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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/pub__field_8cpp_source.html below:

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

((*it)->IsSetAuthors()) {

(seqdesc && seqdesc->

()) {

}

(pubdesc) {

any_change =

;

((*it)->Which()) {

(*it)->SetGen().SetAuthors().Assign(auth_list);

(*it)->SetSub().SetAuthors().Assign(auth_list);

(*it)->SetArticle().SetAuthors().Assign(auth_list);

(*it)->SetBook().SetAuthors().Assign(auth_list);

(*it)->SetProc().SetBook().SetAuthors().Assign(auth_list);

(*it)->SetPatent().SetAuthors().Assign(auth_list);

(*it)->SetMan().SetCit().SetAuthors().Assign(auth_list);

any_change(

);

((*it)->Which()) {

(*it)->SetGen().SetAuthors().SetNames().Assign(

);

(*it)->SetSub().SetAuthors().SetNames().Assign(

);

(*it)->SetArticle().SetAuthors().SetNames().Assign(

);

(*it)->SetBook().SetAuthors().SetNames().Assign(

);

(*it)->SetProc().SetBook().SetAuthors().SetNames().Assign(

);

(*it)->SetPatent().SetAuthors().SetNames().Assign(

);

(*it)->SetMan().SetCit().SetAuthors().SetNames().Assign(

);

}

(

exception &) {

(pub.

()) {

(seqdesc && seqdesc->

()) {

}

(citsub && citsub->

()) {

}

(pubdesc) {

(!title.

() || title.

().size() == 0) {

this_title->SetName(

);

title.

().push_back(this_title);

((*it)->IsName()) {

(*it)->SetName(

);

(*it)->SetName(

);

this_title->SetName(

);

title.

().push_back(this_title);

((*it)->Which()) {

(*it)->SetGen().SetTitle(title);

(skip_sub && !(*it)->GetSub().IsSetDescr()) {

(*it)->SetSub().SetDescr(title);

((*it)->SetProc().SetBook().SetTitle(), title);

(*it)->SetPatent().SetTitle(title);

((*it)->SetMan().SetCit().SetTitle(), title);

(pub.

()) {

(pub.

()) {

(field_type) {

(

.IsSetVolume()) {

rval =

.GetVolume();

(

.IsSetIssue()) {

rval =

.GetIssue();

(

.IsSetPages()) {

rval =

.GetPages();

(

.IsSetDate()) {

.GetDate().GetDate(&rval);

(field_type) {

new_imp->Assign(*imp);

(field_type) {

(field_type) {

new_list->Assign(*

);

rval =

(*new_list, field_type,

, constraint_field, string_constraint, existing_text);

new_list->SetNames().SetStd().push_back(new_auth);

(list<string>::iterator name =

.begin(); name !=

.end(); ++name)

vector<string> full_name;

first_name, last_name, middle_init, suffix;

(full_name.size() == 4)

first_name = full_name[0];

middle = full_name[1];

last_name = full_name[2];

suffix = full_name[3];

(full_name.size() == 3)

first_name = full_name[0];

middle = full_name[1];

last_name = full_name[2];

(full_name.size() == 2)

first_name = full_name[0];

last_name = full_name[1];

(full_name.size() == 1)

last_name = full_name[0];

new_auth->SetName().SetName().SetLast(last_name);

(!first_name.empty())

new_auth->SetName().SetName().SetFirst(first_name);

(!middle_init.empty())

new_auth->SetName().SetName().SetInitials(middle_init);

new_auth->SetName().SetName().SetSuffix(suffix);

auth_list.

().SetStd().push_back(new_auth);

auth_list.

().SetStd().clear();

auth_list.

().SetStd().push_back(new_auth);

rval =

(*auth_list, field_type, constraint_field, string_constraint);

(desc && desc->

()) {

(feat->

().SetPub(), newValue, existing_text);

}

(pubdesc) {

(*pubdesc, newValue, existing_text);

(*citsub, newValue, existing_text);

(!desc.

()) {

macro::CMacroFunction_SetPubStatus::s_SetStatus(pdesc, newValue);

pdesc.

().Set().push_back(pub);

orig_val =

;

curr_val =

;

(seqdesc && seqdesc->

()) {

}

(pubdesc) {

(*pubdesc);

}

(citsub) {

vector<string> vals =

(pdesc);

(vals.size() > 0) {

vector<string> vals =

(pub);

(vals.size() > 0) {

vector<string> vals =

(sub);

(vals.size() > 0) {

vector<string> vals;

(seqdesc && seqdesc->

()) {

}

(pubdesc) {

}

(citsub) {

}

(block && block->

()) {

vector<string> vals;

vals.push_back(

);

((*it)->IsPmid())

vector<string> vals;

vals.push_back(

);

vector<string> vals;

vals.push_back(

);

vector<string> vals;

(field_type) {

rval = macro::CMacroFunction_AuthorFix::s_InsertInitialPeriods(rval);

first_init = macro::CMacroFunction_AuthorFix::s_GetFirstNameInitials(auth.

