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

min_unknown,

max_unknown,

min_known,

vector<pair<

,

>>& start_length_locs,

vector<

> &vec_is_known)

|| !inst.IsSetSeq_data()) {

(inst.GetSeq_data().Which()) {

iupacna = inst.GetSeq_data().GetIupacna();

element =

;

(

, it, iupacna) {

is_unknown =

;

is_known =

;

(n_len >= min_unknown && (max_unknown < 0 || (

)n_len <= max_unknown)) {

(n_len >= min_known && (max_known < 0 || (

)n_len <= max_known)) {

(is_unknown || is_known) {

(element.length() > n_len) {

element = element.substr(0, element.length() - n_len);

pos += element.length();

start_length_locs.emplace_back((

)pos, (

)n_len);

vec_is_known.push_back(is_known);

is_unknown =

;

is_known =

;

(n_len >= min_unknown && (max_unknown < 0 || (

)n_len <= max_unknown)) {

(n_len >= min_known && (max_known < 0 || (

)n_len <= max_known)) {

(is_unknown || is_known) {

(element.length() > n_len) {

element = element.substr(0, element.length() - n_len);

pos += element.length();

start_length_locs.emplace_back((

)pos, (

)n_len);

vec_is_known.push_back(is_known);

pos += element.length();

vector<pair<int, int>>& start_length_locs,

vector<bool> &vec_is_known,

found_row =

;

(

= 0;

< num_rows;

++)

found_overlap =

;

(

= 0;

< start_length_locs.size();

++)

(!vec_is_known[

])

num_segs = lens.size();

start = start_length_locs[

].first;

stop = start + start_length_locs[

].second - 1;

(

j = 0; j<num_segs; j++)

found_overlap =

;

(found_overlap && deleted_aligns.

(&align) == deleted_aligns.

())

deleted_aligns.

(&align);

pair<vector<pair<int, int>>, vector<bool>>>& map_gaps,

keep_gap_length,

create_general_only,

create_xref_map)

(

&gap : map_gaps)

bsh = gap.first;

&start_length_locs = gap.second.first;

&vec_is_known = gap.second.second;

gaps.reserve(start_length_locs.size());

(

= 0;

< start_length_locs.size(); ++

)

gap.

= start_length_locs[

].first;

gap.

= start_length_locs[

].second;

new_map_gaps[bsh] = gaps;

create_general_only, max_feat_id, old_to_new, create_xref_map);

((*xit)->IsSetId() && (*xit)->GetId().IsLocal() && (*xit)->GetId().GetLocal().IsId())

it = old_to_new.

((*xit)->GetId().GetLocal().GetId());

(it != old_to_new.

())

(*xit)->SetId().SetLocal().SetId(it->second);

((*it)->IsSetQual() && (*it)->IsSetVal() &&

(id_label.empty() ||

((*it)->GetVal(), id_label) ||

((*it)->GetVal(), id_label +

))) {

(id_label.empty()) {

id_label = (*it)->GetVal();

keep_gap_length)

CCdregion::TCode_break::iterator cit = cdr.

().begin();

do_remove =

;

((*cit)->IsSetLoc()) {

vector<CRef<CSeq_loc> > locations;

comment =

;

(!locations.empty()) {

(new_loc && !new_loc->

() && !new_loc->

()) {

(*cit)->SetLoc().

(*new_loc);

vector<CRef<CSeq_loc> > locations;

comment =

;

(!locations.empty()) {

(new_loc && !new_loc->

() && !new_loc->

()) {

split_gene_locations,

keep_gap_length,

create_general_only,

create_xref_map)

vector<CRef<CSeq_loc>> locations;

comment =

;

->Assign(*feat_loc.

