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NCBI C++ ToolKit: src/objmgr/util/create_defline.cpp Source File

(

.find_first_of(

) != string::npos) {

(!

.empty()) {

(; (p2 =

.find(replace_what, p1)) != string::npos;

p1 = p2 + 1, p2 =

.length()) {

left = instr.

();

*

= instr.

();

(left && *

==

)

(left &&

[left - 1] ==

)

(left < 1)

;

*

= (

*)dest.c_str();

two_chars = curr;

two_chars =

((two_chars << 8) |

);

(

==

||

==

) {

(

==

||

==

) {

(curr > 0 && curr !=

) {

dest.resize(

- dest.c_str());

=

;

=

;

=

;

=

;

=

;

=

;

unverified_count = 0;

(unverified_count > 1) {

(sid.

()) {

& tsid = *

->GetTextseq_Id ();

& gen_id =

->GetGeneral ();

}

(oid.

()) {

ENeededDescChoices {

needed_desc_choices = fMolinfo | fUser | fSource | fGenbank | fEmbl | fComment;

desc_choices.reserve(7);

needed_desc_choices |= fTitle;

needed_desc_choices |= fPdb;

list <string> *keywords =

;

num_super_kingdom = 0;

super_kingdoms_different =

;

needed_desc_choices != 0 && desc_it; ++desc_it) {

(desc_it->Which()) {

((needed_desc_choices & fMolinfo) == 0) {

& molinf = desc_it->GetMolinfo();

needed_desc_choices &= ~fTitle;

needed_desc_choices &= ~fMolinfo;

((needed_desc_choices & fUser) == 0) {

unverified_count = 0;

needed_desc_choices &= ~fUser;

(unverified_count > 1) {

}

(user_obj.

().

() ==

) {

}

(user_obj.

().

() ==

) {

((needed_desc_choices & fComment) == 0) {

(

(

,

) != string::npos) {

((needed_desc_choices & fSource) != 0) {

needed_desc_choices &= ~fSource;

&bsrc = desc_it->GetSource();

(

& omd : onp.

()) {

(omd->IsSetSubname()) {

&

= omd->GetSubname();

(! pon.

())

;

& lvl = te.

();

num_super_kingdom++;

super_kingdoms_different =

;

(num_super_kingdom > 1 && super_kingdoms_different) {

((needed_desc_choices & fTitle) != 0) {

(

|| desc_it.GetSeq_entry_Handle().IsSeq() ) {

needed_desc_choices &= ~fTitle;

((needed_desc_choices & fGenbank) == 0) {

& gbk = desc_it->GetGenbank();

needed_desc_choices &= ~(fGenbank | fEmbl);

((needed_desc_choices & fEmbl) == 0) {

needed_desc_choices &= ~fEmbl;

((needed_desc_choices & fPdb) == 0) {

needed_desc_choices &= ~fPdb;

(keywords !=

) {

& clause = *kw_itr;

&

= *k_itr;

(!

.IsRsite())

;

(rsite.

()) {

}

(

exception& ) {

(pon.

()) {

& lvl = te.

();

& omd = **omd_itr;

}

(

exception& ) {

vector<CTempString>& desc,

desc.push_back(

);

desc.push_back(

);

desc.push_back(

);

desc.push_back(

);

desc.push_back(

);

(strain.

() >= taxname.

()) {

pos = taxname.

(

, pos + 1);

(pos == taxname.

() - strain.

()) {

ch = taxname[pos - 1];

}

(pos == taxname.

() - strain.

() - 1

&& taxname[pos - 1] ==

&& taxname[taxname.

() - 1] ==

) {

[](

c) {

c ==

|| c ==

|| c ==

; }),

[](

c) {

c ==

|| c ==

; }),

(!specimen_voucher.

()) {

joiner.

(

, specimen_voucher);

(!isolate.

() && (isolate != specimen_voucher)) {

joiner.

(

, isolate);

joiner.

(

, add);

joiner.

(

, add);

joiner.

(

,

,

);

vector<CTempString> clnvec;

(vector<CTempString>, it, clnvec) {

add_gen_tag =

;

add_gen_tag =

;

(pos > 0 && !

((

)s[pos - 1]) ) {

(pos + 3 <

&&

((

)s[pos])) {

(s[pos] ==

&& s[pos + 1] ==

&&

((

)s[pos + 2]) &&

(pos + 3 ==

|| strchr(

, s[pos + 3])) ) {

genes = 0, cdregions = 0;

& sft = feat_it->GetOriginalFeature();

cdregion.

(&sft);

cds_label, gene_label;

.

(gene_label).

(

);

& sft = feat_it->GetOriginalFeature();

joiner.

(

).

(seqno).

(

)

joiner.

(

, add);

joiner.

(

, add);

vector<CTempString> clnvec;

(vector<CTempString>, it, clnvec) {

joiner.

