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

(

.GetLength() <

.GetLength());

(iter != sm_NameTypeMap.end()) {

(iter = sm_NameTypeMap.begin(); iter != sm_NameTypeMap.end(); ++iter) {

(iter->second ==

) {

view = reg.

(

);

(view.

(

)) {

* named_annots[] = {

(

** p = named_annots; p && *p; ++p) {

incl = view.

(*p,

);

(view.

(

,

)) {

include_naas =

;

(include_naas && annots.empty()) {

(vector<string>, iter, annots) {

& annot = *iter;

adaptive,

)

sel.AddUnnamedAnnots();

sel.ExcludeUnnamedAnnots();

include_naas =

;

sel.IncludeNamedAnnotAccession(

);

sel.AddNamedAnnots(annot);

sel.IncludeNamedAnnotAccession(annot);

reg.

(

);

view.

(

, 0);

max_search_segs_action = view.

(

,

);

(max_search_segs_action ==

) {

}

(max_search_segs_action ==

) {

MaxSearchSegmentsAction;

(

> 0 && actual >

) {

);

(

);

view.

(

, 0);

adaptive,

)

sel.SetAdaptiveDepth(

);

sel.SetExactDepth(

);

sel.SetMaxSearchSegments(max_search_segs);

(max_search_segs > 0) {

sel.SetResolveDepth(

);

}

(

>= 0) {

sel.SetResolveDepth(

);

sel.SetExactDepth(

);

sel.SetAdaptiveDepth(

);

<

T,

U>

(

pair<T,U>& p1,

pair<T,U>& p2)

p1.first < p2.first;

feature::CFeatTree

;

.SetFeatIdMode(feature::CFeatTree::EFeatIdMode(

));

.AddFeature(curr_feat->GetMappedFeature());

fmap[curr_feat->GetMappedFeature()] = curr_feat;

parent_feat =

.GetParent(curr_feat->GetMappedFeature());

fmap[parent_feat]->AddChild(curr_feat);

out_feats.push_back(curr_feat);

out_feats.swap(feats);

converter(dummy_parent, child, scope);

converter.

(scope);

( !it_r->Empty() ) {

p_int.

(

, it_r->GetFrom(), it_r->GetTo());

(p_int.

().size()) {

(it != loc_map.

()) {

}

;

bioseq->

().SetLength((

)seq_string.size());

bioseq->

().SetSeq_data().SetIupacaa(*

(seq_string));

bioseq->

().SetSeq_data().SetIupacna(*

(seq_string));

bioseq->

().push_back(

);

->GetLabel(&title_str);

bioseq->

().Set().push_back(title);

(handle.

(iter.GetSeq_id())) {

( !range.

() ) {

range.

(), iter.GetStrand());

(p_int.

().size()) {

}

(annot_handle.

()) {

name = annot_handle.

();

((*descrIter)->IsTitle()) {

name = (*descrIter)->GetTitle();

}

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

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

((*descrIter)->IsUser()) {

& user((*descrIter)->GetUser());

(user.GetType().IsStr() && user.GetType().GetStr() ==

&& user.HasField(

)) {

user.GetFieldRef(

);

((*descrIter)->IsComment()) {

(*descrIter)->GetComment();

(

& annot,

div)

is_naa =

;

= annot.size();

(

>= acc_len && annot[0] ==

&& annot[1] ==

) {

(

< acc_len && annot[

] >=

&& annot[

] <=

) {

(

== acc_len) {

(annot[

++] == div) {

(

<

&& annot[

] >=

&& annot[

] <=

) {

+ sSuffix;

sFileType ==

|| sFileType ==

|| sFileType ==

|| sFileType ==

;

posHashSign{sAnnotName.find(

)};

(posHashSign ==

) {

(sAnnotName, div);

(!

(sAnnotName.substr(0, posHashSign), div))

(posHashSign == sAnnotName.length() - 1) {

(

= posHashSign+1;

<sAnnotName.length(); ++

) {

(sAnnotName[

] <

|| sAnnotName[

] >

) {

vector<string> parts;

parts.size() > 1 ? parts[1] :

();

vector<string> parts;

parts.size() > 2 ? parts[2] :

(

);

(acc.size() < 3 || acc[1] !=

)

(

.IsGene() &&

.GetGene().IsSetPseudo()) {

.GetGene().GetPseudo();

}

(

.IsRna() &&

.GetRna().IsSetPseudo()) {

.GetRna().GetPseudo();

base_url =

;

;

+

+ (

.empty() ?

:

) +

+

+

+

;

+

+

;

&

,

+

+

+

+ url +

+

+

;

(; aln_iter; ++aln_iter) {

aln.

().

().front()->GetSeqRange(target_row);

(r_map.count(target_gi) == 0) {

r_map[target_gi] =

(from, to);

r_map[target_gi].CombineWith(

(from, to));

(TRangeMap, iter, r_map) {

->SetGi(iter->first);

iter->second.GetTo()));

mapped_locs.push_back(loc);

;

LinksUrl;

(LinksUrl.empty()) {

timeout.

= time_out_sec;

*obj_stream >> align_set;

(

<<

<< gi <<

<< e.

());

*obj_stream >> align_set;

timeout.

= time_out_sec;

SourceFrom = loc.GetInt().GetFrom();

SourceTo = loc.GetInt().GetTo();

(loc.GetInt().GetId().IsGi()) {

SourceGi = loc.GetInt().GetId().GetGi();

}

(loc.IsPnt()) {

SourceFrom = loc.GetPnt().GetPoint();

SourceTo = SourceFrom;

(loc.GetPnt().GetId().IsGi()) {

SourceGi = loc.GetPnt().GetId().GetGi();

(SourceTo < SourceFrom) {

(SourceTo, SourceFrom);

*obj_stream >> align_set;

(

<<

<< SourceGi <<

<< e.

());

TRangeMap range_map;

(; aln_iter; ++aln_iter) {

aln.

().

().front()->GetSeqRange(source_row);

(i_source_from > i_source_to) {

(i_source_from, i_source_to);

(i_source_from <= SourceFrom && SourceTo <= i_source_to) {

aln.

().

