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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/phy__tree__view_8cpp_source.html below:

NCBI C++ ToolKit: src/gui/packages/pkg_alignment/phy_tree_view.cpp Source File

((

==1 ||

==0) && !(*node).GetSeqID().Empty()){

= s.size();

= s.size();

uncompressed_len;

uncompressed_len;

() {

; }

uo_id->

(

);

() {

; }

TNodeList::value_type::element_type

;

(sel_cmd !=

&&

) {

& fvalue = it->second;

feat_list.push_back(d);

update_count = 0;

TCNode::TId uid = cnode->GetId();

(*node)->GetBioTreeFeatureList() = iter->GetPrevFeatures();

(*node)->GetBioTreeFeatureList() = iter->GetFeatures();

cnode->ResetFeatures();

& fvalue = (*it).value;

cfeat->SetFeatureid(fid);

cfeat->SetValue(fvalue);

fset.Set().push_back(cfeat);

(

<<

<<

() {

; }

TNodeList::value_type::element_type

;

has_feature =

;

(fdesc->GetName() ==

) {

collapse_fid = fdesc->GetId();

max_fid =

(max_fid, fdesc->GetId());

collapse_fid = max_fid + 1;

d->SetId(collapse_fid);

d->SetName(

);

feat_list.push_back(d);

(node_ids.begin(), node_ids.end());

nodes_updated = 0;

TCNode::TId uid = cnode->GetId();

(std::binary_search(node_ids.begin(), node_ids.end(), uid)) {

(

<< uid);

collapse_feature_found =

;

(feature->GetFeatureid() == collapse_fid) {

feature->SetValue(collapse_value);

collapse_feature_found =

;

(!collapse_feature_found) {

cfeat->SetFeatureid(collapse_fid);

cfeat->SetValue(collapse_value);

features.push_back(cfeat);

(nodes_updated != node_ids.size()) {

(

);

feature_value =

;

feature_value =

;

feature_value;

feature_value =

;

feature_value =

;

() {

; }

"View

graphical presentation of hierarchical

(phylogenetic

, taxonomy

, etc.) using various layout methods",

, m_EditUpdate(

)

wxMenu* view_menu =

wxMenu();

view_menu->Append( wxID_SEPARATOR,

(

) );

wxMenu* bar_menu =

wxMenu();

bar_menu->Append(

,

(

), view_menu );

(event.IsCommandEvent()) {

wxEventType

=

.GetEventType();

wxWindow* child = FindWindow(

);

wxEvtHandler* evtHandler = child->GetEventHandler();

(evtHandler && evtHandler->ProcessEventLocally(event))

wxPanel::ProcessEvent(event);

wxBoxSizer* sizer =

wxBoxSizer(wxVERTICAL);

sizer->Add(queryPanel, 0, wxEXPAND);

sizer->Add(phyWidget, 1, wxEXPAND);

*

= it->object.GetPointer();

(!ws)

;

(uo.

(

) &&

(uo.

(

) &&

first_update = (phyWidget->

() ==

);

(uo.

(

) &&

label_format ==

&&

label_format ==

&&

(label_format ==

)

label_format ==

) {

->SetTreetype(

);

vector<CPhyloTree::TTreeIdx> sel_nodes;

(vector<CPhyloTree::TTreeIdx>, it, sel_nodes) {

(!(*n).GetSeqID().Empty()) {

vector<CPhyloTree::TTreeIdx> sel_nodes;

(sel_nodes.size() > 0) {

evt.

