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NCBI C++ ToolKit: src/misc/biosample_util/biosample_util.cpp Source File

(

use_dev_server,

&args)

host = use_dev_server ?

:

;

path =

;

url =

+ host + path +

+ args;

(it != cache->

())

args =

+ accession +

;

unique_ptr<CObjectIStream> in_stream;

*in_stream >> *response;

(*cache)[accession] = response;

suffix(1);

ofstream ostr(filename);

(it != item.

()) {

(it != cache->

())

args =

+ accession;

response(http_stream, &errors);

status.second;

(it != root.

())

(*cache)[accession] = status;

args =

+ list +

;

response(http_stream, &errors);

(it != root.

())

status[response.first] = response.second;

list +=

+ it->first;

;

;

edit::CDBLinkField dblink_field(edit::CDBLinkField::eDBLinkFieldType_BioSample);

vector<CConstRef<CObject> > objs = dblink_field.GetObjects(bh);

vector<string> new_ids = dblink_field.GetVals(**it);

(vector<string>, s, new_ids) {

vector<string> new_ids =

(*desc_ci,

);

(vector<string>, s, new_ids) {

stream <<

;

stream <<

;

stream <<

<< endl;

(blank_sample && blank_src) {

stream << m_BiosampleID <<

;

(use_geo_loc_name && m_FieldName ==

) {

stream <<

<<

;

stream << m_FieldName <<

;

stream << m_SequenceID <<

;

stream << (blank_sample ?

: m_SampleVal) <<

;

stream << (blank_src ?

: m_SrcVal) << endl;

formattedValue = (

+

(width,

)).substr(0, width);

ostr << formattedValue;

(m_FieldName ==

|| m_FieldName ==

|| m_FieldName ==

) {

(m_FieldName ==

|| m_FieldName ==

|| m_FieldName ==

) {

valueWidth)

newValue = GetSampleVal();

oldValue = GetSrcVal();

(oldValue.empty() && !newValue.empty()) {

newValue =

(

) + newValue;

(!oldValue.empty() && newValue.empty()) {

oldValue =

(

) + oldValue;

stream << m_FieldName;

stream << m_SequenceID <<

;

stream << (blank_sample ?

: m_SampleVal) <<

;

stream << m_SrcVal <<

;

= CompareAllButSequenceID(other);

name1 = f1->GetLabel();

name2 = f2->GetLabel();

fields.insert(fields.end(), src_fields.begin(), src_fields.end());

(fields.size() < 2) {

TStructuredCommentTableColumnList::iterator f_prev = fields.begin();

TStructuredCommentTableColumnList::iterator f_next = f_prev;

(f_next != fields.end()) {

(

((*f_prev)->GetLabel(), (*f_next)->GetLabel())) {

f_next = fields.erase(f_next);

rval.push_back(diff);

vector<CConstRef<CUser_object> > src_list;

src_list.push_back(s1);

src_list.push_back(s2);

(

((*it)->GetLabel(),

)

||

((*it)->GetLabel(),

)) {

src_val = (*it)->GetFromComment(src);

sample_val = (*it)->GetFromComment(sample);

rval.push_back(diff);

vector<CConstRef<CUser_object> > src_list;

src_list.push_back(src);

src_list.push_back(sample);

src_val =

;

src_val = (*it)->GetFromComment(*src);

sample_val =

;

(*it)->GetFromComment(*sample);

rval.push_back(diff);

printed_header =

;

src_val = (*it)->GetSrcVal();

(!printed_header) {

*

<<

<< (*it)->GetSequenceId() <<

<< (*it)->GetBioSample() << endl;

printed_header =

;

*

<<

<< (*it)->GetFieldName() <<

<< src_val <<

<< (*it)->GetSampleVal() <<

<< endl;

((*cit)->IsSetHeader() && (*cit)->GetHeader().IsSetTitle()

&&

((*cit)->GetHeader().GetTitle(), column_name)) {

(

->SetData().SetString().size() <

+ 1) {

->SetData().SetString().push_back (

);

((*cit)->IsSetHeader() && (*cit)->GetHeader().IsSetTitle()

new_col->SetHeader().SetTitle(column_name);

.SetColumns().push_back(new_col);

(

.IsSetData() &&

.GetData().IsString() &&

.GetData().GetString().size() >

) {

((*cit)->IsSetHeader() && (*cit)->GetHeader().IsSetTitle()

((*it)->IsSub()) {

include_comments,

& expected_prefix)

(biosample_ids.size() > 0 && !with_id) {

(pub_desc_ci && !

