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NCBI C++ ToolKit: src/gui/objutils/na_utils.cpp Source File

(num_row < 2)

aln_type;

(

= 0;

< num_row; ++

) {

( !handle )

;

}

(this_type !=

) {

aln_type =

;

aln_type =

;

aln_type =

;

f_subtype = (*feat_it)->GetData().GetSubtype();

CSeqTable_column_info::GetTypeInfo_enum_EField_id();

(type_iter != temp_types.

()) {

subtypes.

(

);

temp_types.

(type_iter);

type_iter = temp_types.

(subtype_iter->GetStoragekey());

(type_iter != temp_types.

()) {

temp_types.

(type_iter);

(*iter ==

) {

subtypes.

(

);

subtypes.

(

);

( ; header_names && *header_names; ++header_names) {

(headers.count(

(*header_names)) == 0) {

* graph_headers[] = {

,

,

,

* bins_headers[] = {

,

,

,

,

,

,

,

,

,

* GWAS_headers[] = {

,

,

,

* HapMap_headers[] = {

,

,

,

((*descrIter)->IsName()) {

->m_DataId = (*descrIter)->GetName();

feat_info->m_Subtype = *subtype_iter;

info_list.push_back(feat_info);

}

(annot.

()) {

( !aligns.empty() ) {

( !aln_type.empty() ) {

->m_Subtype = aln_type;

info_list.push_back(

);

}

(annot.

()) {

->m_Subtype =

;

info_list.push_back(

);

( !subtypes.

() ) {

info_list.push_back(

);

( !

->m_Subtype.empty() ) {

info_list.push_back(

);

& subtype,

(annot_type == align) {

track_key =

;

}

(annot_type ==

) {

(subtype ==

) {

track_key =

;

}

(subtype ==

) {

track_key =

;

}

(subtype ==

) {

track_key =

;

track_key =

;

}

(annot_type == graph) {

(subtype ==

) {

track_key =

;

}

(subtype ==

) {

track_key =

;

}

(annot_type == seq_table) {

(subtype ==

) {

track_key =

;

}

(subtype ==

) {

track_key =

;

}

(subtype ==

) {

track_key =

;

}

(subtype ==

) {

track_key =

;

track_key =

;

(subtype ==

) {

track_key =

;

}

(subtype ==

) {

track_key =

;

}

(subtype ==

) {

track_key =

;

(

<<

<< e.

());

isGetLinks)

(md_set, naas, filtering, pMDSource, pUidsSource, isGetLinks);

isGetLinks)

(TEntrezIds::const_iterator it = uids.begin(); it != uids.end();) {

(

=

;

!= 0 && it != uids.end(); ++it, --

)

(canceledCallback && canceledCallback->

())

& naa)

(md_set.

())

;

(iter != md_set.

()) {

->m_Dbname =

;

->m_AnnotType =

.m_AnnotType;

feat_info->m_Subtype = *subtype_iter;

track_info.push_back(feat_info);

}

(

.m_AnnotType == align) {

(

.m_Subtypes.empty()) {

( !aln_type.empty() ) {

->m_Subtype = aln_type;

track_info.push_back(

);

}

(

.m_Subtypes.size() == 1) {

->m_Subtype = *

.m_Subtypes.begin();

track_info.push_back(

);

}

(

.m_AnnotType == graph &&

.m_Subtypes.size() < 2) {

(

.m_Subtypes.empty()) {

->m_Subtype =

;

->m_Subtype = *

.m_Subtypes.begin();

track_info.push_back(

);

}

(

.m_AnnotType == seq_table) {

(

.m_Subtypes.size() == 1) {

->m_Subtype = *

.m_Subtypes.begin();

track_info.push_back(

);

( !subtypes.

() ) {

track_info.push_back(

);

( !

->m_Subtype.empty() ) {

track_info.push_back(

);

& naas)

(md_set.

())

;

;

(

: uids_from) {

+=

.AsString();

(query_key_str.empty() || web_env.empty())

(

<<

<<

<<

<< query_key_str <<

<< e.

