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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/autodef__mod__combo_8cpp_source.html below:

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

m_AllowModAtEndOfTaxname(

),

m_KeepCountryText(

),

m_ExcludeSpOrgs(

),

m_ExcludeCfOrgs(

),

m_ExcludeNrOrgs(

),

m_ExcludeAffOrgs(

),

m_KeepAfterSemicolon(

),

(

it :

->GetGroupList()) {

(k = 0; k <

->GetNumSubSources(); k++) {

(k = 0; k <

->GetNumOrgMods(); k++) {

(it->IsOrgMod()) {

(

k = 0; k <

.size(); k++) {

(

k = 0; k <

.size(); k++) {

(it->GetSrcList().size() > 0

&& src->Compare (**(it->GetSrcList().begin())) == 0) {

(

,

, even_if_not_uniquifying);

(

,

, even_if_not_uniquifying);

=

;

=

;

string::size_type pos =

(tax_name,

);

(pos != NCBI_NS_STD::string::npos) {

tax_name = tax_name.substr(0, pos);

((*it)->IsSetSubtype() && (*it)->GetSubtype() == subtype) {

((*it)->IsSetSubtype() && (*it)->GetSubtype() == subtype) {

((*subSrcI)->IsSetSubtype() && (*subSrcI)->GetSubtype() ==

) {

= (*subSrcI)->GetName();

(pos != NCBI_NS_STD::string::npos) {

=

.substr(0, pos);

(pos != NCBI_NS_STD::string::npos) {

=

.substr(0, pos);

source_description +=

+

;

(pos == string::npos) {

keep_looking =

;

(pos != 0 && find_in.c_str()[pos - 1] !=

&& find_in.c_str()[pos - 1] !=

) {

keep_looking =

;

}

(find_in.c_str()[pos + find_this.length()] !=

&&

find_in.c_str()[pos + find_this.length()] !=

&&

find_in.c_str()[pos + find_this.length()] != 0) {

keep_looking =

;

at_end = (pos == find_in.length() - find_this.length());

}

(at_end && ignore_at_end) {

((*modI)->IsSetSubtype() && (*modI)->GetSubtype() ==

) {

= (*modI)->GetSubname();

(pos != NCBI_NS_STD::string::npos) {

=

.substr(0, pos);

source_description +=

;

source_description +=

;

has_tricky =

;

(

k = 0; k <

.size() && !has_tricky; k++) {

src_has_clone =

;

src_has_isolate =

;

src_has_strain =

;

(!

(source_description,

) &&

use_isolate =

;

|| !src_has_clone)) {

|| (!src_has_isolate && !src_has_strain))) {

(influenza_type) {

default_exclude =

;

(

k = 0; k <

.size() && default_exclude; k++) {

default_exclude =

[k]->GetDefaultExcludeSp ();

default_exclude;

(*it)->IsSetSubname() &&

((*it)->GetSubname(),

) != string::npos) {

modifier_list.clear();

[k]->GetAvailableModifiers(modifier_list);

source_description;

no_extras =

;

string::size_type pos =

(source_description,

);

(pos != NCBI_NS_STD::string::npos

&& (pos < 2 || !

(source_description.substr(pos - 2),

))) {

string::size_type pos =

(source_description,

);

(pos != NCBI_NS_STD::string::npos) {

string::size_type pos =

(source_description,

);

(pos != NCBI_NS_STD::string::npos) {

string::size_type pos =

(source_description,

);

(pos != NCBI_NS_STD::string::npos) {

source_description =

+ source_description;

(

k = 0; k <

.size(); k++) {

(

k = 0; k <

.size(); k++) {

paren =

;

paren += it->GetSubname();

serotype = it->GetSubname();

paren +=

+ serotype +

;

source_description += paren;

source_description +=

;

(orgmods.

(

) != orgmods.

() &&

(subsrcs.

(

) != subsrcs.