().front()->GetSeqRange(target_row);

range_map[target_gi] =

(from + (SourceFrom - i_source_from), from + (SourceTo - i_source_from));

(TRangeMap, iter, range_map) {

->SetGi(iter->first);

mapped_locs.push_back(loc);

& from,

& to)

=

.length();

(

== 0)

;

space_before_this =

;

separator_before_this =

;

(

= 0;

<

; ++

) {

( !separator_before_this )

space_before_this =

;

(separator_before_this)

;

space_before_this =

;

(separator_before_this)

;

space_before_this =

;

out_str.append(

);

(separator_before_this)

;

space_before_this =

;

out_str.append(

);

space_before_this =

;

separator_before_this =

;

(separator_before_this) {

out_str.append(

);

separator_before_this =

;

}

(space_before_this) {

out_str.append(

);

space_before_this =

;

out_str.append(1,

[

]);

vector<string> TPositions;

(pos.size() < 3) {

is_from =

;

(iter->empty())

;

uids_from.push_back(gi);

(

<<

<< gi <<

<< e.

());

(uids_to.empty())

(itNode = nodes.

(); itNode != nodes.

(); ++itNode) {

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

));

assm->

(idh, sequences);

(replicon->IsSetName()) {

replicon->GetName();

(

<<

<< *iGCId);

(

it : top_level_seqs) {

& tls_seq_id = it->GetSeq_id();

ids.emplace_back(&tls_seq_id);

sNormalizedSeqId(seq_id.

() +

+ assm_acc);

(scope && !assembly_ids.empty() && assembly_ids.front()->IsGi()) {

all_checked =

;

(

&

: assembly_ids) {

all_checked =

;

(id->GetGi() == gi) {

(

&

: assembly_ids) {

(

(seq_id, *

, scope)) {

}

(exception& e) {

(

<<

<< assm_acc <<

<< e.what());

(!id_str.empty() ) {

seq_id->Set(id_str);

objects::CBioseq_Handle bsh = scope.GetBioseqHandle(*seq_id);

objects::CSeq_id_Handle shdl = bsh.GetAccessSeq_id_Handle();

(itAcc = doc_sums.

(); itAcc != doc_sums.

(); ++itAcc) {

<

T1,

T2>

(

&db_from,

&db_to,

vector<T1> &uids_from, vector<T2> &uids_to,

&

,

&xpath)

(itLink = links.

(); itLink != links.

(); ++itLink) {

uids_to.push_back(NStr::StringToNumeric<T2>(

));

ecli.

(db_from, db_to, uids_from,

,

);

docstr(sb.str());

linkset.

(doc);

(

&db,

&term, vector<T> &uids,

&

,

ret_max,

&xpath)

docstr(sb.str());

(itLink = links.

(); itLink != links.

(); ++itLink) {

uids.push_back(NStr::StringToNumeric<T>(

));

(!countStr.empty())

= uids.size();

(

&db,

&term,

&web_env,

&query_key, vector<T> &uids,

&

,

retstart,

&xpath)

(itLink = links.

(); itLink != links.

(); ++itLink) {

uids.push_back(NStr::StringToNumeric<T>(

));

(!countStr.empty())

= uids.size();

ecli.

(db, term, web_env, NStr::StringToNumeric<Int8>(query_key), retstart,

);

docstr(sb.str());

searchset.

(doc);

(parent.

() == itNode)

uids_from.push_back(gi);

(

<<

<< gi <<

<< e.

());

(annot && annot.

()) {

& annot_str = annot.

();

align_iter(scope, *aln_loc, sel);

(align_iter && !align_ref) {

(num_row != 2)

;

align_ref.

(&align);

locs.push_back(prod_loc);

locs.push_back(gen_loc);

(it1 && it2) {

.GetLength() !=

.GetLength()) {

int1->

(*prod_id);

int2->

(*gen_id);

.emplace_back(int1, int2);

objects::CSeq_loc& feat_loc,

objects::CBioseq_Handle& handle)

(locs.size() == 2) {

cout <<

;

(

& it : cds_map_info) {

gen_int = get<1>(it);

prod_int = get<0>(it);

cout << gen_int->GetFrom() <<

<< gen_int->GetTo() <<

<< prod_int->GetFrom() <<

<< prod_int->GetTo() << endl;

cout <<

;

curr_prod_pos = -1;

last_prod_pos = -1;

cds_map_it = cds_map_info.begin();

(cds_map_it != cds_map_info.end()) {

gen_int = cds_map_it->second;

((gen_int->GetTo() - gen_int->GetFrom()) + 1 < 3) {

cds_map_it = cds_map_info.erase(cds_map_it);

prod_loc =

(

(gen_int->SetId(), gen_int->GetFrom(), gen_int->GetTo(), gen_int->GetStrand()));

mapped_prod_loc = map2prod.

(*prod_loc);

mapped_gen_loc = map2loc.

(*mapped_prod_loc);

cout <<

;

list<TSeqRange> rngs;

(

= 0;

< sz; ++

, ++lit) {

(

== 0 &&

.GetLength() < 3) {

(

== sz - 1 &&

.GetLength() < 3)

rngs.push_back(

);

(!rngs.empty()) {

reverse = gen_int->CanGetStrand() && gen_int->GetStrand() ==

;

prod_int = cds_map_it->first;

r_it = rngs.begin();

gen_int->SetFrom(max<int>(r_it->GetFrom(), gen_int->GetFrom()));

gen_int->SetTo(gen_int->GetTo());

gen_int->SetFrom(gen_int->GetFrom());

gen_int->SetTo(min<int>(r_it->GetTo(), gen_int->GetTo()));

(curr_prod_pos == -1) {

curr_prod_pos = prod_int->SetFrom();

(last_prod_pos != -1) {

(prod_int->SetFrom() - last_prod_pos > 0) {

curr_prod_pos += (prod_int->SetFrom() - last_prod_pos);

last_prod_pos = prod_int->GetTo() + 1;

prod_int->SetFrom(curr_prod_pos);

curr_prod_pos += (gen_int->GetTo() - gen_int->GetFrom());

prod_int->SetTo(curr_prod_pos);

(r_it != rngs.end()) {

from = curr_prod_pos;

curr_prod_pos += r_it->GetLength() - 1;

cds_map_it = cds_map_info.emplace(++cds_map_it, int1, int2);

cout <<

;

(

& it : cds_map_info) {

& gen_int = get<1>(it);

& prod_int = get<0>(it);

cout << gen_int->GetFrom() <<

<< gen_int->GetTo() <<

<< prod_int->GetFrom() <<

<< prod_int->GetTo() << endl;

cout <<

;

feat_offset)

cds_offset = -1;

(; feat_iter; ++feat_iter) {

prod_id->

(product_id);

TMappingInfo::const_iterator iter = mapping_info.begin();

(iter != mapping_info.end() && !