());

transcript_id_offset = 1;

transcript_id_label;

protein_id_offset = 1;

protein_id_label;

(locations.empty() || locations.front()->IsNull())

prot_seq->

().ResetExt();

prot_seq->

().SetSeq_data().SetIupacaa().Set(

);

prot_feat->

().SetInt().SetId().Assign(*(prot_seq->

().front()));

(

j = 1; j < locations.size(); j++)

(!locations[j]->IsNull())

add_feat->

().SetLocal().SetId(max_feat_id);

(!create_xref_map)

(*add_feat, transcript_id_offset, transcript_id_label,

);

(*add_feat, protein_id_offset, protein_id_label,

);

vector<CRef<CSeq_feat>> other_prot_feats;

vector<CRef<CSeq_id>> new_prot_id;

new_prot_id.push_back(

(bsh, id_offset, id_label, create_general_only));

add_feat->

().SetWhole().Assign(*new_prot_id.front());

(

prot_feat_ci(product); prot_feat_ci; ++prot_feat_ci)

prot_feat->

(*(prot_feat_ci->GetSeq_feat()));

prot_feat->

().SetLocal().SetId(max_feat_id);

(!create_xref_map)

(*feat.

(), *add_feat, prot_feat_ci->GetSeq_feat_Handle(), other_prot_feats, max_feat_id, old_to_new, create_xref_map);

(

j = 1; j < locations.size(); j++)

(!locations[j]->IsNull())

add_feat->

().SetLocal().SetId(max_feat_id);

(!create_xref_map)

(*add_feat, transcript_id_offset, transcript_id_label,

);

(*add_feat, protein_id_offset, protein_id_label,

);

split_gene_locations,

keep_gap_length,

create_general_only,

create_xref_map)

(map_gaps.empty())

seh = map_gaps.cbegin()->first.GetTopLevelEntry();

&scope = seh.GetScope();

(

feat_it(seh); feat_it; ++feat_it) {

(*feat_it, scope, map_gaps, composite, split_gene_locations, break_features,

keep_gap_length, create_general_only, max_feat_id, old_to_new, create_xref_map);

keep_gap_length)

new_loc->

(feat_loc);

vector<vector<CRef<CSeq_loc>>> all_locs;

vector<vector<pair<bool, bool>>> all_partials;

vector<CRef<CSeq_loc>> locs;

vector<pair<bool, bool>> partials;

(

loc_it(*new_loc); loc_it; ++loc_it)

(loc_it.IsEmpty()) {

strand = loc_it.GetStrand();

->Assign(loc_it.GetSeq_id());

it = map_gaps.find(bsh);

(it != map_gaps.end()) {

partial5 =

;

(

= 0;

< gaps.size(); ++

)

new_gap_length = (keep_gap_length ? gaps[

].length : 100);

(feat_stop < igap_start)

locs.emplace_back(

(*

, new_start, new_stop, strand));

partials.emplace_back(partial5,

);

(!gaps[

].is_replace && igap_start <= feat_start)

(gaps[

].is_known)

(gaps[

].is_replace && gaps[

].is_known && igap_start + gaps[

].length <= feat_start)

(gaps[

].is_replace && !gaps[

].is_known && igap_start + gaps[

].length <= feat_start)

+= new_gap_length - gaps[

].length;

(!gaps[

].is_replace && gaps[

].is_known && igap_start > feat_start && igap_start <= feat_stop)

offset_middle += gaps[

].length;

(!gaps[

].is_replace && !gaps[

].is_known && igap_start > feat_start && igap_start <= feat_stop)

offset_middle += new_gap_length;

+= offset_middle + new_gap_length;

locs.emplace_back(

(*

, new_start, new_stop, strand));

partials.emplace_back(partial5,

);

feat_start = gaps[

].start;

all_locs.push_back(locs);

all_partials.push_back(partials);

(gaps[

].is_replace && gaps[

].is_known && igap_start >= feat_start && igap_start + gaps[

].length - 1 <= feat_stop)

(gaps[

].is_replace && !gaps[

].is_known && igap_start <= feat_start && igap_start + gaps[

].length - 1 >= feat_start && igap_start + gaps[

].length - 1 < feat_stop)

+= offset_middle + new_gap_length - gaps[

].length;

feat_start = gaps[

].start + gaps[

].length;

