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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/edit__seq__id_8cpp_source.html below:

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

IMPLEMENT_DYNAMIC_CLASS(

, wxDialog )

(parent,

, caption, pos,

, style);

( wxWindow* parent, wxWindowID

,

wxString& caption,

wxPoint& pos,

wxSize&

,

style )

SetExtraStyle(wxWS_EX_BLOCK_EVENTS);

wxDialog::Create( parent,

, caption, pos,

, style );

GetSizer()->SetSizeHints(

);

wxBoxSizer* itemBoxSizer2 =

wxBoxSizer(wxVERTICAL);

itemDialog1->SetSizer(itemBoxSizer2);

wxStaticBox* itemStaticBoxSizer3Static =

wxStaticBox(itemDialog1,

,

(

));

wxStaticBoxSizer* itemStaticBoxSizer3 =

wxStaticBoxSizer(itemStaticBoxSizer3Static, wxVERTICAL);

itemBoxSizer2->Add(itemStaticBoxSizer3, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

=

wxRadioButton( itemStaticBoxSizer3->GetStaticBox(),

,

(

), wxDefaultPosition, wxDefaultSize, wxRB_GROUP );

itemStaticBoxSizer3->Add(

, 0, wxALIGN_LEFT|wxALL, 5);

=

wxRadioButton( itemStaticBoxSizer3->GetStaticBox(),

,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemStaticBoxSizer3->Add(

, 0, wxALIGN_LEFT|wxALL, 5);

=

wxRadioButton( itemStaticBoxSizer3->GetStaticBox(),

,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemStaticBoxSizer3->Add(

, 0, wxALIGN_LEFT|wxALL, 5);

wxBoxSizer* itemBoxSizer7 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer2->Add(itemBoxSizer7, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

=

wxRadioButton( itemDialog1,

,

(

), wxDefaultPosition, wxDefaultSize, wxRB_GROUP );

->SetValue(

);

itemBoxSizer7->Add(

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

=

wxRadioButton( itemDialog1,

,

(

), wxDefaultPosition, wxDefaultSize, 0 );

->SetValue(

);

itemBoxSizer7->Add(

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

=

wxRadioButton( itemDialog1,

,

(

), wxDefaultPosition, wxDefaultSize, 0 );

->SetValue(

);

itemBoxSizer7->Add(

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

=

wxRadioButton( itemDialog1,

,

(

), wxDefaultPosition, wxDefaultSize, 0 );

->SetValue(

);

itemBoxSizer7->Add(

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

=

wxRadioButton( itemDialog1,

,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer7->Add(

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxBoxSizer* itemBoxSizer12 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer2->Add(itemBoxSizer12, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

wxStaticText* itemStaticText11 =

wxStaticText( itemDialog1, wxID_STATIC,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer12->Add(itemStaticText11, 0, wxALIGN_TOP|wxALL, 5);

wxStaticText* itemStaticText12 =

wxStaticText( itemDialog1, wxID_STATIC,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer2->Add(itemStaticText12, 0, wxALIGN_LEFT|wxALL, 5);

itemBoxSizer2->Add(

, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

wxBoxSizer* itemBoxSizer13 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer2->Add(itemBoxSizer13, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

wxStaticText* itemStaticText14 =

wxStaticText( itemDialog1, wxID_STATIC,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer13->Add(itemStaticText14, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

=

wxTextCtrl( itemDialog1,

, wxEmptyString, wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer13->Add(

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxBoxSizer* itemBoxSizer16 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer2->Add(itemBoxSizer16, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

wxStaticText* itemStaticText17 =

wxStaticText( itemDialog1, wxID_STATIC,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer16->Add(itemStaticText17, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

=

wxTextCtrl( itemDialog1,

, wxEmptyString, wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer16->Add(

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxBoxSizer* itemBoxSizer6 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer2->Add(itemBoxSizer6, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

=

wxCheckBox( itemDialog1,

,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer6->Add(

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxButton* itemButton7 =

wxButton( itemDialog1, wxID_OK,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer6->Add(itemButton7, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxButton* itemButton8 =

wxButton( itemDialog1, wxID_CANCEL,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer6->Add(itemButton8, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

(

->GetValue())

(CBioseq_Handle::TId::const_iterator id_it = b_iter->GetId().begin(); id_it != b_iter->GetId().end(); ++id_it)

(constraint && !constraint->DoesTextMatch(

))

(constraint && !constraint->DoesTextMatch(db))

db =

->GetValue().ToStdString() + db +

->GetValue().ToStdString();

(constraint && !constraint->DoesTextMatch(

))

(desc_ci->GetUser().IsSetType() && desc_ci->GetUser().GetType().IsStr()

(CSeq_hist::TAssembly::iterator align_it = hist.

