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NCBI C++ ToolKit: src/algo/gnomon/asn1.cpp Source File

bioseq_set.

().push_back(gnomon_models_annot_ref);

(*seq_annot,

);

bioseq_set.

().push_back(seq_annot);

contig_name(a_contig_name),

contig_sid(

::ToSeq_id(a_contig_name)),

gencode(genetic_code),

genetic_code,

shift) :

->main_seq_entry;

->push_back(model_products);

(models_in_internal_feature_table.find(

) == models_in_internal_feature_table.end()) {

internal_feature_table->push_back(internal_feat);

models_in_internal_feature_table.insert(

);

cds_feat = create_cdregion_feature(md);

nucprots->push_back(model_products);

mrna_feat = feature_generator->ConvertAlignToAnnot(*align, *gnomon_models_annot, model_products->

(), model.

(), cds_feat_ptr);

mrna_feat->

().push_back(user_obj);

AddInternalFeature(md);

cdrcode->SetId(gencode);

cdregion_feature->

().SetCdregion().SetCode().Set().push_back(cdrcode);

(model.

()) {

code_break->

(*pstop);

aa->SetNcbieaa(

);

aa->SetNcbieaa(

);

code_break->

(*aa);

code_breaks.push_back(code_break);

cdregion_feature->

().SetCdregion().SetFrame(ncbi_frame);

(0 < altstart && altstart != start)

cdregion_location->

().SetFuzz_from().SetAlt().push_back(altstart);

cdregion_feature->

(*cdregion_location);

cdregion_feature;

(

=0;

< model.

().

(); ++

) {

(interval_range_on_mrna.

())

extends_to_left = interval_range_on_mrna.

() > limits_on_mrna.

();

extends_to_right = interval_range_on_mrna.

() < limits_on_mrna.

();

(extends_to_left,extends_to_right);

(

> 0 && (!e->

|| (model.

()[

-1].Limits().Empty() && extends_to_left))) {

(

< model.

().size()-1 && (!e->

|| (model.

()[

+1].Limits().Empty() && extends_to_right))) {

evidence.GetModel(model.

());

(*seq_annot,

+ id_str);

annot_id->SetGeneral().SetDb(

);

seq_annot->

().push_back(annot_id);

= s->GetId();

(

.NotEmpty()) {

aligns->push_back(

);

unique_ptr<SModelData> smd;

smd.reset(

(*m, contig_seq, shift) );

AddInternalFeature(*smd);

CreateModelProducts(*smd);

aligns->push_back(model2spliced_seq_align(*smd));

(!aligns->empty())

(strs.begin(), strs.end(), back_inserter(values));

(

= 1;

< (

)model.

().size() && !ggap; ++

) {

ggap = model.

()[

-1].m_ssplice_sig ==

|| model.

()[

].m_fsplice_sig ==

;

method = ggap ?

:

;

method =

;

method = ggap ?

:

;

->SetStr(

);

support_field->

().SetStr(

);

vector<string> chains;

vector<string> cores;

vector<string> proteins;

vector<string> mrnas;

vector<string> short_reads;

vector<string> long_sras;

vector<string> others;

vector<string> unknown;

long_sras_count = 0;

others_count = 0;

= s->GetId();

cores.push_back(accession);

chains.push_back(accession);

proteins.push_back(accession);

mrnas.push_back(accession);

ests.push_back(accession);

ests_count += m->

();

long_sras.push_back(accession);

long_sras_count += m->

();

others.push_back(accession);

others_count += m->

();

short_reads.push_back(accession);

unknown.push_back(accession);

have_something =

;

(!chains.empty()) {

support_field->

(

,chains);

have_something =

;

(!cores.empty()) {

support_field->

(

,cores);

have_something =

;

(!proteins.empty()) {

(proteins.begin(),proteins.end());

support_field->

(

,proteins);

have_something =

;

(!mrnas.empty()) {

(mrnas.begin(),mrnas.end());

support_field->

(

,mrnas);

have_something =

;

(ests.begin(),ests.end());

support_field->

(

,ests);

support_field->

().SetFields().back()->SetNum(ests_count);

have_something =

;

(!short_reads.empty()) {

(short_reads.begin(),short_reads.end());

support_field->

(

,short_reads);

have_something =

;

(!long_sras.empty()) {

(long_sras.begin(),long_sras.end());

support_field->

(

,long_sras);

support_field->

().SetFields().back()->SetNum(long_sras_count);

have_something =

;

(!others.empty()) {

(others.begin(),others.end());

support_field->

(

,others);

support_field->

().SetFields().back()->SetNum(others_count);

have_something =

;

(!unknown.empty()) {

support_field->

(

,unknown);

have_something =

;

user_obj->

().push_back(support_field);

user_obj->

(

,

(

));

feature->

().push_back(feat_id);

user->

().SetStr(

);

feature->

().push_back(user);

(!