(

,

,

);

& feat = feat_it->GetOriginalFeature();

(prot_length > longest) {

longest = prot_length;

bestprocessed = processed;

}

(prot_length == longest) {

(processed < bestprocessed) {

longest = prot_length;

bestprocessed = processed;

(longest == seq_len && prot_feat) {

}

(

exception& ) {

cleaned_location->

( *cds_loc );

cleaned_location->

(*rev_loc);

current_state = 0;

ch = *str_itr;

current_state = next_state;

,

(

.empty())

;

(taxname.empty())

;

(

< 5)

;

(

[

- 1] !=

)

;

suffix =

.substr(cp+1);

(suffix.length() != taxlen + 1)

;

* prefix =

;

&

= *prp_itr;

comma =

;

comma =

;

(! locus_tag.

()) {

(! isoform.empty()) {

&

= *act_itr;

&

= *syn_itr;

(! locus_tag.

()) {

& low_qual =

;

( organelle[0] !=

&& ! taxname.

()

((taxname.

() ||

taxname.

(

) ==

&&

taxname.

(

) ==

)) &&

}

(! taxname.

()

) {

* prefix =

;

&

= *prp_itr;

comma =

;

comma =

;

(! locus_tag.

()) {

&

= *act_itr;

&

= *syn_itr;

(! locus_tag.

()) {

& low_qual =

;

( organelle[0] !=

&& ! taxname.

()

((taxname.

() ||

taxname.

(

) ==

&&

taxname.

(

) ==

)) &&

}

(! taxname.

()

) {

*& completeness,

& cds = it->GetOriginalFeature();

completeness =

;

(locus.empty()) {

* completeness =

;

cds_found =

;

locus, product;

vector<CTempString> clnvec;

(vector<CTempString>, it, clnvec) {

(! product.empty()) {

(! locus.empty()) {

((! product.empty()) || (! locus.empty())) {

vector<CTempString> clnvec;

(vector<CTempString>, it, clnvec) {

(!

.empty()) {

prefix =

;

prefix =

;

prefix =

;

nucx = bsxp.

();

(nucx->IsTPAExp()) {

prefix =

;

}

(nucx->IsTPAInf()) {

prefix =

;

}

(nucx->IsTPAReasm()) {

prefix =

;

(prefix.empty()) {

prefix =

;

prefix =

;

prefix =

;

=

;

=

;

=

;

pieces = 1;

+

+ un +

);

=

;

=

;

=

;

=

;

(

.find (

) ==

){

=

;

}

(

.find (

) ==

) {

+=

;

(

.find(

) ==

) {

=

;

=

;

=

;

=

;

=

;

=

;

+=

;

(appendComplete) {

comp =

;

comp =

;

comp =

;

comp =

;

comp =

;

num_gaps = 0;

+

);

(! study.empty()) {

suffix =

+ study +

+

+ comp;

suffix =

+ comp;

pos =

.find_last_not_of (

);

.erase (pos + 1);

len1 = title.length();

len2 = taxname.

();

idx = len1 - len2 - 3;

(len1 > len2 + 4 && title [idx] ==

&& title [idx + 1] ==

&& title [len1 - 1] ==

) {

(pos == idx + 2) {

pos, tpos =

, opos =

;

(len1 > len2 + 4) {

(tpos ==

) {

(tpos ==

) {

(tpos ==

) {

(tpos ==

)

;

( !

.empty() ) {

paren =

+

+

;

(opos !=

) {

( organelle[0] !=

&& ! taxname.

()

((taxname.

() ||

taxname.

(

) ==

&&

taxname.

(

) ==

)) &&

nucx = bsxp.

();

}

(! taxname.

()

) {

pos, tpos =

, opos =

;

(len1 > len2 + 4) {

(tpos ==

) {

(tpos ==

) {

(tpos ==

)

;

( !

.empty() ) {

paren =

+

+

;

(opos !=

) {

( organelle[0] !=

&& ! taxname.

()

((taxname.

() ||

taxname.

(

) ==

&&

taxname.

(

) ==

)) &&

nucx = bsxp.

();

}

(! taxname.

()

) {

,

,

strain_seen =

;

(

.IsSetSubtype() &&

.IsSetSubname()) {

(

.GetSubtype()) {

<<

);

strain_seen =

;

joiner.

(

,

);

joiner.

(

,

);

joiner.

(

,

);

gcode = std::to_string(icode);

joiner.

(

, gcode);

gcode = std::to_string(icode);

joiner.

(

, gcode);

joiner.

(

,

);

gcode = std::to_string(icode);

joiner.

(

, gcode);

joiner.

(

,

);

joiner.

(

,

);

joiner.

(

,

);

joiner.

(

,

);

joiner.

(

,

);

joiner.

(

,

);

joiner.

(

,

);

( primers.

() ) {

( (*it)->IsSetForward() ) {

( forward.

() ) {

&fwd_name = ( (*it2)->CanGetName() ? (*it2)->GetName().Get() :

);

( ! fwd_name.empty() ) {

joiner.

(

, fwd_name);

&fwd_seq = ( (*it2)->CanGetSeq() ? (*it2)->GetSeq().Get() :

);

( ! fwd_seq.empty() ) {

joiner.

(

, fwd_seq);

( (*it)->IsSetReverse() ) {

( reverse.

() ) {

&rev_name = ((*it2)->CanGetName() ? (*it2)->GetName().Get() :

);

( ! rev_name.empty() ) {

joiner.

