Tdata TNodeList

TTreeType::TNodeType TTreeNodeType

ETreeTraverseCode operator()(TTreeType &tree, TTreeIdx node_idx, int delta_level)

TCNodeFeatureSet::Tdata TNodeFeatureList

TBioTreeContainer * m_Container

TNodeList & GetChildren()

Return the indices of this node's child nodes.

static TTreeIdx Null()

Static function that returns the null value.

static TTreeIdx Null()

Return the index value that represents a NULL node.

TNodeType & GetNode(TTreeIdx idx)

Return a reference to the node at the given index.

virtual bool x_Allowed(TNodeType &)

IPhyloTreeFilter(TTreeType *tree)

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 ~IPhyloTreeVisitor()

virtual ETreeTraverseCode x_OnStepRight(TTreeIdx x_node)

IPhyloTreeVisitor(TTreeType *tree)

CPhyloTree::TTreeIdx TTreeIdx

CPhyloTree::TNodeType TNodeType

virtual ETreeTraverseCode x_OnStepLeft(TTreeIdx x_node)

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

const_iterator end() const

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

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

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NCBI_THROW(exception_class, err_code, message)

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

void Reset(void)

Reset reference object.

bool IsNull(void) const THROWS_NONE

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

#define numeric_limits

Pre-declaration of the "numeric_limits<>" template Forcibly overrides (using preprocessor) the origin...

#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.

static double StringToDouble(const CTempStringEx str, TStringToNumFlags flags=0)

Convert string to double.

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.

unsigned int TBioTreeFeatureId

Feature Id.

TBioTreeFeatureId Register(const string &feature_name)

Register new feature, return its 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.

@ eTreeTraverse

Keep traversal.

@ eTreeTraverseStepOver

Do not traverse current node (pick the next one)

constexpr auto sort(_Init &&init)

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

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 TreeConvertSelected2Container(TBioTreeContainer &tree_container, TPhyloTree &phylo_tree, typename TPhyloTree::TTreeIdx node_idx=TPhyloTree::Null())

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

void TreeConvert2ContainerPartial(TBioTreeContainer &tree_container, TPhyloTree &phylo_tree, const set< string > &features, typename TPhyloTree::TTreeIdx node_idx=TPhyloTree::Null())

Convert tree to ASN.1 BioTree container but only include the requested features.

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.

set< CPhyloTree::TTreeIdx > GetTreeNeighborhood(TPhyloTree &phylo_tree, const vector< CPhyloTree::TID > &node_ids, float d)

Find all nodes within 'd' distance of the nodes 'node_ids' If tree does not have distance information...

void DictConvert2ContainerFeatureDict(TContainerDict &fd, CBioTreeFeatureDictionary &dict)

Convert CBioTreeFeatureDictionary to ASN.1 BioTree dictionary.

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

AttrKey(const string &id, unsigned int idx)

unsigned int m_AttrTableIdx

bool operator<(const AttrKey &rhs) const

Sort keys on seq-id string value.

SChildMaxDist(TTreeIdx idx, float dist)

bool operator<(const SChildMaxDist &rhs) const

Sort keys on seq-id string value.

virtual bool operator()(const CPhyloTreeNode &n)

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

Depth-first tree traversal algorithm.

size_t TTreeIdx

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

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