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NCBI C++ ToolKit: src/objtools/readers/source_mod_parser.cpp Source File

->IsSetSubtype() && (

->GetSubtype() == m_st);

<

TEnum,

TSModEnumMap * s_InitSmodToEnumMap(

TSModNameSet & skip_enum_names,

TEnumNameToValMap & extra_enum_names_to_vals )

unique_ptr<TSModEnumMap> smod_enum_map(

TSModEnumMap);

& enum_name = it->first;

TEnum enum_val =

TEnum

(it->second);

( skip_enum_names.find(enum_name.c_str()) !=

skip_enum_names.end() )

emplace_result =

smod_enum_map->emplace(

( ! emplace_result.second) {

<< enum_name);

(

extra_smod_to_enum : extra_enum_names_to_vals) {

emplace_result =

smod_enum_map->emplace(

extra_smod_to_enum.second);

( ! emplace_result.second) {

<< extra_smod_to_enum.first);

smod_enum_map.release();

TSModOrgSubtypeMap * s_InitSModOrgSubtypeMap(

)

TSModNameSet kDeprecatedOrgSubtypes{

,

,

};

s_InitSmodToEnumMap<COrgMod::ESubtype>(

kDeprecatedOrgSubtypes,

extra_smod_to_enum_names

TSModSubSrcSubtype * s_InitSModSubSrcSubtypeMap(

)

TSModNameSet skip_enum_names {

,

,

,

,

,

,

,

,

,

s_InitSmodToEnumMap<CSubSource::ESubtype>(

extra_smod_to_enum_names);

s_InitSModSubSrcSubtypeMap,

);

x_FindBrackets(

&

,

& start,

& stop,

& eq_pos)

* s =

.data() + start;

nested_brackets = -1;

(

<

.size())

(nested_brackets == 0)

(nested_brackets >= 0)

(nested_brackets == 0)

(nested_brackets < 0)

x_AppendIfNonEmpty(

& s,

& o)

;

(d->IsUser() && d->GetUser().IsDBLink())

(

& u : d->SetUser().SetData())

(u->IsSetLabel() && u->GetLabel().IsStr() &&

* operator->();

(!m_bioseq.Empty())

m_descr = &m_bioseq->SetDescr();

(!m_bioset.Empty())

m_descr = &m_bioset->SetDescr();

m_ptr = &Set().SetSource();

m_ptr = &Set().SetMolinfo();

m_ptr = &Set().SetGenbank();

iMaxModsToParse )

stripped_title;

iModsFoundSoFar = 0;

(; (pos < title.

()) && (iModsFoundSoFar < iMaxModsToParse);

lb_pos, end_pos, eq_pos;

(x_FindBrackets(title, lb_pos, end_pos, eq_pos))

(eq_pos < end_pos) {

x_AppendIfNonEmpty(stripped_title, skipped);

x_AppendIfNonEmpty(stripped_title, rest);

stripped_title;

had_ftable =

;

((*it)->GetData().IsFtable()) {

feat->

().SetGene(*gene);

->SetData().SetFtable().push_back(feat);

(

.IsInitialized() ) {

->SetData().SetFtable().push_back(feat);

( !had_ftable &&

.IsInitialized() ) {

seq.

().SetHist(*hist);

seq.

().Set().push_back(desc);

seq.

().Set().push_back(desc);

((

=

(s_Mod_topology, s_Mod_top)) !=

) {

bMolSetViaMolMod =

;

((

=

(s_Mod_molecule, s_Mod_mol)) !=

) {

bMolSetViaMolMod =

;

bMolSetViaMolMod =

;

( ! bMolSetViaMolMod ) {

((

=

(s_Mod_moltype, s_Mod_mol_type)) !=

) {

(it == sc_BiomolMap.end()) {

seq.

().SetMol(it->second.m_eMol);

((

=

(s_Mod_strand)) !=

) {

((

=

(s_Mod_comment)) !=

) {

seq.