->second.empty())

feature->

(*create_packed_int_seqloc(model,rcds_on_mrna));

feature->

().SetCdregion().SetCode().Set().push_back(cdrcode);

feature->

().SetCdregion().SetFrame(ncbi_frame);

se->SetGenomic_start(e.

());

se->SetGenomic_end(e.

());

se->SetGenomic_id(*fillerid);

scr->SetValue().SetReal(e.

);

->SetStr(

);

se->SetScores().Set().push_back(scr);

(strand==

) {

(strand==

) {

(model.

() > 0) {

seq_align->

().push_back(

);

product_length = model.

()/3;

TInDels::const_iterator indel_i = indels.begin();

(

= 0;

< (

)model.

().size(); ++

) {

se->SetProduct_start().SetNucpos(transcript_exon.

());

se->SetProduct_end().SetNucpos(transcript_exon.

());

last_chunk = e->

();

( ;indel_i != indels.end() && indel_i->Loc() <= e->

()+1; ++indel_i) {

(indel.

()-last_chunk > 0) {

chunk->SetDiag(indel.

()-last_chunk);

chunk->SetMatch(indel.

()-last_chunk);

chunk->SetMatch(indel.

()-last_chunk);

se->SetParts().push_back(chunk);

last_chunk = indel.

();

chunk->SetMismatch(indel.

());

se->SetParts().push_back(chunk);

last_chunk += indel.

();

chunk->SetGenomic_ins(indel.

());

se->SetParts().push_back(chunk);

last_chunk += indel.

();

chunk->SetProduct_ins(indel.

());

se->SetParts().push_back(chunk);

(e->

() <= last_chunk && last_chunk <= e->GetTo()) {

chunk->SetDiag(e->

()-last_chunk+1);

chunk->SetMatch(e->

()-last_chunk+1);

chunk->SetMatch(e->

()-last_chunk+1);

se->SetParts().push_back(chunk);

se->SetParts().push_back(chunk);

( indel_i == indels.end() );

(!model.

().empty() && !is_protalign) {

left_not_aligned = tlim.

();

(left_not_aligned, right_not_aligned);

mismatches(left_not_aligned,

);

TInDels::const_iterator indl = model.

().begin();

(

e = 0; e < (

)model.

().size(); ++e) {

(model.

()[e].Limits().Empty())

(e > 0 && !model.

()[e].m_fsplice) {

( ; indl != model.

().end() && indl->IntersectingWith(model.

()[e].GetFrom(), model.

()[e].GetTo()); ++indl) {

(indl->GetStatus()) {

mismstatus.push_back(

);

;

mismstatus.push_back(

);

;

mismstatus.push_back(

);

;

(!indl->IsInsertion())

mismatches += indl->GetInDelV();

mismatches +=

(right_not_aligned,

);

(mismatches.find_first_not_of(

) != string::npos) {

typem->

(

);

userm->

(

, mismatches);

seq_align->

().push_back(userm);

(mismstatus.find_first_not_of(

) != string::npos) {

->SetStr(

);

users->

(

, mismstatus);

seq_align->

().push_back(users);

is_align = !(

()&(eChain|eGnomon));

(is_align && (

()&eProt) && HasStop()) {

(GetCdsInfo().IsMappedToGenome());

lim = GetCdsInfo().Start()+GetCdsInfo().ReadingFrame();

model.

(lim,eRemoveExons);

mrna_sid->

(*GetTargetId());

(Status()&eBestPlacement)

(Status()&eUnknownOrientation)

(

()&eProt) {

modi->SetStart_codon_found(

);

modi->SetStop_codon_found(

);

->SetStr(

);

seq_align->

().push_back(user);

((*uo)->GetType().GetStr() ==

) {

(method.find(

) != string::npos || method.find(

) != string::npos)

(method.find(

) != string::npos)

(ncbi_frame) {

((*u)->CanGetClass() && (*u)->GetClass() ==

&&

(annot == seq_annot_map.