());

(; ds_iter; ++ds_iter) {

(c_i != ds_iter->end() && sum_i != ds_iter->end()) {

(uids.size() == 0) {

md_set[iCacheHit->second->m_Name] = iCacheHit->second;

non_cached_uids.push_back(*iuids);

(uids.size() == 0) {

(non_cached_uids.size() > 0) {

(non_cached_uids.size() == uids.size()) {

(non_cached_uids.size() > 0) {

+

;

(

: non_cached_uids) {

(; ds_iter; ++ds_iter) {

(c_i != ds_iter->end() && sum_i != ds_iter->end()) {

->m_Id = a_i->get_value();

(!

->m_Id.empty())

uid(NStr::StringToNumeric<TEntrezId>(

->m_Id));

(

exception&) {

filtered_ids.push_back(*i_uids);

uids.swap(filtered_ids);

isMatch(

);

EUidsSource* pUidsSource)

uids_from.push_back(uid);

!gis_to.empty() && gis_to[0] ==

;

(

<<

<< uid <<

<< e.

());

(!

(na_uid, naa, pUidsSource)) {

(!isIncremental) {

gis.

(iCacheHit->second.begin(), iCacheHit->second.end());

uids_from.push_back(uid);

container_path[] = {

,

,

};

container_path_length = 3;

content_path[] = {

,

};

content_path_length = 2;

found =

;

(container->

() == container_path[cp++]) {

(; cp < container_path_length; ++cp) {

(it = container->

(); it != container->

(); ++it) {

(it1 = container->

(); it1 != container->

(); ++it1) {

(it1->

())

;

found =

;

(content->

() == content_path[cp++]) {

(; cp < content_path_length; ++cp) {

(it2 = content->

(); it2 != content->

(); ++it2) {

(!

.

()) {

gis_to.push_back(NStr::StringToNumeric<TGi>(

));

(gis_to.begin(), gis_to.end());

(

<<

<< uid <<

<< e.

());

cached_gis.

(*i_gis_to);

(

(uid, *inaas, pUidsSource)) {

uids.push_back(uid);

uid = iCacheHit->second;

ecli.

(

, naa, uids);

(

<<

<< naa <<

<< e.

());

(uids.size() == 1,

);

(

(

->get_name(),

))

;

node_name =

->get_name();

(node_name ==

) {

.m_Title = e_i->get_content();

}

(

(e_i->get_name(),

)) {

tmp_str = e_i->get_content();

.m_Descr = tmp_str;

.m_OtherName = a_i->get_value();

}

(

(a_i->get_name(),

)) {

.m_Scope = a_i->get_value();

(

.m_Title.empty()) {

(node_name ==

) {

(!

(e_i->get_name(),

))

.m_AnnotChain = e_i->get_content();

}

(node_name ==

) {

.m_xClass = a_i->get_value();

}

(node_name ==

) {

e_name = e_i->get_name();

(e_name ==

) {

.m_AssmAcc = a_i->get_value();

}

(e_name ==

) {

( !

(ln_i->get_name(),

) ) {

(

(url_entrez_i->get_name(),

)) {

= lln_i->get_content();

}

(

(lln_i->get_name(),

)) {

url = lln_i->get_content();

}

(

(url_entrez_i->get_name(),

)) {

= lln_i->get_content();

}

(

(lln_i->get_name(),

)) {

url = lln_i->get_content();

( !

.empty() && !url.empty() ) {

url =

+

( !

.empty() && !url.empty() ) {

}

(node_name ==

) {

e_name = e_i->get_name();

(e_name ==

) {

annot_types.

(a_i->get_value());

.m_Subtypes.insert(

(a_i->get_value()));

( !

.m_Subtypes.empty() ) {

vector<string> priorytized_types;

priorytized_types.push_back(

priorytized_types.push_back(

priorytized_types.push_back(

(vector<string>, type_iter, priorytized_types) {

(at_iter != annot_types.

()) {

.m_AnnotType = *type_iter;

uids_from.push_back(NStr::StringToNumeric<TEntrezId>(

.m_Id));

(

<<

<<

.m_Id <<

<< e.

());

(itLinkInfo = nodes.

(); itLinkInfo != nodes.

(); ++itLinkInfo) {

html_tag(itLinkInfo->

(

)->

());

link_name(itLinkInfo->

(

)->

());

(db_to ==

)

(

<<

<< link_name <<

<< e.

