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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/autodef__tool__manager_8cpp_source.html below:

NCBI C++ ToolKit: src/gui/packages/pkg_sequence_edit/autodef_tool_manager.cpp Source File

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(*autodef_opts);

User-defined methods of the data storage class.

void SetExcludeCfOrgs(bool exclude)

void SetHIVCloneIsolateRule(CAutoDefOptions::EHIVCloneIsolateRule rule_num)

void SetKeepAfterSemicolon(bool keep)

void SetExcludeNrOrgs(bool exclude)

void AddOrgMod(COrgMod::ESubtype st, bool even_if_not_uniquifying=false)

void AddSubsource(CSubSource::ESubtype st, bool even_if_not_uniquifying=false)

void SetMaxModifiers(int max_mods)

void SetUseModifierLabels(bool use)

void SetExcludeSpOrgs(bool exclude)

void SetExcludeAffOrgs(bool exclude)

void SetKeepParen(bool keep)

void SetKeepCountryText(bool keep)

void SetKeepIntrons(bool keep)

void SetUseFakePromoters(bool use_fake)

void SetSpecifyNuclearProduct(bool specify_nuclear_product)

void SetKeep5UTRs(bool keep)

void SetKeepExons(bool keep)

void SetSuppressLocusTags(bool suppress_locus_tags)

void SetKeepRegulatoryFeatures(bool keep)

void SetProductFlag(CBioSource::EGenome product_flag)

void SetSuppressFeatureAltSplice(bool suppress_alt_splice)

void AddSources(CSeq_entry_Handle se)

CRef< CUser_object > GetOptionsObject() const

void SetGeneClusterOppStrand(bool gene_opp_strand)

void SetKeep3UTRs(bool keep)

void SetNuclearCopyFlag(CBioSource::EGenome product_flag)

void SetFeatureListType(CAutoDefOptions::EFeatureListType feature_list_type)

string GetOneDefLine(CAutoDefModifierCombo *mod_combo, const CBioseq_Handle &bh, CRef< feature::CFeatTree > featTree=null)

CRef< CAutoDefModifierCombo > FindBestModifierCombo()

void SetMiscFeatRule(CAutoDefOptions::EMiscFeatRule misc_feat_rule)

void SetUseNcRNAComment(bool use_comment)

void SuppressFeature(const objects::CFeatListItem &feat)

void SetAltSpliceFlag(bool alt_splice_flag)

void SuppressMobileElementAndInsertionSequenceSubfeatures(bool suppress)

CAutoDefModifierCombo * GetEmptyCombo()

bool Create(wxWindow *parent, wxWindowID id=10025, const wxString &caption=_("Autodef Params Panel"), const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL)

Creation.

void SetParams(SAutodefParams *params, TConstScopedObjects *objects)

virtual void SetRegistryPath(const string &path)

CAlgoToolManagerParamsPanel.

virtual void LoadSettings()

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

CEditAppJob - a base class for Jobs modifying existing data in projects.

CDataLoadingAppTask - a task that executes CDataLoadingAppJob.

static void Convert(objects::CScope &scope, const CObject &obj, const CTypeInfo *info, TObjList &objs, TFlags flags=eDefault)

Convert an object of potentially unknown type to a set of objects of known type.

ITypeConverter::TObjList TObjList

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

@ eObjectType_AutodefOptions

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

@ fConvert_NoExpensive

do not perform any expensive tests tests (such as fetching from the network)

vector< SObject > TObjList

set< objects::CFeatListItem > m_SuppressedFeatures

bool m_SuppressMobileElementSubfeatures

unsigned int m_MiscFeatRule

objects::CAutoDefSourceDescription::TAvailableModifierVector m_ModifierList

bool m_LeaveParenthetical

bool m_KeepRegulatoryFeatures

bool m_KeepAfterSemicolon

bool m_SuppressFeatureAltSplice

unsigned int m_ProductFlag

unsigned int m_NuclearCopyFlag

unsigned int m_FeatureListType

bool m_IncludeCountryText

bool m_SpecifyNuclearProduct

bool m_GeneClusterOppStrand

TConstScopedObjects m_SeqEntries

#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.

CIRef< T > GetServiceByType()

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

virtual string GetExtensionIdentifier() const

returns the unique human-readable identifier for the extension the id should use lowercase letters se...

virtual bool x_CreateParamsPanelIfNeeded()

returns / creates Parameters panel, override in derived classes see cpp file for example

TConstScopedObjects m_SeqEntries

virtual bool x_ValidateParams()

validates user input in Parameters panel, report errors if any

virtual IRegSettings * x_GetParamsAsRegSetting()

return a pointer to Parameters object as IRegSettings interface

virtual void x_CreateProjectPanelIfNeeded()

returns / creates Project panel

CEditAppJob * x_CreateEditJob()

virtual string GetExtensionLabel() const

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

virtual void InitUI()

override this function in a derived class and initialize extra members

virtual void CleanUI()

override this function in a derived class and clean extra members

CAutodefToolManager()

CAutodefToolManager.

virtual IAppTask * GetTask()

Once parameters are gathered and validated this function is called to produce the final Task object t...

virtual CDataLoadingAppJob * x_CreateLoadingJob()

factory method for creating the job that executes the tool algorithm override in derived classes

virtual void x_SelectCompatibleInputObjects()

select only Seq-entries

virtual CAlgoToolManagerParamsPanel * x_GetParamsPanel()

returns a pointer to the parameters panel, override in derived classes

virtual void x_MakeChanges()

override this function in derived classes, populate m_TextResult

CAutodefJob(CProjectService *service, const SAutodefParams &params)

CAutodefJob.

CAutodefParamsPanel * m_ParamsPanel

string m_Descr

mutex to sync our internals

void NcbiErrorBox(const string &message, const string &title="Error")

specialized Message Box function for reporting critical errors

virtual void SetLogEvent(const string &log_event)

virtual const string & GetLabel() const

vector< SConstScopedObject > TConstScopedObjects

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Set object to copy of another one.

CSeq_entry_Handle GetSeq_entryHandle(CDataLoader *loader, const TBlobId &blob_id, EMissing action=eMissing_Default)

Get Seq-entry handle by its blob-id, with possible loading.

CBioseq_EditHandle GetEditHandle(void) const

Get 'edit' version of handle.

bool AddSeqdesc(CSeqdesc &d) const

CRef< CSeqdesc > RemoveSeqdesc(const CSeqdesc &d) const

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

TObjectType * Release(void)

Release a reference to the object and return a pointer to the object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

EGenome

biological context

TTitle & SetTitle(void)

Select the variant.

TUser & SetUser(void)

Select the variant.

@ e_User

user defined object

@ e_Title

a title for this sequence

struct SObject provides an interface for defining what is returned from object conversion.

const CObject * GetObjectPtr(void) const

named function

static wxAcceleratorEntry entries[3]

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