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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/bioseq__editor_8cpp_source.html below:

NCBI C++ ToolKit: src/gui/widgets/edit/bioseq_editor.cpp Source File

sid(

);

slabel(

);

feat->

().SetCdregion();

feat->

().SetComment();

;

;

registered =

;

,

,

));

,

,

));

,

,

));

,

,

));

,

,

));

,

,

));

,

,

));

,

,

));

,

,

));

,

,

));

description =

+ feature_name +

;

vector<CUICommand*> commands;

(

= 0;

< commands.size();

++)

wxAcceleratorEntry accelerator3(wxACCEL_CTRL, WXK_RETURN,

);

kTextViewTopMenu;

wxEvtHandler::ProcessEvent(event);

* szCommand =

;

}

(

std::exception& e) {

* szCommand =

;

(

<<

<< szCommand <<

);

}

(

std::exception& e) {

* szCommand =

;

}

(

std::exception& e) {

* szCommand =

;

}

(

std::exception& e) {

* szCommand =

;

(objList.empty()) {

(TEditObjectList::iterator it = objList.begin(); it != objList.end(); ++it) {

* pSeqFeat =

*

(it->m_Obj.GetPointer());

bsh = it->m_Scope->GetBioseqHandle(pSeqFeat->

());

vector<CConstRef<CSeq_feat>> propagatedFeats;

(

ci(bsh); ci; ++ci) {

propagatedFeats.push_back(ci->GetSeq_feat());

(

std::exception& e) {

* szCommand =

;

(objList.empty()) {

vector<CConstRef<CSeq_feat>> propagatedFeats;

(TEditObjectList::iterator it = objList.begin(); it != objList.end(); ++it) {

* pSeqFeat =

*

(it->m_Obj.GetPointer());

propagatedFeats.push_back(

(pSeqFeat));

}

(

std::exception& e) {

* szCommand =

;

(

<<

<< szCommand <<

);

seqFeat->

(*featData);

seq_id->

(*bseq_seq_id);

}

(

std::exception& e) {

* szCommand =

;

}

(

std::exception& e) {

feat_name =

+ feature->

().

();

* szCommand = feat_name.c_str();

seq_id->

(*bseq_seq_id);

}

(

std::exception& e) {

.Enable(!bh.

());

.Enable(bh.

());

.Enable(

);

seqFeat->

().SetCdregion();

seqFeat->

().SetGene();

seqFeat->

().SetProt();

(event.GetId()) {

seqFeat->

().SetRegion();

seqFeat->

().SetSite();

seqFeat->

().SetBond();

seqFeat->

().SetPub();

cmd_name =

+ descriptor_type +

;

* szCommand = cmd_name.c_str();

(

<<

<< szCommand <<

);

}

(

std::exception& e) {

(seq_submit && seq_submit->

()) {

submitBlock = &seq_submit->

();

(entry && entry->

()) {

seq_set = &(entry->

());

(titleEdit) {

(submitBlock) {

=

;

(objList.empty())

CSeq_loc* loc =

CSeq_loc*

(editObj.

.

());

wxApp *app =

wxApp*

(wxApp::GetInstance());

wxApp *app =

wxApp*

(wxApp::GetInstance());

wxMessageBox(

(

),

(

), wxOK | wxICON_ERROR);

(submit && submit->

())

res = wxMessageBox(

(

),

(

), wxYES_NO | wxICON_QUESTION);

create =

;

(seqDesc && seqDesc->

())

wxMessageBox(

(

) +

(

), wxOK|wxICON_ERROR);

}

(

std::exception& e) {

(objList.empty())

(

std::exception&) {

.Enable(

);

(objList.empty())

.Enable(

(objList.front()));

(

std::exception&) {

num_selected = 0;

(objList.empty())

* seqDesq =

*

(editObj->m_Obj.GetPointer());

* seqFeat =

*

(editObj->m_Obj.GetPointer());

(seqDesq || seqFeat || seqAnnot || seqAlign)

}

(

std::exception&) {

(num_selected == 0)

(num_selected > 1)

res = wxMessageBox(

(

),

(

), wxYES_NO | wxICON_QUESTION);

delete_genes =

;

res = wxMessageBox(

(

),

(

), wxYES_NO | wxCANCEL | wxICON_QUESTION);

(res == wxCANCEL)

delete_genes =

;

* szCommand =

;

(objList.empty()) {

* seqDesq =

*

(obj->m_Obj.GetPointer());

wxMessageDialog dlg(

,

(

),

(

), wxOK | wxCANCEL);