(*pub_desc_ci)) {

(!src_desc_ci && !comm_desc_ci && bioproject_ids.size() == 0 && !pub_desc_ci) {

(bioproject_ids.size() > 0) {

= bioproject_ids[0];

(

= 1;

< bioproject_ids.size();

++) {

+= bioproject_ids[

];

((*it)->IsSub() && (*it)->GetSub().IsSetAuthors() && (*it)->GetSub().GetAuthors().IsSetAffil()) {

& affil = (*it)->GetSub().GetAuthors().GetAffil();

(affil.

()) {

}

(affil.

()) {

(include_comments) {

(comm_desc_ci) {

= (*it)->GetLabel();

(with_id && biosample_ids.size() > 0) {

num_rows = (

)

+ 1;

.SetNum_rows(num_rows);

(biosample_ids.size() == 0) {

biosample_ids.push_back(biosample_accession);

(vector<string>, it, biosample_ids) {

biosample_ids.clear();

biosample_ids.push_back(biosample_accession);

vector<CRef <CSeq_id> > id_list;

id_list.push_back(ic);

->GetLabel(&

);

& biosample_accession,

& num_processed,

vector<string>& unprocessed_ids,

compare_structured_comments,

& expected_prefix,

vector<string> user_labels;

vector<CConstRef<CUser_object> > user_objs;

(comm_desc_ci) {

user_labels.push_back(prefix);

user_objs.push_back(obj);

(biosample_ids.size() == 0) {

(vector<string>,

, biosample_ids) {

((*it)->IsSource()) {

diffs.insert(diffs.end(), these_diffs.begin(), these_diffs.end());

(compare_structured_comments) {

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

vector<CConstRef<CUser_object> >::iterator uit = user_objs.begin();

(sit != user_labels.end() && uit != user_objs.end()) {

diffs.insert(diffs.end(), these_diffs.begin(), these_diffs.end());

diffs.insert(diffs.end(), these_diffs.begin(), these_diffs.end());

unprocessed_ids.push_back(*

);

street =

;

country =

;

add_address =

;

(auth_list && auth_list->

()) {

affil = &(auth_list->

());

(affil && affil->IsStd()) {

add_address =

;

&& auth_list->

().

().front()->GetName().IsName()) {

address->

(

(

, street.c_str()));

address->

(

(

, city.c_str()));

address->

(

(

, sub.c_str()));

address->

(

(

, country.c_str()));

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

attribute_name =

;

attribute_name =

;

= (*it)->GetName();

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

attribute_name =

;

attribute_name =

;

= (*it)->GetLabel();

= (*it)->GetFromComment(usr);

found =

;

(

!= sample_attrs.

() && !found) {

name_match =

;

(at !=

->get_attributes().end() && !name_match) {

list<string> sbm_info;

(affil.

()) {

}

(affil.

()) {

sbm_info.push_back(affil.

());

& id_prefix,

& bioproject_accession,

& default_owner,

& hup_date,

& comment,

first_seq_only,

report_structured_comments,

& expected_prefix)

(biosample_ids.size() > 0) {

(bioproject_ids.size() > 0) {

found =

;

(vector<string>, it, bioproject_ids) {

+ bioproject_ids[0];

bioproject_ids.clear();

bioproject_ids.push_back(bioproject_accession);

bioproject_ids.push_back(bioproject_accession);

(pub_desc_ci){

((*it)->IsSub() && (*it)->GetSub().IsSetAuthors()) {

auth_list = &((*it)->GetSub().GetAuthors());

}

((*it)->IsGen() && (*it)->GetGen().IsSetAuthors()) {

auth_list = &((*it)->GetGen().GetAuthors());

(!src_desc_ci && !comm_desc_ci && bioproject_ids.size() == 0) {

title =

+ sequence_id;

description->

(

(

, title.c_str()));

(auth_list && auth_list->

()) {

affil = &(auth_list->

());

attrs.

