NCBI C++ ToolKit
Macros | Typedefs | Functions | Variables
common_commands.cpp File Reference
#include <ncbi_pch.hpp>
#include <objects/valerr/ValidErrItem.hpp>
#include <gui/core/project_service.hpp>
#include <gui/core/selection_service_impl.hpp>
#include <gui/objects/GBWorkspace.hpp>
#include <gui/widgets/edit/init.hpp>
#include <gui/widgets/edit/edit_object.hpp>
#include <gui/widgets/edit/edit_object_seq_feat.hpp>
#include <gui/widgets/edit/edit_object_seq_desc.hpp>
#include <gui/packages/pkg_sequence_edit/common_commands.hpp>
#include <gui/packages/pkg_sequence_edit/create_seq_hist_for_tpa.hpp>
#include <gui/packages/pkg_sequence_edit/edit_history.hpp>
#include <gui/packages/pkg_sequence_edit/remove_sequences.hpp>
#include <gui/packages/pkg_sequence_edit/trim_n.hpp>
#include <gui/packages/pkg_sequence_edit/apply_gcode.hpp>
#include <gui/packages/pkg_sequence_edit/remove_structured_comment.hpp>
#include <gui/objutils/cmd_del_desc.hpp>
#include <gui/widgets/edit/generic_report_dlg.hpp>
#include <gui/widgets/edit/bioseq_editor.hpp>
#include <gui/widgets/edit/edit_obj_view_dlg.hpp>
#include <gui/widgets/edit/alignment_assistant.hpp>
#include <gui/widgets/edit/edit_sequence.hpp>
#include <gui/objutils/util_cmds.hpp>
#include <gui/packages/pkg_sequence_edit/retranslate_cds.hpp>
#include <gui/packages/pkg_sequence_edit/rem_prot_titles.hpp>
#include <gui/packages/pkg_sequence_edit/raw_seq_to_delta_by_n.hpp>
#include <gui/widgets/wx/wx_utils.hpp>
#include <array>
#include "wx/wxprec.h"
#include "wx/wx.h"
#include "wx/imaglist.h"
#include <wx/display.h>
#include <wx/filename.h>
+ Include dependency graph for common_commands.cpp:

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Macros

#define REGISTER_HANDLER(code)
 

Typedefs

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

Functions

ICommandProccessor * CommandProcessorFromWorkbench (IWorkbench *wb, CScope &scope)
 
wxWindow * MainWindowFromWorkbench (IWorkbench *wb)
 
wxString GetWorkDirFromWorkbench (IWorkbench *wb, CScope &scope)
 
void LaunchDescEditor (CRef< CSeqdesc > seqdesc, CSeq_entry_Handle seh, ICommandProccessor *cmdProcessor, const wxString &workDir)
 
void LaunchDescEditorForSeq (CRef< CSeqdesc > seqdesc, const objects::CBioseq &bioseq, ICommandProccessor *cmdProcessor, CScope &scope, const wxString &workDir)
 
void LaunchMolInfoEditor (CSeq_entry_Handle seh, IWorkbench *wb)
 
void LaunchSrcEditor (CSeq_entry_Handle seh, IWorkbench *wb)
 
void RemoveSequence (CSeq_entry_Handle seh, IWorkbench *wb)
 
void TrimTerminalNRichRegions (CSeq_entry_Handle seh, IWorkbench *wb)
 
void OfferToDeleteDescriptor (const string &label, CSeq_entry_Handle seh, const CSeqdesc &seqDesc, ICommandProccessor *cmdProcessor)
 
void LaunchAlignmentAssistant (CSeq_entry_Handle seh, IWorkbench *wb, const CSeq_align *align)
 
void LaunchBioseqEditor (CSeq_entry_Handle seh, IWorkbench *wb)
 
void LaunchDefaultEditor (CSeq_entry_Handle seh, IWorkbench *wb, const CSerialObject &obj)
 
static void handler_eErr_SEQ_DESCR_NoPubFound (CSeq_entry_Handle seh, IWorkbench *wb, const CSerialObject &obj)
 
static void handler_eErr_GENERIC_MissingPubRequirement (CSeq_entry_Handle seh, IWorkbench *wb, const CSerialObject &obj)
 