(

, *bioTreeSelection);

(vector<CPhyloTree::TTreeIdx>, it, sel_nodes) {

(!(*n).GetSeqID().Empty()) {

(vector<CPhyloTree::TTreeIdx>, it, sel_nodes) {

& tax_id = (*n).GetBioTreeFeatureList()[feature_id];

(tax_id !=

) {

& tax_id = (*tree_node).GetBioTreeFeatureList()[

];

(tax_id !=

) {

& feat_val = (*tree_node).GetBioTreeFeatureList()[

];

(feat_val !=

) {

(phyWidget ==

)

vector<TTreeIdx> sel_nodes;

vector<CPhyloTree::TID> sel_node_ids;

select_seqids =

;

select_taxids =

;

(objs.size() > 0) {

select_seqids =

;

select_taxids =

;

bioTreeSelection =

*

(objs[0].GetNonNullPointer());

(bioTreeSelection !=

&& bioTreeSelection->

().size()) {

select_by_id =

;

select_by_id =

;

(!select_by_id && bioTree->IsSetFdict()) {

feature_id = bioTreeSelection->

(feat_name);

sel_node_ids.reserve(nodeIds.size());

(nodeIds.begin(), nodeIds.end(), back_inserter(sel_node_ids));

(feature_id != -1) {

(feat_name ==

)

select_seqids =

;

(feat_name ==

|| feat_name ==

)

select_taxids =

;

(!select_seqids && !select_taxids) {

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

feat_val = bioTreeSelection->

(*iter,feature_id);

(feat_val.empty())

selected_feature_values.

(feat_val);

ids.push_back((*it_loc)->m_Id);

(ids.size() != 0 && select_seqids) {

(select_taxids) {

(feature_id != -1) {

(!sel_nodes.empty()) {

(!sel_node_ids.empty()) {

(bioTreeSelection !=

) {

phyWidget->SetCursor(*wxHOURGLASS_CURSOR);

sb_srv->SetStatusMessage(

);

sb_srv->SetStatusMessage(

);

phyWidget->SetCursor(*wxSTANDARD_CURSOR);

(dlgExport.ShowModal() != wxID_OK)

uo_id->

(

);

uo.

(

, current_layout);

(uo.

(

) &&

uo.

(

, use_distances);

(uo.

(

) &&

uo.

(

, rotate_labels);

(sel_edit !=

) {

uo_id->

(

);

(uo.

(

) &&

uo.

(

, label_format);

uo_id->

(

);

(fedit !=

) {

(expand_collapse !=

) {

in_project->

();

(!queryEvt)

;

sb_srv->SetStatusMessage(queryEvt->

());

sid(

);

slabel(

);

found_good =

;

found_bad =

;

(

= 0;

<

.size();

++) {

type_info&

=

(*obj);

.

(

objects::CBioTreeContainer*

(btc));

=

;

item->SetItem().SetOther().Set(*

);

item->SetLabel(

);

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.

User-defined methods of the data storage class.

Defines CBioTreeSelection, class used to broadcast selected tree nodes between views.

CAppJobTask CAppJobTask is an adapter that allows for running IAppJobs as Tasks in App Task Service.

const TNodeIdsVector & GetNodeIds() const

Returns const list of selected nodes.

std::vector< objects::CNode::TId > TNodeIdsVector

Vector of node IDs.

const TNodeIdsVector & GetExplicitlySelectedNodeIds() const

Returns const list of explicitly selected nodes.

std::string GetFeatureValue(objects::CNode::TId nodeId, objects::CFeatureDescr::TId featureId) const

Gets the value of a feature for the specified node id.

objects::CFeatureDescr::TId GetFeatureId(const std::string &feature) const

Gets the id of the specified feature.

bool HasFeature(const std::string &feature) const

Checks if the BioTree has the specified feature.

CConstRef< objects::CBioTreeContainer > GetBioTree() const

Returns the BioTree.

CBioTreeContainer::TFdict TContainerDict

TCNode::TFeatures TCNodeFeatureSet

virtual void Execute()

Do the editing action.

