TaxonomyTree Class Reference

Search Toolkit Book for TaxonomyTree

#include "taxonomy_tree.hpp"
(Private to src/app/cn3d.)

Inheritance diagram for TaxonomyTree:

Collaboration diagram for TaxonomyTree:

Public Member Functions
	TaxonomyTree (void)
	~TaxonomyTree (void)
void	ShowTreeForAlignment (wxFrame *parent, const BlockMultipleAlignment *alignment, bool abbreviated)

Private Types
typedef std::map< const MoleculeIdentifier *, int >	TaxonomyIDMap
typedef std::map< int, ncbi::CRef< ncbi::objects::CTaxon2_data > >	TaxonomyInfoMap
typedef std::map< int, int >	TaxonomyParentMap
typedef std::list< TaxonomyWindow ** >	TaxonomyWindowList

Private Member Functions
bool	Init (void)
int	GetTaxIDForSequence (const Sequence *seq)
const ncbi::objects::CTaxon2_data *	GetTaxInfoForTaxID (int taxid)
int	GetParentTaxID (int taxid)

Private Attributes
TaxonomyIDMap	taxonomyIDs
TaxonomyInfoMap	taxonomyInfo
TaxonomyParentMap	taxonomyParents
ncbi::objects::CTaxon1	taxonomyServer
TaxonomyWindowList	taxonomyWindows

Detailed Description

Definition at line 55 of file taxonomy_tree.hpp.

Member Typedef Documentation

TaxonomyIDMap

typedef std::map< const MoleculeIdentifier * , int > TaxonomyTree::TaxonomyIDMap

private

Definition at line 66 of file taxonomy_tree.hpp.

TaxonomyInfoMap

typedef std::map< int , ncbi::CRef < ncbi::objects::CTaxon2_data > > TaxonomyTree::TaxonomyInfoMap

private

Definition at line 70 of file taxonomy_tree.hpp.

TaxonomyParentMap

typedef std::map< int , int > TaxonomyTree::TaxonomyParentMap

private

Definition at line 74 of file taxonomy_tree.hpp.

TaxonomyWindowList

typedef std::list< TaxonomyWindow ** > TaxonomyTree::TaxonomyWindowList

private

Definition at line 84 of file taxonomy_tree.hpp.

Constructor & Destructor Documentation

TaxonomyTree()

TaxonomyTree::TaxonomyTree

(

void

)

Definition at line 157 of file taxonomy_tree.cpp.

~TaxonomyTree()

TaxonomyTree::~TaxonomyTree

(

void

)

Definition at line 175 of file taxonomy_tree.cpp.

References NULL, taxonomyServer, and taxonomyWindows.

Member Function Documentation

GetParentTaxID()

int TaxonomyTree::GetParentTaxID ( int  taxid )

private

Definition at line 385 of file taxonomy_tree.cpp.

References Init(), taxonomyParents, taxonomyServer, and WARNINGMSG.

Referenced by ShowTreeForAlignment().

GetTaxIDForSequence()

int TaxonomyTree::GetTaxIDForSequence ( const Sequence *  seq )

private

Definition at line 319 of file taxonomy_tree.cpp.

References Sequence::bioseqASN, MoleculeIdentifier::gi, MoleculeIdentifier::GI_NOT_SET, Sequence::identifier, Init(), NULL, taxonomyIDs, taxonomyServer, MoleculeIdentifier::ToString(), and WARNINGMSG.

Referenced by ShowTreeForAlignment().

GetTaxInfoForTaxID()

const ncbi::objects::CTaxon2_data * TaxonomyTree::GetTaxInfoForTaxID ( int  taxid )

private

Definition at line 365 of file taxonomy_tree.cpp.

References data, i, Init(), NULL, taxonomyInfo, taxonomyServer, and WARNINGMSG.

Referenced by ShowTreeForAlignment().

Init()

bool TaxonomyTree::Init ( void  )

private

Definition at line 161 of file taxonomy_tree.cpp.

References ERRORMSG, INFOMSG, and taxonomyServer.

Referenced by GetParentTaxID(), GetTaxIDForSequence(), and GetTaxInfoForTaxID().

ShowTreeForAlignment()

void TaxonomyTree::ShowTreeForAlignment	(	wxFrame *	parent,
		const BlockMultipleAlignment *	alignment,
		bool	abbreviated
	)

Definition at line 265 of file taxonomy_tree.cpp.

References AddNode(), AppendChildrenToTree(), map_checker< Container >::begin(), TaxonomyTreeNode::childTaxids, ExpandAll(), GetParentTaxID(), BlockMultipleAlignment::GetSequenceOfRow(), GetTaxIDForSequence(), GetTaxInfoForTaxID(), INFOMSG, TaxonomyTreeNode::name, TaxonomyTreeNode::nDescendentLeaves, BlockMultipleAlignment::NRows(), NULL, row, map_checker< Container >::size(), taxonomyWindows, TRACEMSG, and TaxonomyWindow::tree.

Referenced by SequenceViewerWindow::OnTaxonomy().

Member Data Documentation

taxonomyIDs

TaxonomyIDMap TaxonomyTree::taxonomyIDs

private

Definition at line 67 of file taxonomy_tree.hpp.

Referenced by GetTaxIDForSequence().

taxonomyInfo

TaxonomyInfoMap TaxonomyTree::taxonomyInfo

private

Definition at line 71 of file taxonomy_tree.hpp.

Referenced by GetTaxInfoForTaxID().

taxonomyParents

TaxonomyParentMap TaxonomyTree::taxonomyParents

private

Definition at line 75 of file taxonomy_tree.hpp.

Referenced by GetParentTaxID().

taxonomyServer

ncbi::objects::CTaxon1 TaxonomyTree::taxonomyServer

private

Definition at line 78 of file taxonomy_tree.hpp.

Referenced by GetParentTaxID(), GetTaxIDForSequence(), GetTaxInfoForTaxID(), Init(), and ~TaxonomyTree().

taxonomyWindows

TaxonomyWindowList TaxonomyTree::taxonomyWindows

private

Definition at line 85 of file taxonomy_tree.hpp.

Referenced by ShowTreeForAlignment(), and ~TaxonomyTree().

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The documentation for this class was generated from the following files:

• src/app/cn3d/taxonomy_tree.hpp
• src/app/cn3d/taxonomy_tree.cpp