(break_features && !locs.empty())

all_locs.push_back(locs);

all_partials.push_back(partials);

(gaps[

].is_replace && !gaps[

].is_known && igap_start <= feat_start && igap_start + gaps[

].length - 1 >= feat_stop)

(break_features && !locs.empty())

all_locs.push_back(locs);

all_partials.push_back(partials);

(gaps[

].is_replace && !gaps[

].is_known && igap_start > feat_start && igap_start <= feat_stop && igap_start + gaps[

].length - 1 > feat_stop)

locs.emplace_back(

(*

, new_start, new_stop, strand));

partials.emplace_back(partial5,

);

all_locs.push_back(locs);

all_partials.push_back(partials);

(gaps[

].is_replace && !gaps[

].is_known && igap_start > feat_start && igap_start <= feat_stop && igap_start + gaps[

].length - 1 <= feat_stop)

+= offset_middle + new_gap_length - gaps[

].length;

locs.emplace_back(

(*

, new_start, new_stop, strand));

partials.emplace_back(partial5,

);

feat_start = gaps[

].start + gaps[

].length;

all_locs.push_back(locs);

all_partials.push_back(partials);

offset_middle += new_gap_length - gaps[

].length;

locs.emplace_back(

(*

, new_start, new_stop, strand));

partials.emplace_back(partial5,

);

all_locs.push_back(locs);

all_partials.push_back(partials);

(!all_partials.empty())

(!all_partials.front().empty())

(!all_partials.back().empty())

(

j = 0; j < all_locs.size(); j++)

(all_locs[j].

())

(

= 0;

< all_locs[j].size();

++)

(!all_partials[j].

())

locations.push_back(changed_loc);

*cds_gap_comment =

;

comment = comment +

+ cds_gap_comment;

(

feat_ci(bh); feat_ci; ++feat_ci)

&loc = feat_ci->GetLocation();

new_feat->

(feat_ci->GetOriginalFeature());

create_xref_map)

(!prot_loc->

())

new_feat->

().SetLocal().SetId(max_feat_id);

(!create_xref_map)

other_prot_feats.push_back(new_feat);

& remove_alignments,

create_xref_map)

vector<pair<int, int>> start_length_locs;

vector<bool> vec_is_known;

start_length_locs, vec_is_known);

(start_length_locs.empty())

(; align_ci; ++align_ci) {

map_gaps[bsh] = make_pair(start_length_locs, vec_is_known);

create_general_only, max_feat_id,

old_to_new, create_xref_map);

remove_alignments = (!deleted_aligns.

());

create_xref_map =

;

create_xref_map =

;

& remove_alignments,

create_xref_map)

vector<pair<int, int>> start_length_locs;

vector<bool> vec_is_known;

start_length_locs, vec_is_known);

(start_length_locs.empty())

(; align_ci; ++align_ci) {

map_gaps[bsh] = make_pair(start_length_locs, vec_is_known);

create_general_only, max_feat_id,

old_to_new, create_xref_map);

remove_alignments = (!deleted_aligns.

());

create_xref_map =

;

create_xref_map =

;

User-defined methods of the data storage class.

@ eExtreme_Positional

numerical value

bool AdjustProteinFeaturePartialsToMatchCDS(CSeq_feat &new_prot, const CSeq_feat &cds)

AdjustProteinFeaturePartialsToMatchCDS A function to change an existing MolInfo to match a coding reg...

CRef< objects::CSeq_id > GetNewProtId(objects::CBioseq_Handle bsh, int &offset, string &id_label, bool general_only)

vector< CRef< objects::CSeq_id > > GetNewProtIdFromExistingProt(objects::CBioseq_Handle bsh, int &offset, string &id_label)

bool IsGeneralIdProtPresent(objects::CSeq_entry_Handle tse)

TSeqPos GetLength(void) const

void AddCommand(IEditCommand &command)

virtual void Unexecute()

Undo (opposite to Execute())

virtual void Execute()

Do the editing action.

static TId s_FindHighestFeatureId(const objects::CSeq_entry_Handle &entry)

static SIZE_TYPE Convert(const CTempString &src, TCoding src_coding, TSeqPos pos, TSeqPos length, string &dst, TCoding dst_coding)

SeqVector related exceptions.

