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

pooled_clones =

);

prefix, title, suffix;

third_party =

;

tpa_exp =

;

tpa_inf =

;

is_tsa =

;

wgs_master =

;

tsa_master =

;

htg_tech =

;

htgs_draft =

;

htgs_cancelled =

;

htgs_pooled =

;

htgs_unfinished =

;

use_biosrc =

;

tsid =

->GetTextseq_Id();

(id->

()) {

(

.IsSetAccession()) {

& acc =

.GetAccession();

general_id = &

->GetGeneral();

pdb_id = &

->GetPdb();

pat_id = &

->GetPatent();

= &it->GetSource();

( (found |= 1) == 3 ) {

mol_info = &it->GetMolinfo();

( (found |= 2) == 3 ) {

htgs_unfinished =

;

(htg_tech || third_party) {

(gb->GetGenbank().IsSetKeywords()) {

keywords = &gb->GetGenbank().GetKeywords();

(embl->GetEmbl().IsSetKeywords()) {

keywords = &embl->GetEmbl().GetKeywords();

htgs_cancelled =

;

search_depth = 0;

(title.empty() && use_biosrc &&

.NotEmpty()) {

htgs_unfinished && htgs_pooled);

(title.empty() && is_nc &&

.NotEmpty()

(!title.empty()) {

}

(title.empty() && is_nm &&

.NotEmpty()

genes = 0, cdregions = 0, prots

= 0;

(it->GetData().Which()) {

gene.Reset(&it->GetMappedFeature());

cdregion.

(&it->GetMappedFeature());

(genes == 1 && cdregions == 1

&&

->GetOrg().IsSetTaxname()) {

title =

->GetOrg().GetTaxname() +

;

)) {

);

}

(title.empty() && is_nr &&

.NotEmpty()

(it->GetData().IsGene()) {

title =

->GetOrg().GetTaxname() +

;

title.erase(title.end() - 1);

(title.empty() && pdb_id.

()) {

(

((

) pdb_id->GetChain())) {

title =

(

) + (char)pdb_id->GetChain() +

;

(title.empty() && pat_id.

()) {

+

+ pat_id->GetCit().GetCountry()

+

+ pat_id->GetCit().GetSomeNumber();

( !title.empty() ) {

(title.empty() && !htg_tech

(title.empty() && !htg_tech &&

.NotEmpty()) {

title =

;

(is_tsa && !title.empty() ) {

}

(third_party && !title.empty() ) {

prefix =

;

}

(tpa_inf) {

prefix =

;

}

( !tpa_start ) {

(title.find(

) ==

) {

suffix =

;

(htgs_draft && title.find(

) ==

) {

suffix =

;

}

( !htgs_draft && !htgs_cancelled

&& title.find(

) ==

) {

suffix =

;

pieces = 1;

+

+ un +

);

(title.find(

) ==

) {

suffix =

;

(title.find(

) ==

) {

suffix =

;

(title.find(

) ==

) {

suffix =

;

(title.find(

) ==

) {

suffix =

;

(title.find(

) ==

){

suffix =

;

}

(title.find(

) ==

) {

(

.NotEmpty()) {

(orgnl[0] && title.find(orgnl) ==

) {

suffix =

(1,

) + orgnl;

suffix +=

;

(title.find(

) ==

){

suffix =

;

}

(title.find(

) ==

) {

suffix +=

;

org = &

->GetOrg();

(organism.empty() && org.

() && org->IsSetTaxname()) {

organism = org->GetTaxname();

( !organism.empty() && title.find(organism) ==

) {

suffix +=

+ organism +

;

prefix + title + suffix;

prefix, title, suffix;

third_party =

;

tpa_exp =

;

tpa_inf =

;

is_tsa =

;

wgs_master =

;

tsa_master =

;

htg_tech =

;

htgs_draft =

;

htgs_cancelled =

;

htgs_pooled =

;

htgs_unfinished =

;

use_biosrc =

;

tsid =

->GetTextseq_Id();

(id->

()) {

(

.IsSetAccession()) {

& acc =

.GetAccession();

general_id = &

->GetGeneral();

pdb_id = &

->GetPdb();

pat_id = &

->GetPatent();

= &desc->GetSource();

mol_info = &desc->GetMolinfo();

htgs_unfinished =

;

(htg_tech || third_party) {

( level <= max_level ) {

title = desc->GetTitle();

(title.empty() && use_biosrc &&

.NotEmpty()) {

htgs_unfinished && htgs_pooled);

(title.empty() && is_nc &&

.NotEmpty()

(!title.empty()) {

}

(title.empty() && is_nm &&

.NotEmpty()) {

}

(title.empty() && is_nr &&

.NotEmpty()

&&

->GetOrg().IsSetTaxname()) {

title.erase(title.end() - 1);

(title.empty() && pdb_id.