().Set().push_back(desc);

vector<string>

;

num_names =

.size();

num_seqs = seqs.size();

num_primers =

(num_names, num_seqs);

(

=0;

<num_primers; ++

) {

primer->SetName().Set(

[

]);

primer->SetSeq().Set(seqs[

]);

primer_set.

().push_back(primer);

vector<pair<string, string>>& reaction_info)

reaction_info.clear();

vector<string>

;

(seqs.front().front() ==

) {

seqs.front().erase(0,1);

(seqs.back().back() ==

) {

seqs.back().erase(seqs.back().size()-1, 1);

num_names =

.size();

num_seqs = seqs.size();

num_reactions =

(num_names, num_seqs);

(

=0;

<num_reactions; ++

) {

name = (

<num_names) ?

[

] :

;

seq = (

<num_seqs) ? seqs[

] :

;

reaction_info.push_back(make_pair(name, seq));

TNameSeqPair = pair<string, string>;

* pNameMod =

;

* pSeqMod =

;

pNameMod =

(s_Mod_fwd_primer_name, s_Mod_fwd_pcr_primer_name);

pSeqMod =

(s_Mod_fwd_primer_seq, s_Mod_fwd_pcr_primer_seq);

vector<TNameSeqPair> fwd_primer_info;

pNameMod =

(s_Mod_rev_primer_name, s_Mod_rev_pcr_primer_name);

pSeqMod =

(s_Mod_rev_primer_seq, s_Mod_rev_pcr_primer_seq);

vector<TNameSeqPair> rev_primer_info;

(fwd_primer_info.empty() &&

rev_primer_info.empty()) {

num_fwd_primer_info = fwd_primer_info.size();

num_rev_primer_info = rev_primer_info.size();

(num_fwd_primer_info == num_rev_primer_info) {

(

=0;

<num_fwd_primer_info; ++

) {

pcr_reaction_set->

().push_back(pcr_reaction);

(num_fwd_primer_info > num_rev_primer_info) {

diff = num_fwd_primer_info - num_rev_primer_info;

(

=0;

<diff; ++

) {

pcr_reaction_set->

().push_back(pcr_reaction);

(

=diff;

<num_fwd_primer_info; ++

) {

pcr_reaction_set->

().push_back(pcr_reaction);

(num_fwd_primer_info < num_rev_primer_info) {

(

=0;

<num_fwd_primer_info; ++

) {

pcr_reaction_set->

().push_back(pcr_reaction);

(

=num_fwd_primer_info;

<num_rev_primer_info; ++

) {

pcr_reaction_set->

().push_back(pcr_reaction);

reset_taxid =

;

(organism.

())

((

=

(s_Mod_organism, s_Mod_org)) !=

) {

organism =

->value;

((

=

(s_Mod_taxname)) !=

) {

organism =

->value;

( !organism.

())

(!(bsrc->GetOrg().IsSetTaxname() &&

(bsrc->GetOrg().GetTaxname(), organism)))

(bsrc->GetOrg().IsSetTaxname())

bsrc->SetOrg().SetTaxname(organism);

((

=

(s_Mod_location)) !=

) {

->FindValue(

->value));

((

=

(s_Mod_origin)) !=

) {

->FindValue(

->value));

(

& smod_orgsubtype : kSModOrgSubtypeMap.Get()) {

& smod = smod_orgsubtype.first;

bsrc->SetOrg().SetOrgname().SetMod().push_back(org_mod);

reset_taxid =

;

(

& smod_subsrcsubtype : kSModSubSrcSubtypeMap.Get() ) {

& smod = smod_subsrcsubtype.first;

& subtype = bsrc->SetSubtype();

(subtype.begin(), subtype.end(),

equal_subtype(e_subtype)),

subtype.push_back(subsource);

(!bsrc->IsSetPcr_primers()) {

bsrc->SetPcr_primers(*pcr_reaction_set);

bsrc->SetPcr_primers().

().splice(

bsrc->SetPcr_primers().

().end(),

pcr_reaction_set->

());

(

db_xref_iter = db_xref_mods_range.first;

db_xref_iter != db_xref_mods_range.second;

db_xref_str = db_xref_iter->value;

colon_location = db_xref_str.

