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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/edit__object__seq__desc_8cpp_source.html below:

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

);

wxTopLevelWindow* gui_widget =

wxTopLevelWindow*

(parent);

(

.IsSeq()) {

orig_bioseq =

.GetSeq().GetCompleteBioseq();

new_bioseq->

(*bioseq);

& edited_seq_desc =

&

(*m_EditedDescriptor);

wxBoxSizer* holder_sizer = 0;

holder_sizer =

wxBoxSizer(wxHORIZONTAL);

holder->SetSizer(holder_sizer);

holder_sizer->Add(

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

holder_sizer =

wxBoxSizer(wxVERTICAL);

parent->SetSizer(holder_sizer);

replace_all =

;

(desc_type.first) {

gui_widget->SetTitle(

(

));

gui_widget->SetTitle(

(

));

gui_widget->SetTitle(

(

));

gui_widget->SetTitle(

(

));

gui_widget->SetTitle(

(

));

help_client->

(

(

));

& edited_bioseq =

&

(*m_EditedBioseq);

bioseq = &(edited_bioseq);

gui_widget->SetTitle(

(

));

gui_widget->SetTitle(

(

));

(desc_type.second ==

)

gui_widget->SetTitle(

(

));

gui_widget->SetTitle(

(

));

(desc_type.second ==

)

help_client->

(

(

));

gui_widget->SetTitle(

(

));

gui_widget->SetTitle(

(

));

gui_widget->SetTitle(

(

));

gui_widget->SetTitle(

(

));

gui_widget->SetTitle(

(

));

parent->SetMinSize(wxSize(810, 650));

gui_widget->SetTitle(

(

));

->ChangeSeqdesc(edited_seq_desc);

holder_sizer->Add(

, 1, wxGROW|wxALL, 5);

=

wxCheckBox( parent,

,

(

), wxDefaultPosition, wxDefaultSize, 0 );

holder_sizer->Add(

, 0, wxALIGN_BOTTOM|wxALL, 0);

holder_sizer->Add(

, 1, wxGROW|wxALL, 0);

=

wxCheckBox( parent,

,

(

), wxDefaultPosition, wxDefaultSize, 0 );

holder_sizer->Add(

, 0, wxALIGN_RIGHT|wxALL, 0);

ConsolidateObjectList(vector<SeqdescEntryPair>& obj_list)

(obj_list.size() < 2) {

vector<SeqdescEntryPair>::iterator it = obj_list.begin();

vector<SeqdescEntryPair>::iterator

= it;

(

!= obj_list.end()) {

(it != obj_list.end()) {

(it->first.GetPointer() ==

->first.GetPointer()) {

it = obj_list.erase(it);

vector<SeqdescEntryPair>

;

(

desc_it(*bi, choice); desc_it; ++desc_it) {

.emplace_back(

(&(*desc_it)), desc_it.GetSeq_entry_Handle());

(

.begin(),

.end(), [](

SeqdescEntryPair&

,

SeqdescEntryPair&

) { return a.first < b.first; });

ConsolidateObjectList(

);

(seh.

() && propagate) {

->AddCommand(*subcmd);

->AddCommand(*subcmd);

->AddCommand(*chgd_cmd);

->AddCommand(*subcmd);

new_bioseq->

(*bioseq);

->AddCommand(*chgInst);

(!entry_it->IsSet())

->AddCommand(*cmdDelDesc);

(num_nuc > 1 && num_desc != 0)

prompt <<

<< num_desc <<

<< num_nuc <<

;

choice = wxMessageBox(prompt,

(

), wxYES_NO | wxICON_WARNING,

);

& orig_inst = orig_bseq.

();

(

b_iter(seh); b_iter; ++b_iter) {

same_inst = same_mol && same_strand && same_topology;

updated =

;

(desc_it->Equals(orig_desc)) {

replacement->

(edited_desc);

->AddCommand(*chgd_cmd);

new_bioseq->

(*bioseq);

new_bioseq->

().ResetTopology();

new_bioseq->

().ResetStrand();

new_bioseq->

().ResetMol();

->AddCommand(*chgInst);

->TransferDataFromWindow();

(specific && specific.

()) {

new_bioseq->

(*bioseq);

& edited_seq_desc =

&

(*m_EditedDescriptor);

->UpdateSeqdesc(edited_seq_desc);

& edited_bioseq =

&

(*m_EditedBioseq);

(edited_seq_desc.

