SAutodefParams Class Reference

Search Toolkit Book for SAutodefParams

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

Inheritance diagram for SAutodefParams:

Collaboration diagram for SAutodefParams:

Public Member Functions
	SAutodefParams ()
	SAutodefParams. More...
void	Init ()
IRegSettings interface implementation
virtual void	SetRegistryPath (const string &reg_path)
virtual void	LoadSettings ()
virtual void	SaveSettings () const
Public Member Functions inherited from IRegSettings
virtual	~IRegSettings ()

Public Attributes
string	m_RegPath
TConstScopedObjects	m_SeqEntries
bool	m_UseLabels
bool	m_LeaveParenthetical
bool	m_DoNotApplyToSp
bool	m_DoNotApplyToNr
bool	m_DoNotApplyToCf
bool	m_DoNotApplyToAff
bool	m_IncludeCountryText
bool	m_KeepAfterSemicolon
unsigned int	m_MaxMods
unsigned int	m_HIVRule
bool	m_NeedHIVRule
unsigned int	m_FeatureListType
unsigned int	m_MiscFeatRule
unsigned int	m_ProductFlag
unsigned int	m_NuclearCopyFlag
bool	m_SpecifyNuclearProduct
bool	m_AltSpliceFlag
bool	m_SuppressLocusTags
bool	m_GeneClusterOppStrand
bool	m_SuppressFeatureAltSplice
bool	m_SuppressMobileElementSubfeatures
bool	m_SuppressMiscFeatSubfeatures
bool	m_KeepExons
bool	m_KeepIntrons
bool	m_UseFakePromoters
bool	m_KeepRegulatoryFeatures
bool	m_KeepLTRs
bool	m_Keep3UTRs
bool	m_Keep5UTRs
bool	m_UseNcRNAComment
bool	m_KeepMiscRecomb
bool	m_KeepRepeatRegion
set< objects::CFeatListItem >	m_SuppressedFeatures
objects::CAutoDefSourceDescription::TAvailableModifierVector	m_ModifierList
string	m_CustomFeatureClause

Detailed Description

Definition at line 52 of file autodef_params.hpp.

Constructor & Destructor Documentation

SAutodefParams()

SAutodefParams::SAutodefParams

(

)

SAutodefParams.

Definition at line 44 of file autodef_params.cpp.

References Init().

Member Function Documentation

Init()

void SAutodefParams::Init

(

void

)

Definition at line 49 of file autodef_params.cpp.

References set< Key, Compare >::clear(), CAutoDefOptions::eDelete, CAutoDefOptions::eListAllFeatures, CAutoDefOptions::ePreferClone, kEmptyStr, m_AltSpliceFlag, m_CustomFeatureClause, m_DoNotApplyToAff, m_DoNotApplyToCf, m_DoNotApplyToNr, m_DoNotApplyToSp, m_FeatureListType, m_GeneClusterOppStrand, m_HIVRule, m_IncludeCountryText, m_Keep3UTRs, m_Keep5UTRs, m_KeepAfterSemicolon, m_KeepExons, m_KeepIntrons, m_KeepLTRs, m_KeepMiscRecomb, m_KeepRegulatoryFeatures, m_KeepRepeatRegion, m_LeaveParenthetical, m_MaxMods, m_MiscFeatRule, m_NeedHIVRule, m_NuclearCopyFlag, m_ProductFlag, m_SpecifyNuclearProduct, m_SuppressedFeatures, m_SuppressFeatureAltSplice, m_SuppressLocusTags, m_SuppressMiscFeatSubfeatures, m_SuppressMobileElementSubfeatures, m_UseFakePromoters, m_UseLabels, and m_UseNcRNAComment.

Referenced by CAutodefParamsPanel::RestoreDefaults(), and SAutodefParams().

LoadSettings()

void SAutodefParams::LoadSettings ( )

virtual

Implements IRegSettings.

Definition at line 112 of file autodef_params.cpp.

References CRegistryReadView::GetBool(), CGuiRegistry::GetInstance(), CGuiRegistry::GetReadView(), kDoNotApplyToSp, kIncludeCountryTextTag, kLeaveParentheticalTag, kUseLabelsTag, m_DoNotApplyToSp, m_IncludeCountryText, m_LeaveParenthetical, m_RegPath, and m_UseLabels.

SaveSettings()

void SAutodefParams::SaveSettings ( ) const

virtual

Implements IRegSettings.

Definition at line 98 of file autodef_params.cpp.