(

);

(colon_location == string::npos) {

new_db->

() =

;

db_xref_str.

(new_db->

(), 0, colon_location);

new_db->

( *object_id );

bsrc->SetOrg().SetDb().push_back( new_db );

((

=

(s_Mod_division, s_Mod_div)) !=

) {

bsrc->SetOrg().SetOrgname().SetDiv(

->value );

((

=

(s_Mod_lineage)) !=

) {

bsrc->SetOrg().SetOrgname().SetLineage(

->value );

((

=

(s_Mod_gcode)) !=

) {

((

=

(s_Mod_mgcode)) !=

) {

((

=

(s_Mod_pgcode)) !=

) {

(

= 0;

< 2;

++)

(

it = mods[

].

; it != mods[

].second; it++)

new_subsource->

(it->value);

bsrc->SetSubtype().push_back(new_subsource);

((

=

(s_Mod_focus)) !=

) {

bsrc->SetIs_focus();

((

=

(s_Mod_taxid)) !=

) {

(reset_taxid && bsrc->IsSetOrgname() && bsrc->GetOrg().GetTaxId() !=

) {

((

=

(s_Mod_moltype, s_Mod_mol_type)) !=

) {

(it == sc_BiomolMap.end()) {

mi->SetBiomol(it->second.m_eBiomol);

((

=

(s_Mod_tech)) !=

) {

(it == sc_TechMap.end()) {

mi->SetTech(it->second);

((

=

(s_Mod_completeness, s_Mod_completedness)) !=

) {

(it == sc_CompletenessMap.end()) {

mi->SetCompleteness(it->second);

((

=

(s_Mod_gene)) !=

) {

gene->SetLocus(

->value);

((

=

(s_Mod_allele)) !=

) {

gene->SetAllele(

->value );

((

=

(s_Mod_gene_syn, s_Mod_gene_synonym)) !=

) {

gene->SetSyn().push_back(

->value );

((

=

(s_Mod_locus_tag)) !=

) {

gene->SetLocus_tag(

->value );

((

=

(s_Mod_protein, s_Mod_prot)) !=

) {

->SetName().push_back(

->value);

((

=

(s_Mod_prot_desc, s_Mod_protein_desc)) !=

) {

->SetDesc(

->value );

((

=

(s_Mod_EC_number)) !=

) {

->SetEc().push_back(

->value );

((

=

(s_Mod_activity, s_Mod_function)) !=

) {

->SetActivity().push_back(

->value );

((

=

(s_Mod_secondary_accession,

s_Mod_secondary_accessions)) !=

)

list<CTempString> ranges;

(list<CTempString>, it, ranges) {

gbb->SetExtra_accessions().push_back(*it2);

gbb->SetExtra_accessions().push_back(s);

((

=

(s_Mod_keyword, s_Mod_keywords)) !=

) {

list<string> keywordList;

gbb->SetKeywords().push_back( *keyword_iter );

((

=

(s_Mod_secondary_accession,

s_Mod_secondary_accessions)) !=

)

list<CTempString> ranges;

(list<CTempString>, it, ranges) {

hist->SetReplaces().SetIds().push_back(it2.GetID());

hist->SetReplaces().SetIds()

((

=

(s_Mod_primary, s_Mod_primary_accessions)) !=

) {

list<CTempString> accns;

(list<CTempString>, it, accns) {

field->SetLabel().SetId(0);

subfield->

().SetStr(

);

field->SetData().SetFields().push_back(subfield);

.push_back(field);

( !

.empty() ) {

(

&

(*pParentSet)).SetDescr() :

(

pDesc : descriptors.

()) {

(pDesc->IsUser() && pDesc->GetUser().IsDBLink()) {

descriptors.

().push_back(pDBLinkDesc);

list<CTempString>& vals,

& user_obj = dblink_desc.

