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CUnculTaxTool Class Reference

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#include <gui/packages/pkg_sequence_edit/uncul_tax_tool.hpp>

+ Inheritance diagram for CUnculTaxTool:
+ Collaboration diagram for CUnculTaxTool:

Classes

struct  SUnindexedObject
 

Public Member Functions

 CUnculTaxTool ()
 Constructors. More...
 
 CUnculTaxTool (wxWindow *parent, objects::CSeq_entry_Handle seh, IWorkbench *workbench, wxWindowID id=11300, const wxString &caption=_("Uncultured Taxonomy Tool"), const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(1400, 840), long style=wxMINIMIZE_BOX|wxMAXIMIZE_BOX|wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL)
 
bool Create (wxWindow *parent, wxWindowID id=11300, const wxString &caption=_("Uncultured Taxonomy Tool"), const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(1400, 840), long style=wxMINIMIZE_BOX|wxMAXIMIZE_BOX|wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL)
 Creation. More...
 
 ~CUnculTaxTool ()
 Destructor. More...
 
void Init ()
 Initialises member variables. More...
 
void CreateControls ()
 Creates the controls and sizers. More...
 
wxBitmap GetBitmapResource (const wxString &name)
 Retrieves bitmap resources. More...
 
wxIcon GetIconResource (const wxString &name)
 Retrieves icon resources. More...
 
CRef< CCmdCompositeGetCommand ()
 
CRef< objects::CSeq_table > GetValuesTableFromSeqEntry ()
 
CRef< CCmdCompositeGetCommandFromValuesTable (CRef< CSeq_table > values_table)
 
CRef< objects::CSeq_table > GetChoices (CRef< objects::CSeq_table > values_table)
 
int GetCollapsible ()
 
bool IsReadOnlyColumn (string column_name)
 
void OnAddSp (wxCommandEvent &event)
 
void OnAddBacterium (wxCommandEvent &event)
 
void OnCancel (wxCommandEvent &event)
 
void OnApply (wxCommandEvent &event)
 
void OnRefreshBtn (wxCommandEvent &event)
 
void TrimSuggestions (wxCommandEvent &event)
 

Static Public Member Functions

static bool ShowToolTips ()
 Should we show tooltips? More...
 

Private Types

typedef vector< SUnindexedObjectTUnindexedObjects
 

Private Member Functions

void AddBioSource (const objects::CSeq_entry &seq, const objects::CSeqdesc &desc)
 
void GetDesc (const CSeq_entry &se)
 
void FindBioSource (objects::CSeq_entry_Handle tse)
 
bool OkToTaxFix (const string &taxname)
 
void LookupSuggestions (vector< string > &suggestions, vector< bool > &verified)
 
string StandardFixes (const CBioSource &biosource)
 
bool IsSpeciesSpecific (const CBioSource &biosource)
 
string MakeUnculturedName (const string &taxname, const string suffix="")
 
bool CompareOrgnameLineage (CRef< CT3Reply > reply, const string &lineage)
 
string GetSuggestion (CRef< CT3Reply > reply)
 
string GetRank (CRef< CT3Reply > reply)
 
CRef< CT3ReplyGetReply (const CBioSource &biosource, const string &standard_taxname)
 
bool CheckSuggestedFix (const CBioSource &biosource, string &suggestion)
 
bool IsAmbiguous (CRef< CT3Reply > reply)
 
string TryRankFix (CRef< CT3Reply > reply, unsigned int i, string &name)
 
int GetColumn ()
 
void ConvertSpeciesSpecificNote (CBioSource &biosource, const string &new_note)
 
void PreloadCache ()
 

Private Attributes

objects::CSeq_entry_Handle m_TopSeqEntry
 
vector< pair< CConstRef< objects::CSeq_entry >, CConstRef< objects::CSeqdesc > > > m_BioSource
 
map< string, CRef< CT3Reply > > m_ReplyCache
 
wxGrid * m_Grid
 
CSeqTableGridPanelm_GridPanel
 
IWorkbenchm_Workbench
 
set< unsigned intm_ConvertNote
 
set< unsigned intm_RemoveNote
 
TUnindexedObjects m_UnindexedObjects
 

Detailed Description

Definition at line 65 of file uncul_tax_tool.hpp.

Member Typedef Documentation

◆ TUnindexedObjects

Definition at line 149 of file uncul_tax_tool.hpp.

Constructor & Destructor Documentation

◆ CUnculTaxTool() [1/2]

CUnculTaxTool::CUnculTaxTool ( )

Constructors.

CUnculTaxTool event table definition

CUnculTaxTool constructors

Definition at line 86 of file uncul_tax_tool.cpp.

References Init().