() &&

source_description;

any_change =

;

vector<CTempString> tokens;

(vector<CTempString>,

, tokens) {

(

(*

,

) != string::npos ||

(*

,

) != string::npos) {

source_description +=

+ add;

any_change =

;

((*it)->IsSetSubtype() && (*it)->IsSetName() &&

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

any_change |=

(source_description, (*it)->GetSubname());

num = 0;

((*it)->GetSrcList().size() == 1) {

num = 0;

((*it)->GetSrcList().size() > num) {

num = (*it)->GetSrcList().size();

num_this, num_other;

(num_this > num_other) {

}

(num_this < num_other) {

(num_this > num_other) {

}

(num_this < num_other) {

(num_this < num_other) {

}

(num_this > num_other) {

(num_this < num_other) {

}

(num_this > num_other) {

added =

, rval =

;

vector <CRef<CAutoDefSourceGroup> > new_groups;

(*it)->SortDescriptions();

= (*it)->SplitGroup();

new_groups.emplace_back(

);

(!new_groups.empty()) {

(rval || even_if_not_uniquifying) {

rval |= (*it)->RemoveQual (IsOrgMod, subtype);

vector<CRef<CAutoDefModifierCombo>> expanded;

(it->GetSrcList().size() == 1) {

mods = it->GetModifiersPresentForAny();

(

mod_it : mods) {

(cpy->AddQual(mod_it.IsOrgMod(), mod_it.GetSubtype())) {

expanded.emplace_back(cpy);

(!expanded.empty()) {

vector<string> clauses;

CAutoDefSourceGroup::TSourceDescriptionVector::iterator s = src_list.begin();

(s != src_list.end()) {

clauses.push_back((*s)->GetFeatureClauses());

(clauses.size() < 2) {

(clauses.begin(), clauses.end());

unique =

;

vector<string>::iterator sit = clauses.begin();

(sit != clauses.end() && unique) {

static const size_t kNumPreferred

static const SPreferredQual s_PreferredList[]

bool CompareAutoDefSourceGroupByStrings(CRef< CAutoDefSourceGroup > s1, CRef< CAutoDefSourceGroup > s2)

static string GetOrgModLabel(COrgMod::ESubtype st)

static string GetSubSourceLabel(CSubSource::ESubtype st)

unsigned int GetNumGroups()

static bool IsModifierRequiredByDefault(bool is_orgmod, int subtype)

static bool x_BioSourceHasOrgMod(const CBioSource &src, COrgMod::ESubtype subtype)

void x_AddTypeStrainModifiers(TExtraOrgMods &extra_orgmods, TExtraSubSrcs &extra_subsrcs, const CBioSource &bsrc)

bool HasSubSource(CSubSource::ESubtype st)

TGroupListVector m_GroupList

void AddSource(const CBioSource &bs, const string &feature_clauses="")

bool AreFeatureClausesUnique()

static bool x_HasTypeStrainComment(const CBioSource &bsrc)

void GetAvailableModifiers(CAutoDefSourceDescription::TAvailableModifierVector &modifier_list)

static bool IsUsableInDefline(CSubSource::ESubtype subtype)

void x_AddHIVModifiers(TExtraOrgMods &extra_orgmods, TExtraSubSrcs &extra_subsrcs, const CBioSource &bsrc)

vector< CRef< CAutoDefSourceGroup > > TGroupListVector

unsigned int GetNumUnique() const

static bool x_AddMinicircle(string &source_description, const CBioSource &bsrc)

CSubSource::ESubtype GetSubSource(unsigned int index)

static bool x_SpecialHandlingForInfluenza(EInfluenzaType influenza_type, CSubSource::ESubtype subtype)

void x_AddRequiredSubSourceModifiers(TExtraOrgMods &extra_orgmods, TExtraSubSrcs &extra_subsrcs, const CBioSource &bsrc)

string x_GetOrgModLabel(COrgMod::ESubtype st)

unsigned int GetMaxInGroup() const

bool HasOrgMod(COrgMod::ESubtype st)

bool m_KeepAfterSemicolon

void x_CleanUpTaxName(string &tax_name)

void AddOrgMod(COrgMod::ESubtype st, bool even_if_not_uniquifying=false)

string GetSourceDescriptionString(const CBioSource &bsrc)

bool AddQual(bool IsOrgMod, int subtype, bool even_if_not_uniquifying=false)

void AddSubsource(CSubSource::ESubtype st, bool even_if_not_uniquifying=false)

bool GetDefaultExcludeSp()

TOrgModTypeVector m_OrgMods

int Compare(const CAutoDefModifierCombo &other) const

string x_GetSubSourceLabel(CSubSource::ESubtype st)

unsigned int GetNumSubSources()