) {

& gen_int = iter->second;

& prod_int = iter->first;

gen_from = gen_int->GetFrom();

gen_to = gen_int->GetTo();

prod_from = prod_int->GetFrom();

prod_to = prod_int->GetTo();

reverse = gen_int->CanGetStrand() && gen_int->GetStrand() ==

;

(cds_map_info.empty()) {

(bio_start >= gen_from && bio_start <= gen_to) {

off1 = reverse ? gen_to - bio_start : bio_start - gen_from;

.Set(prod_from + off1, prod_to);

.Set(gen_from, gen_to - off1);

.Set(gen_from + off1, gen_to);

(cds_offset < 0 || (

)cds_offset >

.GetFrom()) {

cds_offset =

(

.GetFrom());

.Set(prod_from, prod_to);

.Set(gen_from, gen_to);

(!

.Empty() && !

.Empty()) {

(bio_stop >= gen_from && bio_stop <= gen_to) {

off2 = reverse ? bio_stop - gen_from : gen_to - bio_stop;

.SetTo(

.GetTo() - off2);

(reverse)

.SetFrom(

.GetFrom() + off2);

.SetTo(

.GetTo() - off2);

int1->

(

.GetFrom() - cds_offset);

int1->

(

.GetTo() - cds_offset);

int1->

(*prod_id);

int2->

(*gen_id);

cds_map_info.emplace_back(int1, int2);

( !cds_map_info.empty() ) {

cds_map_info.clear();

(!cds_map_info.empty() && (0 != feat_offset)) {

(feat_offset > 0) {

& prod_int = cds_map_info.begin()->first;

prod_int->SetFrom(prod_int->GetFrom() + feat_offset);

& gen_int = cds_map_info.begin()->second;

gen_int->SetFrom(gen_int->GetFrom() + feat_offset);

& prod_int = cds_map_info.begin()->first;

prod_int->SetFrom(prod_int->GetFrom() - feat_offset);

& gen_int = cds_map_info.begin()->second;

gen_int->SetTo(gen_int->GetTo() + feat_offset);

cds_map_info;

objects::CSeq_loc &feat_loc,

objects::CSeq_id &product_id,

feat_offset

gen_id->

(*feat_loc.GetId());

prod_id->

(product_id);

start +=

.GetLength();

.emplace_back(int1, int2);

(!

.empty() && (0 != feat_offset)) {

(feat_offset > 0) {

& prod_int =

.begin()->first;

prod_int->SetFrom(prod_int->GetFrom() + feat_offset);

& gen_int =

.begin()->second;

gen_int->SetFrom(gen_int->GetFrom() + feat_offset);

& prod_int =

.begin()->first;

prod_int->SetFrom(prod_int->GetFrom() - feat_offset);

& gen_int =

.begin()->second;

gen_int->SetTo(gen_int->GetTo() + feat_offset);

( !loc_obj.

() ) {

loc.

(&loc_obj);

(!named_acc.empty()) {

GetCDSFrame = [&]() {

= GetCDSFrame();

(mrna_info.empty())

id_num{ 0 };

= GetCDSFrame();

=

;

(!gi_str)

;

(

= pos + 3;

< sid.length(); ++

) {

c = sid.at(

);

gi_str->append(1, c);

shown_desc->

().SetStr(

);

shown_desc->

(

, isShown);

annot.AddUserObject(*shown_desc);

(!

&&

.find(

) !=

) {

mapper->MapObject(*

);

(

loc_it(loc); loc_it; ++loc_it) {

fuzz = loc_it.GetFuzzFrom();

fuzz = loc_it.GetFuzzTo();

pos = exon->GetGenomic_start();

(

bioseq_it(*handle); bioseq_it; ++bioseq_it) {

(bioseq_it->IsSetDescr()) {

(dit->GetPointer() == &seq_desc) {

(entry_ci->IsSetDescr()) {

((*dit)->IsPub()) {

(&desc_pub == &pubdesc) {

(entry_ci->IsSeq()) {

(&(fi->GetData().GetPub()) == &pubdesc) {

(handles.size() > 0) {

(

->GetSeq_feat() == &feat) {

(

.IsSetLocation()) {

(subloc && !subloc.

()) {

(seh.

()) {

objects::CSeq_entry* seqEntry =

objects::CSeq_entry*

(ptr);

objects::CBioseq* bioseq =

objects::CBioseq*

(ptr);

objects::CBioseq_set* bioseq_set =

objects::CBioseq_set*

(ptr);

objects::CSeq_annot* seqannot =

objects::CSeq_annot*

(ptr);

objects::CSeq_feat* seqfeat =

objects::CSeq_feat*

(ptr);

objects::CSeqdesc* seqdesc =

objects::CSeqdesc*

(ptr);

objects::CSeq_submit* seqsubmit =

objects::CSeq_submit*

(ptr);

objects::CPubdesc* pubdesc =

objects::CPubdesc*

(ptr);

objects::CSeq_loc* loc =

objects::CSeq_loc*

(ptr);

objects::CSeq_id* seq_id =

objects::CSeq_id*

(ptr);

objects::CSeq_entry_Handle seh;

seh = seh.GetTopLevelEntry();

}

(bioseq) {

}

(bioseq_set) {

}

(seqannot) {

seh = sah.GetTopLevelEntry();

}

(seqfeat) {

}

(seqdesc) {

seh = seh.GetTopLevelEntry();

}

(pubdesc) {

seh = seh.GetTopLevelEntry();

}

(seqsubmit) {

(seqsubmit->IsEntrys() && seqsubmit->GetData().GetEntrys().front()) {

}

(seq_id) {

= str1.c_str()[0];

= str2.c_str()[0];

(

==

&&

==

) {

}

(

==

) {

}

(

==

) {

(

==

&&

==

) {

}

(

==

) {

}

(

==

) {

vector<const CFeatListItem * > r_list;

vector<const CFeatListItem * > used;

vector<const CFeatListItem * > popular;

vector<const CFeatListItem * > import_feats;

vector<const CFeatListItem * > least_liked;

vector<const CFeatListItem * >

;

subtype =

->GetSubtype();

desc =

->GetDescription();

(existing.

(desc) == existing.