(

,

);

attrs.

(

,

);

owner(

);

owner_str =

;

owner_str = default_owner;

organization->

(

(

, owner_str.c_str()));

owner.

(

(

, owner_str.c_str()));

description->

(hup);

->get_attributes().insert(

,

);

sample_id = sequence_id;

(first_seq_only) {

sample_id = id_prefix;

sample_id = id_prefix +

+ sequence_id;

node_iter = ids->

(

(

, sample_id.c_str()));

descr->

(

(

, comment.c_str()));

(bioproject_ids.size() > 0) {

links(

);

(vector<string>, it, bioproject_ids) {

(! it->empty()) {

node_iter = links.

(

(

, it->c_str()));

sample->

(

(

,

));

sample_attrs(

);

(report_structured_comments) {

(comm_desc_ci) {

sample->

(sample_attrs);

node_iter = identifier->

(

(

, sample_id.c_str()));

(report_stream) {

*report_stream << doc << endl;

path = sequence_id;

path = path +

;

*xml_out << doc << endl;

(

pSampleDesc: bioSample.

()) {

& sampleDesc = *pSampleDesc;

,

, bioSource, sampleDesc.

());

diffs.insert(diffs.end(), these_diffs.begin(), these_diffs.end());

& filename,

ostr << asnText << object;

& existingBiosampleAcc,

existingBiosampleAcc,

,

);

assigned =

;

(

pExistingDesc: pExistingBiosampleDescrs->

()) {

& existingDesc = *pExistingDesc;

,

, newBioSource, existingSource);

(!diffs.empty()) {

proposedNewBiosource.

(existingSource);

!diffs.empty();

(existingBiosource.

()) {

& existingOrg = existingBiosource.

();

(existingOrg.IsSetTaxname()) {

newBiosource.

().SetTaxname(existingOrg.GetTaxname());

existingTaxId = existingOrg.GetTaxId();

newBiosource.

().SetTaxId(existingTaxId);

& newOrgs = newBiosource.

().SetOrgname().SetMod();

(

& pExistingMod: existingOrgs) {

existingSubtype = pExistingMod->GetSubtype();

existingSubname = pExistingMod->GetSubname();

alreadyThere =

;

(

& pNewMod: newOrgs) {

newSubtype = pNewMod->GetSubtype();

( newSubtype == existingSubtype) {

alreadyThere =

;

newOrgs.push_back(pNewMod);

& existingSubtypes = existingBiosource.

();

(

& pExistingSubSource: existingSubtypes) {

(!pExistingSubSource->CanGetName()) {

existingSubtype = pExistingSubSource->GetSubtype();

(newBiosource.

(existingSubtype)) {

pNewSubsource->

(*pExistingSubSource);

newBiosource.

().push_back(pNewSubsource);

& fieldName)

(

pDiff: diffs) {

(pDiff->GetFieldName() == fieldName) {

(existingBiosource.

()) {

& existingOrg = existingBiosource.

();

(fromDiff && !fromDiff->GetSrcVal().empty()) {

newBiosource.

().SetTaxname(existingOrg.GetTaxname());

existingTaxId = existingOrg.GetTaxId();

newBiosource.

().SetTaxId(existingTaxId);

& newOrgs = newBiosource.

().SetOrgname().SetMod();

(

& pExistingMod: existingOrgs) {

existingSubtype = pExistingMod->GetSubtype();

(fromDiff && !fromDiff->GetSrcVal().empty()) {

newOrgs.push_back(pNewMod);

& existingSubtypes = existingBiosource.

();

& newSubtypes = newBiosource.

();

(

& pExistingSubSource: existingSubtypes) {

(!pExistingSubSource->CanGetName()) {

existingSubtype = pExistingSubSource->GetSubtype();

(pFromDiff && !pFromDiff->GetSrcVal().empty()) {

(existingSubtype, pFromDiff->GetSrcVal()));

newSubtypes.push_back(pNewSubsource);

ostr <<

(keyWidth + 2 * valueWidth,

) <<

;

(

diff: diffList) {

diff->PrettyPrint(ostr, keyWidth, valueWidth);

vector< CRef< CFieldDiff > > TFieldDiffList

User-defined methods of the data storage class.