static void handler_eErr_SEQ_DESCR_NoSourceDescriptor (CSeq_entry_Handle seh, IWorkbench *wb, const CSerialObject &obj)
 
static void handler_eErr_SEQ_INST_MitoMetazoanTooLong (CSeq_entry_Handle seh, IWorkbench *wb, const CSerialObject &obj)
 
static void handler_eErr_SEQ_DESCR_NoMolInfoFound (CSeq_entry_Handle seh, IWorkbench *wb, const CSerialObject &obj)
 
static void handler_eErr_SEQ_INST_MolNuclAcid (CSeq_entry_Handle seh, IWorkbench *wb, const CSerialObject &obj)
 
static void handler_eErr_SEQ_INST_HistAssemblyMissing (CSeq_entry_Handle seh, IWorkbench *wb, const CSerialObject &obj)
 
static void handler_eErr_SEQ_INST_HistoryGiCollision (CSeq_entry_Handle seh, IWorkbench *wb, const CSerialObject &obj)
 
static void handler_eErr_SEQ_INST_ShortSeq (CSeq_entry_Handle seh, IWorkbench *wb, const CSerialObject &obj)
 
static void handler_eErr_SEQ_PKG_OrphanedProtein (CSeq_entry_Handle seh, IWorkbench *wb, const CSerialObject &obj)
 
static void handler_eErr_SEQ_INST_TerminalNs (CSeq_entry_Handle seh, IWorkbench *wb, const CSerialObject &obj)
 
static void handler_eErr_SEQ_INST_HighNpercent5Prime (CSeq_entry_Handle seh, IWorkbench *wb, const CSerialObject &obj)
 
static void handler_eErr_SEQ_INST_HighNpercent3Prime (CSeq_entry_Handle seh, IWorkbench *wb, const CSerialObject &obj)
 
static void handler_eErr_SEQ_DESCR_TitleNotAppropriateForSet (CSeq_entry_Handle seh, IWorkbench *wb, const CSerialObject &obj)
 
static void handler_eErr_SEQ_DESCR_MultipleStrucComms (CSeq_entry_Handle seh, IWorkbench *wb, const CSerialObject &obj)
 
static void handler_eErr_SEQ_FEAT_GenCodeMismatch (CSeq_entry_Handle seh, IWorkbench *wb, const CSerialObject &obj)
 
static void handler_eErr_SEQ_DESCR_InconsistentProteinTitle (CSeq_entry_Handle seh, IWorkbench *wb, const CSerialObject &obj)
 
static void handler_eErr_SEQ_INST_AllNs (CSeq_entry_Handle seh, IWorkbench *wb, const CSerialObject &obj)
 
static void handler_eErr_SEQ_INST_InternalNsInSeqRaw (CSeq_entry_Handle seh, IWorkbench *wb, const CSerialObject &obj)
 
void LaunchEditor (int err_code, const CSerialObject &obj, CSeq_entry_Handle seh, IWorkbench *wb)
 
bool IsEditable (int err_code, const CSerialObject &obj, CSeq_entry_Handle seh)
 

Variables

static std::array< handler, eErr_MAX > valerr_to_handler {}
 
static int dummy_eErr_SEQ_DESCR_NoPubFound = (valerr_to_handler[ eErr_SEQ_DESCR_NoPubFound ] = handler_eErr_SEQ_DESCR_NoPubFound , 0)
 
static int dummy_eErr_GENERIC_MissingPubRequirement = (valerr_to_handler[ eErr_GENERIC_MissingPubRequirement ] = handler_eErr_GENERIC_MissingPubRequirement , 0)
 
static int dummy_eErr_SEQ_DESCR_NoSourceDescriptor = (valerr_to_handler[ eErr_SEQ_DESCR_NoSourceDescriptor ] = handler_eErr_SEQ_DESCR_NoSourceDescriptor , 0)
 
static int dummy_eErr_SEQ_INST_MitoMetazoanTooLong = (valerr_to_handler[ eErr_SEQ_INST_MitoMetazoanTooLong ] = handler_eErr_SEQ_INST_MitoMetazoanTooLong , 0)
 
static int dummy_eErr_SEQ_DESCR_NoMolInfoFound = (valerr_to_handler[ eErr_SEQ_DESCR_NoMolInfoFound ] = handler_eErr_SEQ_DESCR_NoMolInfoFound , 0)
 
