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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/OrgName_8cpp_source.html below:

NCBI C++ ToolKit: src/objects/seqfeat/OrgName.cpp Source File

70 switch

(name.

Which

()) {

84 if

( sSpecies.find(

" "

) != string::npos &&

95 if

( sSubspecies.find(

" "

) != string::npos && !bSubspIndicator ) {

97

name_out += sSubspecies;

101 if

( !bSubspIndicator ) {

102 string

sNomenclature;

103 bool

bZooCode =

false

;

105

bZooCode = sNomenclature ==

"Z"

;

108

bZooCode = sLineage.find(

"Metazoa;"

) != string::npos ||

109

sLineage.find(

"Slopalinida;"

) != string::npos ||

110

sLineage.find(

"Blastocystis;"

) != string::npos;

113

name_out +=

" subsp."

;

115 if

( sSubspecies.find_first_not_of(

"abcdefghijklmnopqrstuvwxyz-"

) != string::npos ||

116

sSubspecies[0] ==

'-'

) {

117

name_out +=

" ssp."

;

121

name_out +=

' '

+ sSubspecies;

130

name_out +=

" var. "

;

131

name_out += (*it)->GetSubname();

138

name_out += (*it)->GetSubname();

141

name_out +=

" f.sp. "

;

142

name_out += (*it)->GetSubname();

163 if

((*it)->GetFlatName(

tmp

, &sLineage)) {

165 if

( (*it)->IsSetName() && (*it)->GetName().IsHybrid() ) {

184

name_out += delim + (*it)->GetName();

215

list< CTempString > lVals;

217 for

( list< CTempString >::iterator

= lVals.begin(), li = lVals.end();

!= li; ) {

221 i

= lVals.erase(

);

237

list< CTempString > lVals;

256

list< CTempString > lVals;

261 i

->size() > name.size() && (*

)[name.size()] ==

'='

) {

262

sValue.assign(

->substr(name.size()+1) );

320 #define MAKE_COMMON(o1,o2,o3,Field) if (o1.IsSet##Field() && o2.IsSet##Field() && NStr::Equal(o1.Get##Field(), o2.Get##Field())) o3.Set##Field(o1.Get##Field()); 321 #define MAKE_COMMON_INT(o1,o2,o3,Field) if (o1.IsSet##Field() && o2.IsSet##Field() && o1.Get##Field() == o2.Get##Field()) o3.Set##Field(o1.Get##Field()); 339 if

((*it1)->Equals(**it2)) {

346

common->

SetMod

().push_back(add);

353 MAKE_COMMON

((*

this

), other, (*common), Lineage);

376 result

= (*ci)->GetSubname();

389

memset( norm_nom, 0,

sizeof

(norm_nom) );

390 ITERATE

(

string

, ci, nomenclature ) {

392 case 'b'

case 'B'

: norm_nom[0] =

'B'

;

break

;

393 case 'p'

case 'P'

: norm_nom[1] =

'P'

;

break

;

394 case 'v'

case 'V'

: norm_nom[2] =

'V'

;

break

;

395 case 'z'

case 'Z'

: norm_nom[3] =

'Z'

;

break

;

396 default

return false

;

400 for

(

size_t i

= 0;

sizeof

(norm_nom); ++

) {

401 if

( norm_nom[

] != 0 ) {

402

sNewVal += norm_nom[

];

408 if

( sOldVal == sNewVal ) {

414 if

( !sNewVal.empty() ) {

416 SetMod

().push_back( pMod );

432 for

( TMod::iterator

SetMod

().begin();

SetMod

().end(); ) {

433 if

( (*i)->GetSubtype() == to_remove ) {

#define MAKE_COMMON(o1, o2, o3, Field)

#define MAKE_COMMON_INT(o1, o2, o3, Field)

const CTempString s_flagDelim

User-defined methods of the data storage class.

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

bool x_GetAttribValue(const string &name, string &sValue) const

bool IsFormalName() const

bool x_GetAttribFlag(const string &name, bool bStartsWith=false) const

bool GetFlatName(string &name_out, string *lineage=0) const

unsigned int RemoveModBySubtype(COrgMod::ESubtype to_remove)

void DisableModifierForwarding()

void SetFormalNameFlag(bool bFormalName)

bool IsUncultured() const

void x_SetAttribFlag(const string &name, bool bStartsWith=false)

CRef< COrgName > MakeCommon(const COrgName &other) const

void SetUncultured(bool bUncultured)

void EnableModifierForwarding()

bool GetNomenclature(string &result) const

bool SetNomenclature(const string &nomenclature)

bool IsModifierForwardingDisabled() const

void x_ResetAttribFlag(const string &name, bool bStartsWith=false)

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

#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.

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.

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 void TruncateSpacesInPlace(string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string (in-place)

static string Join(const TContainer &arr, const CTempString &delim)

Join strings using the specified delimiter.

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 string TruncateSpaces(const string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string.

@ fSplit_Tokenize

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

@ eNocase

Case insensitive compare.

const TMod & GetMod(void) const

Get the Mod member data.

void ResetAttrib(void)

Reset Attrib data member.

const TLineage & GetLineage(void) const

Get the Lineage member data.

bool IsSetPgcode(void) const

plastid genetic code Check if a value has been assigned to Pgcode data member.

const TVirus & GetVirus(void) const

Get the variant data.

E_Choice Which(void) const

Which variant is currently selected.

const THybrid & GetHybrid(void) const

Get the variant data.

void SetName(TName &value)

Assign a value to Name data member.

bool IsSetLineage(void) const

lineage with semicolon separators Check if a value has been assigned to Lineage data member.

bool IsSetSubspecies(void) const

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

const TName & GetName(void) const

Get the Name member data.

bool IsSetMgcode(void) const

mitochondrial genetic code Check if a value has been assigned to Mgcode data member.

const TBinomial & GetBinomial(void) const

Get the variant data.

bool IsSetDiv(void) const

GenBank division code Check if a value has been assigned to Div data member.

bool IsSetMod(void) const

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

const Tdata & Get(void) const

Get the member data.

list< CRef< COrgMod > > TMod

bool IsSetAttrib(void) const

attribution of name Check if a value has been assigned to Attrib data member.

list< CRef< COrgName > > Tdata

const TSpecies & GetSpecies(void) const

Get the Species member data.

list< CRef< CTaxElement > > Tdata

bool IsSetGcode(void) const

genetic code (see CdRegion) Check if a value has been assigned to Gcode data member.

TMod & SetMod(void)

Assign a value to Mod data member.

const TGenus & GetGenus(void) const

Get the Genus member data.

const TPartial & GetPartial(void) const

Get the variant data.

TAttrib & SetAttrib(void)

Assign a value to Attrib data member.

const TNamedhybrid & GetNamedhybrid(void) const

Get the variant data.

bool IsSetSpecies(void) const

species required if subspecies used Check if a value has been assigned to Species data member.

bool IsSetName(void) const

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

const Tdata & Get(void) const

Get the member data.

const TSubspecies & GetSubspecies(void) const

Get the Subspecies member data.

const TAttrib & GetAttrib(void) const

Get the Attrib member data.

@ eSubtype_nomenclature

code of nomenclature in subname (B,P,V,Z or combination)

@ eSubtype_forma_specialis

@ e_Hybrid

hybrid between organisms

@ e_Namedhybrid

some hybrids have genus x species name

@ e_Binomial

genus/species type name

@ e_Partial

when genus not known

@ e_Virus

virus names are different

constexpr bool empty(list< Ts... >) noexcept

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