User-defined methods of the data storage class.

bool s_ShouldIgnoreStructuredCommentFieldDiff(const string &label, const string &src_val, const string &sample_val)

bool UpdateBiosourceFromBiosample(const CBioSource &existingBiosource, CBioSource &newBiosource)

void AddBioseqToTable(CBioseq_Handle bh, CSeq_table &table, bool with_id, bool include_comments, const string &expected_prefix)

string OwnerFromAffil(const CAffil &affil)

static const char * kAffilInst

string GetValueFromColumn(const CSeqTable_column &column, size_t row)

void AddBioSourceToAttributes(node &organism, node &sample_attrs, const CBioSource &src)

void HarmonizeAttributeName(string &attribute_name)

vector< string > GetDBLinkIDs(const CUser_object &user, const string &field_name)

bool s_IsReportableStructuredComment(const CSeqdesc &desc, const string &expected_prefix)

void s_AddSamplePair(node &sample_attrs, string attribute_name, string val)

bool ResolveSuppliedBioSampleAccession(const string &biosample_accession, vector< string > &biosample_ids)

EStatus GetBioSampleStatusFromNode(const node &item)

static const char * kSequenceID

static const char * kStructuredCommentPrefix

static const char * kStructuredCommentSuffix

vector< string > GetBioProjectIDs(CBioseq_Handle bh)

CRef< CSeqTable_column > FindSeqTableColumnByName(CRef< CSeq_table > values_table, string column_name)

void AddValueToTable(CSeq_table &table, string column_name, string value, size_t row)

static const char * kAffilDept

string PrepareUrl(bool use_dev_server, const string &args)

bool DoDiffsContainConflicts(const TBiosampleFieldDiffList &diffs, CNcbiOstream *log)

string GetBestBioseqLabel(CBioseq_Handle bsh)

static const char * kBioProject

TStatus ProcessBiosampleStatusNode(node &item)

CRef< CSeq_descr > GetBiosampleData(const string &accession, bool use_dev_server, TBioSamples *cache)

bool s_CompareStructuredCommentFields(CRef< CStructuredCommentTableColumnBase > f1, CRef< CStructuredCommentTableColumnBase > f2)

CConstRef< CBiosampleFieldDiff > sGetDiffByFieldName(const TBiosampleFieldDiffList &diffs, const string &fieldName)

void PrettyPrint(const TBiosampleFieldDiffList &diffList, CNcbiOstream &ostr, size_t keyWidth, size_t valueWidth)

TStructuredCommentTableColumnList GetAvailableFields(vector< CConstRef< CUser_object > > src)

static bool s_IsCitSub(const CSeqdesc &desc)

void AddStructuredCommentToAttributes(node &sample_attrs, const CUser_object &usr)

TBiosampleFieldDiffList GetBioseqDiffs(CBioseq_Handle bh, const string &biosample_accession, size_t &num_processed, vector< string > &unprocessed_ids, bool use_dev_server, bool compare_structured_comments, const string &expected_prefix, TBioSamples *cache)

void PrintBioseqXML(CBioseq_Handle bh, const string &id_prefix, CNcbiOstream *report_stream, const string &bioproject_accession, const string &default_owner, const string &hup_date, const string &comment, bool first_seq_only, bool report_structured_comments, const string &expected_prefix)

string GetBiosampleStatusName(EStatus status)

EStatus GetBiosampleStatus(const string &accession, bool use_dev_server, TStatuses *cache)

void sPrintField(const string &value, size_t width, CNcbiOstream &ostr)

void GenerateDiffListFromBioSource(const CSeq_descr &bioSample, const CBioSource &bioSource, TBiosampleFieldDiffList &diffs)

void AddContact(node::iterator &organization, CConstRef< CAuth_list > auth_list)

bool AttributeNamesAreEquivalent(string name1, string name2)

string GetValueFromTable(const CSeq_table &table, string column_name, size_t row)

void SaveSerialObject(const string &filename, const CSerialObject &object)

void AddValueToColumn(CRef< CSeqTable_column > column, string value, size_t row)

void ProcessBulkBioSample(TStatuses &status, string list, bool use_dev_server)

vector< string > GetBiosampleIDs(CBioseq_Handle bh)