References CGuiRegistry::GetInstance(), CGuiRegistry::GetWriteView(), kDoNotApplyToSp, kIncludeCountryTextTag, kLeaveParentheticalTag, kUseLabelsTag, m_DoNotApplyToSp, m_IncludeCountryText, m_LeaveParenthetical, m_RegPath, m_UseLabels, and CRegistryWriteView::Set().

SetRegistryPath()

void SAutodefParams::SetRegistryPath ( const string &  reg_path )

virtual

Implements IRegSettings.

Definition at line 87 of file autodef_params.cpp.

References m_RegPath.

Member Data Documentation

m_AltSpliceFlag

bool SAutodefParams::m_AltSpliceFlag

Definition at line 87 of file autodef_params.hpp.

Referenced by ConfigureAutodefForSeqEntry(), Init(), CAutodefFeatClausePanel::PopulateParams(), CAutodefFeatClausePanel::SetParams(), CAutodefParamsPanel::TransferDataFromWindow(), CAutodefParamsPanel::TransferDataToWindow(), and CAutodefJob::x_MakeChanges().

m_CustomFeatureClause

string SAutodefParams::m_CustomFeatureClause

Definition at line 108 of file autodef_params.hpp.

Referenced by ConfigureAutodefForSeqEntry(), Init(), CAutodefFeatClausePanel::PopulateParams(), and CAutodefFeatClausePanel::SetParams().

m_DoNotApplyToAff

bool SAutodefParams::m_DoNotApplyToAff

Definition at line 75 of file autodef_params.hpp.

Referenced by ConfigureAutodefForSeqEntry(), Init(), CAutodefOrgPanel::PopulateParams(), CAutodefOrgPanel::SetParams(), CAutodefParamsPanel::TransferDataFromWindow(), CAutodefParamsPanel::TransferDataToWindow(), and CAutodefJob::x_MakeChanges().

m_DoNotApplyToCf

bool SAutodefParams::m_DoNotApplyToCf

Definition at line 74 of file autodef_params.hpp.

Referenced by ConfigureAutodefForSeqEntry(), Init(), CAutodefOrgPanel::PopulateParams(), CAutodefOrgPanel::SetParams(), CAutodefParamsPanel::TransferDataFromWindow(), CAutodefParamsPanel::TransferDataToWindow(), and CAutodefJob::x_MakeChanges().

m_DoNotApplyToNr

bool SAutodefParams::m_DoNotApplyToNr

Definition at line 73 of file autodef_params.hpp.

Referenced by ConfigureAutodefForSeqEntry(), Init(), CAutodefOrgPanel::PopulateParams(), CAutodefOrgPanel::SetParams(), CAutodefParamsPanel::TransferDataFromWindow(), CAutodefParamsPanel::TransferDataToWindow(), and CAutodefJob::x_MakeChanges().

m_DoNotApplyToSp

bool SAutodefParams::m_DoNotApplyToSp

Definition at line 72 of file autodef_params.hpp.

Referenced by ConfigureAutodefForSeqEntry(), Init(), LoadSettings(), CAutodefOrgPanel::PopulateParams(), SaveSettings(), CAutodefOrgPanel::SetParams(), CAutodefParamsPanel::TransferDataFromWindow(), CAutodefParamsPanel::TransferDataToWindow(), and CAutodefJob::x_MakeChanges().

m_FeatureListType

unsigned int SAutodefParams::m_FeatureListType

Definition at line 82 of file autodef_params.hpp.

Referenced by ConfigureAutodefForSeqEntry(), Init(), CAutodefFeatClausePanel::PopulateParams(), CAutodefFeatClausePanel::SetParams(), CAutodefParamsPanel::TransferDataFromWindow(), CAutodefParamsPanel::TransferDataToWindow(), and CAutodefJob::x_MakeChanges().

m_GeneClusterOppStrand

bool SAutodefParams::m_GeneClusterOppStrand

Definition at line 89 of file autodef_params.hpp.

Referenced by ConfigureAutodefForSeqEntry(), Init(), CAutodefFeatClausePanel::PopulateParams(), CAutodefFeatClausePanel::SetParams(), CAutodefParamsPanel::TransferDataFromWindow(), CAutodefParamsPanel::TransferDataToWindow(), and CAutodefJob::x_MakeChanges().

m_HIVRule

unsigned int SAutodefParams::m_HIVRule

Definition at line 79 of file autodef_params.hpp.