().

().

());

rval = rval.substr(first_init.length());

(field_type) {

orig_first_init =

;

orig_first_init = macro::CMacroFunction_AuthorFix::s_GetFirstNameInitials(auth.

().

().

());

orig_first =

;

new_first_init = macro::CMacroFunction_AuthorFix::s_GetFirstNameInitials(

);

initials =

;

initials = macro::CMacroFunction_AuthorFix::s_InsertInitialPeriods(initials);

initials = initials.substr(orig_first_init.length());

initials = new_first_init + initials;

initials = initials +

;

auth.

().SetName().SetInitials(initials);

first_initials =

;

orig_initials =

;

first_initials = macro::CMacroFunction_AuthorFix::s_GetFirstNameInitials(auth.

().

().

());

orig_initials = macro::CMacroFunction_AuthorFix::s_InsertInitialPeriods(orig_initials);

orig_initials = orig_initials.substr(first_initials.length());

first_initials.append(orig_initials);

first_initials = macro::CMacroFunction_AuthorFix::s_InsertInitialPeriods(first_initials);

auth.

().SetName().SetInitials(orig_initials);

orig_val =

;

auth.

().SetName().SetLast(orig_val);

orig_val =

;

auth.

().SetName().SetSuffix(orig_val);

orig_val =

;

auth.

().SetConsortium(orig_val);

new_auth->Assign(*orig_auth);

(field_type) {

(orig_auth && orig_auth->

()) {

(orig_auth && orig_auth->

()) {

(field_type) {

vector<CConstRef<CObject> >

;

.Reset(&(*desc_ci));

vector<CRef<CApplyObject> >

;

vector<CConstRef<CObject> > objs;

bi (seh, objects::CSeq_inst::eMol_na);

(edit::CSeqIdGuesser::DoesSeqMatchConstraint(*bi, string_constraint)) {

vector<CConstRef<CObject> > these_objs =

(*bi);

objs.insert(objs.end(), these_objs.begin(), these_objs.end());

vector<CConstRef<CObject> > these_objs =

(*bi);

objs.push_back (*it);

(seqdesc && seqdesc->

()) {

}

(pubdesc) {

}

(citsub) {

}

(block && block->

()) {

vector<CConstRef<CObject> > related;

related.push_back(obj);

}

(obj_desc) {

(obj_desc->

()) {

related.push_back(obj);

vector<CConstRef<CObject> > related;

* obj_desc =

*

(&(

.GetObject()));

* obj_feat =

*

(&(

.GetObject()));

related.push_back(obj);

}

(obj_desc) {

(obj_desc->

()) {

related.push_back(obj);

}

(desc && desc->

()) {

}

(submit && submit->

()) {

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

@Auth_list.hpp User-defined methods of the data storage class.

void GetDate(string *label, bool year_only=false) const

Append a standardized string representation of the date to the label.

@Name_std.hpp User-defined methods of the data storage class.

static bool IsImprintField(EPubFieldType field_type)

static bool SetImprint(objects::CPub &pub, const objects::CImprint &imp)

static bool IsAffilField(EPubFieldType field_type)

@ ePubFieldType_AffilCountry

@ ePubFieldType_AffilEmail

@ ePubFieldType_AuthorLastName

@ ePubFieldType_AuthorFirstName

@ ePubFieldType_AffilDept

@ ePubFieldType_AffilState

@ ePubFieldType_AuthorConsortium

@ ePubFieldType_AuthorMiddleInitial

@ ePubFieldType_AuthorSuffix

@ ePubFieldType_AffilStreet

@ ePubFieldType_AffilCity

@ ePubFieldType_AffilAffil

static string GetLabelForStatus(EPubFieldStatus status)

static EPubFieldType GetTypeForLabel(string label)

static string GetLabelForType(EPubFieldType field_type)

static bool IsAuthorField(EPubFieldType field_type)

static CConstRef< objects::CImprint > GetImprint(const objects::CPub &pub)

static string GetStatus(const CObject &obj)

static bool SetJournal(CPubdesc &desc, const string &journal, objects::edit::EExistingText existing_text)

static bool SetImprint(CPub &pub, const CImprint &imp)