TNodeList::value_type::element_type TCNode

CChangePhyloExpandCollapseCmd(CPhyTreeView *view, CExpandCollapseNodes *ec_edit, CRef< CPhyloTreeDataSource > ds, CConstRef< objects::CBioTreeContainer > bio_tree)

TCNodeSet::Tdata TNodeList

CConstRef< objects::CBioTreeContainer > m_BioTree

virtual string GetLabel()

CBioTreeContainer::TNodes TCNodeSet

CRef< CPhyloTreeDataSource > m_DS

TCNodeFeatureSet::Tdata TNodeFeatureList

CRef< CExpandCollapseNodes > m_ExpandCollapseEdit

TNodeFeatureList::value_type::element_type TCNodeFeature

virtual void Unexecute()

Undo (opposite to Execute())

TContainerDict::Tdata::value_type::element_type TCFeatureDescr

void PerformEdit(CPhyloNodeData::TDisplayChildren ec, CNodeFeature_Base::TValue &collapse_value)

virtual bool CanMerge(IEditCommand *cmd)

IEditCommand merge commands (macros allow changes to both properties and selection sets,...

CBioTreeContainer::TFdict TContainerDict

TCNodeFeatureSet::Tdata TNodeFeatureList

virtual void Unexecute()

Undo (opposite to Execute())

TNodeFeatureList::value_type::element_type TCNodeFeature

virtual void Execute()

Do the editing action.

CRef< CChangePhyloSelectionSetCmd > m_MergedCmd

TCNode::TFeatures TCNodeFeatureSet

virtual string GetLabel()

CRef< CFeatureEdit > m_FeatureEdit

CChangePhyloPropertyCmd(CPhyTreeView *view, CFeatureEdit *fedit, CRef< CPhyloTreeDataSource > ds, CConstRef< objects::CBioTreeContainer > bio_tree)

CRef< CPhyloTreeDataSource > m_DS

TCNodeSet::Tdata TNodeList

CBioTreeContainer::TNodes TCNodeSet

TContainerDict::Tdata::value_type::element_type TCFeatureDescr

virtual void Merge(IEditCommand *cmd)

CConstRef< objects::CBioTreeContainer > m_BioTree

void PerformFeatureDictEdit(CBioTreeFeatureDictionary &dict)

void PerformEdit(CBioTreeFeatureDictionary &dict, bool prev_features)

TNodeList::value_type::element_type TCNode

SelectionSets are stored in the biotreecontainer's user-data object so we need a special change comma...

CConstRef< objects::CBioTreeContainer > m_BioTree

CRef< CSelectionSetEdit > m_SelectionEdit

CChangePhyloSelectionSetCmd(CPhyTreeView *view, CSelectionSetEdit *sel_edit, CRef< CPhyloTreeDataSource > ds, CConstRef< objects::CBioTreeContainer > bio_tree)

virtual void Execute()

Do the editing action.

CRef< CPhyloTreeDataSource > m_DS

virtual void Unexecute()

Undo (opposite to Execute())

virtual string GetLabel()

static CLZOCompression m_Compressor

CChangePhyloTreeCommand(CPhyTreeView *view, CConstRef< CBioTreeContainer > prev_tree, CRef< CBioTreeContainer > new_tree)

virtual string GetLabel()

struct CChangePhyloTreeCommand::SBTree TBTree

static vector< char > m_UtilVec

virtual void Unexecute()

Undo (opposite to Execute())

virtual void Execute()

Do the editing action.

CDataLoadingAppJob - a base class for Jobs loading data into projects.

void AddProjectItem(objects::CProjectItem &item)

CRef< objects::CScope > m_Scope

CDataLoadingAppTask - a task that executes CDataLoadingAppJob.

CEvent - generic event implementation TODO TODO - Attachments.

CPhyExportParams & GetData()

Data access.

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

void Clear(objects::CScope *scope)

void Add(ISelObjectHandle *obj_handle, CObject &obj)

void GetMatches(const CObject &object, objects::CScope &scope, TResults &results) const

void SetLabelFormat(const wxString &value)

void SetBioTree(CBioTreeContainer *value)

CPhyRebuildIndexVisitor(CObjectIndex &idx)

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

CPhyTreePanel(wxWindow *parent, long childId)

virtual bool ProcessEvent(wxEvent &event)

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.

void SaveToUserObject(objects::CBioTreeContainer_Base::TUser &uo)

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.