(dlg.ShowModal() == wxID_CANCEL) {

from_single =

;

* seqDesq =

*

(obj->m_Obj.GetPointer());

any_deleted =

;

* seqDesq =

*

(editObj->m_Obj.GetPointer());

* seqFeat =

*

(editObj->m_Obj.GetPointer());

any_deleted =

;

}

(seqFeat) {

any_deleted =

;

(seqAnnot) {

any_deleted =

;

(seqAlign) {

any_deleted =

;

}

(

std::exception& e) {

.Enable(

);

(objList.empty())

}

(

std::exception&) {

wxWindow* editorWindow =

->CreateWindow(edit_dlg);

(!title.empty()) {

edit_dlg->SetTitle(title);

askSeqSet =

;

askSeqSet = (seh.IsSeq() && sehDesc != seh);

(dlg.ShowModal() != wxID_OK) {

cancel =

;

(cancel || !sehDesc) {

(!seqFeat.IsSetData()) {

(

<<

);

(seqFeat.IsSetLocation() && !seqFeat.GetLocation().IsNull()) {

(

mf(seh.GetScope(), seqFeat.GetLocation(), sel); mf; ++mf) {

(mf->GetOriginalFeature().Equals(seqFeat)) {

fh = mf->GetSeq_feat_Handle();

(

<<

);

(

.IsGene()) {

res = wxMessageBox(

(

),

(

), wxYES_NO | wxICON_QUESTION);

addCommand.

();

.Reset(&*composite);

(seqFeat.IsSetId() && seqFeat.GetId().IsLocal()) {

(

feat_it(seh); feat_it; ++feat_it) {

((*it)->IsSetId() && (*it)->GetId().IsLocal()) {

(local_id.

((*it)->GetId().GetLocal())) {

feat_list.push_back(seh.GetScope().GetSeq_featHandle(

));

(!feat_list.empty()) {

(dlg.ShowModal() == wxID_OK) {

->AddCommand(*chgfeats);

(

<<

);

(!seqFeat.IsSetData()) {

(

<<

);

(seqFeat.IsSetLocation() && !seqFeat.GetLocation().IsNull()) {

(

mf(seh.GetScope(), seqFeat.GetLocation(), sel); mf; ++mf) {

(mf->GetOriginalFeature().Equals(seqFeat)) {

fh = mf->GetSeq_feat_Handle();

(

<<

);

(

.IsGene()) {

res = wxMessageBox(

(

),

(

), wxYES_NO | wxICON_QUESTION );

addCommand.

();

.Reset(&*composite);

(seqFeat.IsSetId() && seqFeat.GetId().IsLocal()) {

(

feat_it(seh); feat_it; ++feat_it) {

((*it)->IsSetId() && (*it)->GetId().IsLocal()) {

(local_id.

((*it)->GetId().GetLocal())) {

feat_list.push_back(seh.GetScope().GetSeq_featHandle(

));

(!feat_list.empty()) {

(dlg.ShowModal() == wxID_OK) {

->AddCommand(*chgfeats);

(

<<

);

(annot_it->GetCompleteSeq_annot().GetPointer() == &annot) {

(

<<

);

->AddCommand(*cmdDelAnnot);

(

feat_it(ah); feat_it; ++feat_it) {

->AddCommand(*cmdDelFeat);

(

<<

);

(

align_it(seh); align_it; ++align_it) {

(&align_it.GetOriginalSeq_align() == &align) {

ah = align_it.GetSeq_align_Handle();

(

<<

);

(

<<

);

(

std::exception&) {

!bh.

();

(

std::exception&) {

(

std::exception&) {

(objList.empty()) {

(

&& it : objList) {

* pSeqFeat =

*

(it.m_Obj.GetPointer());

bsh = it.m_Scope->GetBioseqHandle(pSeqFeat->

());

->GetHandle();

(featheader_item)

(startsection_item)

(endsection_item)

(; dsrc_it; ++dsrc_it) {

& seqDesc = *dsrc_it;

(; dsrc_it; ++dsrc_it) {

& seqDesc = *dsrc_it;

CSeq_loc* loc =

CSeq_loc*

(editObj.

.