TBiosampleFieldDiffList GetFieldDiffs(const string &sequence_id, const string &biosample_id, const CBioSource &src, const CBioSource &sample)

vector< CRef< CBiosampleFieldDiff > > TBiosampleFieldDiffList

map< string, CRef< CSeq_descr > >::iterator TBioSamplesIterator

pair< string, biosample_util::EStatus > TStatus

map< string, EStatus >::iterator TStatusesIterator

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

static bool ShouldIgnoreConflict(const string &label, string src_val, string sample_val, bool is_local_copy=false)

TNameValList GetNameValPairs() const

static bool IsStopWord(const string &value)

bool HasSubtype(CSubSource::TSubtype subtype) const

vector< TNameVal > TNameValList

bool IsSetTaxname(void) const

TFieldDiffList GetBiosampleDiffs(const CBioSource &biosample, bool is_local_copy=false) const

string GetSampleVal() const

int Compare(const CBiosampleFieldDiff &other)

static void PrintHeader(ncbi::CNcbiOstream &stream, bool show_seq_id=true)

void PrettyPrint(ncbi::CNcbiOstream &stream, size_t keyWidth=20, size_t valueWidth=40) const

void Print(ncbi::CNcbiOstream &stream, bool show_seq_id=true) const

int CompareAllButSequenceID(const CBiosampleFieldDiff &other)

This stream exchanges data with an HTTP server located at the URL: http[s]://host[:port]/path[?...

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

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

static string GetSubtypeName(TSubtype stype, EVocabulary vocabulary=eVocabulary_raw)

bool IsSetOrgMod(void) const

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

Base class for all serializable objects.

static bool NCBI_UseGeoLocNameForCountry(void)

static string GetSubtypeName(CSubSource::TSubtype stype, EVocabulary vocabulary=eVocabulary_raw)

static bool NeedsNoText(const TSubtype &subtype)

const CUser_field & GetField(const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const

Access a named field in this user object.

container_type::iterator iterator

const_iterator begin() const

const_iterator end() const

const_iterator find(const key_type &key) const

const char * get_value(void) const

Get the value of this attribute.

const char * get_name(void) const

Get the name of this attribute.

Const Iterator class for accessing attribute pairs.

Iterator class for accessing attribute pairs.

The xml::attributes class is used to access all the attributes of one xml::node.

iterator begin(void)

Get an iterator that points to the first attribute.

iterator end(void)

Get an iterator that points one past the the last attribute.

void insert(const char *name, const char *value, const ns *nspace=NULL)

Add an attribute to the attributes list.

The xml::document class is used to hold the XML tree and various bits of information about it.

void set_encoding(const char *encoding)

Set the XML encoding string.

const node & get_root_node(void) const

Get a reference to the root node of this document.

void set_is_standalone(bool sa)

Set the standalone flag.

The xml::error_messages class is used to store all the error message which are collected while parsin...

The xml::node::iterator provides a way to access children nodes similar to a standard C++ container.

The xml::node class is used to hold information about one XML node.

const char * get_name(void) const

Get the name of this xml::node.

iterator end(void)

Get an iterator that points one past the last child for this node.

iterator begin(void)

Get an iterator that points to the beginning of this node's children.

iterator insert(const node &n)

Insert a new child node.

xml::attributes & get_attributes(void)

Get the list of attributes.

void Print(const CCompactSAMApplication::AlignInfo &ai)

Include a standard set of the NCBI C++ Toolkit most basic headers.

The NCBI C++ standard methods for dealing with std::string.

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

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

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

static const char * column

#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 NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

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

Set object to copy of another one.

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

vector< CSeq_id_Handle > TId

const TId & GetId(void) const

TObjectType * GetPointer(void) const THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

#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.

IO_PREFIX::ofstream CNcbiOfstream

Portable alias for ofstream.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

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 bool IsBlank(const CTempString str, SIZE_TYPE pos=0)

Check if a string is blank (has no text).

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

Convert int to string.

static string Join(const TContainer &arr, const CTempString &delim)

Join strings using the specified delimiter.

static int Compare(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2, ECase use_case=eCase)

Compare of a substring with another 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.

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.

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

Case-sensitive compare of a substring with another string.

@ eNocase

Case insensitive compare.