(

, rev_name);

&rev_seq = ( (*it2)->CanGetSeq() ? (*it2)->GetSeq().Get() :

);

( ! rev_seq.empty() ) {

joiner.

(

, rev_seq);

(pMolInfo !=

) {

& molinfo = *pMolInfo;

(find_iter != sc_TechMap.end()) {

joiner.

(&modifiers);

capitalize =

;

appendComplete =

;

pos =

.find_last_not_of (

);

capitalize =

;

appendComplete =

;

pos = decoded.find_last_not_of (

);

decoded.erase (pos + 1);

( prefix.empty() ) {

penult = mag + prefix + decoded + suffix;

(!

.

() &&

((

)

[0]) && capitalize) {

[0] =

((

)

[0]);

feature::CFeatTree& ftree,

feature::CFeatTree& ftree,

(

, 1);

(

, 2);

(

, 3);

User-defined methods of the data storage class.

User-defined methods of the data storage class.

void remove_if(Container &c, Predicate *__pred)

void SetOptions(const CAutoDefOptions &options)

void InitFromUserObject(const CUser_object &obj)

void SetOptionsObject(const CUser_object &user)

string GetOneDefLine(CAutoDefModifierCombo *mod_combo, const CBioseq_Handle &bh, CRef< feature::CFeatTree > featTree=null)

const string & GetTaxname(void) const

const COrgName & GetOrgname(void) const

bool IsSetOrgname(void) const

bool IsSetTaxname(void) const

CTempString GetSubstrain(void)

int GetPatentSequence(void) const

CSeq_inst::TLength GetLength(void) const

CTempString GetCultivar(void)

CTempString GetMetaGenomeSource(void)

CTempString GetBreed(void)

CTempString GetGenus(void)

CMolInfo::TTech GetTech(void)

CRef< CFeatureIndex > GetFeatureForProduct(void)

CTempString GetStrain(void)

bool IsTSAMaster(void) const

bool IsHTGSCancelled(void)

bool IsThirdParty(void) const

bool IsPatent(void) const

bool IsUnverifiedFeature(void)

CTempString GetSpecies(void)

CConstRef< CBioSource > GetBioSource(void)

bool IsWGSMaster(void) const

bool IsTLSMaster(void) const

string GetSecondSuperKingdom(void)

CMolInfo::TCompleteness GetCompleteness(void)

int GetPDBChain(void) const

string GetPatentCountry(void) const

bool IsCrossKingdom(void)

string GetPDBChainID(void) const

CTempString GetIsolate(void)

CTempString GetPDBCompound(void)

const string & GetTitle(void)

string GetPatentNumber(void) const

bool IsUnreviewedUnannotated(void)

CTempString GetSegment(void)

CTempString GetLinkageGroup(void)

const string & GetTaxname(void)

CSeq_inst::TTopology GetTopology(void) const

CWeakRef< CBioseqIndex > GetBioseqForProduct(void)

int GetGeneralId(void) const

const string & GetOrganelle(void)

CRef< CFeatureIndex > GetBestProteinFeature(void)

string GetGeneralStr(void) const

bool IsVirtual(void) const

CTempString GetSpecimenVoucher(void)

CTempString GetClone(void)

CBioSource::TGenome GetGenome(void)

CTempString GetChromosome(void)

bool IsUnverifiedMisassembled(void)

CMolInfo::TBiomol GetBiomol(void)

bool IsHTGSUnfinished(void)

CTempString GetPlasmid(void)

string GetFirstSuperKingdom(void)

bool IsUnverifiedContaminant(void)

bool IsMultispecies(void)

const string & GetComment(void)

bool IsUnverifiedOrganism(void)

CTempString GetTargetedLocus(void)

const string & GetDescTaxname(void)

bool IsSkippable(void) const

void ReplaceAndAdd(const CTempString &value, const CTempString &replace_what, const CTempString &replace_with)

void Add(const CTempString &name, const CTempString &value, EHidePart hide=eHideNone)

CDefLineJoiner(bool show_mods=false)

CTextJoiner< 64, CTempString > m_Joiner

void Join(std::string *result) const

CRef< CFeatureIndex > GetBestGene(void)

const CMappedFeat GetMappedFeat(void) const

const string & GetSomeNumber(void) const

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

CRef< CBioseqIndex > GetBioseqIndex(void)

namespace ncbi::objects::

class CStaticArrayMap<> is an array adaptor that provides an STLish interface to statically-defined a...