CTreeLabel GetTreeLabel() const

TClusterID GetMaxClusterID()

void Relabel(CPhyloTreeScheme *scheme, string labelFmt)

void Sort(bool ascending)

CPhyloSelectionSetMgr & GetSelectionSets()

const CBioTreeFeatureDictionary & GetDictionary() const

CTreeGraphicsModel & GetModel()

Get model for rendering.

string GenerateTooltipFormat()

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

void SetScheme(CPhyloTreeScheme &sl, const CPhyloTree *tree)

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

Set this node to be expanded/collapsed.

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

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

virtual bool LoadCurrentSettings()

string & SetTooltipFormat(void)

void SetLabelStyle(const TLabelStyle &ls)

string & SetLabelFormat(void)

void SetLabelVisibility(const TLabelsVisibility &lv)

CPhyloTreeSelectionRoot()

int m_CurrentRootDistance

int m_SelectionRootDistance

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

TTreeIdx GetSelectionRootIdx() const

TTreeIdx m_SelectionRootIdx

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

void SetExplicitlySelected(const vector< TID > &esel)

Reset explicitly selected nodes to those currently selected nodes that are also found in the vector '...

void SetSelectionIDs(const vector< TID > &ids, bool sel=true, bool sel_children=true)

Select a set of nodes - equivalent to calling SetSelection(idx, true, true, true) on each of the node...

void SetLeavesExplicitlySelected()

Set the nodes used for iteration to default to the leaf nodes.

void ClearSelection()

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

void GetSelectedIDs(vector< TID > &sel) const

Returns the node ids of selected nodes.

CPhyloNodeData::TClusterID TClusterID

CPhyloSelectionSetMgr & GetSelectionSets()

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()).

bool HasCurrentNode() const

Return true if the currently active node is not Null()

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().

CBioTreeFeatureDictionary & GetFeatureDict()

Return feature dictionary.

void GetSelected(vector< TTreeIdx > &sel) const

Returns indices of selected nodes.

size_t GetNumSelected() const

Returns the number of selected nodes.

CProjectService - a service providing API for operations with Workspaces and Projects.

virtual void x_ReportInvalidInputData(TConstScopedObjects &objects)

use this function to report incompatible data in InitView()

virtual void OnProjectChanged()

virtual void x_UpdateContentLabel()

unique_ptr< const wxMenu > m_MenuBarMenu

virtual objects::CScope * x_GetScope() const

virtual void x_AttachToProject(CGBDocument &doc)

virtual bool x_HasProject() const

EEventSubtype GetSubtype() const

CProjectViewTypeDescriptor - holds description of a project view type.

virtual CUndoManager * x_GetUndoManager()

gets undo manager

const string & GetStatus() const

virtual void Create(wxWindow *parent, wxWindowID id=wxID_ANY, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxDefaultSize)

Create window.

TTreeIdx GetNodeIdx() const

CSelNodeHandle(CPhyloTree::TTreeIdx node_idx)

CProjectSelectOptions - describes how new Project Items shall be added to a workspace.

void Set_AddToExistingProject(TProjectId &project_id, const string &folder=kEmptyStr)

CSelectionEvent CSelectionEvent is used for broadcasting selection between views.

vector< CConstRef< objects::CSeq_id > > TIds

const TIdLocs & GetIdLocs() const

const TTaxIds & GetTaxIDs() const

static bool sm_TreeBroadcastOneToOne

Node properties used to compare trees when broadcasting.

void AddTaxIDSelection(TTaxId tid)

void GetIndexed(const string &area_name, TConstObjects &objs) const

Get Objects from the private broadcasting area (caller has to make sure output objs is empty)

static vector< string > sm_TreeBroadcastProperties

broadcast sel. between documents

vector< CConstRef< CIdLoc > > TIdLocs

void AddIndexed(const string &area_name, const CObject &obj)

