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

feature_val =

->GetBioTreeFeatureList().GetFeatureValue(

);

, m_Color(0.0f, 0.0f, 0.0f, 1.0f)

, m_FontSize(font_size)

objects::CScope& scope,

expand_all=

);

(

objects::CBioTreeContainer&

,

objects::CScope& scope,

expand_all=

);

GenerateTooltipFormat();

ComputeLengthsFromRoot();

GetClosestLen(

pct)

;

& labelfmt=

);

ReRootEdge(

edge_child_node);

ReRootMidpoint();

Sort(

ascending);

SortDist(

ascending);

SortLabel(

ascending);

SortLabelRange(

ascending);

FilterDistances(

x_dist);

(

) {

m_Calc ? m_Calc->GetNumNodes() : 0; }

(

) {

m_Calc ? m_Calc->GetVisibleNodes() : 0;}

(

) {

m_Calc ? m_Calc->GetNumEdges() : 0; }

(

) {

m_Calc ? m_Calc->GetWidth() : 0; }

(

) {

m_Calc ? m_Calc->GetHeight() : 0; }

(

) {

m_Calc ? m_Calc->GetMinDistance() : 0.0; }

GetColumnLabel(

col)

;

GetColsCount()

;

ClearQueryResults();

ExecuteStringQuery(

&

,

& num_selected,

& num_queried,

IterateOverSelNodes(

direction,

highlight);

NewNode(

after =

);

Remove(

subtree =

);

RemoveSelected();

MoveNode(

up);

()

{

m_sTreeClipboard.GetRootIdx() == TNodeType::Null(); }

SetCollapsedLabels(

vector<CPhyloNodeData::TID>& node_ids);

CollapseSelected();

[node].GetValue().Init(

.GetFeatureDict(), m_ColorTable);

static CRef< CScope > m_Scope

User-defined methods of the data storage class.

Things for representing and manipulating bio trees.

Features storage for the bio tree node.

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

void RemoveDuplicateIDs()

Remove duplicate IDs from individual sets.

visitor_read_properties(CRgbaGradColorTable *t)

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

CRgbaGradColorTable * m_ColorTable

unsigned int GetVisibleNodes(void)

const TClusterToColorMap & GetClusterToColorMap() const

Get map that translates cluster-ids to color indices.

TTreeIdx GetCurrentSearchNode() const

vector< CPhyloTree::TID > m_StringQueryIDs

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

double GetMinDistance(void)

CRef< objects::CScope > m_Scope

TTreeIdx m_SearchCurrentNode

CPhyloTree::TNodeType TNodeType

CPhyloTree::TClusterID TClusterID

void SetCurrentSearchNode(TTreeIdx node_idx)

CTreeLabel GetTreeLabel() const

TClusterID GetMaxClusterID()

const CPhyloTree * GetTree() const

std::map< int, size_t > TClusterToColorMap

virtual CRef< objects::CScope > GetScope()

Return a scope for the data source, if available.

CRef< CPhyloTree > m_TreeModel

CAppJobDispatcher::TJobID TJobID

unsigned int GetNumEdges(void)

CPhyloSelectionSetMgr & GetSelectionSets()

static CPhyloTree m_sTreeClipboard

static (to allow copying between trees)

CPhyloTreeCalculator * m_Calc

CPhyloTree::TTreeIdx TTreeIdx

const vector< CPhyloTree::TID > & GetStringQueryIDs() const

Get IDs selected by most recent call to FindNodes.

unsigned int GetNumNodes(void)

std::vector< float > m_LenDistribution

double GetNormDistance(void)

const CBioTreeFeatureDictionary & GetDictionary() const

CTreeGraphicsModel & GetModel()

Get model for rendering.

bool ClipboardEmpty() const

bool HasLenDistribution() const

Return true if data is available (for trees without distances, may not be)

TClusterToColorMap m_ClusterToColorMap

void SetTreeLabel(const CTreeLabel &l)

Label for tree (optional element of biotreecontainer)

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

CPhyloNodeData::TClusterID TClusterID

CBioTreeFeatureDictionary & GetFeatureDict()

Return feature dictionary.

class CRgbaColor provides a simple abstraction for managing colors.