());

link(

);

(c_link->second == link) {

.m_Links.erase(c_link);

.m_Links[html_tag] = link;

static CRef< CScope > m_Scope

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 SetMaxReturn(int ret_max)

Uint8 Search(const string &db, const string &term, vector< objects::CSeq_id_Handle > &uids, const string &xml_path=kEmptyStr)

void Summary(const string &db, const vector< objects::CSeq_id_Handle > &uids, xml::document &docsums, const string &version="")

CConfigurableItems - a static list of items that can be configured.

string GetStoragekey(int type, int subtype) const

Get the key used to store this type of feature.

help class for iterating through the NA DocSum one by one.

CNADocSumIterator(const CNAUtils::TEntrezIds &uids, const int max_nas)

xml::node::const_iterator operator->() const

xml::node::const_iterator m_Iter

unique_ptr< xml::document > m_Doc

xml::node::const_iterator m_DocSumRoot

const xml::node & operator*() const

static const CFeatList * GetFeatList()

TDim CheckNumRows(void) const

Validatiors.

const CSeq_id & GetSeq_id(TDim row) const

Get seq-id (the first one if segments have different ids).

bool IsSeq_table(void) const

bool IsFtable(void) const

Data structure for holding basic data track information.

Interface for testing cancellation request in a long lasting operation.

container_type::const_iterator const_iterator

const_iterator end() const

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

const_iterator begin() const

const_iterator find(const key_type &key) const

const_iterator end() const

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

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

const node & get_root_node(void) const

Get a reference to the root node of this document.

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

The xml::node_set::const_iterator class is used to iterate over nodes in a node set.

The xml::node_set class is used to store xpath query result set.

iterator begin()

Get an iterator that points to the beginning of the xpath query result node set.

bool empty() const

Inform if the xpath query result node set is empty.

iterator end()

Get an iterator that points one past the last node in the xpath query result node set.

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

bool is_text(void) const

Find out if this node is a text node or sometiming like a text node, CDATA for example.

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 find(const char *name, const ns *nspace=NULL)

Find the first child node that has the given name and namespace.

iterator begin(void)

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

node_set run_xpath_query(const xpath_expression &expr)

Run the given XPath query.

const char * get_content(void) const

Get the content for this text node.

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

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.

#define NCBI_ASSERT(expr, mess)

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

void Error(CExceptionArgs_Base &args)

const string & GetMsg(void) const

Get message string.

const string & FindName(TEnumValueType value, bool allowBadValue) const

Find name of the enum by its numeric value.

void x_SearchNAIds(TEntrezIds &uids, const TNAAs &naas, bool filtering, EUidsSource *pUidsSource=NULL) const

Search all NAAs for a given term.

static void GetColumnHeader(set< string > &headers, const objects::CSeq_annot &annot)

Collect all column header names for a given seq-table.

static void ELinkQuery(const string &db_from, const string &db_to, const TEntrezIds &uids_from, TEntrezIds &uids_to, const string &cmd="neighbor", const string &xpath="//Link/Id/text()")

Queries elink.fcgi with a vector of uids/seq-ids (seq-ids preferred for future compatibility) and ret...

TGi m_Gi

GI of m_TargetSeq; it may be ZERO_GI for one of two reasons: either a target seq is not given at all ...

CTrackInfo::TTrackInfoList TTrackInfoList

objects::CBioseq_Handle m_BioseqHandle

Derived values which make sense only if m_TargetSeq is set.

static TNAAtoUidCache sm_NAAtoUidCache

static void ESearchQuery(const string &db, const string &term, TEntrezIds &uids, size_t &count, const int ret_max, const string &xpath="//IdList/Id/text()")

Queries esearch.fcgi and returns a vector of uids/seq-ids (seq-ids preferred for future compatibility...

void x_FilterNAIds(TEntrezIds &uids, EUidsSource *pUidsSource=NULL) const

filter a given list of NA uids and keep only the ones that are related to a given gi (m_GI)

EMetaDataSource

source of obtained NA metadata were internal caches hit, partially hit or totally missed during some ...