Add private selection broadcasting info.

objects::CScope & GetScope()

const TIds & GetIds() const

bool HasObjectSelection()

Object Selection - represents select Objects (such as features, alignments, etc)

bool AddObjectSelection(const CObject &obj)

Class designed to hold a set of tax-ids represented as (on) bits in a bit vector.

bool IsSelected(TTaxId tid) const

CRgbaGradColorTable * GetColorTable()

Get color table used a 1D texture map for edges and nodes.

void SaveToUserObject(CBioTreeContainer_Base::TUser &uo)

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.

TTreeIdx GetRootIdx() const

Return the index of the root node.

CUICommandRegistry is a centralized registry where all application commands should be registered.

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.

CViewTypeDescriptor - holds description of a view type.

Undo/Redo interface for editing operations.

virtual void Execute(IEditCommand *command, wxWindow *window=0)=0

Interface (functor) for object editing.

object, that will be attached to event

virtual const CViewTypeDescriptor & GetViewTypeDescriptor() const

returns a Descriptor for the View Type supported by the Factory

IRegSettings An interface for objects that save / restore settings using CGuiRegistry.

virtual void SaveSettings() const =0

virtual void LoadSettings()=0

virtual void SetRegistryPath(const string &path)=0

IView - represents a standard visual part of Workbench UI.

CFingerprint identifies an instance of IWMClient and is used for labeling layout positions.

bool operator()(const CUpdatedFeature &lhs, const CUpdatedFeature &rhs) const

SUpdateFeatureCompare(const CPhyloNodeData::TID id)

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

const_iterator end() const

TBioTreeFeatureId m_FeatureId

const set< string > & m_FeatureValues

visitor_string_query(TBioTreeFeatureId feat_id, const set< string > &feat_values)

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

const vector< CPhyloTree::TTreeIdx > & GetNodes()

visitor_string_query & operator=(const visitor_string_query &rhs)

vector< CPhyloTree::TTreeIdx > m_SelNodes

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

visitor_taxid_query & operator=(const visitor_taxid_query &rhs)

visitor_taxid_query(const CSelectionEvent::TTaxIds &tids, TBioTreeFeatureId tax_feat_id)

const vector< CPhyloTree::TTreeIdx > & GetNodes()

vector< CPhyloTree::TTreeIdx > m_SelNodes

TBioTreeFeatureId m_TaxFeatureId

const CSelectionEvent::TTaxIds & m_TaxIds

virtual void RegisterFileAlias(const wxArtID &anId, const wxArtClient &aClient, const wxSize &aSize, const wxString &aName, long aType=wxBITMAP_TYPE_ANY, int anIndex=-1)

static ulg compressed_len

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

virtual bool DecompressBuffer(const void *src_buf, size_t src_len, void *dst_buf, size_t dst_size, size_t *dst_len)

Decompress data in the buffer.

virtual bool CompressBuffer(const void *src_buf, size_t src_len, void *dst_buf, size_t dst_size, size_t *dst_len)

Compress data in the buffer.

virtual size_t EstimateCompressionBufferSize(size_t src_len)

Estimate buffer size for data compression.

#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)

const string & GetMsg(void) const

Get message string.

CIRef< T > GetServiceByType()

retrieves a typed reference to a service, the name of C++ type is used as the name of the service.

void AddTask(IAppTask &task)

Add a task to the queue.

virtual CAppTaskService * GetAppTaskService()=0

virtual void RegisterCommands(CUICommandRegistry &cmd_reg, wxFileArtProvider &provider)

called by the framework to give Factory a chance to register commands used by view

CPhyloTree::TTreeIdx m_CurrentNode

void RebuildObjectIndex()

CRef< CPhyloTreeDataSource > m_DataSource

int m_InitialRotateLabels

If rendering parms are stored in biotreecontainer, set them first time.