Referenced by ConfigureAutodefForSeqEntry(), Init(), CAutodefOrgPanel::PopulateParams(), CAutodefOrgPanel::SetParams(), CAutodefParamsPanel::TransferDataFromWindow(), CAutodefParamsPanel::TransferDataToWindow(), and CAutodefJob::x_MakeChanges().

m_IncludeCountryText

bool SAutodefParams::m_IncludeCountryText

Definition at line 76 of file autodef_params.hpp.

Referenced by ConfigureAutodefForSeqEntry(), Init(), LoadSettings(), CAutodefOrgPanel::PopulateParams(), SaveSettings(), CAutodefOrgPanel::SetParams(), CAutodefParamsPanel::TransferDataFromWindow(), CAutodefParamsPanel::TransferDataToWindow(), and CAutodefJob::x_MakeChanges().

m_Keep3UTRs

bool SAutodefParams::m_Keep3UTRs

Definition at line 98 of file autodef_params.hpp.

Referenced by ConfigureAutodefForSeqEntry(), Init(), CAutodefOptFeatPanel::PopulateParams(), CAutodefOptFeatPanel::SetParams(), CAutodefParamsPanel::TransferDataFromWindow(), CAutodefParamsPanel::TransferDataToWindow(), and CAutodefJob::x_MakeChanges().

m_Keep5UTRs

bool SAutodefParams::m_Keep5UTRs

Definition at line 99 of file autodef_params.hpp.

Referenced by ConfigureAutodefForSeqEntry(), Init(), CAutodefOptFeatPanel::PopulateParams(), CAutodefOptFeatPanel::SetParams(), CAutodefParamsPanel::TransferDataFromWindow(), CAutodefParamsPanel::TransferDataToWindow(), and CAutodefJob::x_MakeChanges().

m_KeepAfterSemicolon

bool SAutodefParams::m_KeepAfterSemicolon

Definition at line 77 of file autodef_params.hpp.

Referenced by ConfigureAutodefForSeqEntry(), Init(), CAutodefOrgPanel::PopulateParams(), CAutodefOrgPanel::SetParams(), CAutodefParamsPanel::TransferDataFromWindow(), CAutodefParamsPanel::TransferDataToWindow(), and CAutodefJob::x_MakeChanges().

m_KeepExons

bool SAutodefParams::m_KeepExons

Definition at line 93 of file autodef_params.hpp.

Referenced by ConfigureAutodefForSeqEntry(), Init(), CAutodefOptFeatPanel::PopulateParams(), CAutodefOptFeatPanel::SetParams(), CAutodefParamsPanel::TransferDataFromWindow(), CAutodefParamsPanel::TransferDataToWindow(), and CAutodefJob::x_MakeChanges().

m_KeepIntrons

bool SAutodefParams::m_KeepIntrons

Definition at line 94 of file autodef_params.hpp.

Referenced by ConfigureAutodefForSeqEntry(), Init(), CAutodefOptFeatPanel::PopulateParams(), CAutodefOptFeatPanel::SetParams(), CAutodefParamsPanel::TransferDataFromWindow(), CAutodefParamsPanel::TransferDataToWindow(), and CAutodefJob::x_MakeChanges().

m_KeepLTRs

bool SAutodefParams::m_KeepLTRs

Definition at line 97 of file autodef_params.hpp.

Referenced by ConfigureAutodefForSeqEntry(), and Init().

m_KeepMiscRecomb

bool SAutodefParams::m_KeepMiscRecomb

Definition at line 101 of file autodef_params.hpp.

Referenced by ConfigureAutodefForSeqEntry(), Init(), CAutodefOptFeatPanel::PopulateParams(), and CAutodefOptFeatPanel::SetParams().

m_KeepRegulatoryFeatures

bool SAutodefParams::m_KeepRegulatoryFeatures

Definition at line 96 of file autodef_params.hpp.

Referenced by ConfigureAutodefForSeqEntry(), Init(), CAutodefOptFeatPanel::PopulateParams(), CAutodefOptFeatPanel::SetParams(), CAutodefParamsPanel::TransferDataFromWindow(), CAutodefParamsPanel::TransferDataToWindow(), and CAutodefJob::x_MakeChanges().

m_KeepRepeatRegion

bool SAutodefParams::m_KeepRepeatRegion

Definition at line 102 of file autodef_params.hpp.

Referenced by ConfigureAutodefForSeqEntry(), Init(), CAutodefOptFeatPanel::PopulateParams(), and CAutodefOptFeatPanel::SetParams().

m_LeaveParenthetical

bool SAutodefParams::m_LeaveParenthetical

Definition at line 71 of file autodef_params.hpp.