static string GetAuthorField(const CAuthor &auth, CPubFieldType::EPubFieldType field_type)

virtual bool IsEmpty(const CObject &object) const

string x_GetAuthorField(const CPubdesc &pdesc, CPubFieldType::EPubFieldType field_type, CPubFieldType::EPubFieldType constraint_field, CRef< edit::CStringConstraint > string_constraint)

static bool DoesAuthorMatchConstraint(const CAuthor &auth, CPubFieldType::EPubFieldType constraint_field, CRef< edit::CStringConstraint > string_constraint)

static CConstRef< CImprint > GetImprint(const CPub &pub)

virtual vector< string > GetVals(const CObject &object)

bool x_SetAuthorField(CPubdesc &pdesc, CPubFieldType::EPubFieldType field_type, string value, CPubFieldType::EPubFieldType constraint_field, CRef< edit::CStringConstraint > string_constraint, objects::edit::EExistingText existing_text)

virtual void ClearVal(CObject &object)

static bool SetAuthorField(CAuthor &auth, CPubFieldType::EPubFieldType field_type, string val, objects::edit::EExistingText existing_text)

CRef< objects::edit::CStringConstraint > m_StringConstraint

virtual string GetLabel() const

virtual bool AllowMultipleValues()

static string GetJournal(const CPubdesc &pdesc)

virtual vector< CConstRef< CObject > > GetRelatedObjects(const CObject &object, CRef< CScope > scope)

virtual void SetConstraint(const string &field_name, CConstRef< edit::CStringConstraint > string_constraint)

static CRef< CDate > GuessDate(const string &val)

virtual vector< CRef< objects::edit::CApplyObject > > GetApplyObjects(CBioseq_Handle bsh)

virtual bool SetVal(CObject &object, const string &newValue, objects::edit::EExistingText existing_text)

bool x_SetAffilField(CPubdesc &pdesc, CPubFieldType::EPubFieldType field_type, string value, objects::edit::EExistingText existing_text)

CPubFieldType::EPubFieldType m_FieldType

static bool SetPubTitle(CPubdesc &pdesc, const string &title, objects::edit::EExistingText existing_text, bool skip_sub=false)

string x_GetAffilField(const CPubdesc &pdesc, CPubFieldType::EPubFieldType field_type)

virtual string GetVal(const CObject &object)

CPubFieldType::EPubFieldType m_ConstraintFieldType

virtual vector< CConstRef< CObject > > GetObjects(CBioseq_Handle bsh)

bool x_SetImprintField(CPubdesc &desc, CPubFieldType::EPubFieldType field_type, const string &val, objects::edit::EExistingText existing_text)

static string GetPubTitle(const CPubdesc &pdesc)

string x_GetImprintField(const CPubdesc &pdesc, CPubFieldType::EPubFieldType field_type)

const CAuth_list & GetAuthors(void) const

bool IsSetAuthors(void) const

@Pubdesc.hpp User-defined methods of the data storage class.

namespace ncbi::objects::

bool DoesTextMatch(const string &text)

const string & GetTitle(C_E::E_Choice type=C_E::e_not_set) const

If the internal list contains a title (of the specified type, if given), returns the corresponding st...

static vector< string > arr

const char * kFieldTypeSeqId

static const struct name_t names[]

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

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

const TPrim & Get(void) const

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

CScope & GetScope(void) const

Get scope this handle belongs to.

const CSeq_feat & GetOriginalFeature(void) const

Get original feature with unmapped location/product.

TObjectType * GetPointer(void) const 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 int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

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 bool EndsWith(const CTempString str, const CTempString end, ECase use_case=eCase)

Check if a string ends with a specified suffix value.

static bool IsBlank(const CTempString str, SIZE_TYPE pos=0)

Check if a string is blank (has no text).

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

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 enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

@ fConvErr_NoThrow

Do not throw an exception on error.

@ fSplit_Tokenize

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

const TDescr & GetDescr(void) const

Get the Descr member data.

const TTitle & GetTitle(void) const

Get the Title member data.

bool IsSetVolume(void) const

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

bool IsSetDescr(void) const

description of changes for public view Check if a value has been assigned to Descr data member.

const TCit & GetCit(void) const

Get the Cit member data.

void SetPages(const TPages &value)

Assign a value to Pages data member.

bool IsSetAffil(void) const

author affiliation Check if a value has been assigned to Affil data member.

const TBook & GetBook(void) const

Get the Book member data.

const TJournal & GetJournal(void) const

Get the variant data.

bool IsSetTitle(void) const

title of journal Check if a value has been assigned to Title data member.