())

(!present[subtype]) {

import_feats.push_back(

);

popular.push_back(

);

popular.push_back(

);

least_liked.push_back(

);

used.push_back(

);

r_list.insert(r_list.begin(), popular.begin(), popular.end());

r_list.insert(r_list.end(), used.begin(), used.end());

r_list.insert(r_list.end(), least_liked.begin(), least_liked.end());

r_list.insert(r_list.end(), import_feats.begin(), import_feats.end());

r_list.insert(r_list.end(),

.begin(),

.end());

r_list.insert(r_list.begin(),

);

vector<string> range_pairs;

(vector<string>, iter, range_pairs) {

(pos.size() != 2)

;

( !f_str.empty() && !t_str.empty() ) {

ranges.push_back(

(from, to));

->Assign(*idh.GetSeqId());

mapped_loc =

(*loc);

(mapped_loc && !mapped_loc->IsNull() && !mapped_loc->IsEmpty() && mapped_loc->GetId())

(; idit; ++idit) {

(ids.emplace(&

).second ==

)

mapped_loc =

(*loc);

(!mapped_loc || !mapped_loc->GetId())

.Assign(*mapped_loc->GetId());

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.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

@ eExtreme_Positional

numerical value

@ eExtreme_Biological

5' and 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.

CRef< CSeq_align > ConvertSeq_align(const CSeq_align &src, CSeq_align::TSegs::E_Choice dst_choice, CSeq_align::TDim anchor_row=-1, CScope *scope=NULL)

Convert source alignment to a new type.

CSeq_entry_Handle GetSeqEntryForSeqdesc(CRef< CScope > scope, const CSeqdesc &seq_desc)

int GetGenCode(int def=1) const

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

void SetMaxReturn(int ret_max)

void SearchHistory(const string &db, const string &term, const string &web_env, Int8 query_key, int retstart, CNcbiOstream &ostr)

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="")

void Link(const string &db_from, const string &db_to, const vector< objects::CSeq_id_Handle > &uids_from, vector< objects::CSeq_id_Handle > &uids_to, const string &xml_path=kEmptyStr, const string &command="neighbor")

CFeatListItem - basic configuration data for one "feature" type.

string GetDescription() const

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

string GetAccession() const

Retrieve the accession for this assembly.

void Find(const CSeq_id_Handle &id, TSequenceList &sequences) const

Find all references to a given sequence within an assembly.

bool IsRefSeq() const

Is this assembly a RefSeq assembly?

list< CConstRef< CGC_Sequence > > TSequenceList

void GetMolecules(TSequenceList &molecules, ESubset subset) const

Retrieve a subset of molecules.

CRef< objects::CSeq_loc > Map(const objects::CSeq_loc &Loc, const SIdSpec &Spec) const

static bool isGenCollSequence(const objects::CBioseq_Handle &handle)

static CRef< CGencollSvc > GetInstance(void)

static CRef< objects::CGenomicCollectionsService > GetGenCollService(int timeout_sec=-1)

static CGuiRegistry & GetInstance()

access the application-wide singleton

CRegistryReadView GetReadView(const string &section) const

get a read-only view at a particular level.

static CNcbiApplication * Instance(void)

Singleton method.

void AddInterval(const CSeq_interval &ival)

for convenience

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

TThisType & CombineWith(const TRange &r)

class CRegistryReadView provides a nested hierarchical view at a particular key.

int GetInt(const string &key, int default_val=0) const

access a named key at this level, with no recursion

bool GetBool(const string &key, bool default_val=false) const

list< SKeyInfo > TKeys

retrieve information about all keys in the registry

string GetString(const string &key, const string &default_val=kEmptyStr) const

void GetKeys(TKeys &keys) const

Retrieve information about all keys in this view.

ESubtype GetSubtype(void) const

static const CFeatList * GetFeatList()

@ eSubtype_transit_peptide

@ eSubtype_bad

These no longer need to match the FEATDEF values in the C toolkit's objfdef.h.

TDim CheckNumRows(void) const

Validatiors.

const CSeq_id & GetSeq_id(TDim row) const

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

ENa_strand GetSeqStrand(TDim row) const

Get strand (the first one if segments have different strands).

namespace ncbi::objects::

int Compare(const CSeq_feat &f2) const

Compare relative order of this feature and feature f2, ordering first by features' coordinates,...

Seq-loc iterator class – iterates all intervals from a seq-loc in the correct order.

static TSeqPos Pack(CSeq_data *in_seq, TSeqPos uLength=ncbi::numeric_limits< TSeqPos >::max())

Base class for all serializable objects.

class CStaticArrayMap<> provides access to a static array in much the same way as CStaticArraySet<>,...

TBase::const_iterator const_iterator

static CSeq_id_Handle GetSeq_id_Handle(const const_iterator &iter)

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

Template class for iteration on objects of class C.

CUser_object & AddField(const string &label, const string &value, EParseField parse=eParse_String)

add a data field to the user object that holds a given value

General IdMapper interface.

Task clients implement this callback interface.

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 find(const key_type &key) const

const_iterator end() const

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

void swap(document &other)

Swap one xml::document object for another.

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.

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.

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.

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.

string GetSeqIdString(const CSeq_id &id)

static unsigned char depth[2 *(256+1+29)+1]

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

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

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

SStrictId_Entrez::TId TEntrezId

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

#define ENTREZ_ID_TO(T, entrez_id)

const CNcbiRegistry & GetConfig(void) const

Get the application's cached configuration parameters (read-only).

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

int TSignedSeqPos

Type for signed sequence position.

#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)

unsigned int THTTP_Flags

Bitwise OR of EHTTP_Flag.

@ fHTTP_AutoReconnect

See HTTP_CreateConnectorEx()

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

#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)

#define NCBI_THROW(exception_class, err_code, message)

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

const string & GetMsg(void) const

Get message string.

static CConstRef< objects::CSeq_loc > GetFeatLocation(const objects::CSeq_feat &feat, const objects::CBioseq_Handle &bsh)

static bool StringToRange(const string &range_str, long &from, long &to)

Convert a range string to a range.

virtual void SetTaskName(const string &name)=0

virtual void SetTaskCompleted(int completed)=0

set total finished task number.

static int GetMaxSearchTime(const CRegistryReadView &view)

static string CreateLinkRow(const string &tag, const string &label, const string &url)

static TMappingInfo GetMappingInfoFromLocation(const objects::CSeq_loc &feat_loc, const objects::CSeq_id &product_id, const int feat_offset=0)

static TMappingInfo GetRnaMappingInfo(const objects::CSeq_loc &feat_loc, const objects::CMappedFeat &feat, const objects::CBioseq_Handle &handle)

Helper function to generate mapping info between the specified product sequence and genomic sequence ...