TBase::const_iterator const_iterator

static bool NCBI_UseGeoLocNameForCountry(void)

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

@ eObjectType_AutodefOptions

bool IsUnverifiedMisassembled() const

bool IsUnverifiedOrganism() const

bool IsUnverifiedContaminant() const

bool IsUnverifiedFeature() const

bool IsUnverified() const

bool IsUnreviewedUnannotated() const

bool IsUnreviewed() const

EObjectType GetObjectType() const

static size_t s_TitleEndsInOrganism(string &title, CTempString taxname)

static bool x_GetSegSeqInfoViaCDS(string &locus, string &product, const char *&completeness, const CBioseq_Handle &bsh)

static void s_AddVoucherAndIsolate(const CTempString &taxname, const CTempString &strain, const CTempString &specimen_voucher, const CTempString &isolate, CDefLineJoiner &joiner)

#define FOR_EACH_SEQID_ON_BIOSEQ_HANDLE(Itr, Var)

void x_CleanAndCompress(string &dest, const CTempString &instr, bool isProt)

#define FOR_SELECTED_SEQFEAT_ON_BIOSEQ_HANDLE(Itr, Var, Sel)

static string s_RemoveWhiteSpace(string str)

static string s_RemoveBracketedOrgFromEnd(string str, string taxname)

#define FOR_EACH_SEQFEAT_ON_BIOSEQ_HANDLE(Itr, Var, Chs)

static void x_FlyCG_PtoR(string &s)

#define FOR_EACH_SEQFEAT_ON_SCOPE(Itr, Var, Loc, Chs)

static void s_TrimMainTitle(string &str)

static bool s_EndsWithStrain(const CTempString &taxname, const CTempString &strain)

static const char * s_proteinOrganellePrefix[]

static string s_RemoveColonsAndWhiteSpace(string str)

static CConstRef< CBioSource > x_GetSourceFeatViaCDS(const CBioseq_Handle &bsh)

static const char * s_tpaPrefixList[]

static bool s_IsVirusOrPhage(const CTempString &taxname)

API (CDeflineGenerator) for computing sequences' titles ("definitions").

std::ofstream out("events_result.xml")

main entry point for tests

static DLIST_TYPE *DLIST_NAME() next(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

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

#define FOR_EACH_USERFIELD_ON_USEROBJECT(Itr, Var)

FOR_EACH_USERFIELD_ON_USEROBJECT EDIT_EACH_USERFIELD_ON_USEROBJECT.

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define ERR_POST_X(err_subcode, message)

Error posting with default error code and given error subcode.

void Warning(CExceptionArgs_Base &args)

static EAccessionInfo IdentifyAccession(const CTempString &accession, TParseFlags flags=fParse_AnyRaw)

Deduces information from a bare accession a la WHICH_db_accession; may report false negatives on prop...

CConstRef< CSeq_id > GetSeqId(void) const

EAccessionInfo

For IdentifyAccession (below)

CSeq_id::E_Choice Which(void) const

string GetLabel(const CSeq_id &id)

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

Override Assign() to incorporate cache invalidation.

CMappedFeat GetBestGeneForCds(const CMappedFeat &cds_feat, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0, CFeatTree::EBestGeneType lookup_type=CFeatTree::eBestGene_TreeOnly)

CMappedFeat GetBestOverlappingFeat(const CMappedFeat &feat, CSeqFeatData::ESubtype need_subtype, sequence::EOverlapType overlap_type, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0)

@ fFGL_Content

Include its content if there is any.

TSeqPos GetLength(const CSeq_id &id, CScope *scope)

Get sequence length if scope not null, else return max possible TSeqPos.

CSeq_loc * SeqLocRevCmpl(const CSeq_loc &loc, CScope *scope)

Get reverse complement of the seq-loc (?)

@ eOverlap_SubsetRev

1st is a subset of 2nd ranges

@ eOverlap_Contained

2nd contained within 1st extremes

void x_AdjustProteinTitleSuffixIdx(const CBioseq_Handle &bsh)

CRef< feature::CFeatTree > m_Feat_Tree

CTempString m_Chromosome

subsource fields

CTempString m_SpecimenVoucher

CDeflineGenerator(void)

Constructor.

void x_SetTitleFromNR(const CBioseq_Handle &bsh)

bool m_Reconstruct

ignore existing title is forced for certain types

const CSeq_feat * GetCDSForProduct(const CBioseq &product, CScope *scope)

Get the encoding CDS feature of a given protein sequence.

void x_SetTitleFromGPipe(void)

int TUserFlags

Binary "OR" of EUserFlags.

CTempString m_PDBCompound

pdb block fields

bool m_HTGSCancelled

genbank or embl block keyword fields

void x_DescribeClones(vector< CTempString > &desc, string &buf)

CTempString m_UnreviewedPrefix

void x_SetTitleFromMap(void)

string GenerateDefline(const CBioseq_Handle &bsh, TUserFlags flags=0)

Main method.

bool m_ConstructedFeatTree

string m_FirstSuperKingdom

CTempString m_LinkageGroup

void x_SetTitleFromWGS(void)

bool m_UsePDBCompoundForDefline

bool m_IsNA

seq-inst fields

void x_SetTitleFromProtein(const CBioseq_Handle &bsh)

void x_SetBioSrcIdx(const CBioseq_Handle &bsh)

void x_SetFlagsIdx(const CBioseq_Handle &bsh, TUserFlags flags)

CSeq_inst::TLength m_Length

string m_rEnzyme

map fields

const char * x_OrganelleName(CBioSource::TGenome genome) const

CConstRef< CGene_ref > x_GetGeneRefViaCDS(const CMappedFeat &mapped_cds)

CConstRef< CSeq_feat > x_GetLongestProtein(const CBioseq_Handle &bsh)

CTempString m_UnverifiedPrefix

void x_AdjustProteinTitleSuffix(const CBioseq_Handle &bsh)

void x_SetTitleFromProteinIdx(const CBioseq_Handle &bsh)

const CBioSource * GetBioSource(const CBioseq &bioseq)

Retrieve the BioSource object for a given bioseq handle.

bool m_InitializedFeatTree

CBioSource::TGenome m_Genome

string x_GetModifiers(const CBioseq_Handle &handle)

void x_SetTitleFromPatent(void)

const CMolInfo * GetMolInfo(const CBioseq &bioseq)

Retrieve the MolInfo object for a given bioseq handle.