()) {

(title.empty() && pat_id.

()) {

+

+ pat_id->GetCit().GetCountry()

+

+ pat_id->GetCit().GetSomeNumber();

(title.empty() && seq.

()) {

(title.empty() && !htg_tech &&

(title.empty() && !htg_tech &&

.NotEmpty()) {

title =

;

(is_tsa && !title.empty() ) {

}

(third_party && !title.empty() ) {

prefix =

;

}

(tpa_inf) {

prefix =

;

}

( !tpa_start ) {

(title.find(

) ==

) {

suffix =

;

(htgs_draft && title.find(

) ==

) {

suffix =

;

}

( !htgs_draft && !htgs_cancelled

&& title.find(

) ==

) {

suffix =

;

(title.find(

) ==

) {

suffix =

;

(title.find(

) ==

) {

suffix =

;

(title.find(

) ==

) {

suffix =

;

(title.find(

) ==

) {

suffix =

;

(title.find(

) ==

){

suffix =

;

}

(title.find(

) ==

) {

(

.NotEmpty()) {

(orgnl[0] && title.find(orgnl) ==

) {

suffix =

(1,

) + orgnl;

suffix +=

;

(title.find(

) ==

){

suffix =

;

}

(title.find(

) ==

) {

suffix +=

;

org = &

->GetOrg();

org = &desc->GetOrg();

(organism.empty() && org.

() && org->IsSetTaxname()) {

organism = org->GetTaxname();

( !organism.empty() && title.find(organism) ==

) {

suffix +=

+ organism +

;

*title_ptr = prefix + title + suffix;

pos = clone.find(

, pos + 1)) {

;

}

(

> 3) {

+ clone;

(strain.size() >= name.size()) {

pos = name.find(

, pos + 1);

(pos ==

|| pos + strain.size() >= name.size()) {

(pos == name.size() - strain.size()) {

}

(pos == name.size() - strain.size() - 1

&& name[pos - 1] ==

&& name[name.size() - 1] ==

) {

& suffix,

name, chromosome, clone, map_, plasmid, strain, sfx;

(suffix.size() > 0) {

(

.IsSetSubtype()) {

((*it)->GetSubtype()) {

chromosome =

+ (*it)->GetName();

(suffix == (*it)->GetName()) {

map_ =

+ (*it)->GetName();

plasmid =

+ (*it)->GetName();

(suffix == (*it)->GetName()) {

&

= (*it)->GetSubname();

+ map_ + plasmid + sfx);

( !title.empty() &&

((

) title[0])) {

title[0] = (char)

((

) title[0]);

;

;

;

;

;

;

;

;

;

;

;

;

;

;

;

;

name, chromosome, segment, plasmid_name, orgnl;

seq_tag, gen_tag;

is_plasmid =

;

(

.GetOrg().IsSetTaxname()) {

name =

.GetOrg().GetTaxname();

lc_name = name;

(lc_name.find(

) !=

|| lc_name.find(

) !=

) {

(

.IsSetSubtype()) {

((*it)->GetSubtype()) {

chromosome = (*it)->GetName();

segment = (*it)->GetName();

plasmid_name = (*it)->GetName();

lc_plasmid = plasmid_name;

(lc_plasmid.find(

) ==

&& lc_plasmid.find(

) ==

) {

plasmid_name =

+ plasmid_name;

seq_tag =

;

gen_tag =

;

seq_tag =

;

gen_tag =

;

(lc_name.find(

) !=

) {

name + seq_tag;

}

(is_plasmid) {

(plasmid_name.empty()) {

name +

+ seq_tag;

name +

+ plasmid_name + seq_tag;

}

( !plasmid_name.empty() ) {

(orgnl.empty()) {

name +

+ plasmid_name + seq_tag;

name +

+ orgnl +

+ plasmid_name + seq_tag;

}

( !orgnl.empty() ) {

( chromosome.empty() ) {

name +

+ orgnl + gen_tag;

name +

+ orgnl +

+ chromosome + seq_tag;

}

( !segment.empty() ) {

(segment.find(

) ==

&& segment.find(

) ==

&& segment.find(

) ==

&& segment.find(

) ==

) {

name +

+ segment + seq_tag;

name +

+ segment + seq_tag;

}

( !chromosome.empty() ) {

name +

+ chromosome + seq_tag;

name + gen_tag;

(

.NotEmpty() &&

->IsSetName() && !