◆ CUnculTaxTool() [2/2]

CUnculTaxTool::CUnculTaxTool ( wxWindow *  parent,
objects::CSeq_entry_Handle  seh,
IWorkbench workbench,
wxWindowID  id = 11300,
const wxString &  caption = _("Uncultured Taxonomy Tool"),
const wxPoint &  pos = wxDefaultPosition,
const wxSize &  size = wxSize(1400, 840),
long  style = wxMINIMIZE_BOX|wxMAXIMIZE_BOX|wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL 
)

◆ ~CUnculTaxTool()

CUnculTaxTool::~CUnculTaxTool ( )

Destructor.

CUnculTaxTool destructor

Definition at line 127 of file uncul_tax_tool.cpp.

Member Function Documentation

◆ AddBioSource()

void CUnculTaxTool::AddBioSource ( const objects::CSeq_entry &  seq,
const objects::CSeqdesc &  desc 
)
private

◆ CheckSuggestedFix()

bool CUnculTaxTool::CheckSuggestedFix ( const CBioSource biosource,
string suggestion 
)
private

Definition at line 578 of file uncul_tax_tool.cpp.

References GetRank(), GetReply(), and GetSuggestion().

Referenced by LookupSuggestions().

◆ CompareOrgnameLineage()

bool CUnculTaxTool::CompareOrgnameLineage ( CRef< CT3Reply reply,
const string lineage 
)
private

◆ ConvertSpeciesSpecificNote()

void CUnculTaxTool::ConvertSpeciesSpecificNote ( CBioSource biosource,
const string new_note 
)
private

◆ Create()

bool CUnculTaxTool::Create ( wxWindow *  parent,
wxWindowID  id = 11300,
const wxString &  caption = _("Uncultured Taxonomy Tool"),
const wxPoint &  pos = wxDefaultPosition,
const wxSize &  size = wxSize(1400, 840),
long  style = wxMINIMIZE_BOX|wxMAXIMIZE_BOX|wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL 
)

Creation.

CVectorTrimDlg creator

Definition at line 105 of file uncul_tax_tool.cpp.

References CreateControls(), and ncbi::grid::netcache::search::fields::size.

◆ CreateControls()

void CUnculTaxTool::CreateControls ( )

◆ FindBioSource()

void CUnculTaxTool::FindBioSource ( objects::CSeq_entry_Handle  tse)
private

◆ GetBitmapResource()

wxBitmap CUnculTaxTool::GetBitmapResource ( const wxString &  name)

Retrieves bitmap resources.

Get bitmap resources

Definition at line 330 of file uncul_tax_tool.cpp.

◆ GetChoices()

CRef<objects::CSeq_table> CUnculTaxTool::GetChoices ( CRef< objects::CSeq_table >  values_table)
inline

Definition at line 100 of file uncul_tax_tool.hpp.

Referenced by CreateControls().

◆ GetCollapsible()

int CUnculTaxTool::GetCollapsible ( )
inline

Definition at line 101 of file uncul_tax_tool.hpp.

Referenced by CreateControls(), OnRefreshBtn(), and TrimSuggestions().

◆ GetColumn()

int CUnculTaxTool::GetColumn ( void  )
private

Definition at line 857 of file uncul_tax_tool.cpp.

References _, i, and m_Grid.

Referenced by OnAddBacterium(), and OnAddSp().

◆ GetCommand()

CRef< CCmdComposite > CUnculTaxTool::GetCommand ( void  )

◆ GetCommandFromValuesTable()

CRef< CCmdComposite > CUnculTaxTool::GetCommandFromValuesTable ( CRef< CSeq_table values_table)

◆ GetDesc()

void CUnculTaxTool::GetDesc ( const CSeq_entry se)
private

◆ GetIconResource()

wxIcon CUnculTaxTool::GetIconResource ( const wxString &  name)

Retrieves icon resources.

Get icon resources

Definition at line 341 of file uncul_tax_tool.cpp.

◆ GetRank()

string CUnculTaxTool::GetRank ( CRef< CT3Reply reply)
private

◆ GetReply()

CRef< CT3Reply > CUnculTaxTool::GetReply ( const CBioSource biosource,
const string standard_taxname 
)
private

◆ GetSuggestion()

string CUnculTaxTool::GetSuggestion ( CRef< CT3Reply reply)
private

◆ GetValuesTableFromSeqEntry()

CRef< CSeq_table > CUnculTaxTool::GetValuesTableFromSeqEntry ( )

◆ Init()

void CUnculTaxTool::Init ( void  )

Initialises member variables.

Member initialisation

Definition at line 138 of file uncul_tax_tool.cpp.

References m_GridPanel, and NULL.