CTempString m_Comment

comment fields

bool x_IsComplete() const

void x_SetTitleFromSegSeq(const CBioseq_Handle &bsh)

void x_SetTitleFromNC(void)

~CDeflineGenerator(void)

Destructor.

bool m_IsNC

seq-id fields

CMappedFeat GetMappedCDSForProduct(const CBioseq_Handle &product)

CConstRef< CBioSource > m_Source

biosource fields

CTempString m_TargetedLocus

static CSafeStatic< CLowQualityTextFsm > ms_p_Low_Quality_Fsa

void x_SetBioSrc(const CBioseq_Handle &bsh)

bool m_IsUnverified

user object fields

void x_SetTitleFromBioSrc(void)

void x_Init(void)

internal methods

void x_SetTitleFromPDB(void)

CSeq_entry_Handle m_TopSEH

internal feature tree for parent mapping

void x_SetSuffix(string &suffix, const CBioseq_Handle &bsh, bool appendComplete)

CMolInfo::TCompleteness m_MICompleteness

string m_SecondSuperKingdom

void x_SetTitleFromNM(const CBioseq_Handle &bsh)

bool x_CDShasLowQualityException(const CSeq_feat &sft)

void x_SetFlags(const CBioseq_Handle &bsh, TUserFlags flags)

CTempString m_Breed

orgmod fields

CRef< CSeqEntryIndex > m_Idx

index with feature tree for each Bioseq

CTempString m_MetaGenomeSource

CSeq_inst::TTopology m_Topology

void x_SetPrefix(string &prefix, const CBioseq_Handle &bsh)

CMolInfo::TBiomol m_MIBiomol

molinfo fields

@ fLocalAnnotsOnly

Never use related sequences' annotations.

@ fDevMode

Development mode for testing new features.

@ fDoNotUseAutoDef

Disable internal call to auto-def.

@ fLeavePrefixSuffix

Do not remove and recreate prefix or suffix.

@ fGpipeMode

Use GPipe defaults.

@ fOmitTaxonomicName

Do not add organism suffix to proteins.

@ fFastaFormat

Generate FASTA defline.

@ fShowModifiers

Show key-value pair modifiers (e.g. "[organism=Homo sapiens]")

@ fIgnoreExisting

Generate fresh titles unconditionally.

@ fAllProteinNames

List all relevant proteins, not just one.

CBioseq_Handle AddBioseq(CBioseq &bioseq, TPriority pri=kPriority_Default, EExist action=eExist_Throw)

Add bioseq, return bioseq handle.

@ kPriority_Default

Use default priority for added data.

const TInst_Ext & GetInst_Ext(void) const

bool IsSetInst_Ext(void) const

const CSeqFeatData & GetData(void) const

CConstRef< CSeq_id > GetSeqId(void) const

Get id which can be used to access this bioseq handle Throws an exception if none is available.

bool IsSetInst_Length(void) const

TInst_Topology GetInst_Topology(void) const

TInst_Length GetInst_Length(void) const

bool IsSetInst(void) const

bool IsSetInst_Repr(void) const

bool CanGetInst_Topology(void) const

TInst_Repr GetInst_Repr(void) const

CScope & GetScope(void) const

Get scope this handle belongs to.

SAnnotSelector & SetResolveTSE(void)

SetResolveTSE() is equivalent to SetResolveMethod(eResolve_TSE).

SAnnotSelector & SetFeatType(TFeatType type)

Set feature type (also set annotation type to feat)

const CSeq_feat & GetOriginalFeature(void) const

Get original feature with unmapped location/product.

SAnnotSelector & IncludeFeatType(TFeatType type)

Include feature type in the search.

vector< CSeqdesc::E_Choice > TDescChoices

bool Empty(void) const THROWS_NONE

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

void Reset(void)

Reset reference object.

void Reset(void)

Reset reference object.

TRefType Lock(void) const

Lock the object and return reference to it.

bool NotEmpty(void) const THROWS_NONE

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

bool Empty(void) const THROWS_NONE

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

uint16_t Uint2

2-byte (16-bit) unsigned integer

void AddWord(const string &word, const int &match)

static string HtmlDecode(const CTempString str, EEncoding encoding=eEncoding_Unknown, THtmlDecode *result_flags=NULL)

Decode HTML entities and character references.

NCBI_NS_STD::string::size_type SIZE_TYPE

CTextJoiner & Add(const TIn &s)

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 SIZE_TYPE FindNoCase(const CTempString str, const CTempString pattern, SIZE_TYPE start, SIZE_TYPE end, EOccurrence which=eFirst)

Find the pattern in the specified range of a string using a case insensitive search.