())

(!processed_ids.

(

).second)

cds_handle = feat_handle;

unique_ptr<CAlignModel> model(

(feat_handle, cds_handle, seq_align) );

evidence_models.push_back(*model);

(

, evidence_models, evidence_alignments, seq_entry_handle, seq_annot_map, processed_ids);

evidence_alignments.push_back(align_ref);

CAnnot_descr::Tdata::const_iterator iter = (*annot)->GetDesc().Get().begin();

( ; iter != (*annot)->GetDesc().

().end(); ++iter) {

((*iter)->IsName() ) {

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

((*iter)->IsRegion() ) {

(!name.empty()) {

seq_annot_map[name] = *annot;

(name==

) {

internal_feature_table = seq_annot_map[

];

(contig.empty() && feat_ci) {

(; feat_ci; ++feat_ci) {

model_list.push_back(*model);

processed_ids.

(model->ID());

(model->ID(), evidence_models, evidence_alignments, seq_entry_handle, seq_annot_map, processed_ids);

(; internal_feat_ci; ++internal_feat_ci) {

(processed_ids.

(

) != processed_ids.

())

(model.get() ==

)

evidence_models.push_back(*model);

processed_ids.

(

);

(model->ID(), evidence_models, evidence_alignments, seq_entry_handle, seq_annot_map, processed_ids);

@ eExtreme_Biological

5' and 3'

CRef< CUser_object > GetModelEvidenceUserObject(const CSeq_feat_Handle &feat)

CAlignModel * RestoreModelFromPublicMrnaFeature(const CSeq_feat_Handle &feat)

void ParseAttributes(TAttributes &attributes, CAlignModel &a)

CRef< CSpliced_exon > spliced_exon(const CModelExon &e, EStrand strand)

bool IsGnomonConstructed(const CSeq_align &seq_align)

USING_SCOPE(ncbi::objects)

CRef< CProduct_pos > NucPosToProtPos(int nultripos)

int CollectUserField(const CUser_field &field, const string &name, vector< string > &values)

void ExpandSupport(const CSupportInfoSet &src, CSupportInfoSet &dst, IEvidence &evidence)

void CollectAttributes(const CAlignModel &a, TAttributes &attributes)

void RestoreModelMethod(const CSeq_feat_Handle &feat, CAlignModel &model)

void NameAnnot(CSeq_annot &annot, const string &name)

void ExtractSupportModels(Int8 model_id, TAlignModelList &evidence_models, list< CRef< CSeq_align > > &evidence_alignments, CSeq_entry_Handle seq_entry_handle, map< string, CRef< CSeq_annot > > &seq_annot_map, set< Int8 > &processed_ids)

void RestoreModelAttributes(const CSeq_feat_Handle &feat_handle, CAlignModel &model)

void RestoreModelReadingFrame(const CSeq_feat_Handle &feat, CAlignModel &model)

Int8 GetModelId(const CSeq_align &seq_align)

const string kGnomonConstructed

CAlignModel * RestoreModel(const CSeq_feat_Handle &internal_feat, const CSeq_feat_Handle &cds_feat, const CSeq_align &align)

string ModelMethod(const CGeneModel &model)

CAlignModel * RestoreModelFromInternalGnomonFeature(const CSeq_feat_Handle &feat)

CRef< CSeq_align > AlignModelToSeqalign(const CAlignModel &model, CSeq_id &mrnaid, CSeq_id &contigid, bool is_align, bool is_protalign, bool stop_found)

void MoveOrigin(TSignedSeqPos shift)

TSignedSeqRange MapRangeEditedToOrig(TSignedSeqRange edited_range, bool withextras=true) const

void EditedSequence(const In &original_sequence, Out &edited_sequence, bool includeholes=false) const

TSignedSeqRange MapRangeOrigToEdited(TSignedSeqRange orig_range, ERangeEnd lend, ERangeEnd rend) const

CRef< objects::CSeq_align > MakeSeqAlign(const string &contig) const

virtual void Clip(TSignedSeqRange limits, EClipMode mode, bool ensure_cds_invariant=true)

CConstRef< objects::CSeq_id > GetTargetId() const

virtual CAlignMap GetAlignMap() const

CBioseq_set::TSeq_set * nucprots

void AddModel(const CAlignModel &model)