().begin(); align_it != hist.

().end(); ++align_it)

(CSeq_hist_rec::TIds::iterator id_it = hist.

().SetIds().begin(); id_it != hist.

().SetIds().end(); ++id_it)

(CSeq_hist_rec::TIds::iterator id_it = hist.

().SetIds().begin(); id_it != hist.

().SetIds().end(); ++id_it)

(CSeg_ext::Tdata::iterator loc_it = ext.

().

().begin(); loc_it != ext.

().

().end(); ++loc_it)

(CMap_ext::Tdata::iterator feat_it = ext.

().

().begin(); feat_it != ext.

().

().end(); ++feat_it)

(CDelta_ext::Tdata::iterator delta_it = ext.

().

().begin(); delta_it != ext.

().

().end(); ++delta_it)

((*delta_it)->IsLoc())

new_entry->

(*new_seq);

(

annot_ci(seh, sel); annot_ci; ++annot_ci)

(annot_ci->IsFtable())

(

feat_it(*annot_ci); feat_it; ++feat_it)

new_feat->

(feat_it->GetOriginalFeature());

(annot_ci->IsAlign())

(

align_it(*annot_ci); align_it; ++align_it)

new_align->

(align_it.GetOriginalSeq_align());

(annot_ci->IsGraph())

(

graph_it(*annot_ci); graph_it; ++graph_it)

new_graph->

(graph_it->GetOriginalGraph());

(CBioseq::TId::iterator it = new_seq->

().begin(); it != new_seq->

().end(); ++it)

((*codebreak)->IsSetLoc())

(clone_set.

())

(CClone_seq_set::Tdata::iterator clone_it = clone_set.

().begin(); clone_it != clone_set.

().end(); ++clone_it)

((*clone_it)->IsSetLocation())

((*clone_it)->IsSetSeq())

(CSeqFeatSupport::TInference::iterator inf_it = feat.

().SetInference().begin(); inf_it != feat.

().SetInference().end(); ++inf_it)

((*inf_it)->IsSetBasis() && (*inf_it)->GetBasis().IsSetAccessions())

(CEvidenceBasis::TAccessions::iterator id_it = (*inf_it)->SetBasis().SetAccessions().begin(); id_it != (*inf_it)->SetBasis().SetAccessions().end(); ++id_it)

(CSeqFeatSupport::TModel_evidence::iterator mod_it = feat.

().SetModel_evidence().begin(); mod_it != feat.

().SetModel_evidence().end(); ++mod_it)

((*mod_it)->IsSetIdentification())

((*mod_it)->IsSetMrna())

(CModelEvidenceSupport::TMrna::iterator item_it = (*mod_it)->SetMrna().begin(); item_it != (*mod_it)->SetMrna().end(); ++item_it)

((*item_it)->IsSetId())

((*mod_it)->IsSetEst())

(CModelEvidenceSupport::TEst::iterator item_it = (*mod_it)->SetEst().begin(); item_it != (*mod_it)->SetEst().end(); ++item_it)

((*item_it)->IsSetId())

((*mod_it)->IsSetProtein())

(CModelEvidenceSupport::TEst::iterator item_it = (*mod_it)->SetProtein().begin(); item_it != (*mod_it)->SetProtein().end(); ++item_it)

((*item_it)->IsSetId())

(CVariation_inst::TDelta::iterator delta_it = var.

().SetInstance().SetDelta().begin(); delta_it != var.

().SetInstance().SetDelta().end(); ++delta_it)

((*delta_it)->IsSetSeq() && (*delta_it)->GetSeq().IsLoc())

( CVariation_ref::C_Data::C_Set::TVariations::iterator var_it = var.

().SetSet().SetVariations().begin(); var_it != var.

().SetSet().SetVariations().end(); ++var_it)

((*con_it)->IsVariation())

(CSeq_annot::C_Data::TGraph::iterator graph_it = annot.

().SetGraph().begin(); graph_it != annot.