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

Check if a string ends with a specified suffix value.

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

Truncate whitespace in a string (in-place)

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.

void Join(TOut *result) const

const char * data(void) const

Return a pointer to the array represented.

bool empty(void) const

Return true if the represented string is empty (i.e., the length is zero)

static SIZE_TYPE FindCase(const CTempString str, const CTempString pattern, SIZE_TYPE start, SIZE_TYPE end, EOccurrence which=eFirst)

Find the pattern in the specified range of a string using a case sensitive search.

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

Check if a string starts with a specified prefix value.

void clear(void)

Clears the string.

size_type length(void) const

Return the length of the represented array.

CTempString substr(size_type pos) const

Obtain a substring from this string, beginning at a given offset.

size_type find_first_not_of(const CTempString match, size_type pos=0) const

Find the first occurrence of any character not in the matching string within the current 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 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.

size_type find(const CTempString match, size_type pos=0) const

Find the first instance of the entire matching string within the current string, beginning at an opti...

static string & ReplaceInPlace(string &src, const string &search, const string &replace, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a string.

const char *const kEmptyCStr

Empty "C" string (points to a '\0').

size_type size(void) const

Return the length of the represented array.

@ fSplit_Tokenize

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

@ eReverseSearch

Search in a backward direction.

@ eNocase

Case insensitive compare.

const TKeywords & GetKeywords(void) const

Get the Keywords member data.

bool IsSetKeywords(void) const

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

const TKeywords & GetKeywords(void) const

Get the Keywords member data.

bool IsSetKeywords(void) const

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

const TCountry & GetCountry(void) const

Get the Country member data.

const Tdata & Get(void) const

Get the member data.

const TSubtype & GetSubtype(void) const

Get the Subtype member data.

const TPcr_primers & GetPcr_primers(void) const

Get the Pcr_primers member data.

TGenome GetGenome(void) const

Get the Genome member data.

const Tdata & Get(void) const

Get the member data.

bool IsSetOrg(void) const

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

list< CRef< CSubSource > > TSubtype

bool IsSetSubtype(void) const

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

bool IsSetPcr_primers(void) const

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

bool CanGetGenome(void) const

Check if it is safe to call GetGenome method.

const TOrg & GetOrg(void) const

Get the Org member data.

TSubtype GetSubtype(void) const

Get the Subtype member data.

bool CanGet(void) const

Check if it is safe to call Get method.

bool IsSetGenome(void) const

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

bool IsSetSubtype(void) const

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

bool CanGet(void) const

Check if it is safe to call Get method.

const TName & GetName(void) const

Get the Name member data.

list< CRef< CPCRReaction > > Tdata

bool IsSetName(void) const

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

list< CRef< CPCRPrimer > > Tdata

@ eSubtype_collection_date

DD-MMM-YYYY format.

@ eSubtype_insertion_seq_name

@ eSubtype_transposon_name

@ eSubtype_lat_lon

+/- decimal degrees

@ eSubtype_collected_by

name of person who collected the sample

@ eSubtype_isolation_source

@ eSubtype_environmental_sample

@ eSubtype_endogenous_virus_name

@ eSubtype_identified_by

name of person who identified the sample

@ eSubtype_whole_replicon

@ eGenome_plasmid_in_mitochondrion

@ eGenome_plasmid_in_plastid

const TDesc & GetDesc(void) const

Get the Desc member data.

bool IsSetLocus_tag(void) const

systematic gene name (e.g., MI0001, ORF0069) Check if a value has been assigned to Locus_tag data mem...

bool IsSetLocus(void) const

Official gene symbol Check if a value has been assigned to Locus data member.

bool IsSetDesc(void) const

descriptive name Check if a value has been assigned to Desc data member.

const TLocus_tag & GetLocus_tag(void) const

Get the Locus_tag member data.

const TLocus & GetLocus(void) const

Get the Locus member data.

const TStr & GetStr(void) const

Get the variant data.

bool IsStr(void) const

Check if variant Str is selected.

const TTag & GetTag(void) const

Get the Tag member data.

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.

bool IsStr(void) const

Check if variant Str is selected.

const TStr & GetStr(void) const

Get the variant data.

const TLabel & GetLabel(void) const

Get the Label member data.

const TType & GetType(void) const

Get the Type member data.

bool IsSetData(void) const

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

TId GetId(void) const

Get the variant data.

const TMod & GetMod(void) const

Get the Mod member data.

bool IsSetPgcode(void) const

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

TFixed_level GetFixed_level(void) const

Get the Fixed_level member data.

TMgcode GetMgcode(void) const

Get the Mgcode member data.

TGcode GetGcode(void) const

Get the Gcode member data.

const TSubname & GetSubname(void) const

Get the Subname member data.

bool IsSetFixed_level(void) const

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

bool IsPartial(void) const

Check if variant Partial is selected.

const TName & GetName(void) const

Get the Name member data.