();

(user_obj.IsSetData()) {

(

pUserField : user_obj.SetData()) {

(pUserField->IsSetLabel() &&

pUserField->GetLabel().IsStr() &&

pField = pUserField;

user_obj.SetData().push_back(pField);

pField->

().SetStrs().clear();

(

&

: vals) {

pField->

().SetStrs().push_back(

);

& vals,

list<CTempString> value_list;

(

&

: value_list) {

(value_list.empty()) {

((

=

(s_Mod_SRA)) !=

) {

((

=

(s_Mod_bioproject)) !=

) {

((

=

(s_Mod_biosample)) !=

) {

((

=

(s_Mod_project, s_Mod_projects)) !=

) {

list<CTempString> ids;

(list<CTempString>, it, ids) {

field->SetLabel().SetId(0);

subfield->

().SetStr(

);

subfield->

().SetInt(

);

field->SetData().SetFields().push_back(subfield);

subfield->

().SetStr(

);

subfield->

().SetInt(0);

field->SetData().SetFields().push_back(subfield);

.push_back(field);

( !

.empty() ) {

it != range.second; ++it) {

bioseq.

().Set().push_back(pubdesc);

SMod & badMod,

& sAllowedValues )

: runtime_error(x_CalculateErrorString(badMod, sAllowedValues)),

m_BadMod(badMod), m_sAllowedValues(sAllowedValues)

& badMod,

& sAllowedValues )

stringstream str_strm;

str_strm <<

<<

<< badMod.

<<

<< badMod.

<<

<< sAllowedValues <<

;

str_strm.str();

& unkMod )

: runtime_error(x_CalculateErrorString(unkMod)), m_UnkMod(unkMod)

& unkMod)

stringstream str_strm;

str_strm <<

<<

<< unkMod.

<<

;

str_strm.str();

(

tries = 0; tries < 2; ++tries) {

( modkey.

() ) {

&

(*it).

=

;

alt_smod(alt_key);

(

.second =

.first;

&

(*

.second).used =

;

delim = s->empty() ?

:

;

*s += delim +

+ it->key +

+ it->value +

;

TMapModToValidValues s_mapModToValidValues;

TMapModToValidValues::const_iterator find_iter =

s_mapModToValidValues.find(

);

( find_iter != s_mapModToValidValues.end() ) {

find_iter->second;

set_valid_values.

(

);

set_valid_values.

(

);

set_valid_values.

(

);

set_valid_values.

(

);

set_valid_values.

(map_iter->first);

set_valid_values.

(

);

set_valid_values.

(

);

set_valid_values.

(

);

set_valid_values.

(

);

set_valid_values.

(

);

set_valid_values.

(

);

set_valid_values.

(

);

set_valid_values.

(

);

set_valid_values.

(

);

set_valid_values.

( enum_iter->first );

set_valid_values.

(tech_it->first);

set_valid_values.

(comp_it->first);

set_valid_values.

(

);

set_valid_values;

TMapModNameToStringOfAllAllowedValues mapModNameToStringOfAllAllowedValues;

TMapModNameToStringOfAllAllowedValues::const_iterator find_iter =

mapModNameToStringOfAllAllowedValues.

(

);

( find_iter != mapModNameToStringOfAllAllowedValues.end() ) {

find_iter->second;

& sAllValuesAsOneString =

mapModNameToStringOfAllAllowedValues[

];

( ! sAllValuesAsOneString.empty() ) {

sAllValuesAsOneString +=

;

sAllValuesAsOneString +=

+ *value_it +

;

sAllValuesAsOneString;

cerr << badModError.what() << endl;

cerr << unkModError.what() << endl;

,

&

(*it).

=

;

newmod.

=

;

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.

void remove_if(Container &c, Predicate *__pred)

CRef< CSeqdesc > m_user_obj

bool IsInitialised() const

CRef< CUser_field > m_dblink

CAutoAddDBLink(CBioseq &seq, const CTempString &id)

CRef< CSeq_descr > m_descr

CSeqdesc & Set(bool skip_lookup=false)

CAutoInitDesc(CSeq_descr &descr, CSeqdesc::E_Choice which)

CRef< CBioseq_set > m_bioset

bool IsInitialized(void) const

void Set(T *object)

Initialize with an existing object.