->GetName().empty()) {

}

(

.NotEmpty() &&

->IsSetDesc()

&& !

->GetDesc().empty()) {

->GetDesc();

}

(

.NotEmpty() &&

->IsSetActivity()

&& !

->GetActivity().empty()) {

->GetActivity().front();

gene_name = *gene->

().begin();

gene_name = gene->

();

( !gene_name.empty() ) {

gene_name +

;

;

=

;

org = &it->GetSource().GetOrg();

org = &it->GetData().GetBiosrc().GetOrg();

(org.

() && org->IsSetTaxname()) {

organism = org->GetTaxname();

organism, product, locus, strain, clone, isolate;

completeness =

;

cds_found =

;

&

= (*mod)->GetSubname();

(organism.empty()) {

organism =

;

completeness =

;

(product.empty() && prot_feat.

()

(locus.empty() && gene_feat.

()) {

= organism;

( !strain.empty() ) {

+=

+ strain;

}

( !clone.empty() && clone.find(

) !=

) {

}

( !isolate.empty() ) {

+=

+ isolate;

( !product.empty() ) {

( !locus.empty() ) {

+=

+ locus +

;

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

+=

+ completeness +

;

(pos > 0 && !

((

)s[pos - 1]) ) {

(pos + 3 <

&&

((

)s[pos])) {

(s[pos] ==

&& s[pos + 1] ==

&&

((

)s[pos + 2])

&& (pos + 3 ==

|| strchr(

, s[pos + 3])) ) {

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

CConstRef< CSeqdesc > GetClosestDescriptor(CSeqdesc::E_Choice choice, int *level=NULL) const

bool IsSkippable(void) const

Template class for iteration on objects of class C (non-medifiable version)

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

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...

EAccessionInfo

For IdentifyAccession (below)

string GetLabel(const CSeq_id &id)

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.

@ eOverlap_Interval

at least one pair of intervals must overlap

@ eOverlap_Contained

2nd contained within 1st extremes

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

Get the encoding CDS feature of a given protein sequence.

CConstRef< CSeq_feat > GetOverlappingGene(const CSeq_loc &loc, CScope &scope, ETransSplicing eTransSplicing=eTransSplicing_Auto)

string GetTitle(const CBioseq_Handle &hnd, TGetTitleFlags flags)

@ fGetTitle_Organism

append [organism]

@ fGetTitle_Reconstruct

ignore existing title Seqdesc.

@ fGetTitle_NoExpensive

skip potential expensive operations

@ fGetTitle_AllProteins

normally just names the first

vector< CSeq_id_Handle > TId

const TInst_Ext & GetInst_Ext(void) const

bool IsSetProduct(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.

CConstRef< CSeq_entry > GetCompleteSeq_entry(void) const

Complete and get const reference to the seq-entry.

TInst_Repr GetInst_Repr(void) const

CScope & GetScope(void) const

Get scope this handle belongs to.

CSeq_entry_Handle GetTopLevelEntry(void) const

Get top level Seq-entry handle.

const TId & GetId(void) const

TMol GetBioseqMolType(void) const

Get some values from core:

bool IsSetPartial(void) const

const CSeq_loc & GetLocation(void) const

const CSeq_loc & GetProduct(void) const

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.

bool IsNull(void) const THROWS_NONE

Check if pointer is null – same effect as Empty().

void Reset(void)

Reset reference object.

bool NotEmpty(void) const THROWS_NONE

Check if CConstRef 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.

NCBI_NS_STD::string::size_type SIZE_TYPE

static string SizetToString(size_t value, TNumToStringFlags flags=0, int base=10)

Convert size_t to string.

static int CompareNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive compare of a substring with another string.

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 string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

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

Replace occurrences of a substring within a string.

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.

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.

const char *const kEmptyCStr

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

static string & ToLower(string &str)

Convert string to lower case – string& version.

@ eNocase

Case insensitive compare.

const TSubtype & GetSubtype(void) const

Get the Subtype member data.

list< CRef< CSubSource > > TSubtype

bool IsSetSubtype(void) const

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

const TOrg & GetOrg(void) const

Get the Org member data.

@ eGenome_endogenous_virus

bool IsSetSyn(void) const

synonyms for locus Check if a value has been assigned to Syn data member.

const TSyn & GetSyn(void) const

Get the Syn member data.