TDim CheckNumRows(void) const

Validatiors.

const CSeq_id & GetSeq_id(TDim row) const

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

namespace ncbi::objects::

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

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

void RemapOtherProtFeats(const CSeq_feat &old_cds, CSeq_feat &cds, CBioseq_Handle bh, CRef< CCmdComposite > composite, bool &any_actions)

void FindNewLocations(const CSeq_loc &feat_loc, CScope &scope, const map< CBioseq_Handle, vector< SGap >> &map_gaps, vector< CRef< CSeq_loc >> &locations, bool &comment, bool break_features, bool keep_gap_length)

static CRef< CCmdComposite > ConvertRawToDeltaByNsHugeFileCmd_impl(const CSeq_entry_Handle &seh, const SGapRequestInfo &request, CObject_id::TId &max_feat_id, bool &remove_alignments, int &count, map< CObject_id::TId, CObject_id::TId > &old_to_new, bool create_xref_map)

static CRef< CCmdComposite > ConvertRawToDeltaByNsCommand_impl(const CSeq_entry_Handle &seh, const SGapRequestInfo &request, bool &remove_alignments, int &count, map< CObject_id::TId, CObject_id::TId > &old_to_new, bool create_xref_map)

CRef< CCmdComposite > ConvertRawToDeltaByNsCommand(const CSeq_entry_Handle &seh, const SGapRequestInfo &request, bool &remove_alignments, int &count)

static void AdjustSingleFeature(const CMappedFeat &feat, CScope &scope, const map< CBioseq_Handle, vector< SGap >> &gaps, CRef< CCmdComposite > composite, bool split_gene_locations, bool break_features, bool keep_gap_length, bool create_general_only, CObject_id::TId &max_feat_id, map< CObject_id::TId, CObject_id::TId > &old_to_new, bool create_xref_map)

CRef< CCmdComposite > ConvertRawToDeltaByNsHugeFileCmd(const CSeq_entry_Handle &seh, const SGapRequestInfo &request, CObject_id::TId &max_feat_id, bool &remove_alignments, int &count)

static void UpdateFeaturesForGaps(const map< CBioseq_Handle, pair< vector< pair< int, int >>, vector< bool >>> &map_gaps, CRef< CCmdComposite > composite, bool break_features, bool keep_gap_length, bool create_general_only, CObject_id::TId &max_feat_id, map< CObject_id::TId, CObject_id::TId > &old_to_new, bool create_xref_map)

void GapLocationsFromNs(const CSeq_inst &inst, const size_t min_unknown, const long max_unknown, const size_t min_known, const long max_known, vector< pair< int, int >> &start_length_locs, vector< bool > &vec_is_known)

CRef< CSeq_feat > UpdateFeat(CRef< CSeq_loc > changed_loc, const CSeq_feat &feat, bool comment, CScope &scope)

static void s_ReplaceFeatureIdXref(CSeq_feat &f, map< CObject_id::TId, CObject_id::TId > &old_to_new)

void UpdateDensegAlignment(CSeq_align_Handle ah, CBioseq_Handle bsh, CRef< CCmdComposite > composite, const vector< pair< int, int >> &start_length_locs, const vector< bool > &vec_is_known, set< const CSeq_align * > &deleted_aligns)

static void x_AdjustOrigLabel(CSeq_feat &feat, size_t &id_offset, string &id_label, const string &qual)

void AdjustFeatureLocations(const map< CBioseq_Handle, vector< SGap >> &map_gaps, CRef< CCmdComposite > composite, bool split_gene_locations, bool break_features, bool keep_gap_length, bool create_general_only, CObject_id::TId &max_feat_id, map< CObject_id::TId, CObject_id::TId > &old_to_new, bool create_xref_map)

static void s_UpdateCodeBreaksAndAnticodons(CSeq_feat &feat, CScope &scope, const map< CBioseq_Handle, vector< SGap >> &gaps, bool break_features, bool keep_gap_length)

static void s_AddComment(CRef< CSeq_feat > new_feat)

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.

