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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/Org__ref_8cpp_source.html below:

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

(TDb::const_iterator

= lDbTags.begin();

&&

->GetObject().GetDb().compare(

) == 0 ) {

(TDb::iterator

= lDbTags.begin();

().push_back( ref );

taxname =

;

(pos == string::npos) {

taxname = taxname.substr(pos + 1);

(pos == string::npos) {

taxname = taxname.substr(pos + 1);

value_len =

.length();

(pos != string::npos

&& ( ( (pos != 0 &&

(taxname.c_str()[pos - 1]))

||

(taxname.c_str()[pos + value_len])))) {

(pos == string::npos) {

&& (*it)->IsSetSubname() && !

((*it)->GetSubname())

(list< string >, it1, list1) {

(list< string >, it2, list2) {

list3.push_back(*it1);

(taxid1 != taxid2) {

common->

(*

);

((*

), other, (*common), Taxname);

(common->

().empty()) {

(common->

().empty()) {

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

common->

().push_back(add);

vector<string> tokens;

(tokens.size() != 8) {

taxon->

(

);

org->

().push_back(taxon);

(!

.empty()) {

(

+

+

);

(

);

num_orgrefs =

(kOrgRefList) /

(

*);

(

= 0;

< num_orgrefs;

++) {

*p = kOrgRefList[

];

}

(!

->AtEOF());

(

->IsSetGcode()) {

(

->IsSetMgcode()) {

(

->IsSetDivision()) {

(

->IsSetDb()) {

((*it)->IsSetDb() &&

(*it)->GetTag().IsId() &&

taxid = (*it)->GetTag().GetId();

(

->IsSetLineage()) {

(TDb::iterator

= lDbTags.begin();

!= lDbTags.end(); ) {

= lDbTags.erase(

);

bool s_FindWholeWord(string taxname, string value)

static const string s_nomenclature

static TOrgrefMap s_OrgRefMap

static void s_ProcessOrgRefMapLine(const CTempString &line)

static bool s_OrgRefMapInitialized

void s_MakeCommonStringList(const list< string > &list1, const list< string > &list2, list< string > &list3)

static vector< string > s_CommonTaxnameList

static void s_InitializeOrgRefMap(void)

map< string, CRef< COrg_ref >, PNocase > TOrgrefMap

DEFINE_STATIC_FAST_MUTEX(s_OrgRefMapMutex)

static const char *const s_taxonName

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

unsigned int RemoveModBySubtype(COrgMod::ESubtype to_remove)

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

void EnableModifierForwarding()

bool IsModifierForwardingDisabled() const

void GetLabel(string *label) const

const string & GetLineage(void) const

static CConstRef< COrg_ref > TableLookup(const string &taxname)

unsigned int fOrgref_parts

const string & GetDivision(void) const

TTaxId SetTaxId(TTaxId tax_id)

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

int GetPgcode(void) const

bool IsSetDivision(void) const

bool HasValidVariety() const

bool IsSetPgcode(void) const

bool IsSetGcode(void) const

bool IsSetMgcode(void) const

int GetMgcode(void) const

void FilterOutParts(fOrgref_parts to_remain)

string x_GetTaxnameAfterFirstTwoWords() const

static const vector< string > & GetTaxnameList()

bool IsVarietyValid(const string &variety) const

bool IsSetOrgMod(void) const

bool IsSubspeciesValid(const string &subspecies) const

bool IsSetLineage(void) const

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

container_type::iterator iterator

const_iterator end() const

const_iterator find(const key_type &key) const

static int lookup(const char *name, const struct lookup_int *table)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define TAX_ID_TO(T, tax_id)

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

SStrictId_Tax::TId TTaxId

Taxon id type.

#define TAX_ID_FROM(T, value)

#define LOG_POST(message)

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

#define NCBI_CATCH(message)

Catch CExceptions as well This macro is deprecated - use *_X or *_XX variant instead of it.