static int dummy_eErr_SEQ_INST_MolNuclAcid = (valerr_to_handler[ eErr_SEQ_INST_MolNuclAcid ] = handler_eErr_SEQ_INST_MolNuclAcid , 0)
 
static int dummy_eErr_SEQ_INST_HistAssemblyMissing = (valerr_to_handler[ eErr_SEQ_INST_HistAssemblyMissing ] = handler_eErr_SEQ_INST_HistAssemblyMissing , 0)
 
static int dummy_eErr_SEQ_INST_HistoryGiCollision = (valerr_to_handler[ eErr_SEQ_INST_HistoryGiCollision ] = handler_eErr_SEQ_INST_HistoryGiCollision , 0)
 
static int dummy_eErr_SEQ_INST_ShortSeq = (valerr_to_handler[ eErr_SEQ_INST_ShortSeq ] = handler_eErr_SEQ_INST_ShortSeq , 0)
 
static int dummy_eErr_SEQ_PKG_OrphanedProtein = (valerr_to_handler[ eErr_SEQ_PKG_OrphanedProtein ] = handler_eErr_SEQ_PKG_OrphanedProtein , 0)
 
static int dummy_eErr_SEQ_INST_TerminalNs = (valerr_to_handler[ eErr_SEQ_INST_TerminalNs ] = handler_eErr_SEQ_INST_TerminalNs , 0)
 
static int dummy_eErr_SEQ_INST_HighNpercent5Prime = (valerr_to_handler[ eErr_SEQ_INST_HighNpercent5Prime ] = handler_eErr_SEQ_INST_HighNpercent5Prime , 0)
 
static int dummy_eErr_SEQ_INST_HighNpercent3Prime = (valerr_to_handler[ eErr_SEQ_INST_HighNpercent3Prime ] = handler_eErr_SEQ_INST_HighNpercent3Prime , 0)
 
static int dummy_eErr_SEQ_DESCR_TitleNotAppropriateForSet = (valerr_to_handler[ eErr_SEQ_DESCR_TitleNotAppropriateForSet ] = handler_eErr_SEQ_DESCR_TitleNotAppropriateForSet , 0)
 
static int dummy_eErr_SEQ_DESCR_MultipleStrucComms = (valerr_to_handler[ eErr_SEQ_DESCR_MultipleStrucComms ] = handler_eErr_SEQ_DESCR_MultipleStrucComms , 0)
 
static int dummy_eErr_SEQ_FEAT_GenCodeMismatch = (valerr_to_handler[ eErr_SEQ_FEAT_GenCodeMismatch ] = handler_eErr_SEQ_FEAT_GenCodeMismatch , 0)
 
static int dummy_eErr_SEQ_DESCR_InconsistentProteinTitle = (valerr_to_handler[ eErr_SEQ_DESCR_InconsistentProteinTitle ] = handler_eErr_SEQ_DESCR_InconsistentProteinTitle , 0)
 
static int dummy_eErr_SEQ_INST_AllNs = (valerr_to_handler[ eErr_SEQ_INST_AllNs ] = handler_eErr_SEQ_INST_AllNs , 0)
 
static int dummy_eErr_SEQ_INST_InternalNsInSeqRaw = (valerr_to_handler[ eErr_SEQ_INST_InternalNsInSeqRaw ] = handler_eErr_SEQ_INST_InternalNsInSeqRaw , 0)
 

Macro Definition Documentation

◆ REGISTER_HANDLER

#define REGISTER_HANDLER (   code)
Value:
static void handler_##code (CSeq_entry_Handle seh, IWorkbench* wb, const CSerialObject& obj); \
static int dummy_##code = (valerr_to_handler[code] = handler_##code, 0); \
void handler_##code (CSeq_entry_Handle seh, IWorkbench* wb, const CSerialObject& obj) \
CSeq_entry_Handle
CSeq_entry_Handle –.
Definition: seq_entry_handle.hpp:107
CSerialObject
Base class for all serializable objects.
Definition: serialbase.hpp:150
IWorkbench
IWorkbench is the central interface in the application framework.
Definition: workbench.hpp:113
valerr_to_handler
static std::array< handler, eErr_MAX > valerr_to_handler
Definition: common_commands.cpp:296
code
Definition: inftrees.h:24

Definition at line 298 of file common_commands.cpp.