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

Set object to copy of another one.

CRef< CSeq_loc > MakeSeq_loc(EMakeType make_type=eMake_CompactType) const

return constructed CSeq_loc with all changes

bool IsPartialStart(ESeqLocExtremes ext) const

check start or stop of location for e_Lim fuzz

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

Override Assign() to incorporate cache invalidation.

TSeqPos GetStart(ESeqLocExtremes ext) const

Return start and stop positions of the seq-loc.

CSeq_loc_I InsertInterval(const CSeq_id_Handle &id, const TRange &range, ENa_strand strand=eNa_strand_unknown)

Insert new element before the current one (.

const CSeq_id * GetId(void) const

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

void SetPartialStart(bool val, ESeqLocExtremes ext)

set / remove e_Lim fuzz on start or stop (lt/gt - indicating partial interval)

CRef< CSeq_loc > Intersect(const CSeq_loc &other, TOpFlags flags, ISynonymMapper *syn_mapper) const

Find the intersection with the seq-loc, merge/sort resulting ranges depending on flags.

void SetPartialStop(bool val, ESeqLocExtremes ext)

bool IsPartialStop(ESeqLocExtremes ext) const

CSeq_loc_I InsertNull(void)

Set of Insert*() methods.

TSeqPos GetStop(ESeqLocExtremes ext) const

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,...

static CCdregion::EFrame FindBestFrame(const CSeq_feat &cds, CScope &scope)

Find "best" frame for a coding region.

static void Translate(const string &seq, string &prot, const CGenetic_code *code, bool include_stop=true, bool remove_trailing_X=false, bool *alt_start=NULL, bool is_5prime_complete=true, bool is_3prime_complete=true)

Translate a string using a specified genetic code.

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.

CSeq_loc_Mapper_Base & SetMergeAbutting(void)

Merge only abutting intervals, keep overlapping.

@ 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.

CConstRef< CSeq_align > GetSeq_align(void) const

Get const reference to current seq-align.

virtual const CSeq_loc & GetLocation(void) const

CSeq_entry_Handle GetParentEntry(void) const

Get parent Seq-entry handle.

CScope & GetScope(void) const

Get scope this handle belongs to.

CScope & GetScope(void) const

Get scope this handle belongs to.

CConstRef< CSeq_feat > GetOriginalSeq_feat(void) const

CSeqFeatData::ESubtype GetFeatSubtype(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,...

bool IsPlainFeat(void) const

Check if this is plain feature.

bool IsSynonym(const CSeq_id &id) const

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

const CSeq_loc & GetLocation(void) const

const CSeq_feat & GetOriginalFeature(void) const

Get original feature with unmapped location/product.

const CSeq_feat_Handle & GetSeq_feat_Handle(void) const

Get original feature handle.

CSeq_align_Handle GetSeq_align_Handle(void) const

Get original alignment handle.

CConstRef< CSeq_feat > GetSeq_feat(void) const

Get current seq-feat.

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.

static bool EndsWith(const CTempString str, const CTempString end, ECase use_case=eCase)

Check if a string ends with a specified suffix value.

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

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

static SIZE_TYPE Find(const CTempString str, const CTempString pattern, ECase use_case=eCase, EDirection direction=eForwardSearch, SIZE_TYPE occurrence=0)

Find the pattern in the string.

static bool 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.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

bool IsId(void) const

Check if variant Id is selected.