EEntrezDB m_SeqDB

Entrez db name for m_TargetSeq: nucleotide/protein or Undef if no TargetSeq is given.

void x_GetAllNAIdsWithContext(TEntrezIds &uids, const string &context) const

get all available NA ids applied to a viewer context for a given gi.

static void GetAllGIs(const TNAA &naa, EEntrezDB eedb, TGis &gis, EUidsSource *pUidsSource=NULL)

string TNAA

typedefs for NAA meta-data

void x_GetNAIds(TEntrezIds &uids, const string &context="") const

Get all available NA uids w/wo a context.

void GetNAMetaData(TNAMetaDataSet &md_set, const string &na, bool filtering=false, EMetaDataSource *pMDSource=NULL, EUidsSource *pUidsSource=NULL, bool isGetLinks=true) const

Get meta-data for a specific NA.

vector< objects::CSeq_id_Handle > TSeqIdHandles

static TEntrezIdtoGiCache sm_UidtoGiCache

static string GetAnnotName(const objects::CSeq_annot_Handle &annot_handle)

CRef< objects::CScope > m_Scope

Scope helping resolve sequences and retrieve annotations.

void x_Init()

Initialize some internal states.

static string GetAlignType(const objects::CSeq_align &align, objects::CScope &scope)

Get alignment type.

void GetAllNAMetaData(TNAMetaDataSet &md_set, const string &context="", ICanceled *canceledCallback=0) const

Get meta-data for a given NAA associated with seq_id.

void x_GetNAMetaData(TNAMetaDataSet &md_set, const TEntrezIds &uids, bool isGetLinks, EMetaDataSource *pSource=NULL) const

Retrieve NA meta data for a list of NA uids.

static void FeatSubtypes2TrackSubtypes(set< string > &subtypes, const set< string > &feat_subtypes)

Convert feature subtypes to track subtypes.

static const string & GetUnnamedAnnot()

Get the commonly used symbol representing a unnnamed annotation.

void x_GetAllNAIds(TEntrezIds &uids) const

get all available NA uids for a given gi.

static string GetSeqTableSubtype(const set< string > &headers)

Guess the track subtype based on seq-table headers.

static bool IsGeneModelFeature(int type, int subtype)

Does feature belong to gene model track Gene, RNA, cdregion, exon, C_region, and VDJ segments.

static string CreateIdStr(const vector< T > &uids)

Convert a list of ids into a comma-delimited string.

static string GetAnnotComment(const objects::CSeq_annot_Handle &annot_handle)

static void DataType2TrackType(const string &annot_type, const string &subtype, string &track_key, string &subkey)

Map data type to track type.

objects::CSeq_id_Handle m_SeqIdHandle

sequence handles

static bool GetAnnotShown(const objects::CSeq_annot &annot)

static CTrackInfo::TTrackInfoList GetTrackInfo(objects::CSeq_annot_Handle annot_handle)

Get data track information from a seq-annot.

static bool x_GetNAId(TEntrezId &uid, const string &naa, EUidsSource *pUidsSource=NULL)

get an id for a given NAA string returns false if no id is found

void x_GetNAEntrezLinks(CAnnotMetaData &data) const

Retrieve Entrez links for a given NA.

CSeqUtils::TEntrezIds TEntrezIds

int m_MaxNAMeta

maximal number of NAAs for retrieving meta-data.

static TEntrezIdtoMetaDataCache sm_UidtoMetaDataCache

void GetNATrackInfo(TTrackInfoList &track_info, const string &naa) const

Do data track discovery for a given NA.

bool x_NAIdMatchesGI(TEntrezId uid, EUidsSource *pUidsSource=NULL) const

returns true if an uid is related to a given gi (m_GI) or GI is ZERO_GI

void x_GetNAAs(TNAAs &naas, const TEntrezIds &uids) const

Retrieve NAAs for a list of NA uids.

EEntrezDB

eutils databases that can be used

static void x_GetAllGIs(TEntrezId uid, EEntrezDB eedb, TGis &gis, EUidsSource *pUidsSource=NULL, bool isIncremental=false)

get all GIs for a given uid this needs a given database where to search for GIs

static void GetFeatSubtypes(const objects::CSeq_annot &annot, set< string > &subtypes)

Collect unique list of feature subtypes for all features in a seq-annot.

list< CRef< CTrackInfo > > TTrackInfoList

void GetAllNAAs(TNAAs &naas, const string &context="") const

Get a list of NAAs associated with the target sequence.