TSubSourceTypeVector m_SubSources

void InitFromOptions(const CAutoDefOptions &options)

void x_AddInfluenzaModifiers(TExtraOrgMods &extra_orgmods, TExtraSubSrcs &extra_subsrcs, EInfluenzaType influenza_type)

const TGroupListVector & GetGroupList() const

CAutoDefSourceDescription::TModifierVector m_Modifiers

static bool x_BioSourceHasSubSrc(const CBioSource &src, CSubSource::ESubtype subtype)

bool m_AllowModAtEndOfTaxname

static EInfluenzaType GetInfluenzaType(const string &taxname)

bool x_AddOrgModString(string &source_description, const CBioSource &bsrc, COrgMod::ESubtype st)

static bool IsModifierInString(const string &find_this, const string &find_in, bool ignore_at_end)

pair< CSubSource::ESubtype, bool > TExtraSubSrc

unsigned int GetNumOrgMods()

bool x_AddSubsourceString(string &source_description, const CBioSource &bsrc, CSubSource::ESubtype st)

CAutoDefOptions::EHIVCloneIsolateRule m_HIVCloneIsolateRule

vector< CRef< CAutoDefModifierCombo > > ExpandByAnyPresent()

void InitOptions(CAutoDefOptions &options) const

const CAutoDefSourceDescription::TModifierVector & GetModifiers() const

bool RemoveQual(bool IsOrgMod, int subtype)

pair< COrgMod::ESubtype, bool > TExtraOrgMod

COrgMod::ESubtype GetOrgMod(unsigned int index)

bool GetKeepAfterSemicolon() const

THIVRule GetHIVRule() const

void AddOrgMod(COrgMod::TSubtype subtype)

void SetHIVRule(EHIVCloneIsolateRule rule)

void SetLeaveParenthetical(bool val=true)

bool GetDoNotApplyToSp() const

const TOrgMods & GetOrgMods() const

void SetDoNotApplyToAff(bool val=true)

bool GetDoNotApplyToNr() const

bool GetLeaveParenthetical() const

bool GetAllowModAtEndOfTaxname() const

void SetDoNotApplyToNr(bool val=true)

bool GetDoNotApplyToAff() const

void SetUseLabels(bool val=true)

void SetKeepAfterSemicolon(bool val=true)

vector< COrgMod::TSubtype > TOrgMods

bool GetIncludeCountryText() const

void SetDoNotApplyToCf(bool val=true)

bool GetDoNotApplyToCf() const

void SetAllowModAtEndOfTaxname(bool val=true)

void AddSubSource(CSubSource::TSubtype subtype)

void SetDoNotApplyToSp(bool val=true)

void SetIncludeCountryText(bool val=true)

const TSubSources & GetSubSources() const

bool GetUseLabels() const

vector< CSubSource::TSubtype > TSubSources

vector< CAutoDefSourceModifierInfo > TModifierVector

vector< CAutoDefAvailableModifier > TAvailableModifierVector

vector< CRef< CAutoDefSourceDescription > > TSourceDescriptionVector

const_iterator end() const

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

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

#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.

#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.

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 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 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 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.

@ fSplit_Tokenize

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

@ eNocase

Case insensitive compare.

static const char label[]

const TSubtype & GetSubtype(void) const

Get the Subtype member data.

TOrigin GetOrigin(void) const

Get the Origin 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 CanGetOrigin(void) const

Check if it is safe to call GetOrigin method.

const TOrg & GetOrg(void) const

Get the Org member data.

@ eSubtype_endogenous_virus_name

@ eOrigin_mut

artificially mutagenized

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.

@ eSubtype_other

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

@ eSubtype_nat_host

natural host of this specimen

@ eSubtype_specimen_voucher

@ eSubtype_culture_collection

@ eSubtype_forma_specialis

where boath are integers</td > n< td ></td > n</tr > n< tr > n< td > tse</td > n< td > optional</td > n< td > String</td > n< td class=\"description\"> TSE option controls what blob is orig

constexpr auto sort(_Init &&init)

Miscellaneous common-use basic types and functionality.

void split(std::vector< std::string > *strVec, const std::string &str_, const std::string &split_)

static SLJIT_INLINE sljit_ins st(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

int g(Seg_Gsm *spe, Seq_Mtf *psm, Thd_Gsm *tdg)

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