const TVolume & GetVolume(void) const

Get the Volume member data.

const TPages & GetPages(void) const

Get the Pages member data.

const TFrom & GetFrom(void) const

Get the From member data.

bool IsSetTitle(void) const

Title of book Check if a value has been assigned to Title data member.

void SetJournal(TJournal &value)

Assign a value to Journal data member.

void SetIssue(const TIssue &value)

Assign a value to Issue data member.

const TAffil & GetAffil(void) const

Get the Affil member data.

bool IsSetStreet(void) const

street address, not ANSI Check if a value has been assigned to Street data member.

void ResetNames(void)

Reset Names data member.

const TStr & GetStr(void) const

Get the variant data.

void SetName(TName &value)

Assign a value to Name data member.

bool IsSetTitle(void) const

title of paper (ANSI requires) Check if a value has been assigned to Title data member.

const TTitle & GetTitle(void) const

Get the Title member data.

const TAuthors & GetAuthors(void) const

Get the Authors member data.

void SetFrom(TFrom &value)

Assign a value to From data member.

bool IsSetCity(void) const

Author Affiliation, City Check if a value has been assigned to City data member.

const TIssue & GetIssue(void) const

Get the Issue member data.

const TEmail & GetEmail(void) const

Get the Email member data.

void SetAffil(TAffil &value)

Assign a value to Affil data member.

bool IsSetFrom(void) const

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

bool IsSetAuthors(void) const

not necessarily authors of the paper Check if a value has been assigned to Authors data member.

bool IsSetEmail(void) const

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

const TStreet & GetStreet(void) const

Get the Street member data.

const TName & GetName(void) const

Get the Name member data.

void SetAuthors(TAuthors &value)

Assign a value to Authors data member.

const TAffil & GetAffil(void) const

Get the Affil member data.

const TSub & GetSub(void) const

Get the Sub member data.

list< CRef< CAuthor > > TStd

list< CRef< C_E > > Tdata

void SetTitle(TTitle &value)

Assign a value to Title data member.

bool IsStr(void) const

Check if variant Str is selected.

const TTitle & GetTitle(void) const

Get the Title member data.

void SetDescr(const TDescr &value)

Assign a value to Descr data member.

bool IsSetNames(void) const

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

const TJournal & GetJournal(void) const

Get the Journal member data.

bool IsSetTitle(void) const

eg.

void SetVolume(const TVolume &value)

Assign a value to Volume data member.

void SetNames(TNames &value)

Assign a value to Names data member.

bool IsSetIssue(void) const

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

bool IsSetJournal(void) const

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

void SetDate(TDate &value)

Assign a value to Date data member.

bool IsSetDiv(void) const

Author Affiliation, Division Check if a value has been assigned to Div data member.

const TCountry & GetCountry(void) const

Get the Country member data.

const TStd & GetStd(void) const

Get the variant data.

bool IsSetDate(void) const

date of publication Check if a value has been assigned to Date data member.

bool IsSetName(void) const

Author, Primary or Secondary Check if a value has been assigned to Name data member.

bool IsSetTitle(void) const

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

const TImp & GetImp(void) const

Get the Imp member data.

bool IsSet(void) const

Check if a value has been assigned to data member.

bool IsSetBook(void) const

citation to meeting Check if a value has been assigned to Book data member.

bool IsJournal(void) const

Check if variant Journal is selected.

const TNames & GetNames(void) const

Get the Names member data.

bool IsSetCit(void) const

same fields as a book Check if a value has been assigned to Cit data member.

const TStd & GetStd(void) const

Get the variant data.

bool IsSetImp(void) const

this only used to get date.

const TDate & GetDate(void) const

Get the Date member data.

bool IsStd(void) const

Check if variant Std is selected.

const TTitle & GetTitle(void) const

Get the Title member data.

void SetImp(TImp &value)

Assign a value to Imp data member.

bool IsSetCountry(void) const

Author Affiliation, Country Check if a value has been assigned to Country data member.

const TTitle & GetTitle(void) const

Get the Title member data.

bool IsSetPages(void) const

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

const TCity & GetCity(void) const

Get the City member data.

bool IsSetAffil(void) const

Author Affiliation, Name Check if a value has been assigned to Affil data member.

const Tdata & Get(void) const

Get the member data.

const TDiv & GetDiv(void) const

Get the Div member data.

Tdata & Set(void)

Assign a value to data member.

bool IsSetSub(void) const

Author Affiliation, County Sub Check if a value has been assigned to Sub data member.

bool IsStd(void) const

Check if variant Std is selected.