()) {

(original && orig_bseq && edited_bioseq) {

->AddCommand(*chgd_cmd);

->AddCommand(*chgInst);

propagate =

;

choice = wxMessageBox(

(

),

(

),

(choice == wxYES) {

(

& it : obj_list) {

replacement->

(edited_seq_desc);

vector<SeqdescEntryPair> obj_list =

(

& it : obj_list) {

* descriptor =

*

(it.first.GetPointer());

(descriptor && descriptor->

(*original)) {

replacement->

(edited_seq_desc);

(&*desc_it != original) {

*

<< edited_seq_desc;

*

<< edited_seq_desc;

* seqdesc(

);

bioseq = b_iter->GetCompleteBioseq();

->ChangeSeqdesc(*seqdesc);

new_bioseq->

(*bioseq);

& edited_seq_desc =

&

(*m_EditedDescriptor);

(desc_type.first !=

) {

= desc_type.second;

(

==

)

choice = wxMessageBox(

(

) +

+

(

) +

+

(

),

(

), wxYES_NO | wxICON_ERROR, gui_widget);

gui_widget->SetFocus();

(choice == wxYES) {

->ChangeSeqdesc(*di);

(

.IsSeq()) {

new_bioseq->

(*bioseq);

(desc.

()) {

((*it)->IsSetLabel()

&& (*it)->GetLabel().IsStr()

&&

((*it)->GetLabel().GetStr(),

)

&& (*it)->IsSetData()

&& (*it)->GetData().IsStr()) {

sval = (*it)->GetData().GetStr();

make_pair(rval,sval);

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

void SetUser_object(CRef< objects::CUser_object > user)

void SetBioseq(CConstRef< objects::CBioseq > seq)

void SetUser_object(CRef< objects::CUser_object > user)

void AddCommand(IEditCommand &command)

virtual bool TransferDataToWindow()

void PopulateLocationChoices(objects::CSeq_entry_Handle seh)

void SetNotify(IDescEditorNotify *notify)

objects::CSeq_entry_Handle GetLocationChoice()

objects::CSeq_entry_Handle m_SEH

virtual void LocationChange(objects::CSeq_entry_Handle seh, wxTopLevelWindow *gui_widget)

CRef< CSerialObject > m_EditedBioseq

CRef< objects::CScope > m_Scope

void MolInfoLocationChange(objects::CSeq_entry_Handle seh, IDescEditorPanel *edit, CMolInfoPanel *molPanel)

virtual IEditCommand * GetEditCommand()

After placing the window in the Edit Object Dialog ShowModal() method of the dialog is called.

static objects::CSeqdesc::E_Choice GetDescChoiceForType(EDescriptorType desc_type)

CDescPlacementPanel * m_Placement

CConstRef< CObject > m_Object

CRef< CSerialObject > m_EditedDescriptor

CIRef< IEditCommand > m_EditAction

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

virtual wxWindow * CreateWindow(wxWindow *parent)

creates a child (not top level) windows that can contain whatever controls/subwindows etc.

wxCheckBox * m_ReplaceAll

CConstRef< CObject > m_Bioseq

void SetEditor(IDescEditorPanel *editor)

void ChangeBioseq(CConstRef< objects::CBioseq > bioseq)

void SetBioseqValues(CRef< objects::CBioseq > bioseq)

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

bool SameCitation(const CPub_equiv &other) const

void SetUser_object(CRef< objects::CUser_object > user)

CBioseq_Handle GetBioseq_Handle() const

void GetLabel(string *const label, ELabelType label_type) const

Base class for all serializable objects.

void SetUser_object(CRef< objects::CUser_object > user)

void SetUser_object(CRef< objects::CUser_object > user)

@ eObjectType_StructuredComment

EObjectType GetObjectType() const

Interface (functor) for object editing.

virtual void SetHelpUrl(const wxString &url)=0

static bool s_IsTpa(const CUser_object &user)

CRef< CCmdComposite > AddDescToSeqEntry(const CSeqdesc &desc, CSeq_entry_Handle seh, bool propagate)

static CRef< CCmdComposite > s_ReplaceAllMolinfo(CSeq_entry_Handle seh, const CSeqdesc &orig_desc, const CSeqdesc &edited_desc, const CBioseq &orig_bseq, const CBioseq &edited_bseq)

CRef< CCmdComposite > CreateMolInfoDesc(CSeq_entry_Handle seh, CRef< CSerialObject > obj, CMolInfoPanel *molPanel)

std::ofstream out("events_result.xml")

main entry point for tests

static DLIST_TYPE *DLIST_NAME() prev(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#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)

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

const string & GetMsg(void) const

Get message string.

