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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/common__commands_8cpp_source.html below:

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

wxWindow* main_window =

;

wxEmptyString;

doc =

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(ws->GetProjectFromScope(scope));

wxEmptyString;

wxWindow* editorWindow = editor->CreateWindow(edit_dlg);

edit_dlg->Show(

);

objects::CBioseq& bioseq,

wxString& workDir)

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wxWindow* editorWindow = editor->CreateWindow(edit_dlg);

editorWindow->TransferDataToWindow();

edit_dlg->Show(

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report->SetTitle(

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worker.

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cmd_proc->

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User-defined methods of the data storage class.

@ eErr_GENERIC_MissingPubRequirement

@ eErr_SEQ_INST_HistoryGiCollision

@ eErr_SEQ_DESCR_InconsistentProteinTitle

@ eErr_SEQ_DESCR_NoMolInfoFound

@ eErr_SEQ_PKG_OrphanedProtein

@ eErr_SEQ_FEAT_GenCodeMismatch

@ eErr_SEQ_INST_HighNpercent3Prime

@ eErr_SEQ_DESCR_NoPubFound

@ eErr_SEQ_INST_MolNuclAcid

@ eErr_SEQ_DESCR_TitleNotAppropriateForSet

@ eErr_SEQ_DESCR_MultipleStrucComms

@ eErr_SEQ_INST_MitoMetazoanTooLong

@ eErr_SEQ_DESCR_NoSourceDescriptor

@ eErr_SEQ_INST_HistAssemblyMissing

@ eErr_SEQ_INST_InternalNsInSeqRaw

@ eErr_SEQ_INST_TerminalNs

@ eErr_SEQ_INST_HighNpercent5Prime

CIRef< IEditObject > CreateEditorForObject(CConstRef< CObject > obj, objects::CSeq_entry_Handle seh, bool create)

CRef< CCmdComposite > GetCommand()

static CRef< CCmdComposite > GetCreateSeqHistFromTpaCommand(CSeq_entry_Handle tse, string &msg, double word_size, double expect_value)

CRef< CCmdComposite > GetCommand()

void SetEditorWindow(wxWindow *editorWindow)

void SetEditor(CIRef< IEditObject > editor)

virtual void SetWorkDir(const wxString &workDir)

virtual void SetUndoManager(ICommandProccessor *cmdProccessor)

wxString GetWorkDir() const

CUndoManager & GetUndoManager()

void SetText(const wxString &text)

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

void apply(objects::CSeq_entry_Handle tse, ICommandProccessor *cmdProcessor, string title)

bool apply(CSeq_entry_Handle tse, ICommandProccessor *cmdProcessor, string title)

static CRef< CCmdComposite > OrphanedProteins(objects::CSeq_entry_Handle seh)

CRef< CCmdComposite > GetCommand()

void ChooseSequence(CBioseq_Handle bsh)

@ eRetranslateCDSIgnoreStopExceptEnd

static CRef< CCmdComposite > GetCommand(objects::CSeq_entry_Handle seh, string title, ERetranslateMethod method, string &error)

Base class for all serializable objects.

bool apply(CSeq_entry_Handle tse, ICommandProccessor *cmdProcessor, string title, wxWindow *parent, const wxString &workDir, const CSequenceAmbigTrimmer::TTrimRuleVec &trim_rules=CSequenceAmbigTrimmer::GetDefaultTrimRules())

CWorkbench - default implementation of IWorkbench.

Undo/Redo interface for editing operations.

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

IWorkbench is the central interface in the application framework.

void LaunchDefaultEditor(CSeq_entry_Handle seh, IWorkbench *wb, const CSerialObject &obj)

bool IsEditable(int err_code, const CSerialObject &obj, CSeq_entry_Handle seh)

wxString GetWorkDirFromWorkbench(IWorkbench *wb, CScope &scope)

ICommandProccessor * CommandProcessorFromWorkbench(IWorkbench *wb, CScope &scope)

static std::array< handler, eErr_MAX > valerr_to_handler

void(*)(CSeq_entry_Handle seh, IWorkbench *wb, const CSerialObject &obj) handler

void RemoveSequence(CSeq_entry_Handle seh, IWorkbench *wb)

void TrimTerminalNRichRegions(CSeq_entry_Handle seh, IWorkbench *wb)

wxWindow * MainWindowFromWorkbench(IWorkbench *wb)

void LaunchBioseqEditor(CSeq_entry_Handle seh, IWorkbench *wb)

void OfferToDeleteDescriptor(const string &label, CSeq_entry_Handle seh, const CSeqdesc &seqDesc, ICommandProccessor *cmdProcessor)

void LaunchMolInfoEditor(CSeq_entry_Handle seh, IWorkbench *wb)

void LaunchAlignmentAssistant(CSeq_entry_Handle seh, IWorkbench *wb, const CSeq_align *align)

void LaunchSrcEditor(CSeq_entry_Handle seh, IWorkbench *wb)

void LaunchEditor(int err_code, const CSerialObject &obj, CSeq_entry_Handle seh, IWorkbench *wb)

void LaunchDescEditorForSeq(CRef< CSeqdesc > seqdesc, const objects::CBioseq &bioseq, ICommandProccessor *cmdProcessor, CScope &scope, const wxString &workDir)

#define REGISTER_HANDLER(code)

void LaunchDescEditor(CRef< CSeqdesc > seqdesc, CSeq_entry_Handle seh, ICommandProccessor *cmdProcessor, const wxString &workDir)

static void cleanup(void)

CIRef< T > GetServiceByType()

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

virtual wxFrame * GetMainWindow()

returns a pointer to the main application frame window

vector< STrimRule > TTrimRuleVec

Multiple STrimRules are allowed, which are applied from smallest bases_to_check to largest bases_to_c...

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

CSeq_entry_Handle GetSeq_entry_Handle(void) const

Get parent Seq-entry handle.

CSeq_entry_Handle GetTopLevelEntry(void) const

Get top level Seq-entry handle.

CScope & GetScope(void) const

Get scope this handle belongs to.

CRef< CSeq_loc > GetRangeSeq_loc(TSeqPos start, TSeqPos stop, ENa_strand strand=eNa_strand_unknown) const

Return CSeq_loc referencing the given range and strand on the bioseq If start == 0,...

CConstRef< C > ConstRef(const C *object)

Template function for conversion of const object pointer to CConstRef.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

static const char label[]

TSub & SetSub(void)

Select the variant.

void SetPub(TPub &value)

Assign a value to Pub data member.

TPub & SetPub(void)

Select the variant.

TSource & SetSource(void)

Select the variant.

TMolinfo & SetMolinfo(void)

Select the variant.

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

For example, if bases_to_check is 10 and max_bases_allowed_to_be_ambig is 5, then on each iteration w...

CRef< CCmdComposite > CleanupCommand(objects::CSeq_entry_Handle orig_seh, bool extended, bool do_tax)

wxString ToWxString(const string &s)

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