Typedef Documentation

◆ handler

static void handler

Definition at line 295 of file common_commands.cpp.

Function Documentation

◆ CommandProcessorFromWorkbench()

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

Definition at line 86 of file common_commands.cpp.

References IServiceLocator::GetServiceByType(), CGBDocument::GetUndoManager(), and NULL.

Referenced by handler_eErr_GENERIC_MissingPubRequirement(), handler_eErr_SEQ_DESCR_InconsistentProteinTitle(), handler_eErr_SEQ_DESCR_MultipleStrucComms(), handler_eErr_SEQ_DESCR_NoPubFound(), handler_eErr_SEQ_DESCR_TitleNotAppropriateForSet(), handler_eErr_SEQ_FEAT_GenCodeMismatch(), handler_eErr_SEQ_INST_HistAssemblyMissing(), handler_eErr_SEQ_INST_HistoryGiCollision(), handler_eErr_SEQ_INST_InternalNsInSeqRaw(), handler_eErr_SEQ_INST_TerminalNs(), handler_eErr_SEQ_PKG_OrphanedProtein(), LaunchAlignmentAssistant(), LaunchBioseqEditor(), LaunchDefaultEditor(), LaunchMolInfoEditor(), LaunchSrcEditor(), RemoveSequence(), and TrimTerminalNRichRegions().

◆ GetWorkDirFromWorkbench()

wxString GetWorkDirFromWorkbench ( IWorkbench *  wb,
CScope &  scope 
)

Definition at line 118 of file common_commands.cpp.

References _ASSERT, IServiceLocator::GetServiceByType(), and CGBDocument::GetWorkDir().

Referenced by handler_eErr_GENERIC_MissingPubRequirement(), handler_eErr_SEQ_DESCR_NoPubFound(), handler_eErr_SEQ_INST_TerminalNs(), LaunchMolInfoEditor(), LaunchSrcEditor(), and TrimTerminalNRichRegions().

◆ handler_eErr_GENERIC_MissingPubRequirement()

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

Definition at line 312 of file common_commands.cpp.

References CommandProcessorFromWorkbench(), CSeq_entry_Handle::GetScope(), GetWorkDirFromWorkbench(), LaunchDescEditor(), CPubdesc_Base::SetPub(), CSeqdesc_Base::SetPub(), and CPub_Base::SetSub().

◆ handler_eErr_SEQ_DESCR_InconsistentProteinTitle()

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

Definition at line 477 of file common_commands.cpp.

References CRemProtTitles::apply(), CommandProcessorFromWorkbench(), CSeq_entry_Handle::GetScope(), CSeq_entry_Handle::GetTopLevelEntry(), and wxT.

◆ handler_eErr_SEQ_DESCR_MultipleStrucComms()

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

Definition at line 444 of file common_commands.cpp.

References CRemoveStructuredComment::apply(), CommandProcessorFromWorkbench(), CSeq_entry_Handle::GetScope(), CSeq_entry_Handle::GetTopLevelEntry(), and wxT.

◆ handler_eErr_SEQ_DESCR_NoMolInfoFound()

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

Definition at line 334 of file common_commands.cpp.

References LaunchMolInfoEditor().

◆ handler_eErr_SEQ_DESCR_NoPubFound()

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

Definition at line 303 of file common_commands.cpp.

References CommandProcessorFromWorkbench(), CSeq_entry_Handle::GetScope(), GetWorkDirFromWorkbench(), LaunchDescEditor(), and CSeqdesc_Base::SetPub().

◆ handler_eErr_SEQ_DESCR_NoSourceDescriptor()

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

Definition at line 324 of file common_commands.cpp.

References LaunchSrcEditor().

◆ handler_eErr_SEQ_DESCR_TitleNotAppropriateForSet()

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

Definition at line 437 of file common_commands.cpp.

References CommandProcessorFromWorkbench(), CSeq_entry_Handle::GetScope(), and OfferToDeleteDescriptor().

◆ handler_eErr_SEQ_FEAT_GenCodeMismatch()

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

Definition at line 454 of file common_commands.cpp.