TId GetId(void) const

Get the variant data.

const TAnticodon & GetAnticodon(void) const

Get the Anticodon member data.

bool IsTRNA(void) const

Check if variant TRNA is selected.

bool IsSetAnticodon(void) const

location of anticodon Check if a value has been assigned to Anticodon data member.

void SetAnticodon(TAnticodon &value)

Assign a value to Anticodon data member.

bool IsSetExt(void) const

generic fields for ncRNA, tmRNA, miscRNA Check if a value has been assigned to Ext data member.

void ResetAnticodon(void)

Reset Anticodon data member.

const TExt & GetExt(void) const

Get the Ext member data.

const TDenseg & GetDenseg(void) const

Get the variant data.

const TStarts & GetStarts(void) const

Get the Starts member data.

const TLens & GetLens(void) const

Get the Lens member data.

bool IsSetSegs(void) const

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

const TSegs & GetSegs(void) const

Get the Segs member data.

bool IsDenseg(void) const

Check if variant Denseg is selected.

bool IsSetComment(void) const

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

bool IsSetData(void) const

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

bool IsSetQual(void) const

qualifiers Check if a value has been assigned to Qual data member.

void SetLocation(TLocation &value)

Assign a value to Location data member.

bool IsCdregion(void) const

Check if variant Cdregion is selected.

void SetComment(const TComment &value)

Assign a value to Comment data member.

void ResetCode_break(void)

Reset Code_break data member.

void SetPartial(TPartial value)

Assign a value to Partial data member.

void SetProduct(TProduct &value)

Assign a value to Product data member.

const TId & GetId(void) const

Get the Id member data.

const TLocal & GetLocal(void) const

Get the variant data.

const TLocation & GetLocation(void) const

Get the Location member data.

bool IsLocal(void) const

Check if variant Local is selected.

const TData & GetData(void) const

Get the Data member data.

const TExcept_text & GetExcept_text(void) const

Get the Except_text member data.

void SetId(TId &value)

Assign a value to Id data member.

bool IsSetExcept_text(void) const

explain if except=TRUE Check if a value has been assigned to Except_text data member.

void SetData(TData &value)

Assign a value to Data data member.

TCode_break & SetCode_break(void)

Assign a value to Code_break data member.

const TCdregion & GetCdregion(void) const

Get the variant data.

bool IsSetId(void) const

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

const TProduct & GetProduct(void) const

Get the Product member data.

const TComment & GetComment(void) const

Get the Comment member data.

void ResetLocation(void)

Reset Location data member.

vector< CRef< CSeqFeatXref > > TXref

vector< CRef< CGb_qual > > TQual

const TRna & GetRna(void) const

Get the variant data.

TQual & SetQual(void)

Assign a value to Qual data member.

const TCode_break & GetCode_break(void) const

Get the Code_break member data.

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 IsSetCode_break(void) const

individual exceptions Check if a value has been assigned to Code_break data member.

bool IsEmpty(void) const

Check if variant Empty is selected.

bool IsNull(void) const

Check if variant Null is selected.

const TInst & GetInst(void) const

Get the Inst member data.

const TId & GetId(void) const

Get the Id member data.

void SetInst(TInst &value)

Assign a value to Inst data member.

@ eRepr_raw

continuous sequence

@ e_Ncbi2na

2 bit nucleic acid code

@ e_Iupacna

IUPAC 1 letter nuc acid code.

@ e_Ncbi8na

8 bit extended nucleic acid code

@ e_Ncbi4na

4 bit nucleic acid code

@ eMol_na

just a nucleic acid

constexpr auto front(list< Head, As... >, T=T()) noexcept -> Head

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

TLocAdjustmentVector NormalizeUnknownLengthGaps(CSeq_inst &inst, TSeqPos unknown_length=100)

NormalizeUnknownLengthGaps A function to adjust the length of unknown-length gaps to a specific lengt...

void ConvertRawToDeltaByNs(CSeq_inst &inst, size_t min_unknown, int max_unknown, size_t min_known, int max_known, bool is_assembly_gap=false, int gap_type=CSeq_gap::eType_unknown, int linkage=-1, int linkage_evidence=-1)

ConvertRawToDeltaByNs A function to convert a raw sequence to a delta sequence, using runs of Ns to d...

#define row(bind, expected)

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