().SetGraph().end(); ++graph_it)

((*graph_it)->IsSetLoc())

&loc = (*graph_it)->SetLoc();

(CSeq_annot::C_Data::TIds::iterator id_it = annot.

().SetIds().begin(); id_it != annot.

().SetIds().end(); ++id_it)

(CSeq_annot::C_Data::TLocs::iterator loc_it = annot.

().SetLocs().begin(); loc_it != annot.

().SetLocs().end(); ++loc_it)

((*annotdesc_it)->IsSrc())

&

= (*annotdesc_it)->SetSrc();

((*annotdesc_it)->IsRegion())

&loc = (*annotdesc_it)->SetRegion();

(CSeq_table::TColumns::iterator col_it = annot.

().SetSeq_table().SetColumns().begin(); col_it != annot.

().SetSeq_table().SetColumns().end(); ++col_it)

((*col_it)->IsSetData() && (*col_it)->GetData().IsLoc())

(CSeqTable_multi_data::TLoc::iterator loc_it = (*col_it)->SetData().SetLoc().begin(); loc_it != (*col_it)->SetData().SetLoc().end(); ++loc_it)

((*col_it)->IsSetData() && (*col_it)->GetData().IsId())

(CSeqTable_multi_data::TId::iterator id_it = (*col_it)->SetData().SetId().begin(); id_it != (*col_it)->SetData().SetId().end(); ++id_it)

((*col_it)->IsSetDefault() && (*col_it)->GetDefault().IsLoc())

((*col_it)->IsSetDefault() && (*col_it)->GetDefault().IsId())

((*col_it)->IsSetSparse_other() && (*col_it)->GetSparse_other().IsLoc())

((*col_it)->SetSparse_other().SetLoc());

((*col_it)->IsSetSparse_other() && (*col_it)->GetSparse_other().IsId())

((*col_it)->SetSparse_other().SetId());

((*std_it)->IsSetIds())

(CStd_seg::TIds::iterator id_it = (*std_it)->SetIds().begin(); id_it != (*std_it)->SetIds().end(); ++id_it)

((*std_it)->IsSetLoc())

(CStd_seg::TLoc::iterator loc_it = (*std_it)->SetLoc().begin(); loc_it != (*std_it)->SetLoc().end(); ++loc_it)

->Assign(*(new_loc->

()));

new_loc->

(*

);

(CBioseq_Handle::TId::const_iterator id_it = b_iter->GetId().begin(); id_it != b_iter->GetId().end(); ++id_it)

(id_it->Which() == id_type)

remove_id = id_it->GetSeqId();

(

&

: b_iter->GetId())

(

.Which() != id_type)

(!

.

()->IsGeneral() || (

.

()->IsGeneral() &&

.

()->GetGeneral().IsSetDb() &&

.

()->GetGeneral().GetDb() !=

&&

.

()->GetGeneral().GetDb() !=

&&

.

()->GetGeneral().GetDb() !=

))

(prev_nuc != *b_iter_nuc)

prev_nuc = *b_iter_nuc;

(remove_id && replace_id)

(!

.empty())

found_new(

);

(

: new_seq->

())

CBioseq::TId::iterator it = new_seq->

().begin();

( it != new_seq->

().end() )

found_old(

);

it = new_seq->

().erase(it);

:

(seh,

)

ask_user(

);

default_set(

);

vector<string>

;

(

.size() == 2)

db =

.front();

=

.back();

wxTextEntryDialog dlg(

,

(

),

(

));

(dlg.ShowModal() == wxID_OK)

default_db = dlg.GetValue().ToStdString();

default_set =

;

:

(seh,

)

(CBioseq_Handle::TId::const_iterator id_it = b_iter->GetId().begin(); id_it != b_iter->GetId().end(); ++id_it)

=

->GetGeneral().GetTag().GetStr();

:

(seh,

)

(CBioseq_Handle::TId::const_iterator id_it = b_iter->GetId().begin(); id_it != b_iter->GetId().end(); ++id_it)

(

feat_ci(*b_iter); feat_ci; ++feat_ci)

(id->

())

default : text_id.

