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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/cuTaxClient_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/structure/cd_utils/cuTaxClient.cpp Source File

( vector<CSeq_id_Handle>, it, ids ) {

(it->GetSeqId()->IsGi()) {

gi = it->GetSeqId()->GetGi();

is_species, is_uncultured;

orgRef.

(*constOrgRef);

list< CRef< CSeqdesc > >::const_iterator j, jend;

(j=bioseq.

().

().begin(); j!=jend; j++)

org = &((*j)->GetOrg());

((*j)->IsSource())

org = &((*j)->GetSource().GetOrg());

vector < CRef< CDbtag > >::const_iterator k, kend = org->

().end();

(k=org->

().begin(); k != kend; ++k) {

((*k)->GetDb() ==

) {

((*k)->GetTag().IsId()) {

(

->IsSetOrg() &&

->GetOrg().IsSetTaxname()) {

taxName =

->GetOrg().GetTaxname();

(ancestor == taxid1);

v.push_back(rootTaxid);

lineageFromRoot.clear();

lineageFromRoot.push_back(taxid);

root(

);

vector<TTaxId> lineageAsTaxids;

pair<TTaxId, string> p;

lineageFromRoot.clear();

(vector<TTaxId>, vit, lineageAsTaxids) {

(!useCommonName) {

(commonName.length() > 0) {

p.second = (p.first >

(1)) ? commonName : root;

}

(useCommonName &&

(*vit, commonName) && commonName.length() > 0) {

p.second = (p.first >

(1)) ? commonName : root;

lineageFromRoot.push_back(p);

User-defined methods of the data storage class.

static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, CReader *reader=0, CObjectManager::EIsDefault is_default=CObjectManager::eDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

bool GetTaxId4GI(TGi gi, TTaxId &tax_id_out)

CConstRef< COrg_ref > GetOrgRef(TTaxId tax_id, bool &is_species, bool &is_uncultured, string &blast_name, bool *is_specified=NULL)

CRef< CTaxon2_data > GetById(TTaxId tax_id)

bool GetDisplayCommonName(TTaxId tax_id, string &disp_name_out)

bool GetPopsetJoin(const TTaxIdList &ids_in, TTaxIdList &ids_out)

TTaxId GetTaxIdByOrgRef(const COrg_ref &inp_orgRef)

TTaxId GetParent(TTaxId id_tax)

bool SetSynonyms(bool on_off)

TTaxId GetSuperkingdom(TTaxId id_tax)

CRef< ITreeIterator > GetTreeIterator(EIteratorMode mode=eIteratorMode_Default)

bool GetRankName(TTaxRank rank_id, string &rank_name_out)

TTaxId Join(TTaxId taxid1, TTaxId taxid2)

virtual TTaxRank GetRank() const =0

virtual const ITaxon1Node * GetNode() const =0

virtual short GetRankID(TTaxId taxId, string &rankName)

virtual bool GetFullLineage(TTaxId taxid, vector< TTaxId > &lineageFromRoot)

virtual string GetSuperKingdom(TTaxId taxid)

virtual bool SetSynonyms(bool on_off)

static const bool REFRESH_DEFAULT

virtual bool GetDisplayCommonName(TTaxId taxid, string &displayCommonName)

CTaxon1 * m_taxonomyClient

TaxClient(bool refresh=REFRESH_DEFAULT)

TTaxId Join(TTaxId taxid1, TTaxId taxid2)

virtual TTaxId GetTaxIDFromBioseq(const CBioseq &bioseq, bool lookInBioseq)

virtual TTaxId GetTaxIDForSeqId(CConstRef< CSeq_id > sid)

virtual bool ConnectToTaxServer()

virtual TTaxId GetParentTaxID(TTaxId taxid)

virtual TTaxId GetTaxIDForGI(TGi gi)

virtual bool GetOrgRef(TTaxId taxId, COrg_ref &orgRef)

virtual bool IsTaxDescendant(TTaxId tax1, TTaxId tax2)

virtual string GetTaxNameForTaxID(TTaxId taxid)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

SStrictId_Tax::TId TTaxId

Taxon id type.

#define TAX_ID_FROM(T, value)

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

Set object to copy of another one.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

TIds GetIds(const CSeq_id &id, TGetFlags flags=0)

Get "native" bioseq ids without filtering and matching.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

void AddDefaults(TPriority pri=kPriority_Default)

Add default data loaders from object manager.

bool Empty(void) const THROWS_NONE

Check if CConstRef is empty – not pointing to any object which means having a null value.

bool NotEmpty(void) const THROWS_NONE

Check if CRef is not empty – pointing to an object and has a non-null value.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

virtual void Reset(void)

Reset the whole object.

const TDb & GetDb(void) const

Get the Db member data.

TGi GetGi(void) const

Get the variant data.

bool IsGi(void) const

Check if variant Gi is selected.

const Tdata & Get(void) const

Get the member data.

bool IsSetDescr(void) const

descriptors Check if a value has been assigned to Descr data member.

const TDescr & GetDescr(void) const

Get the Descr member data.

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