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.

const TLevel & GetLevel(void) const

Get the Level member data.

bool IsSetName(void) const

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

const TBinomial & GetBinomial(void) const

Get the variant data.

bool IsSetMod(void) const

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

const Tdata & Get(void) const

Get the member data.

const TName & GetName(void) const

Get the Name member data.

list< CRef< COrgMod > > TMod

bool IsSetGenus(void) const

required Check if a value has been assigned to Genus data member.

const TSpecies & GetSpecies(void) const

Get the Species member data.

list< CRef< CTaxElement > > Tdata

bool IsSetOrgname(void) const

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

bool IsSetSubname(void) const

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

bool IsSetTaxname(void) const

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

bool IsSetLevel(void) const

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

bool IsSetGcode(void) const

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

const TGenus & GetGenus(void) const

Get the Genus member data.

const TPartial & GetPartial(void) const

Get the variant data.

bool IsSet(void) const

Check if a value has been assigned to data member.

bool IsSetSpecies(void) const

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

const TOrgname & GetOrgname(void) const

Get the Orgname member data.

bool IsBinomial(void) const

Check if variant Binomial is selected.

@ eSubtype_gb_acronym

used by taxonomy database

@ eSubtype_gb_synonym

used by taxonomy database

@ eSubtype_other

ASN5: old-name (254) will be added to next spec.

@ eSubtype_dosage

chromosome dosage of hybrid

@ eSubtype_nat_host

natural host of this specimen

@ eSubtype_metagenome_source

@ eSubtype_specimen_voucher

@ eSubtype_nomenclature

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

@ eSubtype_gb_anamorph

used by taxonomy database

@ eSubtype_culture_collection

@ eSubtype_forma_specialis

bool IsSetDesc(void) const

description (instead of name) Check if a value has been assigned to Desc data member.

EProcessed

processing status

TProcessed GetProcessed(void) const

Get the Processed member data.

bool IsSetProcessed(void) const

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

const TDesc & GetDesc(void) const

Get the Desc member data.

bool IsStr(void) const

Check if variant Str is selected.

const TStr & GetStr(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

bool IsSetData(void) const

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

bool IsSetPartial(void) const

incomplete in some way? Check if a value has been assigned to Partial data member.

const TLocation & GetLocation(void) const

Get the Location member data.

bool IsGene(void) const

Check if variant Gene is selected.

const TData & GetData(void) const

Get the Data member data.

bool IsSetData(void) const

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

bool IsSetExcept(void) const

something funny about this? Check if a value has been assigned to Except data member.

const TExcept_text & GetExcept_text(void) const

Get the Except_text member data.

bool IsSetExcept_text(void) const

explain if except=TRUE Check if a value has been assigned to Except_text data member.

const TBiosrc & GetBiosrc(void) const

Get the variant data.

bool IsBiosrc(void) const

Check if variant Biosrc is selected.

const TGene & GetGene(void) const

Get the variant data.

const TProt & GetProt(void) const

Get the variant data.

TExcept GetExcept(void) const

Get the Except member data.

bool IsSetLocation(void) const

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

TChain GetChain(void) const

Get the Chain member data.

bool IsSetChain_id(void) const

chain identifier; length-independent generalization of 'chain' Check if a value has been assigned to ...

bool IsSetChain(void) const

Deprecated: 'chain' can't support multiple character PDB chain identifiers (introduced in 2015).

bool IsSetAccession(void) const

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

bool IsSetCit(void) const

patent citation Check if a value has been assigned to Cit data member.

TSeqid GetSeqid(void) const

Get the Seqid member data.

const TChain_id & GetChain_id(void) const

Get the Chain_id member data.

bool IsSetSeqid(void) const

number of sequence in patent Check if a value has been assigned to Seqid data member.

const TCit & GetCit(void) const

Get the Cit member data.

const TAccession & GetAccession(void) const

Get the Accession member data.

bool IsMap(void) const

Check if variant Map is selected.

const TSeg & GetSeg(void) const

Get the variant data.

const TUser & GetUser(void) const

Get the variant data.

ERepr

representation class

const Tdata & Get(void) const

Get the member data.

const TMap & GetMap(void) const

Get the variant data.

TTech GetTech(void) const

Get the Tech member data.

list< CRef< CSeq_feat > > Tdata

TBiomol GetBiomol(void) const

Get the Biomol member data.

ETopology

topology of molecule

bool IsSetTech(void) const

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

TCompleteness GetCompleteness(void) const

Get the Completeness member data.

bool IsSet(void) const

Check if a value has been assigned to data member.

@ eRepr_seg

segmented sequence

@ eRepr_delta

sequence made by changes (delta) to others

@ eRepr_map

ordered map of any kind

@ eRepr_virtual

no seq data

@ eTech_htgs_2

ordered High Throughput sequence contig

@ eTech_physmap

from physical mapping techniques

@ eTech_htc

high throughput cDNA

@ eTech_both

concept transl. w/ partial pept. seq.

@ eTech_seq_pept_homol

sequenced peptide, ordered by homology

@ eTech_composite_wgs_htgs

composite of WGS and HTGS

@ eTech_sts

Sequence Tagged Site.