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...

static string GetAlignDbIsQuery(const string &annot)

get a is_source_assembly_query string from AlignDb annotation suffixed after a second '#'

static bool LinkFeatures(CLinkedFeature::TLinkedFeats &feats, TFeatLinkingMode mode=1, ISeqTaskProgressCallback *p_cb=NULL)

Link features into a hierarchical list.

static bool IsNAA(const string &annot, bool isStrict=false)

check if a given annotation is a named annotation accession[.version][number] when isSctrict == false...

static bool IsException(const objects::CSeq_feat &feat)

static objects::CBioseq * SeqLocToBioseq(objects::CScope &scope, const objects::CSeq_loc &loc)

Construct a bioseq to fit a given location.

static bool isRmtPipelineFileType(const string &sFileType)

check if a file type is one of remote file types

static TLocVec GetAccessionPlacements(const objects::CSeq_id &id, objects::CScope &scope, int time_out_sec=1, THTTP_Flags flags=fHTTP_AutoReconnect)

Retrieve mapped-up sequences.

static bool isTopLevel(const objects::CSeq_id &seq_id, const string &assm_acc, objects::CScope *scope=NULL)

static bool IsPartialStart(const objects::CSeq_loc &loc)

static objects::SAnnotSelector GetAnnotSelector(TAnnotFlags flags=0)

request an annotation selector for a given type

list< CRef< CLinkedFeature > > TLinkedFeats

static bool IsPartialFeature(const objects::CSeq_feat &feat)

static TLocVec GetGiPlacements(TGi gi, int time_out_sec=5, THTTP_Flags flags=fHTTP_AutoReconnect)

Retrieve mapped-up sequences.

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...

vector< CRef< objects::CSeq_loc > > TLocVec

static TMappingInfo GetCdsMappingInfoFromRna(const TMappingInfo &rna_mapping_info, const objects::CSeq_feat &rna_feat, const objects::CMappedFeat &mapped_cds_feat, const objects::CSeq_loc &feat_loc, objects::CScope &scope, const int feat_offset=0)

Derive the CDS feature mapping information based on its parent RNA feature mapping info.

static string GetNcbiBaseUrl()

static int GetMaxSearchSegments(const CRegistryReadView &view)

static bool IsCrossOrigin(const objects::CSeq_loc &loc)

static bool IsAlignDb(const string &annot)

check if a given annotation is AlignDb (potentially suffixed with batch identication string after a '...

static const string & NameTypeValueToStr(TAnnotNameType type)

vector< TEntrezId > TEntrezIds

static void GetAssmAccs_Gi(TAccs &accs, TGi gi)

get all assembly accessions corresponding to a GI

static objects::SAnnotSelector::EMaxSearchSegmentsAction GetMaxSearchSegmentsAction(const CRegistryReadView &view)

virtual objects::CSeq_id_Handle Map(const objects::CSeq_id_Handle &idh) override

static bool IsPseudoFeature(const objects::CSeq_feat &feat)

vector< objects::CSeq_id_Handle > TSeqIdHandles

static string MakeRmtAnnotName(const string &sSuffix)

create an annotation name for a remote file pipeline, appending sSuffix

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

static bool IsPartialStop(const objects::CSeq_loc &loc)

CGencollIdMapper::SIdSpec m_Spec

CSeq_entry_Handle GetTopSeqEntryFromScopedObject(SConstScopedObject &obj)

static bool GetRangeCollection(const objects::CSeq_id &id, const objects::CHandleRangeMap &map, CRangeCollection< TSeqPos > &ranges)

static CRef< objects::CSeq_loc > MixLocToLoc(const objects::CSeq_loc &mix_loc, const objects::CBioseq_Handle &handle)

Create a new seq-loc with a unique seq-id from a "mixed" loc.

static void GetAssmIds_GIChr(TEntrezIds &gc_ids, TGi gi)

get all assembly ids associated with a gi where this gi is a chromosome

static CConstRef< objects::CUser_field > GetAnnotUserField(const objects::CSeq_annot &annot, const string &type, const string &label)

static bool CanHavePlacements(const objects::CSeq_id &seqid)

check that a given seq-id can potentially have placements (to weed out cases like local ids)

static const string & GetUnnamedAnnot()

Get the commonly used symbol representing a unnnamed annotation.

static void GetMappingInfo(const objects::CMappedFeat &mapped_feat, const objects::CBioseq_Handle &bsh, TMappingInfo &info, const string &annot=string())

virtual void SetTaskTotal(int total)=0

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

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

static TLocVec GetLocPlacements(const objects::CSeq_loc &loc, int time_out_sec=1)

Retrieve locations on mapped-up sequences Help method for retrieving upper level sequences for a give...

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

static string CreateSectionRow(const string &tag)

virtual void MapObject(CSerialObject &obj) override

static bool isQuasiLocal(const objects::CBioseq_Handle &handle)

check that a given accession is either local or unrecognizable this can be important to avoid unneces...

static bool IsVDBAccession(const string &acc)

Check if string starts with ("SRA", "SRR", "DRR", "ERR")

static bool IsSameStrands(const objects::CSeq_loc &loc)

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

static CRef< objects::CSeq_loc > CreateSeq_loc(const objects::CSeq_id &id, const CRangeCollection< TSeqPos > &ranges)

vector< TSeqRange > TRanges

CRef< CGencollIdMapper > m_Mapper

static bool IsNAA_Name(const string &annot)

check if a given annotation is a named annotation name with '.' replaced with '_'.

static bool GetGIString(const string &sid, string *gi_str)

ad-hoc GI extraction (for misformed seq-id strings like: "gi|55823257|ref|YP_141698....

static IIdMapper * GetIdMapper(CRef< objects::CGC_Assembly > assm)

static TAnnotNameType NameTypeStrToValue(const string &type)

static bool IsExtendedNAA(const string &annot, bool isStrict=false)

check if a given annotation is an extended NAA (named accession[.version][number],...

static int GetGenCode(const objects::CBioseq_Handle &handle)

Returns Bioseq's Genetic Code.

static string GetChrGI(TGi gi)

try to get a chromosome from a GI

static bool Match(const objects::CSeq_id &id1, const objects::CSeq_id &id2, objects::CScope *scope=NULL)

check to see if two seq-ids are identical.