());

*

= loc->GetId();

(entry && entry->

())

seq_set = &(entry->

());

(submit_block || seq_set || title_edit || align || submit) {

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

CSeq_entry_Handle GetSeqEntryForSeqdesc(CRef< CScope > scope, const CSeqdesc &seq_desc)

static CBioseq_Handle s_GetContext(const IFlatItem &item)

static const int num_feat_cmds

static const FeatTypeCmd feat_type_cmds[]

static bool s_IsLocalFeature(const CSeq_feat &seq_feat, CSeq_entry_Handle ctx)

struct feattypecmd FeatTypeCmd

static string GetKeyFromCmdID(int cmd_id)

static const FeatCmd feat_cmds[]

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

static string s_GetMenuName(int i)

static const int num_feat_type_cmds

@ eCmdCreateRegulatory_ribosome_binding_site

@ eCmdCreateMobileElement

@ eCmdCreateMiscStructure

@ eCmdCreateBiosourceFeat

@ eCmdCreateRefGeneTracking

@ eCmdDeleteBiosourceDesc

@ eCmdCreatePrimTranscript

@ eCmdCreatePubDescriptorLabeled

@ eCmdCreateRegulatory_promoter

@ eCmdCreateRegulatory_riboswitch

@ eCmdCreateCodingRegion_ext

@ eCmdCreateCommentDescriptor

@ eCmdCreateBiosourceDesc

@ eCmdCreatePubFeatureLabeled

@ eCmdCreateRegulatory_enhancer

@ eCmdCreatePubDescriptor

@ eCmdCreateTransitPeptide

@ eCmdPropagateAllFeatures

@ eCmdCreateRegionDescriptor

@ eCmdCreateSecondaryStructure

@ eCmdCreateAuthorizedAccess

@ eCmdPropagateSelectedFeatures

@ eCmdCreateStructuredComment

@ eCmdCreateRegulatory_terminator

@ eCmdCreateMiscDifference

@ eCmdDeleteBiosourceFeat

static void CollectBioseqEditorCommands(vector< CUICommand * > &commands)

virtual CObject * CreateEditor(const string &interface_name, ICommandProccessor &cmdProccessor, IGuiWidgetHost *guiWidgetHost)

virtual string GetExtensionIdentifier() const

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

virtual void RegisterCommands(CUICommandRegistry &, wxFileArtProvider &)

virtual string GetExtensionLabel() const

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

void OnCreateSite(wxCommandEvent &event)

bool x_HasAlignment(void)

bool x_HaveBiosourceDesc()

void OnPropagateSelectedFeatures(wxCommandEvent &event)

static CRef< objects::CSeq_feat > MakeDefaultFeature(objects::CSeqFeatData::ESubtype subtype)

CIRef< IEditCommand > x_GetDeleteCommand(objects::CSeq_entry_Handle &seh, const objects::CSeqdesc &seqDesc, bool from_single)

void OnDeleteBiosourceDesc(wxCommandEvent &event)

static objects::CSeqFeatData::ESubtype GetFeatTypeFromCmdID(int cmd_id)

void OnUpdateEditSelection(wxUpdateUIEvent &event)

void OnUpdateDeleteSelection(wxUpdateUIEvent &event)

void OnUpdateCreateBiosourceDesc(wxUpdateUIEvent &event)

void OnPropagateAllFeatures(wxCommandEvent &event)

void OnUpdateDeleteBiosourceDesc(wxUpdateUIEvent &event)

virtual void EditSelection()

void OnUpdateEditBiosourceFeat(wxUpdateUIEvent &event)

void OnCreateBond(wxCommandEvent &event)

void OnUpdateAnyFeat(wxUpdateUIEvent &event)

void OnUpdateProteinFeat(wxUpdateUIEvent &event)

void OnUpdatePropagateSelectedFeatures(wxUpdateUIEvent &event)

void OnCreateCodingRegion(wxCommandEvent &event)

void OnUpdateCreateBiosourceFeat(wxUpdateUIEvent &event)

void OnCreateDescriptor(wxCommandEvent &evt)

void OnCreateFeature(CRef< objects::CSeq_feat > feat, wxCommandEvent &event)

void OnEditSelection(wxCommandEvent &event)

virtual int GetEditFlags(CEditObject &editObj) const

bool x_DeleteFromSingleSeq(objects::CSeq_entry_Handle &seh, objects::CSeq_entry_Handle &sehdesc, const objects::CSeqdesc &seqDesq, bool &any, bool &cancel)

void OnCreatePubFeat(wxCommandEvent &event)

void OnCreateImport(wxCommandEvent &evt)

void OnCreateBiosourceDesc(wxCommandEvent &event)

bool x_HaveBiosourceFeat()

bool IsEditable(CEditObject &editObj) const

void OnDeleteBiosourceFeat(wxCommandEvent &event)