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.

static CRef< ILineReader > New(const string &filename)

Return a new ILineReader object corresponding to the given filename, taking "-" (but not "....

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static int StringToNonNegativeInt(const CTempString str, TStringToNumFlags flags=0)

Convert string to non-negative integer value.

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 IsBlank(const CTempString str, SIZE_TYPE pos=0)

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

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

Truncate whitespace in a string (in-place)

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 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[]

void SetTag(TTag &value)

Assign a value to Tag data member.

void SetDb(const TDb &value)

Assign a value to Db data member.

void ResetDiv(void)

Reset Div data member.

void ResetMod(void)

Reset Mod data member.

void ResetAttrib(void)

Reset Attrib data member.

bool IsSetDb(void) const

ids in taxonomic or culture dbases Check if a value has been assigned to Db data member.

TCommon & SetCommon(void)

Assign a value to Common 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 TDiv & GetDiv(void) const

Get the Div member data.

void ResetMgcode(void)

Reset Mgcode data member.

void ResetLineage(void)

Reset Lineage data member.

TMgcode GetMgcode(void) const

Get the Mgcode member data.

TGcode GetGcode(void) const

Get the Gcode member data.

void SetCommon(const TCommon &value)

Assign a value to Common data member.

bool IsSetCommon(void) const

common name Check if a value has been assigned to Common data member.

TDb & SetDb(void)

Assign a value to Db data member.

virtual void Reset(void)

Reset the whole object.

void ResetSyn(void)

Reset Syn data member.

bool IsSetLineage(void) const

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

vector< CRef< CDbtag > > TDb

bool IsSetMod(void) const

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

void SetDiv(const TDiv &value)

Assign a value to Div data member.

TSyn & SetSyn(void)

Assign a value to Syn data member.

TOrgname & SetOrgname(void)

Assign a value to Orgname data member.

const TTaxname & GetTaxname(void) const

Get the Taxname member data.

bool IsSetMgcode(void) const

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

void ResetGcode(void)

Reset Gcode data member.

void ResetTaxname(void)

Reset Taxname data member.

const TCommon & GetCommon(void) const

Get the Common member data.

const TDb & GetDb(void) const

Get the Db member data.

void ResetPgcode(void)

Reset Pgcode data member.

const TSyn & GetSyn(void) const

Get the Syn member data.

bool IsSetDiv(void) const

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

void SetTaxname(const TTaxname &value)

Assign a value to Taxname data member.

bool IsSetMod(void) const

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

void ResetCommon(void)

Reset Common data member.

void ResetMod(void)

Reset Mod data member.

list< CRef< COrgMod > > TMod

void ResetOrgname(void)

Reset Orgname data member.

void SetGcode(TGcode value)

Assign a value to Gcode data member.

void SetMgcode(TMgcode value)

Assign a value to Mgcode data member.

bool IsSetAttrib(void) const

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

void ResetDb(void)

Reset Db data member.

bool IsSetOrgname(void) const

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

bool IsSetTaxname(void) const

preferred formal name Check if a value has been assigned to Taxname data member.

void ResetName(void)

Reset Name data member.

TMod & SetMod(void)

Assign a value to Mod data member.

bool IsSetGcode(void) const

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

void SetOrgname(TOrgname &value)

Assign a value to Orgname data member.

const TMod & GetMod(void) const

Get the Mod member data.

bool IsSetSyn(void) const

synonyms for taxname or common Check if a value has been assigned to Syn data member.

TPgcode GetPgcode(void) const

Get the Pgcode member data.

bool IsSetName(void) const

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

void SetLineage(const TLineage &value)

Assign a value to Lineage data member.

const TOrgname & GetOrgname(void) const

Get the Orgname member data.

const GenericPointer< typename T::ValueType > T2 value

static SLJIT_INLINE sljit_ins lr(sljit_gpr dst, sljit_gpr src)

string g_FindDataFile(const CTempString &name, CDirEntry::EType type=CDirEntry::eFile)

Look for an NCBI application data file or directory of the given name and type; in general,...

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