();

((!text_id->IsSetAccession() || text_id->GetAccession().empty()) &&

text_id->IsSetName() && !text_id->GetName().empty() &&

(

(1,text_id->GetName().front())) &&

(text_id->GetName(),

) !=

)

(new_id->

())

(parent,

, caption, pos,

, style);

SetExtraStyle(wxWS_EX_BLOCK_EVENTS);

wxDialog::Create( parent,

, caption, pos,

, style );

GetSizer()->SetSizeHints(

);

wxBoxSizer* itemBoxSizer2 =

wxBoxSizer(wxVERTICAL);

itemDialog1->SetSizer(itemBoxSizer2);

wxBoxSizer* itemBoxSizer12 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer2->Add(itemBoxSizer12, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

wxStaticText* itemStaticText11 =

wxStaticText( itemDialog1, wxID_STATIC,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer12->Add(itemStaticText11, 0, wxALIGN_TOP|wxALL, 5);

wxBoxSizer* itemBoxSizer6 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer2->Add(itemBoxSizer6, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

wxButton* itemButton7 =

wxButton( itemDialog1, wxID_OK,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer6->Add(itemButton7, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxButton* itemButton8 =

wxButton( itemDialog1, wxID_CANCEL,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer6->Add(itemButton8, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxNullBitmap;

(CBioseq_Handle::TId::const_iterator id_it = b_iter->GetId().begin(); id_it != b_iter->GetId().end(); ++id_it)

(CBioseq_Handle::TId::const_iterator id_it = b_iter->GetId().begin(); id_it != b_iter->GetId().end(); ++id_it)

:

(seh,

)

(CBioseq_Handle::TId::const_iterator id_it = b_iter->GetId().begin(); id_it != b_iter->GetId().end(); ++id_it)

(id->

())

default : text_id.

();

(text_id->IsSetAccession() && !text_id->GetAccession().empty())

= text_id->GetAccession();

((

.empty() || force_name) && text_id->IsSetName())

= text_id->GetName();

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

CRef< objects::CSeq_id > GetNewProtId(objects::CBioseq_Handle bsh, int &offset, string &id_label, bool general_only)

CAccessionToLocalId(objects::CSeq_entry_Handle seh, CSeq_inst::EMol filter, bool force_name)

void x_GetReplacementIds(CConstRef< CSeq_id > id, bool force_name)

bool IsSkippable(void) const

CRef< CCmdComposite > GetRemoveOriginalIdCommand(void)

wxRadioButton * m_Proteins

wxBitmap GetBitmapResource(const wxString &name)

Retrieves bitmap resources.

void x_CollectChangedIds(void)

bool Create(wxWindow *parent, wxWindowID id=10420, const wxString &caption=_("Edit Sequence Id"), const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL)

Creation.

wxIcon GetIconResource(const wxString &name)

Retrieves icon resources.

wxRadioButton * m_GeneralTag

CStringConstraintPanel * m_StringConstraintPanel

CEditSeqId()

Constructors.

CParseTextOptionsDlg * m_ParseOptions

static bool ShowToolTips()

Should we show tooltips?

virtual CRef< CCmdComposite > GetCommand(void)

virtual ~CEditSeqId()

Destructor.

void Init()

Initialises member variables.

wxCheckBox * m_RemoveOrig

void CreateControls()

Creates the controls and sizers.

wxRadioButton * m_GeneralDb

CGeneralToLocalId(objects::CSeq_entry_Handle seh, CSeq_inst::EMol filter=CSeq_inst::eMol_not_set)

CLocalToGeneralId(objects::CSeq_entry_Handle seh, CSeq_inst::EMol filter=CSeq_inst::eMol_not_set)

vector< pair< CConstRef< CSeq_id >, CRef< CSeq_id > > > m_old_to_new_id

void x_ChangeId(objects::CSeq_id &id)

virtual CRef< CCmdComposite > GetCommand(void)

void x_UpdateSeqAlign(objects::CSeq_align &align)

virtual void x_UpdateBioseq(CRef< CBioseq > new_seq)

void x_UpdateSeqAnnot(objects::CSeq_annot &annot)

void x_GetRemoveOriginalIdCommand(CRef< CCmdComposite > cmd)

objects::CSeq_entry_Handle m_TopSeqEntry

set< string > m_remove_ids

void x_UpdateLoc(objects::CSeq_loc &loc)

void x_UpdateVariation(objects::CVariation_ref &var)

void x_UpdateFeat(objects::CSeq_feat &feat)

string GetSelectedText(const string &input)