References cleanup(), CleanupCommand(), cmd, CommandProcessorFromWorkbench(), CRetranslateCDS::eRetranslateCDSIgnoreStopExceptEnd, ICommandProccessor::Execute(), CApplyGCode::GetCommand(), CRetranslateCDS::GetCommand(), CSeq_entry_Handle::GetScope(), CSeq_entry_Handle::GetTopLevelEntry(), and MainWindowFromWorkbench().

◆ handler_eErr_SEQ_INST_AllNs()

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

Definition at line 487 of file common_commands.cpp.

References RemoveSequence().

◆ handler_eErr_SEQ_INST_HighNpercent3Prime()

void handler_eErr_SEQ_INST_HighNpercent3Prime ( CSeq_entry_Handle  seh,
IWorkbench *  wb,
const CSerialObject &  obj 
)
static

Definition at line 432 of file common_commands.cpp.

References TrimTerminalNRichRegions().

◆ handler_eErr_SEQ_INST_HighNpercent5Prime()

void handler_eErr_SEQ_INST_HighNpercent5Prime ( CSeq_entry_Handle  seh,
IWorkbench *  wb,
const CSerialObject &  obj 
)
static

Definition at line 427 of file common_commands.cpp.

References TrimTerminalNRichRegions().

◆ handler_eErr_SEQ_INST_HistAssemblyMissing()

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

Definition at line 344 of file common_commands.cpp.

References cmd, CommandProcessorFromWorkbench(), ICommandProccessor::Execute(), CCreateSeqHistForTpa::GetCreateSeqHistFromTpaCommand(), CSeq_entry_Handle::GetScope(), CSeq_entry_Handle::GetTopLevelEntry(), MainWindowFromWorkbench(), msg(), CGenericReportDlg::SetText(), and wxT.

◆ handler_eErr_SEQ_INST_HistoryGiCollision()

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

Definition at line 368 of file common_commands.cpp.

References cmd, CommandProcessorFromWorkbench(), ICommandProccessor::Execute(), CEditHistory::GetCommand(), CSeq_entry_Handle::GetScope(), CSeq_entry_Handle::GetSeq(), CSeq_entry_Handle::IsSeq(), and MainWindowFromWorkbench().

◆ handler_eErr_SEQ_INST_InternalNsInSeqRaw()

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

Definition at line 492 of file common_commands.cpp.

References CRawSeqToDeltaByN::apply(), CommandProcessorFromWorkbench(), CSeq_entry_Handle::GetScope(), CSeq_entry_Handle::GetTopLevelEntry(), CSeq_entry_Handle::IsSeq(), and MainWindowFromWorkbench().

◆ handler_eErr_SEQ_INST_MitoMetazoanTooLong()

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

Definition at line 329 of file common_commands.cpp.

References LaunchSrcEditor().

◆ handler_eErr_SEQ_INST_MolNuclAcid()

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

Definition at line 339 of file common_commands.cpp.

References LaunchMolInfoEditor().

◆ handler_eErr_SEQ_INST_ShortSeq()

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

Definition at line 391 of file common_commands.cpp.

References RemoveSequence().

◆ handler_eErr_SEQ_INST_TerminalNs()

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

Definition at line 410 of file common_commands.cpp.

References CTrimN::apply(), CommandProcessorFromWorkbench(), CSeq_entry_Handle::GetScope(), CSeq_entry_Handle::GetTopLevelEntry(), GetWorkDirFromWorkbench(), MainWindowFromWorkbench(), and wxT.

◆ handler_eErr_SEQ_PKG_OrphanedProtein()

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

Definition at line 396 of file common_commands.cpp.

References cmd, CommandProcessorFromWorkbench(), ICommandProccessor::Execute(), CSeq_entry_Handle::GetScope(), CSeq_entry_Handle::GetTopLevelEntry(), CRemoveProteins::OrphanedProteins(), and wxT.

◆ IsEditable()

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

Definition at line 517 of file common_commands.cpp.

References ConstRef(), CreateEditorForObject(), and valerr_to_handler.

◆ LaunchAlignmentAssistant()

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

Definition at line 225 of file common_commands.cpp.

References CommandProcessorFromWorkbench(), ConstRef(), CSeq_entry_Handle::GetScope(), MainWindowFromWorkbench(), NULL, and wxT.