Referenced by ConfigureAutodefForSeqEntry(), Init(), LoadSettings(), CAutodefOrgPanel::PopulateParams(), SaveSettings(), CAutodefOrgPanel::SetParams(), CAutodefParamsPanel::TransferDataFromWindow(), CAutodefParamsPanel::TransferDataToWindow(), and CAutodefJob::x_MakeChanges().

m_MaxMods

unsigned int SAutodefParams::m_MaxMods

Definition at line 78 of file autodef_params.hpp.

Referenced by ConfigureAutodefForSeqEntry(), Init(), CAutodefOrgPanel::PopulateParams(), CAutodefOrgPanel::SetParams(), CAutodefParamsPanel::TransferDataFromWindow(), CAutodefParamsPanel::TransferDataToWindow(), and CAutodefJob::x_MakeChanges().

m_MiscFeatRule

unsigned int SAutodefParams::m_MiscFeatRule

Definition at line 83 of file autodef_params.hpp.

Referenced by CSequenceEditingEventHandler::Autodef(), CEditingBtnsPanel::AutodefMisc(), ConfigureAutodefForSeqEntry(), Init(), CAutodefOptFeatPanel::PopulateParams(), CAutodefOptFeatPanel::SetParams(), CAutodefParamsPanel::TransferDataFromWindow(), CAutodefParamsPanel::TransferDataToWindow(), and CAutodefJob::x_MakeChanges().

m_ModifierList

objects::CAutoDefSourceDescription::TAvailableModifierVector SAutodefParams::m_ModifierList

Definition at line 106 of file autodef_params.hpp.

Referenced by ConfigureAutodefForSeqEntry(), ConfigureAutodefParamsForBestCombo(), ConfigureAutodefParamsForID(), ConfigureParamsForPrefixCombo(), CAutodefParamsPanel::CreateControls(), CPrefixDeflinedlg::GetCommand(), CPrefixDeflinedlg::PopulateModifierCombo(), CAutodefOrgPanel::PopulateParams(), CAutodefParamsPanel::TransferDataFromWindow(), CAutodefParamsPanel::TransferDataToWindow(), CAutodefParamsPanel::x_AllowHIVRule(), CPrefixDeflinedlg::x_FindModifierBasedOnLabel(), CAutodefOrgPanel::x_ListModifiers(), CAutodefJob::x_MakeChanges(), and CAutodefToolManager::x_SelectCompatibleInputObjects().

m_NeedHIVRule

bool SAutodefParams::m_NeedHIVRule

Definition at line 80 of file autodef_params.hpp.

Referenced by ConfigureAutodefForSeqEntry(), ConfigureAutodefParamsForBestCombo(), CAutodefParamsPanel::CreateControls(), Init(), CAutodefOrgPanel::SetParams(), CAutodefJob::x_MakeChanges(), and CAutodefToolManager::x_SelectCompatibleInputObjects().

m_NuclearCopyFlag

unsigned int SAutodefParams::m_NuclearCopyFlag

Definition at line 85 of file autodef_params.hpp.

Referenced by ConfigureAutodefForSeqEntry(), Init(), CAutodefFeatClausePanel::PopulateParams(), CAutodefFeatClausePanel::SetParams(), CAutodefParamsPanel::TransferDataFromWindow(), CAutodefParamsPanel::TransferDataToWindow(), and CAutodefJob::x_MakeChanges().

m_ProductFlag

unsigned int SAutodefParams::m_ProductFlag

Definition at line 84 of file autodef_params.hpp.

Referenced by ConfigureAutodefForSeqEntry(), Init(), CAutodefFeatClausePanel::PopulateParams(), CAutodefFeatClausePanel::SetParams(), CAutodefParamsPanel::TransferDataFromWindow(), CAutodefParamsPanel::TransferDataToWindow(), and CAutodefJob::x_MakeChanges().

m_RegPath

string SAutodefParams::m_RegPath

Definition at line 67 of file autodef_params.hpp.

Referenced by LoadSettings(), SaveSettings(), and SetRegistryPath().

m_SeqEntries

TConstScopedObjects SAutodefParams::m_SeqEntries

Definition at line 69 of file autodef_params.hpp.

Referenced by CAutodefParamsPanel::TransferDataFromWindow(), CAutodefJob::x_MakeChanges(), CAutodefToolManager::x_SelectCompatibleInputObjects(), and CAutodefToolManager::x_ValidateParams().

m_SpecifyNuclearProduct

bool SAutodefParams::m_SpecifyNuclearProduct

Definition at line 86 of file autodef_params.hpp.