CConstRef< CBioseq_set > GetParentSet(void) const

void Throw(void) const

this function to throw this object.

static CObjReaderLineException * Create(EDiagSev eSeverity, unsigned int uLine, const std::string &strMessage, EProblem eProblem=eProblem_GeneralParsingError, const std::string &strSeqId=string(""), const std::string &strFeatureName=string(""), const std::string &strQualifierName=string(""), const std::string &strQualifierValue=string(""), CObjReaderLineException::EErrCode eErrCode=eFormat, const TVecOfLines &vecOfOtherLines=TVecOfLines())

Please use this instead of the constructor because the ctor is protected.

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

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

namespace ncbi::objects::

Root class for all serialization exceptions.

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

TBase::const_iterator const_iterator

static bool IsMultipleValuesAllowed(TSubtype)

static bool NeedsNoText(const TSubtype &subtype)

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

virtual bool PutError(const ILineError &)=0

Store error in the container, and return true if error was stored fine, and return false if the calle...

@ eProblem_GeneralParsingError

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

const_iterator begin() const

const_iterator end() const

const_iterator lower_bound(const key_type &key) const

parent_type::const_iterator const_iterator

static bool key_equal(const KEY_T *a, const KEY_T *b)

static const struct name_t names[]

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

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

static const char location[]

SStrictId_Entrez::TId TEntrezId

TEntrezId type for entrez ids which require the same strictness as TGi.

#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.

void swap(NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair1, NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair2)

@ eDiag_Warning

Warning message.

@ eDiag_Critical

Critical error message.

#define NCBI_USER_THROW_FMT(message)

Throw a "user exception" with message processed as output to ostream.

list< pair< string, TEnumValueType > > TValues

const TValues & GetValues(void) const

Get the list of name-value pairs.

#define ENUM_METHOD_NAME(EnumName)

void SetAllUnused()

Set all mods to unused.

static const unsigned char kKeyCanonicalizationTable[257]

pair< TModsCI, TModsCI > TModsRange

std::string x_CalculateErrorString(const SMod &badMod, const string &sAllowedValues)

ILineErrorListener * m_pErrorListener

void ApplyMods(CBioSource &bsrc, CTempString organism=kEmptyStr)

const SMod * FindMod(const CTempString &key, const CTempString &alt_key=CTempString())

If a modifier with either key is present, mark it as used and return it; otherwise,...

bool AddMods(const CTempString &name, const CTempString &value)

void x_ApplyDBLinkMods(CBioseq &bioseq)

void x_ProcessError(CObjReaderLineException &err)

TModsRange FindAllMods(const CTempString &key, const CTempString &alt_key)

Return all modifiers with the given key (e.g., db_xref), marking them as used along the way.

void x_AddPCRPrimers(CAutoInitRef< CPCRReactionSet > &pcr_reaction_set)

static const set< string > & GetModAllowedValues(const string &mod)

Given a mod name (e.g.

EHandleBadMod m_HandleBadMod

void ApplyPubMods(CBioseq &seq)

CRef< CModFilter > m_pModFilter

CConstRef< CSeq_id > seqid

static bool EqualKeys(const CTempString &lhs, const CTempString &rhs)

void GetLabel(string *s, TWhichMods which=fAllMods) const

Append a representation of the specified modifiers to s, with a space in between if s is not empty an...

CBadModError(const SMod &badMod, const std::string &sAllowedValues)

std::string x_CalculateErrorString(const SMod &unkMod)

void x_HandleUnkModValue(const SMod &mod)

static CSafeStatic< CSourceModParser::SMod > kEmptyMod

Used for passing an empty mod to some funcs without having to constantly recreate an empty one.

void x_HandleBadModValue(const SMod &mod)

static const string & GetModAllowedValuesAsOneString(const string &mod)

Same as GetModAllowedValues, but returns one string with all the values.

void x_ApplyTPAMods(CAutoInitRef< CUser_object > &tpa)

CUnkModError(const SMod &unkMod)

void ApplyAllMods(CBioseq &seq, CTempString organism=kEmptyStr, CConstRef< CSeq_loc > location=CConstRef< CSeq_loc >())