static void SetAnnot(objects::SAnnotSelector &sel, const string &annot)

help function for setting up an annotation.

static string CreateTableRow(const string &tag="", const string &value="")

static CRef< objects::CSeq_loc > RemapChildToParent(const objects::CSeq_loc &parent, const objects::CSeq_loc &child, objects::CScope *scope=NULL)

remap a location to a parent location.

static string CreateTableStart()

help methods for creating HTML text

static TLocVec GetAccessionPlacementsMsec(const objects::CSeq_id &id, objects::CScope &scope, unsigned long time_out_msec=1000, THTTP_Flags flags=fHTTP_AutoReconnect)

same, with a timeout in milliseconds

static CRegistryReadView GetSelectorRegistry()

helper functions to read selector-related tune-up info (mostly segment limits) from registry:

CGencollIdMapperAdapter(CRef< CGencollIdMapper > mapper, const CGencollIdMapper::SIdSpec &spec)

-------------------------------- CGencollIdMapperAdapter ——————————–

virtual bool StopRequested() const =0

static bool isRmtAnnotName(const string &sAnnotname)

check if a given annotation was created by a remote file pipeline

EAnnotationNameType

flags for classifying annotation names.

static CRef< objects::CSeq_id > MapStringId(const string &str, objects::IIdMapper *mapper)

static objects::CMappedFeat GetMrnaForCds(const objects::CMappedFeat &cds_feat, const string &named_acc=string())

static std::string GetXmlChildNodeValue(const xml::node &parent, const std::string &name)

Returns the contents of the specified child node.

static string GetChrId(const string &id_str, objects::CScope &scope)

same as GetChrGI(), but takes an string with id (that must correspond to some GI)

static void GetAssmIds_GI(TEntrezIds &gc_ids, TGi gi)

get all assembly ids associated with a gi.

static bool IsExtendedNAA_Name(const string &annot)

check if a given annotation is an extended NAA name with '.' replaced with '_'.

static void ParseRanges(const string &sRanges, TRanges &ranges)

vector< TMappedInt > TMappingInfo

static string CreateTableEnd()

static void SetResolveDepth(objects::SAnnotSelector &sel, bool adaptive, int depth=-1)

help function for setting selector resolve depth.

static void SetAnnotShown(objects::CSeq_annot &annot, bool isShown)

static bool CheckMaxSearchSegments(int actual, int max, objects::SAnnotSelector::EMaxSearchSegmentsAction action)

check actual number of segments against max and perform the action if the actual number is more than ...

virtual void AddTaskCompleted(int delta)=0

set to add newly finished task number.

static string GetAlignDbBatch(const string &annot)

get a batch string from AlignDb annotation suffixed with batch identication string after a '#'

@ eAnnot_Unnamed

unnamed annotation

@ eAnnot_All

all annotations

@ eAnnot_Named

all named annotations

@ eAnnot_Other

any given named annots

CRef< objects::CScope > scope

CConstRef< CObject > object

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

Set object to copy of another one.

#define MSerial_AsnText

I/O stream manipulators –.

@ eSerial_AsnText

ASN.1 text.

const string AsFastaString(void) const

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...

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

Optimized implementation of CSerialObject::Assign, which is not so efficient.

static SIZE_TYPE ParseIDs(CBioseq::TId &ids, const CTempString &s, TParseFlags flags=fParse_Default)

Parse a string representing one or more Seq-ids, appending the results to IDS.

EAccessionInfo

For IdentifyAccession (below)

bool MatchesTo(const CSeq_id_Handle &h) const

True if *this matches to h.

bool Match(const CSeq_id &sid2) const

Match() - TRUE if SeqIds are equivalent.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

@ eAcc_refseq_mrna_predicted

@ eAcc_refseq_prot_predicted

@ eAcc_refseq_ncrna_predicted

@ eAcc_refseq_wgs_intermed

void SetPacked_int(TPacked_int &v)

bool IsPartialStart(ESeqLocExtremes ext) const

check start or stop of location for e_Lim fuzz

TRange GetTotalRange(void) const

TSeqPos GetStart(ESeqLocExtremes ext) const

Return start and stop positions of the seq-loc.

CRef< CSeq_loc > Merge(TOpFlags flags, ISynonymMapper *syn_mapper) const

All functions create and return a new seq-loc object.

bool IsSetStrand(void) const

Get strand.

int CompareSubLoc(const CSeq_loc &loc, ENa_strand strand, const ISubLocFilter *filter=NULL) const

Compare first-level sub-locations sequentially to order them by biological "complexity".

bool IsEmpty(void) const

True if the current location is empty.

const CSeq_id * GetId(void) const

Get the id of the location return NULL if has multiple ids or no id at all.

size_t GetSize(void) const

Get number of ranges.

TRange GetRange(void) const

Get the range.

ENa_strand GetStrand(void) const

const CSeq_id & GetSeq_id(void) const

Get seq_id of the current location.

void GetLabel(string *label) const

Appends a label suitable for display (e.g., error messages) label must point to an existing string ob...

bool IsPartialStop(ESeqLocExtremes ext) const

TSeqPos GetStop(ESeqLocExtremes ext) const

static CObjectIStream * Open(ESerialDataFormat format, CNcbiIstream &inStream, bool deleteInStream)

Create serial object reader and attach it to an input stream.

CMappedFeat GetBestMrnaForCds(const CMappedFeat &cds_feat, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0)

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,...

ENa_strand GetStrand(const CSeq_loc &loc, CScope *scope=0)

Returns eNa_strand_unknown if multiple Bioseqs in loc Returns eNa_strand_other if multiple strands in...

CConstRef< CSeq_loc > m_ParentLoc

CRef< CSeq_loc > Resolve(CScope *scope=0, TFlags flags=0) const

TGi GetGiForId(const objects::CSeq_id &id, CScope &scope, EGetIdType flags=0)

Given a Seq-id retrieve the corresponding GI.

@ eGetId_ForceGi

return only a gi-based seq-id

CRef< CSeq_loc > Map(const CSeq_loc &src_loc)

Map seq-loc.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

void GetAllTSEs(TTSE_Handles &tses, enum ETSEKind kind=eManualTSEs)

CConstRef< CSynonymsSet > GetSynonyms(const CSeq_id &id)

Get bioseq synonyms, resolving to the bioseq in this scope.

vector< CSeq_entry_Handle > TTSE_Handles

@ eProductToLocation

Map from the feature's product to location.

@ eLocationToProduct

Map from the feature's location to product.