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.

bool IsStr(void) const

Check if variant Str is selected.

const TTag & GetTag(void) const

Get the Tag member data.

const TStr & GetStr(void) const

Get the variant data.

const TMod & GetMod(void) const

Get the Mod member data.

const TTaxname & GetTaxname(void) const

Get the Taxname member data.

bool IsSetMod(void) const

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

list< CRef< COrgMod > > TMod

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.

const TOrgname & GetOrgname(void) const

Get the Orgname member data.

const TName & GetName(void) const

Get the Name member data.

bool IsSetName(void) const

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

const TLocation & GetLocation(void) const

Get the Location member data.

const TData & GetData(void) const

Get the Data member data.

const TGene & GetGene(void) const

Get the variant data.

const TProt & GetProt(void) const

Get the variant data.

E_Choice Which(void) const

Which variant is currently selected.

const TGeneral & GetGeneral(void) const

Get the variant data.

@ e_Other

for historical reasons, 'other' = 'refseq'

@ e_Tpe

Third Party Annot/Seq EMBL.

@ e_Tpd

Third Party Annot/Seq DDBJ.

@ e_General

for other databases

@ e_Tpg

Third Party Annot/Seq Genbank.

TRepr GetRepr(void) const

Get the Repr member data.

const TSeg & GetSeg(void) const

Get the variant data.

const TInst & GetInst(void) const

Get the Inst member data.

const TTitle & GetTitle(void) const

Get the variant data.

const TSource & GetSource(void) const

Get the variant data.

const TPdb & GetPdb(void) const

Get the variant data.

const TId & GetId(void) const

Get the Id member data.

TTech GetTech(void) const

Get the Tech member data.

bool IsSetInst(void) const

the sequence data Check if a value has been assigned to Inst data member.

const TOrg & GetOrg(void) const

Get the variant data.

list< CRef< CSeq_id > > TId

TBiomol GetBiomol(void) const

Get the Biomol member data.

TCompleteness GetCompleteness(void) const

Get the Completeness member data.

@ eRepr_seg

segmented sequence

@ eRepr_delta

sequence made by changes (delta) to others

@ eCompleteness_no_left

missing 5' or NH3 end

@ eCompleteness_partial

partial but no details given

@ eCompleteness_no_right

missing 3' or COOH end

@ eCompleteness_no_ends

missing both ends

@ eTech_htgs_2

ordered High Throughput sequence contig

@ eTech_sts

Sequence Tagged Site.

@ eTech_htgs_3

finished High Throughput sequence

@ eTech_htgs_1

unordered High Throughput sequence contig

@ eTech_tsa

transcriptome shotgun assembly

@ eTech_wgs

whole genome shotgun sequencing

@ eTech_survey

one-pass genomic sequence

@ eTech_htgs_0

single genomic reads for coordination

@ eTech_est

Expressed Sequence Tag.

@ eBiomol_pre_RNA

precursor RNA of any sort really

@ eBiomol_cRNA

viral RNA genome copy intermediate

@ eBiomol_snoRNA

small nucleolar RNA

@ eBiomol_transcribed_RNA

transcribed RNA other than existing classes

@ eBiomol_other_genetic

other genetic material

@ e_Embl

EMBL specific information.

@ e_Org

if all from one organism

@ e_Genbank

GenBank specific info.

@ 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

const TCompound & GetCompound(void) const

Get the Compound member data.

const CharType(& source)[N]

static string s_GetProteinName(const CBioseq_Handle &handle, CScope &scope, CConstRef< CSeq_loc > &cds_loc, TGetTitleFlags flags)

static string s_TitleFromChromosome(const CBioSource &source, const CMolInfo &mol_info)

static const char * s_OrganelleName(CBioSource::TGenome genome, TOrganelleNameFlags flags)

static string s_TitleFromProtein(const CBioseq_Handle &handle, CScope &scope, string &organism, TGetTitleFlags flags)

static void s_FlyCG_PtoR(string &s)

static string x_TitleFromChromosome(const CBioSource &source, const CMolInfo &mol_info)

static string s_DescribeClones(const string &clone, bool pooled)

static string s_TitleFromSegment(const CBioseq_Handle &handle, CScope &scope, TGetTitleFlags flags)

static string s_TitleFromBioSource(const CBioSource &source, CMolInfo::TTech tech, const string &suffix=kEmptyStr, bool pooled_clones=false)

static bool s_EndsWithStrain(const string &name, const string &strain)

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