@ e_not_set

No variant selected.

@ e_Name

Title, Anal,Coll,Mono AJB.

bool IsConsortium(void) const

Check if variant Consortium is selected.

void SetYear(TYear value)

Assign a value to Year data member.

bool IsSetSuffix(void) const

Jr, Sr, III Check if a value has been assigned to Suffix data member.

const TInitials & GetInitials(void) const

Get the Initials member data.

bool IsName(void) const

Check if variant Name is selected.

TStd & SetStd(void)

Select the variant.

bool IsSetInitials(void) const

first + middle initials Check if a value has been assigned to Initials data member.

bool IsSetLast(void) const

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

const TConsortium & GetConsortium(void) const

Get the variant data.

const TSuffix & GetSuffix(void) const

Get the Suffix member data.

const TFirst & GetFirst(void) const

Get the First member data.

const TLast & GetLast(void) const

Get the Last member data.

const TName & GetName(void) const

Get the variant data.

bool IsSetFirst(void) const

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

bool IsPmid(void) const

Check if variant Pmid is selected.

TPmid & SetPmid(void)

Select the variant.

list< CRef< CPub > > Tdata

const TMan & GetMan(void) const

Get the variant data.

const TPmid & GetPmid(void) const

Get the variant data.

const TArticle & GetArticle(void) const

Get the variant data.

const TJournal & GetJournal(void) const

Get the variant data.

const TSub & GetSub(void) const

Get the variant data.

const TPatent & GetPatent(void) const

Get the variant data.

const Tdata & Get(void) const

Get the member data.

const TProc & GetProc(void) const

Get the variant data.

E_Choice Which(void) const

Which variant is currently selected.

TGen & SetGen(void)

Select the variant.

const TGen & GetGen(void) const

Get the variant data.

TJournal & SetJournal(void)

Select the variant.

TArticle & SetArticle(void)

Select the variant.

bool IsGen(void) const

Check if variant Gen is selected.

const TBook & GetBook(void) const

Get the variant data.

@ e_Pat_id

identify a patent

@ e_Gen

general or generic unparsed

@ e_Proc

proceedings of a meeting

@ e_Equiv

to cite a variety of ways

@ e_Man

manuscript, thesis, or letter

const TPub & GetPub(void) const

Get the variant data.

bool IsSetData(void) const

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

const TLocation & GetLocation(void) const

Get the Location member data.

const TData & GetData(void) const

Get the Data member data.

bool IsPub(void) const

Check if variant Pub is selected.

void SetData(TData &value)

Assign a value to Data data member.

@ e_Pub

publication applies to this seq

void SetPub(TPub &value)

Assign a value to Pub data member.

TPub & SetPub(void)

Select the variant.

const TPub & GetPub(void) const

Get the variant data.

bool IsPub(void) const

Check if variant Pub is selected.

bool IsSetPub(void) const

the citation(s) Check if a value has been assigned to Pub data member.

E_Choice Which(void) const

Which variant is currently selected.

const TPub & GetPub(void) const

Get the Pub member data.

@ e_Pub

a reference to the publication

const TCit & GetCit(void) const

Get the Cit member data.

void SetCit(TCit &value)

Assign a value to Cit data member.

bool IsSetCit(void) const

citation for this submission Check if a value has been assigned to Cit data member.

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

bool DoesObjectMatchFieldConstraint(const CObject &object, const string &field_name, CRef< objects::edit::CStringConstraint > string_constraint, CRef< objects::CScope > scope)

const GenericPointer< typename T::ValueType > T2 value

SPSG_Reply::SState::SStatus s_GetStatus(SPSG_Reply::SItem::TTS &ts, const CDeadline &deadline)

CConstRef< CAuth_list > GetAuthList(const CPub &pub)

bool SetAuthorNames(CPubdesc &pdesc, const CAuth_list &auth_list)

bool SetAuthList(CPubdesc &pdesc, const CAuth_list &auth_list)

USING_SCOPE(ncbi::objects)

string GetTitleName(const CTitle &title)

string GetPubTitle(CConstRef< CObject > sel_pub)

void SetTitleName(CTitle &title, string val)

string GetFirstInitial(string input, bool skip_rest)

CRef< CPub > journal(ParserPtr pp, char *bptr, char *eptr, CRef< CAuth_list > &auth_list, CRef< CTitle::C_E > &title, bool has_muid, CRef< CCit_art > &cit_art, Int4 er)

@ eExistingText_replace_old

bool AddValueToString(string &str, const string &value, EExistingText existing_text)

Add text to an existing string, using the "existing_text" directive to combine new text with existing...

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