Apply previously extracted modifiers to the given object, marking all relevant ones as used.

void x_ApplyGenomeProjectsDBMods(CAutoInitRef< CUser_object > &gpdb)

string ParseTitle(const CTempString &title, CConstRef< CSeq_id > seqid, size_t iMaxModsToParse=std::numeric_limits< size_t >::max())

Extract and store bracketed modifiers from a title string, returning a stripped version (which may we...

void x_ApplyMods(CAutoInitDesc< CBioSource > &bsrc, CTempString organism)

TMods::const_iterator TModsCI

TMods GetMods(TWhichMods which=fAllMods) const

Return all modifiers matching the given criteria (if any) without affecting their status (used vs.

@ eHandleBadMod_PrintToCerr

@ eHandleBadMod_ErrorListener

const string AsFastaString(void) const

static int BestRank(const CRef< CSeq_id > &id)

CRef< C > Ref(C *object)

Helper functions to get CRef<> and CConstRef<> objects.

void Reset(void)

Reset reference object.

TObjectType * GetPointerOrNull(void) const THROWS_NONE

Get pointer value.

bool Empty(void) const THROWS_NONE

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

static CTempString TruncateSpaces_Unsafe(const CTempString str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string.

static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

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 bool EqualCase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-sensitive equality of a substring with another string.

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 CStringUTF8 AsUTF8(const CTempString &src, EEncoding encoding, EValidate validate=eNoValidate)

Convert into UTF8 from a C/C++ string.

size_type length(void) const

Return the length of the represented array.

static unsigned int StringToUInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to unsigned int.

CTempString substr(size_type pos) const

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

static bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another 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.

size_type size(void) const

Return the length of the represented array.

void Copy(string &dst, size_type pos, size_type len) const

Copy a substring into a string Somewhat similar to basic_string::assign()

static const size_type npos

@ fConvErr_NoThrow

Do not throw an exception on error.

@ fSplit_Tokenize

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

@ fSplit_MergeDelimiters

Merge adjacent delimiters.

C::value_type FindBestChoice(const C &container, F score_func)

Find the best choice (lowest score) for values in a container.

static const char label[]

void SetSubtype(TSubtype value)

Assign a value to Subtype data member.

void SetForward(TForward &value)

Assign a value to Forward data member.

void SetReverse(TReverse &value)

Assign a value to Reverse data member.

void SetName(const TName &value)

Assign a value to Name data member.

Tdata & Set(void)

Assign a value to data member.

@ eSubtype_lat_lon

+/- decimal degrees

@ eOrigin_mut

artificially mutagenized

@ eOrigin_natmut

naturally occurring mutant

bool IsStr(void) const

Check if variant Str is selected.

void SetTag(TTag &value)

Assign a value to Tag data member.

const TStrs & GetStrs(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

E_Choice Which(void) const

Which variant is currently selected.

TData & SetData(void)

Assign a value to Data data member.

void SetNum(TNum value)

Assign a value to Num data member.

const TStr & GetStr(void) const

Get the variant data.

void SetLabel(TLabel &value)

Assign a value to Label data member.

TStr & SetStr(void)

Select the variant.

void SetType(TType &value)

Assign a value to Type data member.

void SetData(TData &value)

Assign a value to Data data member.

const TType & GetType(void) const

Get the Type member data.

void SetDb(const TDb &value)

Assign a value to Db data member.

vector< CRef< CUser_field > > TData

@ e_not_set

No variant selected.

void SetSubtype(TSubtype value)

Assign a value to Subtype data member.

void SetSubname(const TSubname &value)

Assign a value to Subname data member.

@ eSubtype_nat_host

natural host of this specimen

TPmid & SetPmid(void)

Select the variant.

void SetLocation(TLocation &value)

Assign a value to Location data member.

void SetData(TData &value)

Assign a value to Data data member.

bool IsSetClass(void) const

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

TClass GetClass(void) const

Get the Class member data.