CStringConstraintPanel * m_StringConstraintPanel

void Init()

Initialises member variables.

static bool ShowToolTips()

Should we show tooltips?

wxBitmap GetBitmapResource(const wxString &name)

Retrieves bitmap resources.

bool Create(wxWindow *parent, wxWindowID id=10420, const wxString &caption=_("Remove General Id"), const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL)

Creation.

void x_CollectChangedIds(void)

CRemoveGeneralId()

Constructors.

wxIcon GetIconResource(const wxString &name)

Retrieves icon resources.

virtual ~CRemoveGeneralId()

Destructor.

void CreateControls()

Creates the controls and sizers.

virtual CRef< CCmdComposite > GetCommand(void)

CRemoveName(objects::CSeq_entry_Handle seh)

void x_GetReplacementIds(CConstRef< CSeq_id > id)

virtual void x_UpdateBioseq(CRef< CBioseq > new_seq)

CRef< CCmdComposite > GetRemoveOriginalIdCommand()

namespace ncbi::objects::

void SetStringSelection(const wxString &str)

CRef< edit::CStringConstraint > GetStringConstraint()

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

const_iterator end() const

static vector< string > arr

USING_SCOPE(ncbi::objects)

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

static const char * str(char *buf, int n)

Utility macros and typedefs for exploring NCBI objects from general.asn.

#define FOR_EACH_USERFIELD_ON_USEROBJECT(Itr, Var)

FOR_EACH_USERFIELD_ON_USEROBJECT EDIT_EACH_USERFIELD_ON_USEROBJECT.

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

Set object to copy of another one.

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

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

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

Override Assign() to incorporate cache invalidation.

void SetId(CSeq_id &id)

set the 'id' field in all parts of this location

const CSeq_id * GetId(void) const

Get the id of the location return NULL if has multiple ids or no id at all.

bool IsSetInst_Mol(void) const

TClass GetClass(void) const

TBioseqCore GetBioseqCore(void) const

Get bioseq core structure.

bool CanGetClass(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.

@ fIncludeGivenEntry

Include the top (given) entry.

@ fRecursive

Iterate recursively.

CConstRef< C > ConstRef(const C *object)

Template function for conversion of const object pointer to CConstRef.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

static SIZE_TYPE Find(const CTempString str, const CTempString pattern, ECase use_case=eCase, EDirection direction=eForwardSearch, SIZE_TYPE occurrence=0)

Find the pattern in the string.

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 bool IsUpper(const CTempString str)

Checks if all letters in the given string have a upper case.

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.

@ fSplit_Tokenize

All delimiters are merged and trimmed, to get non-empty tokens only.

const TStr & GetStr(void) const

Get the variant data.

bool IsStr(void) const

Check if variant Str is selected.

bool IsSetDb(void) const

name of database or system Check if a value has been assigned to Db data member.

const TTag & GetTag(void) const

Get the Tag member data.

void SetTag(TTag &value)

Assign a value to Tag data member.

bool IsId(void) const

Check if variant Id is selected.

const TData & GetData(void) const

Get the Data member data.

bool IsSetTag(void) const

appropriate tag Check if a value has been assigned to Tag data member.

const TDb & GetDb(void) const

Get the Db member data.

void ResetTag(void)

Reset Tag data member.

bool IsStr(void) const

Check if variant Str is selected.

const TStr & GetStr(void) const

Get the variant data.

TStr & SetStr(void)

Select the variant.

const TLabel & GetLabel(void) const

Get the Label member data.

bool IsSetData(void) const

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

void SetDb(const TDb &value)

Assign a value to Db data member.

TId GetId(void) const

Get the variant data.

bool IsTRNA(void) const

Check if variant TRNA is selected.

bool IsSetAnticodon(void) const

location of anticodon Check if a value has been assigned to Anticodon data member.

bool IsSetExt(void) const

generic fields for ncRNA, tmRNA, miscRNA Check if a value has been assigned to Ext data member.

const TExt & GetExt(void) const

Get the Ext member data.

const TTRNA & GetTRNA(void) const

Get the variant data.

bool IsSetColumns(void) const

data in columns Check if a value has been assigned to Columns data member.

void SetSegs(TSegs &value)

Assign a value to Segs data member.

bool IsSetSegs(void) const

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

bool IsDendiag(void) const

Check if variant Dendiag is selected.

bool IsStd(void) const

Check if variant Std is selected.

const TSegs & GetSegs(void) const

Get the Segs member data.

bool IsDenseg(void) const

Check if variant Denseg is selected.

const TClone & GetClone(void) const

Get the variant data.