@ eTech_htgs_3

finished High Throughput sequence

@ eTech_seq_pept_overlap

sequenced peptide, ordered by overlap

@ eTech_htgs_1

unordered High Throughput sequence contig

@ eTech_concept_trans

conceptual translation

@ eTech_tsa

transcriptome shotgun assembly

@ eTech_standard

standard sequencing

@ eTech_wgs

whole genome shotgun sequencing

@ eTech_seq_pept

peptide was sequenced

@ eTech_survey

one-pass genomic sequence

@ eTech_barcode

barcode of life project

@ eTech_htgs_0

single genomic reads for coordination

@ eTech_derived

derived from other data, not a primary entity

@ eTech_fli_cdna

full length insert cDNA

@ eTech_est

Expressed Sequence Tag.

@ eTech_concept_trans_a

conceptual transl. supplied by author

@ eTech_genemap

from genetic mapping techniques

@ e_Embl

EMBL specific information.

@ e_User

user defined object

@ e_Genbank

GenBank specific info.

@ e_Comment

a more extensive comment

@ e_Molinfo

info on the molecule and techniques

@ e_Title

a title for this sequence

@ e_Pdb

PDB specific information.

@ e_Source

source of materials, includes Org-ref

unsigned int

A callback function used to compare two keys in a database.

Definition of all error codes used in objmgr libraries (xobjmgr.lib, xobjutil.lib and others).

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

const GenericPointer< typename T::ValueType > T2 value

const CharType(& source)[N]

Static variables safety - create on demand, destroy on application termination.

std::istream & in(std::istream &in_, double &x_)

Int4 delta(size_t dimension_, const Int4 *score_)

#define NCBI_BIOMOL(Type)

CMolInfo definitions.

#define NCBI_COMPLETENESS(Type)

#define NCBI_SEQTOPOLOGY(Type)

#define FOR_EACH_COMPOUND_ON_PDBBLOCK(Itr, Var)

FOR_EACH_COMPOUND_ON_PDBBLOCK EDIT_EACH_COMPOUND_ON_PDBBLOCK.

#define FOR_EACH_NAME_ON_PROT

#define FOR_EACH_ACTIVITY_ON_PROT

#define NCBI_GENOME(Type)

@NAME Convenience macros for NCBI objects

#define FOR_EACH_SYNONYM_ON_GENEREF(Itr, Var)

FOR_EACH_SYNONYM_ON_GENEREF EDIT_EACH_SYNONYM_ON_GENEREF.

#define SWITCH_ON_SUBSOURCE_CHOICE(Var)

SWITCH_ON_SUBSOURCE_CHOICE.

#define NCBI_ORGMOD(Type)

COrgMod definitions.

#define FOR_EACH_ORGMOD_ON_BIOSOURCE(Itr, Var)

FOR_EACH_ORGMOD_ON_BIOSOURCE EDIT_EACH_ORGMOD_ON_BIOSOURCE.

#define FOR_EACH_SEQFEATXREF_ON_FEATURE

#define SWITCH_ON_ORGMOD_CHOICE(Var)

SWITCH_ON_ORGMOD_CHOICE.

#define NCBI_SEQFEAT(Type)

CSeq_feat definitions.

#define FOR_EACH_SUBSOURCE_ON_BIOSOURCE(Itr, Var)

FOR_EACH_SUBSOURCE_ON_BIOSOURCE EDIT_EACH_SUBSOURCE_ON_BIOSOURCE.

#define FEATURE_CHOICE_IS

FEATURE_CHOICE_IS SWITCH_ON_FEATURE_CHOICE.

#define NCBI_SUBSOURCE(Type)

CSubSource definitions.

CBioSource::TGenome TBIOSOURCE_GENOME

#define SWITCH_ON_FEATURE_CHOICE

#define FOR_EACH_SEQFEATXREF_ON_SEQFEAT(Itr, Var)

FOR_EACH_SEQFEATXREF_ON_SEQFEAT EDIT_EACH_SEQFEATXREF_ON_SEQFEAT.

#define FOR_EACH_SYNONYM_ON_GENE

CSeq_id::EAccessionInfo TACCN_CHOICE

#define NCBI_SEQID(Type)

@NAME Convenience macros for NCBI objects

#define FIELD_IS_SET_AND_IS(Var, Fld, Chs)

FIELD_IS_SET_AND_IS base macro.

#define FIELD_IS(Var, Fld)

Generic FIELD macros.

#define FOR_EACH_STRING_IN_LIST(Itr, Var)

FOR_EACH_STRING_IN_LIST EDIT_EACH_STRING_IN_LIST.

#define FIELD_IS_SET(Var, Fld)

FIELD_IS_SET base macro.

#define GET_FIELD(Var, Fld)

GET_FIELD base macro.

#define FOR_EACH_CHAR_IN_STRING(Itr, Var)

FOR_EACH_CHAR_IN_STRING EDIT_EACH_CHAR_IN_STRING.

static const TTechMapEntry sc_TechArray[]

SStaticPair< const char *, CMolInfo::TTech > TTechMapEntry

CStaticPairArrayMap< const char *, CMolInfo::TTech, CSourceModParser::PKeyCompare > TTechMap

#define DEFINE_STATIC_ARRAY_MAP(Type, Var, Array)

Template structure SStaticPair is simlified replacement of STL pair<> Main reason of introducing this...

Template for collecting and joining strings with a minimum of heap churn.

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