CConstRef< objects::CSeq_id > m_TargetSeq

The target sequence associating with the NAAs.

void x_ParseNAMetaData(CAnnotMetaData &data, const char *xml_str) const

Parse the meta-data xml DocSum.

@ EUidsSource_EmptyRequest

@ EMetaDataSource_EmptyRequest

@ EMetaDataSource_EmptyAfterFilteringRequest

@ EEDB_All

try both nucleotide and protein databases, merge results

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

@ eGetId_ForceGi

return only a gi-based seq-id

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

TBioseqCore GetBioseqCore(void) const

Get bioseq core structure.

CConstRef< CSeq_annot > GetCompleteSeq_annot(void) const

Complete and return const reference to the current seq-annot.

CScope & GetScope(void) const

Get scope this handle belongs to.

SAnnotSelector & IncludeNamedAnnotAccession(const string &acc, int zoom_level=0)

SAnnotSelector & SetCollectNames(bool value=true)

Collect available annot names rather than annots.

SAnnotSelector & IncludeAnnotType(TAnnotType type)

Include annotation type in the search.

SAnnotSelector & SetMaxSize(TMaxSize max_size)

Set maximum number of annotations to find.

SAnnotSelector & AddNamedAnnots(const CAnnotName &name)

Add named annot to set of annots names to look for.

void Reset(void)

Reset reference object.

static TThisType GetWhole(void)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

virtual bool IsCanceled(void) const =0

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 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.

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.

void Stop(void)

Suspend the timer.

string AsSmartString(CTimeSpan::ESmartStringPrecision precision, ERound rounding, CTimeSpan::ESmartStringZeroMode zero_mode=CTimeSpan::eSSZ_SkipZero) const

Transform elapsed time to "smart" string.

void Start(void)

Start the timer.

static const char label[]

TField_id GetField_id(void) const

Get the Field_id member data.

const TColumns & GetColumns(void) const

Get the Columns member data.

bool IsSetFeat_subtype(void) const

subtype of features in this table, defined in header SeqFeatData.hpp Check if a value has been assign...

bool CanGetField_name(void) const

Check if it is safe to call GetField_name method.

TFeat_subtype GetFeat_subtype(void) const

Get the Feat_subtype member data.

vector< CRef< CSeqTable_column > > TColumns

const TField_name & GetField_name(void) const

Get the Field_name member data.

bool CanGetField_id(void) const

Check if it is safe to call GetField_id method.

const Tdata & Get(void) const

Get the member data.

const TInst & GetInst(void) const

Get the Inst member data.

list< CRef< CSeq_align > > TAlign

const TDesc & GetDesc(void) const

Get the Desc member data.

bool IsSetDesc(void) const

used only for stand alone Seq-annots Check if a value has been assigned to Desc data member.

TMol GetMol(void) const

Get the Mol member data.

const TAlign & GetAlign(void) const

Get the variant data.

static string SelectionName(E_Choice index)

Retrieve selection name (for diagnostic purposes).

const TSeq_table & GetSeq_table(void) const

Get the variant data.

const TFtable & GetFtable(void) const

Get the variant data.

list< CRef< CSeq_feat > > TFtable

bool IsFtable(void) const

Check if variant Ftable is selected.

const TData & GetData(void) const

Get the Data member data.

E_Choice Which(void) const

Which variant is currently selected.

list< CRef< CAnnotdesc > > Tdata

@ eMol_na

just a nucleic acid

DEFINE_CLASS_STATIC_FAST_MUTEX(CNAUtils::sm_NAAtoUidCacheMutex)

static string s_MakeUidtoGiCacheKey(TEntrezId uid, CNAUtils::EEntrezDB eedb)

static const char * kSnpSubtypeStr

static string s_EEDBToString(CNAUtils::EEntrezDB eedb)

static bool s_MatchHeaders(const char **header_names, const set< string > &headers)

static string s_GetFeatSubtypeStr(int subtype)

constexpr auto sort(_Init &&init)

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

const struct ncbi::grid::netcache::search::fields::SIZE size

const struct ncbi::grid::netcache::search::fields::SUBKEY subkey

#define row(bind, expected)

static CS_CONTEXT * context

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