@ eCurrent

Use current time. See also CCurrentTime.

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[]

bool IsSetAffil(void) const

author affiliation Check if a value has been assigned to Affil data member.

const TAffil & GetAffil(void) const

Get the Affil member data.

bool IsSetStreet(void) const

street address, not ANSI Check if a value has been assigned to Street data member.

const TStr & GetStr(void) const

Get the variant data.

bool IsSetCity(void) const

Author Affiliation, City Check if a value has been assigned to City data member.

const TEmail & GetEmail(void) const

Get the Email member data.

bool IsSetEmail(void) const

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

const TStreet & GetStreet(void) const

Get the Street member data.

const TAffil & GetAffil(void) const

Get the Affil member data.

const TSub & GetSub(void) const

Get the Sub member data.

bool IsStr(void) const

Check if variant Str is selected.

bool IsSetNames(void) const

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

bool IsSetDiv(void) const

Author Affiliation, Division Check if a value has been assigned to Div data member.

const TCountry & GetCountry(void) const

Get the Country member data.

const TStd & GetStd(void) const

Get the variant data.

const TNames & GetNames(void) const

Get the Names member data.

const TStd & GetStd(void) const

Get the variant data.

bool IsStd(void) const

Check if variant Std is selected.

bool IsSetCountry(void) const

Author Affiliation, Country Check if a value has been assigned to Country data member.

const TCity & GetCity(void) const

Get the City member data.

bool IsSetAffil(void) const

Author Affiliation, Name Check if a value has been assigned to Affil data member.

const TDiv & GetDiv(void) const

Get the Div member data.

bool IsSetSub(void) const

Author Affiliation, County Sub Check if a value has been assigned to Sub data member.

bool IsStd(void) const

Check if variant Std is selected.

const TSubtype & GetSubtype(void) const

Get the Subtype 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.

const TOrg & GetOrg(void) const

Get the Org member data.

void SetOrg(TOrg &value)

Assign a value to Org data member.

TSubtype & SetSubtype(void)

Assign a value to Subtype data member.

bool IsStr(void) const

Check if variant Str is selected.

bool IsSetType(void) const

type of object within class Check if a value has been assigned to Type data member.

bool IsStrs(void) const

Check if variant Strs is selected.

const TStrs & GetStrs(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

bool IsSetLast(void) const

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

const TStr & GetStr(void) const

Get the variant data.

const TType & GetType(void) const

Get the Type member data.

const TFirst & GetFirst(void) const

Get the First member data.

const TLast & GetLast(void) const

Get the Last member data.

bool IsSetData(void) const

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

vector< CStringUTF8 > TStrs

bool IsSetFirst(void) const

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

const TMod & GetMod(void) const

Get the Mod member data.

const TTaxname & GetTaxname(void) const

Get the Taxname member data.

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.

list< CRef< CPub > > Tdata

const Tdata & Get(void) const

Get the member data.

const TColumns & GetColumns(void) const

Get the Columns member data.

vector< CRef< CSeqTable_column > > TColumns

bool IsGenbank(void) const

Check if variant Genbank is selected.

list< CRef< CSeqdesc > > Tdata

const TUser & GetUser(void) const

Get the variant data.

const TSource & GetSource(void) const

Get the variant data.

const TPub & GetPub(void) const

Get the variant data.

bool IsSource(void) const

Check if variant Source is selected.

const Tdata & Get(void) const

Get the member data.

bool IsPub(void) const

Check if variant Pub is selected.

bool IsSetPub(void) const

the citation(s) Check if a value has been assigned to Pub data member.

const TPub & GetPub(void) const

Get the Pub member data.

bool IsUser(void) const

Check if variant User is selected.

@ e_User

user defined object

@ e_Pub

a reference to the publication

@ e_Source

source of materials, includes Org-ref

unsigned int

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

<!DOCTYPE HTML >< html > n< header > n< title > PubSeq Gateway Help Page</title > n< style > n table

constexpr auto sort(_Init &&init)

const GenericPointer< typename T::ValueType > T2 value

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

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

#define row(bind, expected)

vector< CRef< CStructuredCommentTableColumnBase > > TStructuredCommentTableColumnList

TStructuredCommentTableColumnList GetStructuredCommentFields(const CUser_object &src)

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