Referenced by LaunchDefaultEditor().

◆ LaunchBioseqEditor()

void LaunchBioseqEditor ( CSeq_entry_Handle  seh,
IWorkbench *  wb 
)

Definition at line 242 of file common_commands.cpp.

References CommandProcessorFromWorkbench(), CRef< C, Locker >::GetPointer(), CBioseq_Handle::GetRangeSeq_loc(), CSeq_entry_Handle::GetScope(), CSeq_entry_Handle::GetSeq(), CSeq_entry_Handle::IsSeq(), NULL, and wxT.

Referenced by LaunchDefaultEditor().

◆ LaunchDefaultEditor()

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

Definition at line 264 of file common_commands.cpp.

References CommandProcessorFromWorkbench(), ConstRef(), CreateEditorForObject(), CSeq_entry_Handle::GetScope(), LaunchAlignmentAssistant(), LaunchBioseqEditor(), MainWindowFromWorkbench(), CEditObjViewDlg::SetEditor(), CEditObjViewDlg::SetEditorWindow(), and CEditObjViewDlg::SetUndoManager().

Referenced by LaunchEditor().

◆ LaunchDescEditor()

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

Definition at line 139 of file common_commands.cpp.

References CSeq_entry_Handle::GetScope(), NULL, CEditObjViewDlg::SetEditor(), CEditObjViewDlg::SetEditorWindow(), CEditObjViewDlg::SetUndoManager(), and CEditObjViewDlg::SetWorkDir().

Referenced by handler_eErr_GENERIC_MissingPubRequirement(), handler_eErr_SEQ_DESCR_NoPubFound(), LaunchDescEditorForSeq(), LaunchMolInfoEditor(), and LaunchSrcEditor().

◆ LaunchDescEditorForSeq()

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

Definition at line 152 of file common_commands.cpp.

References CScope::GetBioseqHandle(), CBioseq_Handle::GetSeq_entry_Handle(), and LaunchDescEditor().

◆ LaunchEditor()

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

Definition at line 507 of file common_commands.cpp.

References LaunchDefaultEditor(), and valerr_to_handler.

◆ LaunchMolInfoEditor()

void LaunchMolInfoEditor ( CSeq_entry_Handle  seh,
IWorkbench *  wb 
)

Definition at line 165 of file common_commands.cpp.

References CommandProcessorFromWorkbench(), CSeq_entry_Handle::GetScope(), GetWorkDirFromWorkbench(), LaunchDescEditor(), and CSeqdesc_Base::SetMolinfo().

Referenced by handler_eErr_SEQ_DESCR_NoMolInfoFound(), and handler_eErr_SEQ_INST_MolNuclAcid().

◆ LaunchSrcEditor()

void LaunchSrcEditor ( CSeq_entry_Handle  seh,
IWorkbench *  wb 
)

Definition at line 175 of file common_commands.cpp.

References CommandProcessorFromWorkbench(), CSeq_entry_Handle::GetScope(), GetWorkDirFromWorkbench(), LaunchDescEditor(), and CSeqdesc_Base::SetSource().

Referenced by handler_eErr_SEQ_DESCR_NoSourceDescriptor(), and handler_eErr_SEQ_INST_MitoMetazoanTooLong().

◆ MainWindowFromWorkbench()

wxWindow* MainWindowFromWorkbench ( IWorkbench *  wb)

Definition at line 108 of file common_commands.cpp.

References CWorkbench::GetMainWindow(), and NULL.

Referenced by handler_eErr_SEQ_FEAT_GenCodeMismatch(), handler_eErr_SEQ_INST_HistAssemblyMissing(), handler_eErr_SEQ_INST_HistoryGiCollision(), handler_eErr_SEQ_INST_InternalNsInSeqRaw(), handler_eErr_SEQ_INST_TerminalNs(), LaunchAlignmentAssistant(), LaunchDefaultEditor(), RemoveSequence(), and TrimTerminalNRichRegions().

◆ OfferToDeleteDescriptor()

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

Definition at line 217 of file common_commands.cpp.

References cmd, ICommandProccessor::Execute(), label, ToWxString(), and wxT.

Referenced by handler_eErr_SEQ_DESCR_TitleNotAppropriateForSet().