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

EStringMatching

String matching algorithms.

@ ePlainSearch

Plain search.

class CTreeGraphicsModel Model for rendering tree graphics data.

string GetFontName() const

CRgbaColor GetColor() const

void SetFontName(const string &f)

CTreeLabel(string label, string font, int font_size, const CRgbaColor &c, int xpos, int ypos)

void SetLabel(const string &l)

void SetColor(const CRgbaColor &c)

object, that will be attached to event

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

#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.

ECase

Which type of string comparison.

@ fConvErr_NoThrow

Do not throw an exception on error.

@ eCase

Case sensitive compare.

ETreeTraverseCode

Tree traverse code returned by the traverse predicate function.

unsigned int TBioTreeFeatureId

Feature Id.

TBioTreeFeatureId GetId(const string &feature_name) const

If feature is already registered returns its id by name.

const string & GetFeatureValue(TBioTreeFeatureId id) const

Get feature value by id.

const TFeatureDict & GetFeatureDict() const

Get reference on the internal map.

@ eTreeTraverse

Keep traversal.

#define NCBI_GUIWIDGETS_PHYLO_TREE_EXPORT

static const char label[]

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

void Filter(TTimeline &timeline, TServers &servers)

Int4 delta(size_t dimension_, const Int4 *score_)

static SLJIT_INLINE sljit_ins l(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

CPhyloNodeData::TDisplayChildren GetExpanded() const

CPhyloNodeData::TDisplayChildren m_Expanded

Indicates if all nodes are to be expanded or collapsed.

void AddNode(CPhyloNodeData::TID id)

vector< CPhyloNodeData::TID > & GetIds()

void SetExpanded(CPhyloNodeData::TDisplayChildren ec)

vector< CPhyloNodeData::TID > m_NodeIds

Node ids to find node in either tree or biotree.

Edits for one or more nodes.

CBioTreeFeatureDictionary & GetPrevDictionary()

vector< CUpdatedFeature > m_Updated

One entry for each updated node.

vector< CUpdatedFeature > & GetUpdated()

CBioTreeFeatureDictionary m_Dictionary

CBioTreeFeatureDictionary m_PrevDictionary

Store value of dictionary before edit for undo.

CBioTreeFeatureDictionary & GetDictionary()

Edits for one or more nodes.

CPhyloSelectionSetMgr & GetUpdatedSet()

CPhyloSelectionSetMgr m_PrevSet

Previous values (for undo)

CPhyloSelectionSetMgr & GetPrevSet()

CPhyloSelectionSetMgr m_UpdatedSet

Updated set.

CBioTreeFeatureList & GetPrevFeatures()

CPhyloTree::TTreeIdx m_NodeIdx

Node index or pointer (set to NULL after first execute)

CBioTreeFeatureList m_Features

Updated feature list (includes all features, not just those that changed)

bool operator<(const CUpdatedFeature &rhs) const

CBioTreeFeatureList m_PrevFeatures

Feature list prior to edit (for undo)

void SetNode(CPhyloNodeData::TID id, CPhyloTree::TTreeIdx tidx)

CBioTreeFeatureList & GetFeatures()

CPhyloNodeData::TID m_NodeId

Node id to find node in either tree or biotree.

bool FeatureUpdated(TBioTreeFeatureId fid)

Function to exclude nodes during a collapse those nodes that meet a priority threshold.

TBioTreeFeatureId m_PriorityId

SPriorityCollapse(CPhyloTree &m_TreeModel)

virtual bool operator()(const CPhyloTreeNode &n)

size_t TTreeIdx

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

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