virtual string GetExtensionIdentifier() const

CPhyTreeViewFactory.

virtual void x_OnSetSelection(CSelectionEvent &evt)

override in derived classes in order to handle selection broadcast

CObjectIndex m_ObjectIndex

CPhyloTreeJob(const objects::CBioTreeContainer *btc)

virtual int TestInputObjects(TConstScopedObjects &objects)

tests input objects (not using object conversion) and returns a combination of ETestResult flags bett...

virtual const CProjectViewTypeDescriptor & GetProjectViewTypeDescriptor() const

returns a Descriptor for the View Type supported by the Factory

void OnCreateSelectedSubtree(CEvent *evt)

virtual IView * CreateInstance() const

creates a view instance

int m_InitialUseDistances

virtual void RegisterIconAliases(wxFileArtProvider &provider)

called by the framework to give Factory a chance to register images used by view

virtual void SetRegistryPath(const string &reg_path)

CPhyloTreeWidget * GetWidget() const

virtual bool InitView(TConstScopedObjects &objects, const objects::CUser_object *params)

initialize view with data, inside this function the view must call CProjectService::AttachView to con...

virtual string GetExtensionLabel() const

returns a displayable label for this extension ( please capitalize the key words - "My Extension" )

virtual void GetVisibleRanges(CVisibleRange &vrange) const

populate a visible range event for broadcasting

CRef< objects::CBioTreeContainer > m_Cont

virtual void SaveSettings() const

void OnSomethingEdited(CEvent *evt)

void AppliedEditToDataSource()

virtual const CObject * x_GetOrigObject() const

virtual void x_CreateMenuBarMenu()

initializes m_MenuBarMenu; override in derived classes

virtual IView * CreateInstanceByFingerprint(const TFingerprint &fingerprint) const

if fingerprint is recognized - creates and returns a new instance

CRef< CPhyloTreeScheme > m_Scheme

CRef< objects::CBioTreeContainer > m_Btc

virtual void x_CreateProjectItems()

override this function in derived classes and populate m_Items.

CConstRef< objects::CBioTreeContainer > m_BioTreeContainer

void x_QueryStatusChange(CEvent *evt)

void GetSelection(CSelectionEvent &evt) const

get selection for broadcasting

virtual const CViewTypeDescriptor & GetTypeDescriptor() const

return an object providing meta information about thei view type

virtual void DestroyViewWindow()

destroy Window corresponding to the view

virtual void LoadSettings()

void OnExportTree(CEvent *evt)

void CommitTheChanges(CNcbiIstrstream &istr)

virtual void CreateViewWindow(wxWindow *parent)

create Window corresponding to the view

virtual wxWindow * GetWindow()

returns a pointer to the wxWindow representing the client

static void GetLabel(const CObject &obj, string *label, ELabelType type=eDefault)

const TEventID GetID(void) const

Inline Implementation.

string m_Descr

mutex to sync our internals

vector< CConstRef< CObject > > TConstObjects

virtual const string & GetIconAlias() const

#define ON_EVENT(type, id, handler)

#define END_EVENT_MAP()

Ends definition of Command Map.

#define BEGIN_EVENT_MAP(thisClass, baseClass)

Begins definition of Command Map for CEventHandler-derived class.

virtual void AddListener(CEventHandler *listener, int pool_name=ePool_Default)

Add a listener.

vector< SConstScopedObject > TConstScopedObjects

virtual IEventAttachment * GetAttachment(void)

#define MSerial_AsnText

I/O stream manipulators –.

bool Empty(void) const THROWS_NONE

Check if CConstRef is empty – not pointing to any object which means having a null value.

TObjectType * GetPointer(void) const THROWS_NONE

Get pointer,.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

void Reset(void)

Reset reference object.

bool IsNull(void) const THROWS_NONE

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

TObjectType * GetPointerOrNull(void) THROWS_NONE

Get pointer value.