◆ RemoveSequence()

void RemoveSequence ( CSeq_entry_Handle  seh,
IWorkbench *  wb 
)

Definition at line 184 of file common_commands.cpp.

References CRemoveSequencesDlg::ChooseSequence(), cmd, CommandProcessorFromWorkbench(), ICommandProccessor::Execute(), CRemoveSequencesDlg::GetCommand(), CSeq_entry_Handle::GetScope(), CSeq_entry_Handle::GetSeq(), CSeq_entry_Handle::GetTopLevelEntry(), CSeq_entry_Handle::IsSeq(), and MainWindowFromWorkbench().

Referenced by handler_eErr_SEQ_INST_AllNs(), and handler_eErr_SEQ_INST_ShortSeq().

◆ TrimTerminalNRichRegions()

void TrimTerminalNRichRegions ( CSeq_entry_Handle  seh,
IWorkbench *  wb 
)

Definition at line 202 of file common_commands.cpp.

References CTrimN::apply(), CommandProcessorFromWorkbench(), CSeq_entry_Handle::GetScope(), CSeq_entry_Handle::GetTopLevelEntry(), GetWorkDirFromWorkbench(), MainWindowFromWorkbench(), and wxT.

Referenced by handler_eErr_SEQ_INST_HighNpercent3Prime(), and handler_eErr_SEQ_INST_HighNpercent5Prime().

Variable Documentation

◆ dummy_eErr_GENERIC_MissingPubRequirement

int dummy_eErr_GENERIC_MissingPubRequirement = (valerr_to_handler[ eErr_GENERIC_MissingPubRequirement ] = handler_eErr_GENERIC_MissingPubRequirement , 0)
static

Definition at line 312 of file common_commands.cpp.

◆ dummy_eErr_SEQ_DESCR_InconsistentProteinTitle

int dummy_eErr_SEQ_DESCR_InconsistentProteinTitle = (valerr_to_handler[ eErr_SEQ_DESCR_InconsistentProteinTitle ] = handler_eErr_SEQ_DESCR_InconsistentProteinTitle , 0)
static

Definition at line 477 of file common_commands.cpp.

◆ dummy_eErr_SEQ_DESCR_MultipleStrucComms

int dummy_eErr_SEQ_DESCR_MultipleStrucComms = (valerr_to_handler[ eErr_SEQ_DESCR_MultipleStrucComms ] = handler_eErr_SEQ_DESCR_MultipleStrucComms , 0)
static

Definition at line 444 of file common_commands.cpp.

◆ dummy_eErr_SEQ_DESCR_NoMolInfoFound

int dummy_eErr_SEQ_DESCR_NoMolInfoFound = (valerr_to_handler[ eErr_SEQ_DESCR_NoMolInfoFound ] = handler_eErr_SEQ_DESCR_NoMolInfoFound , 0)
static

Definition at line 334 of file common_commands.cpp.

◆ dummy_eErr_SEQ_DESCR_NoPubFound

int dummy_eErr_SEQ_DESCR_NoPubFound = (valerr_to_handler[ eErr_SEQ_DESCR_NoPubFound ] = handler_eErr_SEQ_DESCR_NoPubFound , 0)
static

Definition at line 303 of file common_commands.cpp.

◆ dummy_eErr_SEQ_DESCR_NoSourceDescriptor

int dummy_eErr_SEQ_DESCR_NoSourceDescriptor = (valerr_to_handler[ eErr_SEQ_DESCR_NoSourceDescriptor ] = handler_eErr_SEQ_DESCR_NoSourceDescriptor , 0)
static

Definition at line 324 of file common_commands.cpp.

◆ dummy_eErr_SEQ_DESCR_TitleNotAppropriateForSet

int dummy_eErr_SEQ_DESCR_TitleNotAppropriateForSet = (valerr_to_handler[ eErr_SEQ_DESCR_TitleNotAppropriateForSet ] = handler_eErr_SEQ_DESCR_TitleNotAppropriateForSet , 0)
static

Definition at line 437 of file common_commands.cpp.

◆ dummy_eErr_SEQ_FEAT_GenCodeMismatch

int dummy_eErr_SEQ_FEAT_GenCodeMismatch = (valerr_to_handler[ eErr_SEQ_FEAT_GenCodeMismatch ] = handler_eErr_SEQ_FEAT_GenCodeMismatch , 0)
static

Definition at line 454 of file common_commands.cpp.