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.

bool IsCdregion(void) const

Check if variant Cdregion is selected.

bool IsSetSupport(void) const

will replace /experiment, /inference, model-evidence Check if a value has been assigned to Support da...

bool IsSetModel_evidence(void) const

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

Tdata & Set(void)

Assign a value to data member.

void SetProduct(TProduct &value)

Assign a value to Product data member.

void SetSupport(TSupport &value)

Assign a value to Support data member.

const TData & GetData(void) const

Get the Data member data.

void SetData(TData &value)

Assign a value to Data data member.

const TProduct & GetProduct(void) const

Get the Product member data.

bool IsClone(void) const

Check if variant Clone is selected.

bool IsVariation(void) const

Check if variant Variation is selected.

const TSupport & GetSupport(void) const

Get the Support member data.

bool IsSet(void) const

Check if a value has been assigned to data member.

const TRna & GetRna(void) const

Get the variant data.

bool IsSetProduct(void) const

product of process Check if a value has been assigned to Product data member.

bool IsRna(void) const

Check if variant Rna is selected.

bool IsSetInference(void) const

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

bool IsSetClone_seq(void) const

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

bool IsSetLocation(void) const

feature made from Check if a value has been assigned to Location data member.

TGeneral & SetGeneral(void)

Select the variant.

const TEmbl & GetEmbl(void) const

Get the variant data.

TEmbl & SetEmbl(void)

Select the variant.

const TTpe & GetTpe(void) const

Get the variant data.

TOther & SetOther(void)

Select the variant.

const TGenbank & GetGenbank(void) const

Get the variant data.

const TTpd & GetTpd(void) const

Get the variant data.

bool IsGeneral(void) const

Check if variant General is selected.

TTpe & SetTpe(void)

Select the variant.

const TTpg & GetTpg(void) const

Get the variant data.

TTpg & SetTpg(void)

Select the variant.

E_Choice Which(void) const

Which variant is currently selected.

TTpd & SetTpd(void)

Select the variant.

E_Choice

Choice variants.

TDdbj & SetDdbj(void)

Select the variant.

const TOther & GetOther(void) const

Get the variant data.

TLocal & SetLocal(void)

Select the variant.

const TDdbj & GetDdbj(void) const

Get the variant data.

const TLocal & GetLocal(void) const

Get the variant data.

void ResetName(void)

Reset Name data member.

bool IsLocal(void) const

Check if variant Local is selected.

const TGeneral & GetGeneral(void) const

Get the variant data.

TGenbank & SetGenbank(void)

Select the variant.

@ e_Other

for historical reasons, 'other' = 'refseq'

@ e_Tpe

Third Party Annot/Seq EMBL.

@ e_Tpd

Third Party Annot/Seq DDBJ.

@ e_Tpg

Third Party Annot/Seq Genbank.

bool IsSetLoc(void) const

region this applies to Check if a value has been assigned to Loc data member.

void SetLoc(TLoc &value)

Assign a value to Loc data member.

TSeq & SetSeq(void)

Select the variant.

@ eClass_nuc_prot

nuc acid and coded proteins

bool IsMap(void) const

Check if variant Map is selected.

const TSeg & GetSeg(void) const

Get the variant data.

void SetData(TData &value)

Assign a value to Data data member.

bool IsRef(void) const

Check if variant Ref is selected.

TId & SetId(void)

Assign a value to Id data member.

bool IsSetReplaced_by(void) const

these seqs make this one obsolete Check if a value has been assigned to Replaced_by data member.

const TInst & GetInst(void) const

Get the Inst member data.

bool IsSetAssembly(void) const

how was this assembled? Check if a value has been assigned to Assembly data member.

bool IsSetIds(void) const

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

Tdata & Set(void)

Assign a value to data member.

const TMap & GetMap(void) const

Get the variant data.

const TId & GetId(void) const

Get the Id member data.

bool IsSetHist(void) const

sequence history Check if a value has been assigned to Hist data member.

bool IsSetData(void) const

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

bool IsSetExt(void) const

extensions for special types Check if a value has been assigned to Ext data member.

bool IsSetReplaces(void) const

seq makes these seqs obsolete Check if a value has been assigned to Replaces data member.

bool IsSetInst(void) const

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

TDelta & SetDelta(void)

Select the variant.