@ eClass_nuc_prot

nuc acid and coded proteins

void SetPub(TPub &value)

Assign a value to Pub data member.

const TInst & GetInst(void) const

Get the Inst member data.

TPub & SetPub(void)

Select the variant.

bool IsSetAnnot(void) const

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

TAnnot & SetAnnot(void)

Assign a value to Annot data member.

const TId & GetId(void) const

Get the Id member data.

bool IsSetHist(void) const

sequence history Check if a value has been assigned to Hist data member.

TComment & SetComment(void)

Select the variant.

void SetInst(TInst &value)

Assign a value to Inst data member.

E_Choice

Choice variants.

EMol

molecule class in living organism

void SetDescr(TDescr &value)

Assign a value to Descr data member.

TUser & SetUser(void)

Select the variant.

Tdata & Set(void)

Assign a value to data member.

list< CRef< CSeq_annot > > TAnnot

@ eCompleteness_has_left

5' or NH3 end present

@ eCompleteness_complete

complete biological entity

@ eCompleteness_has_right

3' or COOH end present

@ 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_physmap

from physical mapping techniques

@ eTech_htc

high throughput cDNA

@ eTech_both

concept transl. w/ partial pept. seq.

@ eTech_targeted

targeted locus sets/studies

@ 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

@ eBiomol_pre_RNA

precursor RNA of any sort really

@ eBiomol_cRNA

viral RNA genome copy intermediate

@ eBiomol_transcribed_RNA

transcribed RNA other than existing classes

@ eBiomol_other_genetic

other genetic material

@ e_Genbank

GenBank specific info.

@ e_Molinfo

info on the molecule and techniques

@ e_not_set

No variant selected.

@ e_Source

source of materials, includes Org-ref

@ eStrand_ds

double strand

@ eStrand_ss

single strand

static const CS_INT unused

const struct ncbi::grid::netcache::search::fields::KEY key

const GenericPointer< typename T::ValueType > T2 value

Useful/utility classes and methods.

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

static const GLdouble origin[]

#define FIELD_CHAIN_OF_2_IS_SET(Var, Fld1, Fld2)

FIELD_CHAIN_OF_2_IS_SET.

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

SStaticPair< const char *, SMolTypeInfo > TBiomolMapEntry

static void s_SetDBLinkField(const string &label, const string &vals, CRef< CSeqdesc > &pDBLinkDesc, CBioseq &bioseq)

DEFINE_STATIC_ARRAY_MAP(TBiomolMap, sc_BiomolMap, sc_BiomolArray)

CStaticPairArrayMap< const char *, CMolInfo::TCompleteness, CSourceModParser::PKeyCompare > TCompletenessMap

static const TTechMapEntry sc_TechArray[]

static void s_GetPrimerInfo(const CSourceModParser::SMod *pNamesMod, const CSourceModParser::SMod *pSeqsMod, vector< pair< string, string >> &reaction_info)

static void s_AddPrimers(const pair< string, string > &primer_info, CPCRPrimerSet &primer_set)

static void s_PopulateUserObject(CUser_object &uo, const string &type, CUser_object::TData &data)

static CRef< CSeqdesc > s_SetDBLinkDesc(CBioseq &bioseq)

static const TBiomolMapEntry sc_BiomolArray[]

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

static void s_ApplyPubMods(CBioseq &bioseq, const CSourceModParser::TModsRange &range)

static void s_SetDBLinkFieldVals(const string &label, const list< CTempString > &vals, CSeqdesc &dblink_desc)

static const TCompletenessMapEntry sc_CompletenessArray[]

SStaticPair< const char *, CMolInfo::TCompleteness > TCompletenessMapEntry

CSafeStaticRef< CSeq_descr > fake_descr

CStaticPairArrayMap< const char *, SMolTypeInfo, CSourceModParser::PKeyCompare > TBiomolMap

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

#define STATIC_SMOD(key_str)

SMolTypeInfo(EShown eShown, CMolInfo::TBiomol eBiomol, CSeq_inst::EMol eMol)

CMolInfo::TBiomol m_eBiomol

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

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