◆ dummy_eErr_SEQ_INST_AllNs

int dummy_eErr_SEQ_INST_AllNs = (valerr_to_handler[ eErr_SEQ_INST_AllNs ] = handler_eErr_SEQ_INST_AllNs , 0)
static

Definition at line 487 of file common_commands.cpp.

◆ dummy_eErr_SEQ_INST_HighNpercent3Prime

int dummy_eErr_SEQ_INST_HighNpercent3Prime = (valerr_to_handler[ eErr_SEQ_INST_HighNpercent3Prime ] = handler_eErr_SEQ_INST_HighNpercent3Prime , 0)
static

Definition at line 432 of file common_commands.cpp.

◆ dummy_eErr_SEQ_INST_HighNpercent5Prime

int dummy_eErr_SEQ_INST_HighNpercent5Prime = (valerr_to_handler[ eErr_SEQ_INST_HighNpercent5Prime ] = handler_eErr_SEQ_INST_HighNpercent5Prime , 0)
static

Definition at line 427 of file common_commands.cpp.

◆ dummy_eErr_SEQ_INST_HistAssemblyMissing

int dummy_eErr_SEQ_INST_HistAssemblyMissing = (valerr_to_handler[ eErr_SEQ_INST_HistAssemblyMissing ] = handler_eErr_SEQ_INST_HistAssemblyMissing , 0)
static

Definition at line 344 of file common_commands.cpp.

◆ dummy_eErr_SEQ_INST_HistoryGiCollision

int dummy_eErr_SEQ_INST_HistoryGiCollision = (valerr_to_handler[ eErr_SEQ_INST_HistoryGiCollision ] = handler_eErr_SEQ_INST_HistoryGiCollision , 0)
static

Definition at line 368 of file common_commands.cpp.

◆ dummy_eErr_SEQ_INST_InternalNsInSeqRaw

int dummy_eErr_SEQ_INST_InternalNsInSeqRaw = (valerr_to_handler[ eErr_SEQ_INST_InternalNsInSeqRaw ] = handler_eErr_SEQ_INST_InternalNsInSeqRaw , 0)
static

Definition at line 492 of file common_commands.cpp.

◆ dummy_eErr_SEQ_INST_MitoMetazoanTooLong

int dummy_eErr_SEQ_INST_MitoMetazoanTooLong = (valerr_to_handler[ eErr_SEQ_INST_MitoMetazoanTooLong ] = handler_eErr_SEQ_INST_MitoMetazoanTooLong , 0)
static

Definition at line 329 of file common_commands.cpp.

◆ dummy_eErr_SEQ_INST_MolNuclAcid

int dummy_eErr_SEQ_INST_MolNuclAcid = (valerr_to_handler[ eErr_SEQ_INST_MolNuclAcid ] = handler_eErr_SEQ_INST_MolNuclAcid , 0)
static

Definition at line 339 of file common_commands.cpp.

◆ dummy_eErr_SEQ_INST_ShortSeq

int dummy_eErr_SEQ_INST_ShortSeq = (valerr_to_handler[ eErr_SEQ_INST_ShortSeq ] = handler_eErr_SEQ_INST_ShortSeq , 0)
static

Definition at line 391 of file common_commands.cpp.

◆ dummy_eErr_SEQ_INST_TerminalNs

int dummy_eErr_SEQ_INST_TerminalNs = (valerr_to_handler[ eErr_SEQ_INST_TerminalNs ] = handler_eErr_SEQ_INST_TerminalNs , 0)
static

Definition at line 410 of file common_commands.cpp.

◆ dummy_eErr_SEQ_PKG_OrphanedProtein

int dummy_eErr_SEQ_PKG_OrphanedProtein = (valerr_to_handler[ eErr_SEQ_PKG_OrphanedProtein ] = handler_eErr_SEQ_PKG_OrphanedProtein , 0)
static

Definition at line 396 of file common_commands.cpp.

◆ valerr_to_handler

std::array<handler, eErr_MAX> valerr_to_handler {}
static

Definition at line 296 of file common_commands.cpp.

Referenced by IsEditable(), and LaunchEditor().

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