ICommandProccessor & m_CmdProccessor

void OnCreateRegion(wxCommandEvent &evt)

int x_GetFromPosition(void)

void OnCreateProt(wxCommandEvent &event)

void OnCreateBiosourceFeat(wxCommandEvent &event)

void x_DeleteObject(objects::CSeq_entry_Handle &seh, const objects::CSeqdesc &seqDesq)

void OnUpdateDeleteBiosourceFeat(wxUpdateUIEvent &event)

void OnEditBiosourceFeat(wxCommandEvent &event)

void OnCreateRNA(wxCommandEvent &evt)

void OnEditBiosourceDesc(wxCommandEvent &event)

void OnUpdateNucleotideFeat(wxUpdateUIEvent &event)

void OnUpdateEditBiosourceDesc(wxUpdateUIEvent &event)

void OnUpdatePropagateAllFeatures(wxUpdateUIEvent &event)

bool x_HandleFeatCreationHere(wxCommandEvent &event)

void x_EditObject(CIRef< IEditObject > edit, const string &title=kEmptyStr)

void OnCreateSecondaryStructure(wxCommandEvent &evt)

void x_ReportError(const string &cmd, const std::exception &e)

bool IsDeletable(CEditObject &editObj) const

void OnDeleteSelection(wxCommandEvent &event)

void OnCreateGene(wxCommandEvent &event)

void AddCommand(IEditCommand &command)

static CIRef< IEditCommand > DeleteGeneXRefs(objects::CSeq_entry_Handle &seh, const objects::CGene_ref &gene)

CRef< CCmdComposite > GetCommand()

vector< objects::CSeq_feat_Handle > TFeatVec

void SetEditorWindow(wxWindow *editorWindow)

void SetEditor(CIRef< IEditObject > editor)

virtual void SetUndoManager(ICommandProccessor *cmdProccessor)

static pair< EDescriptorType, string > GetDescriptorType(const objects::CSeqdesc &desc)

objects::CSeq_entry_Handle m_SEH

CConstRef< CObject > m_Obj

CBioseqContext * GetContext(void)

bool Match(const CObject_id &oid2) const

void SetBiosrc(TBiosrc &v)

ESubtype GetSubtype(void) const

string GetKey(EVocabulary vocab=eVocabulary_full) const

@ eSubtype_misc_difference

@ eSubtype_misc_structure

@ eSubtype_bad

These no longer need to match the FEATDEF values in the C toolkit's objfdef.h.

@ eSubtype_mobile_element

@ eSubtype_prim_transcript

@ eSubtype_transit_peptide_aa

@ eSubtype_sig_peptide_aa

@ eSubtype_mat_peptide_aa

static CTempString SubtypeValueToName(ESubtype eSubtype)

Turns a ESubtype into its string value which is NOT necessarily related to the identifier of the enum...

bool IsFtable(void) const

namespace ncbi::objects::

Base class for all serializable objects.

CUICommandRegistry is a centralized registry where all application commands should be registered.

static CUICommandRegistry & GetInstance()

the main instance associated with the application

wxMenu * CreateMenu(const SwxMenuItemRec *items)

create a menu from a static definition (see WX_*_MENU macros)

int RegisterCommand(CUICommand *cmd)

assumes ownership of the given object returns a command id (useful when registry is used for auto id ...

void AddAccelerator(const wxAcceleratorEntry &entry)

virtual objects::CBioseq_Handle GetCurrentBioseq()=0

virtual void GetCurrentSelection(TEditObjectList &)=0

virtual bool MayCreateFeatures() const

virtual wxString GetWorkDir() const =0

Undo/Redo interface for editing operations.

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

virtual const CSerialObject * GetObject(void) const =0

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

void Error(CExceptionArgs_Base &args)

const string & GetMsg(void) const

Get message string.

void Info(CExceptionArgs_Base &args)

objects::CBioseq_Handle GetBioseqForSeqFeat(const objects::CSeq_feat &f, objects::CScope &scope)

objects::CSeq_feat_Handle GetSeqFeatHandleForBadLocFeature(const objects::CSeq_feat &feat, objects::CScope &scope)

virtual const CTypeInfo * GetThisTypeInfo(void) const =0

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

Optimized implementation of CSerialObject::Assign, which is not so efficient.

CConstRef< CSeq_feat > GetGeneForFeature(const CSeq_feat &feat, CScope &scope)

Finds gene for feature, but obeys SeqFeatXref directives.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

CSeq_feat_Handle GetSeq_featHandle(const CSeq_feat &feat, EMissing action=eMissing_Default)

const CSeq_annot_Handle & GetAnnot(void) const

Get handle to seq-annot for this feature.