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

const CSeq_annot_Handle & GetAnnot(void) const

Get handle to seq-annot for this feature.

const CSeqFeatData & GetData(void) const

CConstRef< CSeq_annot > GetCompleteSeq_annot(void) const

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

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.

CSeq_entry_Handle GetParentEntry(void) const

Get parent Seq-entry handle.

CSeq_entry_Handle GetTopLevelEntry(void) const

Get top level Seq-entry handle.

CScope & GetScope(void) const

Get scope this handle belongs to.

const string & GetName(void) const

CRef< CSeq_loc > GetRangeSeq_loc(TSeqPos start, TSeqPos stop, ENa_strand strand=eNa_strand_unknown) const

Return CSeq_loc referencing the given range and strand on the bioseq If start == 0,...

CSeq_entry_Handle GetTopLevelEntry(void) const

Return a handle for the top-level seq-entry.

CSeq_entry_Handle GetTopLevelEntry(void) const

Get top level Seq-entry handle.

bool IsSynonym(const CSeq_id &id) const

Check if this id can be used to obtain this bioseq handle.

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

SAnnotSelector & IncludeFeatSubtype(TFeatSubtype subtype)

Include feature subtype in the search.

SAnnotSelector & SetFeatType(TFeatType type)

Set feature type (also set annotation type to feat)

SAnnotSelector & SetExactDepth(bool value=true)

SetExactDepth() specifies that annotations will be searched on the segment level specified by SetReso...

SAnnotSelector & SetResolveAll(void)

SetResolveAll() is equivalent to SetResolveMethod(eResolve_All).

SAnnotSelector & SetOverlapTotalRange(void)

Check overlapping only of total ranges.

const CSeq_loc & GetLocation(void) const

const CSeq_feat & GetOriginalFeature(void) const

Get original feature with unmapped location/product.

SAnnotSelector & SetAdaptiveDepth(bool value=true)

SetAdaptiveDepth() requests to restrict subsegment resolution depending on annotations found on lower...

SAnnotSelector & SetResolveDepth(int depth)

SetResolveDepth sets the limit of subsegment resolution in searching annotations.

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

SAnnotSelector & SetExcludeExternal(bool exclude=true)

External annotations for the Object Manger are annotations located in top level Seq-entry different f...

SAnnotSelector & SetCollectNames(bool value=true)

Collect available annot names rather than annots.

const CSeq_feat & GetMappedFeature(void) const

Feature mapped to the master sequence.

const CSeq_loc & GetProduct(void) const

SAnnotSelector & SetAnnotType(TAnnotType type)

Set annotation type (feat, align, graph)

SAnnotSelector & AddNamedAnnots(const CAnnotName &name)

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

SAnnotSelector & SetFeatSubtype(TFeatSubtype subtype)

Set feature subtype (also set annotation and feat type)

SAnnotSelector & ExcludeNamedAnnots(const CAnnotName &name)

Add named annot to set of annots names to exclude.

SAnnotSelector & ExcludeUnnamedAnnots(void)

Add unnamed annots to set of annots names to exclude.

SAnnotSelector & AddUnnamedAnnots(void)

Add unnamed annots to set of annots names to look for.

@ fIncludeGivenEntry

Include the top (given) entry.

@ fRecursive

Iterate recursively.

@ eMaxSearchSegmentsSilent

@ eMaxSearchSegmentsThrow

void GetSeqData(TSeqPos start, TSeqPos stop, string &buffer) const

Fill the buffer string with the sequence data for the interval [start, stop).

bool IsProtein(void) const

TObjectType * GetPointer(void) const THROWS_NONE

Get pointer,.

bool IsNull(void) const THROWS_NONE

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

CRef< C > Ref(C *object)

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

void Reset(void)

Reset reference object.

void Reset(void)

Reset reference object.

bool IsNull(void) const THROWS_NONE

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

TObjectType * Release(void)

Release a reference to the object and return a pointer to the object.

CRange< TSeqPos > TSeqRange

typedefs for sequence ranges

CRange< TSignedSeqPos > TSignedSeqRange

static TThisType GetWhole(void)

virtual string GetString(const string &section, const string &name, const string &default_value, TFlags flags=0) const

Get the parameter string value.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

NCBI_NS_STD::string::size_type SIZE_TYPE

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 size_t StringToSizet(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to size_t.

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

Convert int to string.

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 long StringToLong(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to long.

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

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

Convert string to unsigned int.

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 string TruncateSpaces(const string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string.

@ eNocase

Case insensitive compare.

unsigned int usec

microseconds (modulo 1,000,000)

STimeout * NcbiMsToTimeout(STimeout *timeout, unsigned long ms)

static const char label[]

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

bool IsLim(void) const

Check if variant Lim is selected.

const TData & GetData(void) const

Get the Data member data.

TLim GetLim(void) const

Get the variant data.

void SetType(TType &value)

Assign a value to Type data member.

bool IsBool(void) const

Check if variant Bool is selected.

@ eLim_circle

artificial break at origin of circle

@ eGC_SequenceRole_top_level

bool IsSetSegs(void) const

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

const TSpliced & GetSpliced(void) const

Get the variant data.

const TStd & GetStd(void) const

Get the variant data.

const TExons & GetExons(void) const

Get the Exons member data.

bool IsStd(void) const

Check if variant Std is selected.

bool IsSetExons(void) const

set of segments involved each segment corresponds to one exon exons are always in biological order Ch...

bool IsSpliced(void) const

Check if variant Spliced is selected.

const TSegs & GetSegs(void) const

Get the Segs member data.

E_Choice Which(void) const

Which variant is currently selected.

bool IsSetPartial(void) const

incomplete in some way? Check if a value has been assigned to Partial data member.

const TLocation & GetLocation(void) const

Get the Location member data.

E_Choice

Choice variants.

TFrame GetFrame(void) const

Get the Frame member data.

const TData & GetData(void) const

Get the Data member data.

bool IsSetExcept(void) const

something funny about this? Check if a value has been assigned to Except data member.

const TCdregion & GetCdregion(void) const

Get the variant data.

TPseudo GetPseudo(void) const

Get the Pseudo member data.

const TProduct & GetProduct(void) const

Get the Product member data.

bool IsSetPseudo(void) const

annotated on pseudogene? Check if a value has been assigned to Pseudo data member.

TPartial GetPartial(void) const

Get the Partial member data.