TObjectType * GetNonNullPointer(void) const

Get pointer value and throw a null pointer exception if pointer is null.

bool Empty(void) const THROWS_NONE

Check if CRef is empty – not pointing to any object, which means having a null value.

int32_t Int4

4-byte (32-bit) signed integer

#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 unsigned int StringToUInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to unsigned int.

double Restart(void)

Return time elapsed since first Start() or last Restart() call (in seconds).

double Elapsed(void) const

Return time elapsed since first Start() or last Restart() call (in seconds).

void Start(void)

Start the timer.

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.

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.

static const char label[]

list< CRef< CFeatureDescr > > Tdata

const TTreetype & GetTreetype(void) const

Get the Treetype member data.

void SetNodes(TNodes &value)

Assign a value to Nodes data member.

void SetFdict(TFdict &value)

Assign a value to Fdict data member.

list< CRef< CNodeFeature > > Tdata

virtual void Reset(void)

Reset the whole object.

void Reset(void)

Reset data member.

void SetTreetype(const TTreetype &value)

Assign a value to Treetype data member.

list< CRef< CNode > > Tdata

bool IsSetTreetype(void) const

hint on what kind of tree this is Check if a value has been assigned to Treetype data member.

Tdata & Set(void)

Assign a value to data member.

void SetUser(TUser &value)

Assign a value to User data member.

const TStr & GetStr(void) const

Get the variant data.

bool CanGetType(void) const

Check if it is safe to call GetType method.

bool IsSetType(void) const

type of object within class Check if a value has been assigned to Type data member.

const TData & GetData(void) const

Get the Data member data.

TBool GetBool(void) const

Get the variant data.

E_Choice Which(void) const

Which variant is currently selected.

bool IsInt(void) const

Check if variant Int is selected.

bool IsStr(void) const

Check if variant Str is selected.

TInt GetInt(void) const

Get the variant data.

TStr & SetStr(void)

Select the variant.

void SetType(TType &value)

Assign a value to Type data member.

void SetData(TData &value)

Assign a value to Data data member.

const TType & GetType(void) const

Get the Type member data.

bool IsBool(void) const

Check if variant Bool is selected.

@ e_not_set

No variant selected.

unsigned int

A callback function used to compare two keys in a database.

for(len=0;yy_str[len];++len)

constexpr auto sort(_Init &&init)

Defines: CTimeFormat - storage class for time format.

Int4 delta(size_t dimension_, const Int4 *score_)

void copy(Njn::Matrix< S > *matrix_, const Njn::Matrix< T > &matrix0_)

CProjectViewTypeDescriptor s_PhyTreeViewTypeDescr("Tree View", "phylo_tree_view", "Tree View", "View for graphical presentation of hierarchical data (phylogenetic tree, taxonomy tree, etc.) using various layout methods", "PHY_TREE_VIEW", "Alignment", false, "BioTreeContainer", eOneObjectAccepted)

float m_ExecOnBioTreeChanged

float m_CreateProperyUndoCommand

float m_DataSourceInitTimer

float m_ExecutePropertyCommand

float m_ExecuteUndoCommand

float m_CreateUndoCommand

Timers:

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.

@ eCmdRenderingOptionsChanged

wxEVT_COMMAND_MENU_SELECTED

CPhyloNodeData::TDisplayChildren GetExpanded() const

vector< CPhyloNodeData::TID > & GetIds()

Edits for one or more nodes.

CBioTreeFeatureDictionary & GetPrevDictionary()

vector< CUpdatedFeature > & GetUpdated()

CBioTreeFeatureDictionary & GetDictionary()

Edits for one or more nodes.

CPhyloSelectionSetMgr & GetUpdatedSet()

CPhyloSelectionSetMgr & GetPrevSet()

CPhyloNodeData::TID m_NodeId

Node id to find node in either tree or biotree.

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.

wxString ToWxString(const string &s)

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