Referenced by ConfigureAutodefForSeqEntry(), Init(), CAutodefFeatClausePanel::PopulateParams(), CAutodefFeatClausePanel::SetParams(), CAutodefParamsPanel::TransferDataFromWindow(), CAutodefParamsPanel::TransferDataToWindow(), and CAutodefJob::x_MakeChanges().

m_SuppressedFeatures

set<objects::CFeatListItem> SAutodefParams::m_SuppressedFeatures

Definition at line 104 of file autodef_params.hpp.

Referenced by ConfigureAutodefForSeqEntry(), Init(), CAutodefFeatClausePanel::PopulateParams(), CAutodefFeatClausePanel::SetParams(), CAutodefParamsPanel::TransferDataFromWindow(), CAutodefParamsPanel::TransferDataToWindow(), and CAutodefJob::x_MakeChanges().

m_SuppressFeatureAltSplice

bool SAutodefParams::m_SuppressFeatureAltSplice

Definition at line 90 of file autodef_params.hpp.

Referenced by ConfigureAutodefForSeqEntry(), Init(), CAutodefFeatClausePanel::PopulateParams(), CAutodefFeatClausePanel::SetParams(), CAutodefParamsPanel::TransferDataFromWindow(), CAutodefParamsPanel::TransferDataToWindow(), and CAutodefJob::x_MakeChanges().

m_SuppressLocusTags

bool SAutodefParams::m_SuppressLocusTags

Definition at line 88 of file autodef_params.hpp.

Referenced by ConfigureAutodefForSeqEntry(), Init(), CAutodefFeatClausePanel::PopulateParams(), CAutodefFeatClausePanel::SetParams(), CAutodefParamsPanel::TransferDataFromWindow(), CAutodefParamsPanel::TransferDataToWindow(), and CAutodefJob::x_MakeChanges().

m_SuppressMiscFeatSubfeatures

bool SAutodefParams::m_SuppressMiscFeatSubfeatures

Definition at line 92 of file autodef_params.hpp.

Referenced by ConfigureAutodefForSeqEntry(), Init(), CAutodefFeatClausePanel::PopulateParams(), and CAutodefFeatClausePanel::SetParams().

m_SuppressMobileElementSubfeatures

bool SAutodefParams::m_SuppressMobileElementSubfeatures

Definition at line 91 of file autodef_params.hpp.

Referenced by ConfigureAutodefForSeqEntry(), Init(), CAutodefFeatClausePanel::PopulateParams(), CAutodefFeatClausePanel::SetParams(), CAutodefParamsPanel::TransferDataFromWindow(), CAutodefParamsPanel::TransferDataToWindow(), and CAutodefJob::x_MakeChanges().

m_UseFakePromoters

bool SAutodefParams::m_UseFakePromoters

Definition at line 95 of file autodef_params.hpp.

Referenced by ConfigureAutodefForSeqEntry(), Init(), CAutodefOptFeatPanel::PopulateParams(), CAutodefOptFeatPanel::SetParams(), CAutodefParamsPanel::TransferDataFromWindow(), CAutodefParamsPanel::TransferDataToWindow(), and CAutodefJob::x_MakeChanges().

m_UseLabels

bool SAutodefParams::m_UseLabels

Definition at line 70 of file autodef_params.hpp.

Referenced by ConfigureAutodefForSeqEntry(), ConfigureAutodefParamsForBestCombo(), ConfigureAutodefParamsForID(), Init(), LoadSettings(), CAutodefOrgPanel::PopulateParams(), SaveSettings(), CAutodefOrgPanel::SetParams(), CAutodefParamsPanel::TransferDataFromWindow(), CAutodefParamsPanel::TransferDataToWindow(), and CAutodefJob::x_MakeChanges().

m_UseNcRNAComment

bool SAutodefParams::m_UseNcRNAComment

Definition at line 100 of file autodef_params.hpp.

Referenced by ConfigureAutodefForSeqEntry(), Init(), CAutodefFeatClausePanel::PopulateParams(), CAutodefFeatClausePanel::SetParams(), CAutodefParamsPanel::TransferDataFromWindow(), CAutodefParamsPanel::TransferDataToWindow(), and CAutodefJob::x_MakeChanges().

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

• include/gui/packages/pkg_sequence_edit/autodef_params.hpp
• src/gui/packages/pkg_sequence_edit/autodef_params.cpp