◆ IsAmbiguous()

bool CUnculTaxTool::IsAmbiguous ( CRef< CT3Reply reply)
private

◆ IsReadOnlyColumn()

bool CUnculTaxTool::IsReadOnlyColumn ( string  column_name)
inline

Definition at line 102 of file uncul_tax_tool.hpp.

Referenced by CreateControls().

◆ IsSpeciesSpecific()

bool CUnculTaxTool::IsSpeciesSpecific ( const CBioSource biosource)
private

◆ LookupSuggestions()

void CUnculTaxTool::LookupSuggestions ( vector< string > &  suggestions,
vector< bool > &  verified 
)
private

◆ MakeUnculturedName()

string CUnculTaxTool::MakeUnculturedName ( const string taxname,
const string  suffix = "" 
)
private

Definition at line 573 of file uncul_tax_tool.cpp.

References suffix.

Referenced by LookupSuggestions(), PreloadCache(), and TryRankFix().

◆ OkToTaxFix()

bool CUnculTaxTool::OkToTaxFix ( const string taxname)
private

Definition at line 797 of file uncul_tax_tool.cpp.

References NStr::FindNoCase(), i, NPOS, and sUnfixable.

Referenced by AddBioSource().

◆ OnAddBacterium()

void CUnculTaxTool::OnAddBacterium ( wxCommandEvent &  event)

Definition at line 869 of file uncul_tax_tool.cpp.

References GetColumn(), i, m_Grid, and rapidjson::value.

◆ OnAddSp()

void CUnculTaxTool::OnAddSp ( wxCommandEvent &  event)

Definition at line 882 of file uncul_tax_tool.cpp.

References GetColumn(), i, m_Grid, and rapidjson::value.

◆ OnApply()

void CUnculTaxTool::OnApply ( wxCommandEvent &  event)

◆ OnCancel()

void CUnculTaxTool::OnCancel ( wxCommandEvent &  event)

Definition at line 933 of file uncul_tax_tool.cpp.

◆ OnRefreshBtn()

void CUnculTaxTool::OnRefreshBtn ( wxCommandEvent &  event)

◆ PreloadCache()

void CUnculTaxTool::PreloadCache ( )
private

◆ ShowToolTips()

bool CUnculTaxTool::ShowToolTips ( )
static

Should we show tooltips?

Should we show tooltips?

Definition at line 321 of file uncul_tax_tool.cpp.

◆ StandardFixes()

string CUnculTaxTool::StandardFixes ( const CBioSource biosource)
private

◆ TrimSuggestions()

void CUnculTaxTool::TrimSuggestions ( wxCommandEvent &  event)

◆ TryRankFix()

string CUnculTaxTool::TryRankFix ( CRef< CT3Reply reply,
unsigned int  i,
string name 
)
private

Member Data Documentation

◆ m_BioSource

vector<pair<CConstRef<objects::CSeq_entry>, CConstRef<objects::CSeqdesc> > > CUnculTaxTool::m_BioSource
private

◆ m_ConvertNote

set<unsigned int> CUnculTaxTool::m_ConvertNote
private

Definition at line 140 of file uncul_tax_tool.hpp.

Referenced by FindBioSource(), GetCommandFromValuesTable(), and TryRankFix().

◆ m_Grid

wxGrid* CUnculTaxTool::m_Grid
private

◆ m_GridPanel

CSeqTableGridPanel* CUnculTaxTool::m_GridPanel
private

Definition at line 138 of file uncul_tax_tool.hpp.

Referenced by CreateControls(), GetCommand(), Init(), OnRefreshBtn(), and TrimSuggestions().

◆ m_RemoveNote

set<unsigned int> CUnculTaxTool::m_RemoveNote
private

Definition at line 140 of file uncul_tax_tool.hpp.

Referenced by FindBioSource(), GetCommandFromValuesTable(), and TryRankFix().

◆ m_ReplyCache

map<string, CRef<CT3Reply> > CUnculTaxTool::m_ReplyCache
private

Definition at line 136 of file uncul_tax_tool.hpp.

Referenced by GetReply(), and PreloadCache().

◆ m_TopSeqEntry

objects::CSeq_entry_Handle CUnculTaxTool::m_TopSeqEntry
private

◆ m_UnindexedObjects

TUnindexedObjects CUnculTaxTool::m_UnindexedObjects
private

Definition at line 150 of file uncul_tax_tool.hpp.

Referenced by GetCommandFromValuesTable(), and OnApply().

◆ m_Workbench

IWorkbench* CUnculTaxTool::m_Workbench
private

Definition at line 139 of file uncul_tax_tool.hpp.

Referenced by OnApply(), and OnRefreshBtn().


The documentation for this class was generated from the following files:
Modified on Sun Jul 21 04:18:47 2024 by modify_doxy.py rev. 669887