TExcept GetExcept(void) const

Get the Except member data.

bool CanGetProduct(void) const

Check if it is safe to call GetProduct method.

bool IsSetProduct(void) const

product of process Check if a value has been assigned to Product data member.

bool IsRna(void) const

Check if variant Rna is selected.

bool IsSetFrame(void) const

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

@ e_Pub

publication applies to this seq

void SetTo(TTo value)

Assign a value to To data member.

ENa_strand

strand of nucleic acid

const Tdata & Get(void) const

Get the member data.

Tdata & Set(void)

Assign a value to data member.

void SetId(TId &value)

Assign a value to Id data member.

void SetFrom(TFrom value)

Assign a value to From data member.

TGi GetGi(void) const

Get the variant data.

bool IsGi(void) const

Check if variant Gi is selected.

bool IsWhole(void) const

Check if variant Whole is selected.

void SetStrand(TStrand value)

Assign a value to Strand data member.

const TPacked_int & GetPacked_int(void) const

Get the variant data.

@ e_Gi

GenInfo Integrated Database.

list< CRef< CSeqdesc > > Tdata

const Tdata & Get(void) const

Get the member data.

TId & SetId(void)

Assign a value to Id data member.

TTitle & SetTitle(void)

Select the variant.

const TSource & GetSource(void) const

Get the variant data.

const Tdata & Get(void) const

Get the member data.

const TDesc & GetDesc(void) const

Get the Desc member data.

list< CRef< CSeq_id > > TId

bool IsSetDesc(void) const

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

void SetInst(TInst &value)

Assign a value to Inst data member.

void SetDescr(TDescr &value)

Assign a value to Descr data member.

const TPub & GetPub(void) const

Get the Pub member data.

const TDescr & GetDescr(void) const

Get the Descr member data.

@ eRepr_raw

continuous sequence

@ e_Source

source of materials, includes Org-ref

@ eMol_na

just a nucleic acid

unsigned int

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

SStaticPair< const char *, CSeqUtils::TAnnotNameType > TNameTypeStr

static bool s_CompareDescriptions(const CFeatListItem *p1, const CFeatListItem *p2)

static void s_CreateMappingInfo(const CSeq_loc &prod_loc, const CSeq_loc &gen_loc, CSeqUtils::TMappingInfo &info)

Helper function to convert two mapped locations into an interval-to-interval mapping structure.

static TMappedLocs s_GetRnaMappingLocs(const CSeq_loc &feat_loc, const CMappedFeat &feat, const CBioseq_Handle &handle)

static bool s_IsNAA(const string &annot, char div)

static void s_AdjustToAnnotatedCDS(const CMappedFeat &mapped_cds_feat, CScope &scope, CSeqUtils::TMappingInfo &cds_map_info)

map< string, bool > TTopLevels

DEFINE_STATIC_ARRAY_MAP(TNameTypeMap, sm_NameTypeMap, s_NameTypeStrs)

CBioseq_Handle GetBioseqForSeqFeat(const CSeq_feat &f, CScope &scope)

static void s_ESearchQuery(const string &db, const string &term, vector< T > &uids, size_t &count, const int ret_max, const string &xpath)

static void s_ELinkQuery(const string &db_from, const string &db_to, const vector< T1 > &uids_from, vector< T2 > &uids_to, const string &cmd, const string &xpath)

static const TAssemblySeqIds & s_GetAssemblySeqIds(const string &assm_acc)

CConstRef< CBioseq > GetBioseqForSeqdesc(CRef< CScope > scope, const CSeqdesc &seq_desc)

static CSeqUtils::TLocVec s_GetAlnMapplingLocs(const CSeq_align_set &align_set, TGi gi)

static CRWLock m_AssemblySeqIdLock

CSeq_feat_Handle GetSeqFeatHandleForBadLocFeature(const CSeq_feat &feat, CScope &scope)

CStaticArrayMap< string, CSeqUtils::TAnnotNameType > TNameTypeMap

static const string kTaxDb

static bool s_IsExtendedNAA(const string &sAnnotName, char div, bool isStrict)

static map< string, TAssemblySeqIds > s_AssemblySeqIdCache

static const string kAssmDb

static CRWLock m_TopLevelsLock

static const string & GetLinksURL()

CSeq_entry_Handle GetDefaultTopLevelSeqEntry(CScope &scope)

static const string kNucDb

vector< const CFeatListItem * > GetSortedFeatList(CSeq_entry_Handle seh, size_t max)

CSeq_entry_Handle GetSeqEntryForPubdesc(CRef< CScope > scope, const CPubdesc &pubdesc)

static TTopLevels m_TopLevels

vector< CRef< CSeq_loc > > TMappedLocs

For CDS and RNA feature mapping information.

static const char * kLinksUrlDefault

vector< CConstRef< CSeq_id > > TAssemblySeqIds

static const TNameTypeStr s_NameTypeStrs[]

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 smart and slim</td> n<td> orig</td> n</tr> n<tr> n<td> last_modified</td> n<td> optional</td> n<td> Integer</td> n<td class=\"description\"> The blob last modification If provided then the exact match will be requested with n the Cassandra storage corresponding field value</td> n<td> Positive integer Not provided means that the most recent match will be selected</td> n<td></td> n</tr> n<tr> n<td> use_cache</td> n<td> optional</td> n<td> String</td> n<td class=\"description\"> The option controls if the Cassandra LMDB cache and or database should be used It n affects the seq id resolution step and the blob properties lookup step The following n options are BIOSEQ_INFO and BLOB_PROP at all

Lightweight interface for getting lines of data with minimal memory copying.

static const CS_INT unused

constexpr auto sort(_Init &&init)

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

const GenericPointer< typename T::ValueType > T2 value

static const BitmapCharRec ch1

static const BitmapCharRec ch2

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

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

static int match(PCRE2_SPTR start_eptr, PCRE2_SPTR start_ecode, uint16_t top_bracket, PCRE2_SIZE frame_size, pcre2_match_data *match_data, match_block *mb)

static const sljit_gpr r1

static const sljit_gpr r0

static const sljit_gpr r2

#define row(bind, expected)

CSeq_annot::C_Data::E_Choice TAnnotType

bool operator()(const CMappedFeat &feat0, const CMappedFeat &feat1) const

bool operator()(const CMappedFeat &feat0, const CMappedFeat &feat1) const

bool operator()(const pair< T, U > &p1, const pair< T, U > &p2) const

Location relative to a base Seq-loc: one (usually) or more ranges of offsets.

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

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