Tdata & Set(void)

Assign a value to data member.

bool IsSet(void) const

Check if a value has been assigned to data member.

void SetReplaces(TReplaces &value)

Assign a value to Replaces data member.

bool IsSeg(void) const

Check if variant Seg is selected.

Tdata & Set(void)

Assign a value to data member.

bool IsDelta(void) const

Check if variant Delta is selected.

void SetInst(TInst &value)

Assign a value to Inst data member.

bool IsGraph(void) const

Check if variant Graph is selected.

const TSeq_table & GetSeq_table(void) const

Get the variant data.

EMol

molecule class in living organism

const TDelta & GetDelta(void) const

Get the variant data.

TSeg & SetSeg(void)

Select the variant.

bool IsSet(void) const

Check if a value has been assigned to data member.

const TData & GetData(void) const

Get the Data member data.

void SetReplaced_by(TReplaced_by &value)

Assign a value to Replaced_by data member.

bool IsSetId(void) const

equivalent identifiers Check if a value has been assigned to Id data member.

const TReplaces & GetReplaces(void) const

Get the Replaces member data.

bool IsSeq_table(void) const

Check if variant Seq_table is selected.

const TReplaced_by & GetReplaced_by(void) const

Get the Replaced_by member data.

TAssembly & SetAssembly(void)

Assign a value to Assembly data member.

bool IsIds(void) const

Check if variant Ids is selected.

bool IsSet(void) const

Check if a value has been assigned to data member.

TRef & SetRef(void)

Select the variant.

TMap & SetMap(void)

Select the variant.

bool IsLocs(void) const

Check if variant Locs is selected.

@ e_User

user defined object

@ eMol_na

just a nucleic acid

const TInstance & GetInstance(void) const

Get the variant data.

const TSet & GetSet(void) const

Get the variant data.

bool IsSetDelta(void) const

Sequence that replaces the location, in biological order.

TConsequence & SetConsequence(void)

Assign a value to Consequence data member.

void SetData(TData &value)

Assign a value to Data data member.

bool IsSetConsequence(void) const

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

const TData & GetData(void) const

Get the Data member data.

bool IsInstance(void) const

Check if variant Instance is selected.

bool IsSet(void) const

Check if variant Set is selected.

bool IsSetVariations(void) const

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

bool IsSetData(void) const

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

const struct ncbi::grid::netcache::search::fields::SIZE size

const GenericPointer< typename T::ValueType > T2 value

static bool GetSeqId(const T &d, set< string > &labels, const string name="", bool detect=false, bool found=false)

Utility macros and typedefs for exploring NCBI objects from seq.asn.

#define EDIT_EACH_SEQALIGN_ON_SEQANNOT(Itr, Var)

#define EDIT_EACH_SEQFEAT_ON_SEQANNOT(Itr, Var)

#define EDIT_EACH_SEQANNOT_ON_BIOSEQ(Itr, Var)

#define EDIT_EACH_ANNOTDESC_ON_SEQANNOT(Itr, Var)

Utility macros and typedefs for exploring NCBI objects from seqalign.asn.

#define EDIT_EACH_DENDIAG_ON_SEQALIGN(Itr, Var)

EDIT_EACH_DENDIAG_ON_SEQALIGN.

#define EDIT_EACH_SEQID_ON_DENDIAG(Itr, Var)

EDIT_EACH_SEQID_ON_DENDIAG.

#define EDIT_EACH_RECURSIVE_SEQALIGN_ON_SEQALIGN(Itr, Var)

EDIT_EACH_RECURSIVE_SEQALIGN_ON_SEQALIGN.

#define EDIT_EACH_STDSEG_ON_SEQALIGN(Itr, Var)

EDIT_EACH_STDSEG_ON_SEQALIGN.

#define EDIT_EACH_SEQID_ON_DENSEG(Itr, Var)

EDIT_EACH_SEQID_ON_DENSEG.

Utility macros and typedefs for exploring NCBI objects from seqfeat.asn.

#define EDIT_EACH_CODEBREAK_ON_CDREGION(Itr, Var)

Utility macros and typedefs for exploring NCBI objects from seqset.asn.

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