TSeqPos GetBioseqLength(void) const

CSeq_entry_Handle GetSeq_entry_Handle(void) const

Get parent Seq-entry handle.

CConstRef< CSeq_id > GetSeqId(void) const

Get id which can be used to access this bioseq handle Throws an exception if none is available.

CSeq_entry_Handle GetParentEntry(void) const

Get parent Seq-entry handle.

CSeq_entry_EditHandle GetEditHandle(void) const

Get 'edit' version of handle.

CSeq_entry_Handle GetTopLevelEntry(void) const

Get top level Seq-entry handle.

CScope & GetScope(void) const

Get scope this handle belongs to.

CScope & GetScope(void) const

Get scope this handle belongs to.

CConstRef< CSeq_feat > GetOriginalSeq_feat(void) const

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,...

const CSeq_annot_Handle & GetAnnot(void) const

Get handle to the seq-annot.

const CSeq_feat_Handle & GetSeq_feat_Handle(void) const

Get original feature handle.

TObjectType * GetPointer(void) const THROWS_NONE

Get pointer,.

CConstRef< C > ConstRef(const C *object)

Template function for conversion of const object pointer to CConstRef.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another string.

const string & GetName(void) const

Get name of this type.

void SetType(TType &value)

Assign a value to Type data member.

TId GetId(void) const

Get the variant data.

@ eProcessed_signal_peptide

@ eProcessed_transit_peptide

@ eType_ncRNA

non-coding RNA; subsumes snRNA, scRNA, snoRNA

bool IsSetData(void) const

the specific data Check if a value has been assigned to Data data member.

void SetLocation(TLocation &value)

Assign a value to Location data member.

const TLocation & GetLocation(void) const

Get the Location member data.

const TData & GetData(void) const

Get the Data member data.

void SetData(TData &value)

Assign a value to Data data member.

@ ePsec_str_helix

any helix

TFrom GetFrom(void) const

Get the From member data.

const TInt & GetInt(void) const

Get the variant data.

const TSet & GetSet(void) const

Get the variant data.

bool IsSet(void) const

Check if variant Set is selected.

TTitle & SetTitle(void)

Select the variant.

TPub & SetPub(void)

Select the variant.

bool IsSource(void) const

Check if variant Source is selected.

TName & SetName(void)

Select the variant.

TComment & SetComment(void)

Select the variant.

TSource & SetSource(void)

Select the variant.

E_Choice

Choice variants.

TUser & SetUser(void)

Select the variant.

const TMolinfo & GetMolinfo(void) const

Get the variant data.

TMolinfo & SetMolinfo(void)

Select the variant.

TRegion & SetRegion(void)

Select the variant.

@ e_Embl

EMBL specific information.

@ e_User

user defined object

@ e_Pub

a reference to the publication

@ e_Genbank

GenBank specific info.

@ e_Comment

a more extensive comment

@ e_Region

overall region (globin locus)

@ e_Molinfo

info on the molecule and techniques

@ e_Title

a title for this sequence

@ e_Name

a name for this sequence

@ e_Source

source of materials, includes Org-ref

const TSub & GetSub(void) const

Get the Sub member data.

bool IsSetSub(void) const

Check if a value has been assigned to Sub data member.

vector< CEditObject > TEditObjectList

where boath are integers</td > n< td ></td > n</tr > n< tr > n< td > tse</td > n< td > optional</td > n< td > String</td > n< td class=\"description\"> TSE option controls what blob is orig

#define FOR_EACH_SEQFEATXREF_ON_SEQFEAT(Itr, Var)

FOR_EACH_SEQFEATXREF_ON_SEQFEAT EDIT_EACH_SEQFEATXREF_ON_SEQFEAT.

ViewerWindowBase::OnEditMenu ViewerWindowBase::OnJustification EVT_MENU(MID_SHOW_GEOM_VLTNS, ViewerWindowBase::OnShowGeomVltns) EVT_MENU(MID_FIND_PATTERN

CSeqFeatData::ESubtype subtype

#define WX_DEFINE_MENU(name)

New macros for defining menus for use with CUICommandRegistry.

#define WX_SUBMENU(label)

#define WX_MENU_SEPARATOR_L(label)

#define WX_MENU_ITEM(cmd)

#define WX_MENU_ITEM_INT(cmd)

CRef< CCmdComposite > GetDeleteFeatureCommand(const objects::CSeq_feat_Handle &fh, bool remove_proteins=true)

static const char * type_name(CS_INT value)

void SetWorkDir(wxWindow *wnd, const wxString &workDir)

wxString ToWxString(const string &s)

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