CConstRef< objects::CBioseq > GetBioseqForSeqdesc(CRef< objects::CScope > scope, const objects::CSeqdesc &seq_desc)

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

Set object to copy of another one.

virtual bool Equals(const CSerialObject &object, ESerialRecursionMode how=eRecursive) const

Check if both objects contain the same values.

@ eSerial_AsnText

ASN.1 text.

static CObjectOStream * Open(ESerialDataFormat format, CNcbiOstream &outStream, bool deleteOutStream)

Create serial object writer and attach it to an output stream.

bool IsSetInst_Strand(void) const

bool IsSetInst_Mol(void) const

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

TClass GetClass(void) const

TInst_Mol GetInst_Mol(void) const

CBioseq_set_Handle GetParentBioseq_set(void) const

Return a handle for the parent Bioseq-set, or null handle.

TInst_Strand GetInst_Strand(void) const

TInst_Topology GetInst_Topology(void) const

CSeq_entry_Handle GetTopLevelEntry(void) const

Get top level Seq-entry handle.

CSeq_entry_Handle GetParentEntry(void) const

Return a handle for the parent seq-entry of the bioseq.

bool IsSetClass(void) const

CScope & GetScope(void) const

Get scope this handle belongs to.

bool IsSetInst_Topology(void) const

CSeq_entry_Handle GetSeq_entry_Handle(void) const

@ fIncludeGivenEntry

Include the top (given) entry.

@ fRecursive

Iterate recursively.

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.

TObjectType * GetPointerOrNull(void) const THROWS_NONE

Get pointer value.

bool IsNull(void) const THROWS_NONE

Check if pointer is null – same effect as Empty().

TObjectType & GetObject(void)

Get object.

TObjectType * GetPointerOrNull(void) THROWS_NONE

Get pointer value.

TObjectType * GetNonNullPointer(void) const

Get pointer value and throw a null pointer exception if pointer is null.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static void TrimSuffixInPlace(string &str, const CTempString suffix, ECase use_case=eCase)

Trim suffix from a string (in-place)

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

Case-insensitive equality of a substring with another string.

static void TrimPrefixInPlace(string &str, const CTempString prefix, ECase use_case=eCase)

Trim prefix from a string (in-place)

static bool Equal(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2, ECase use_case=eCase)

Test for equality of a substring with another string.

static const char label[]

bool IsSetData(void) const

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

bool IsStr(void) const

Check if variant Str is selected.

bool IsSetType(void) const

type of object within class Check if a value has been assigned to Type data member.

const TStr & GetStr(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

const TType & GetType(void) const

Get the Type member data.

vector< CRef< CUser_field > > TData

@ eClass_nuc_prot

nuc acid and coded proteins

const TUser & GetUser(void) const

Get the variant data.

bool IsMolinfo(void) const

Check if variant Molinfo is selected.

TStrand GetStrand(void) const

Get the Strand member data.

const TInst & GetInst(void) const

Get the Inst member data.

TPub & SetPub(void)

Select the variant.

TTopology GetTopology(void) const

Get the Topology member data.

bool IsSetMol(void) const

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

const TTitle & GetTitle(void) const

Get the variant data.

const TPub & GetPub(void) const

Get the variant data.

bool IsSetStrand(void) const

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

bool IsSetInst(void) const

the sequence data Check if a value has been assigned to Inst data member.

TMol GetMol(void) const

Get the Mol member data.

void SetInst(TInst &value)

Assign a value to Inst data member.

E_Choice

Choice variants.

bool IsPub(void) const

Check if variant Pub is selected.

TUser & SetUser(void)

Select the variant.

E_Choice Which(void) const

Which variant is currently selected.

const TPub & GetPub(void) const

Get the Pub member data.

TMolinfo & SetMolinfo(void)

Select the variant.

bool IsSetTopology(void) const

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

bool IsUser(void) const

Check if variant User is selected.

@ e_User

user defined object

@ e_Pub

a reference to the publication

@ 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_not_set

No variant selected.

@ e_Name

a name for this sequence

@ e_Source

source of materials, includes Org-ref

@ eMol_na

just a nucleic acid

static void text(MDB_val *v)

constexpr auto sort(_Init &&init)

void TestForNonAsciiText(wxWindow *win)

string GetTextObjectDescription(const CSeq_feat &sf, CScope &scope)

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