CRef< CSeq_id > contig_sid

map< Int8, CRef< CSeq_feat > > TGeneMap

CImplementationData(const string &contig_name, const CResidueVec &seq, IEvidence &evdnc, int genetic_code, int sh)

CRef< CUser_object > create_ModelEvidence_user_object(const CGeneModel &model)

CSeq_annot::C_Data::TFtable * feature_table

CRef< CSeq_align > model2spliced_seq_align(SModelData &md)

CRef< CSeq_feat > create_cdregion_feature(SModelData &md)

void DumpEvidence(const SModelData &md)

CRef< CSeq_feat > create_internal_feature(const SModelData &md)

void CreateModelProducts(SModelData &model)

CSeq_annot::C_Data::TFtable * internal_feature_table

CSeq_annot * gnomon_models_annot

unique_ptr< CFeatureGenerator > feature_generator

void AddInternalFeature(const SModelData &md)

CRef< CSeq_loc > create_packed_int_seqloc(const CGeneModel &model, TSignedSeqRange limits_on_mrna=TSignedSeqRange::GetWhole())

set< Int8 > models_in_internal_feature_table

CRef< CSeq_entry > main_seq_entry

static string ExtractModels(objects::CSeq_entry &seq_entry, TAlignModelList &model_list, TAlignModelList &evidence_models, list< CRef< objects::CSeq_align > > &evidence_alignments, map< Int8, CRef< CUser_object > > &model_evidence_uo)

CAnnotationASN1(const string &contig_name, const CResidueVec &seq, IEvidence &evidence, int genetic_code=1, int shift=0)

CRef< objects::CSeq_entry > GetASN1() const

unique_ptr< CImplementationData > m_data

void AddModel(const CAlignModel &model)

CCDSInfo MapFromEditedToOrig(const CAlignMap &amap) const

CCDSInfo MapFromOrigToEdited(const CAlignMap &amap) const

TSignedSeqRange MaxCdsLimits() const

bool IsMappedToGenome() const

void SetScore(double score, bool open=false)

TSignedSeqRange Start() const

TSignedSeqRange Cds() const

TSignedSeqRange ReadingFrame() const

const TPStops & PStops() const

void SetReadingFrame(TSignedSeqRange r, bool protein=false)

TSignedSeqRange TranscriptLimits() const

EStrand Orientation() const

const CSupportInfoSet & Support() const

const TExons & Exons() const

TSignedSeqRange ReadingFrame() const

virtual CAlignMap GetAlignMap() const

TSignedSeqRange TranscriptExon(int i) const

void SetCdsInfo(const CCDSInfo &cds_info)

TSignedSeqRange Limits() const

const CCDSInfo & GetCdsInfo() const

const string & ProteinHit() const

TInDels GetInDels(bool fs_only) const

bool PStop(bool includeall=true) const

static string TypeToString(int type)

static CRef< CSeq_id > GnomonMRNA(Int8 id)

static void SetId(CObject_id &obj, Int8 value)

static CRef< CSeq_id > ToSeq_id(const string &str)

static string ToString(const CSeq_id &id)

static Int8 GetId(const CObject_id &obj)

static CRef< CSeq_id > GnomonProtein(Int8 id)

TSignedSeqPos Loc() const

CInDelInfo::SSource m_source

TSignedSeqPos GetFrom() const

const TSignedSeqRange & Limits() const

TSignedSeqPos GetTo() const

void AddInterval(const CSeq_interval &ival)

for convenience

void SetNamedScore(const string &id, int score)

TSeqPos GetAlignLength(bool include_gaps=true) const

Get the length of this alignment.

void Validate(bool full_test=false) const

void SetNameDesc(const string &name)

void SetTitleDesc(const string &title)

bool IsFtable(void) const

namespace ncbi::objects::

CSpliced_seg_modifier –.

CSeq_feat_Handle GetFeatureWithId(CSeqFeatData::E_Choice type, TFeatureIdInt id) const

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

Access a named field in this user field.

CUser_field & AddField(const string &label, int value)

add fields to the current user field

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

Verify that a named field exists.

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

Verify that a named field exists.

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

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

Access a named field in this user object.

virtual const CAlignModel * GetModel(Int8 id)=0

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

static const struct attribute attributes[]

static const struct type types[]

vector< TResidue > CResidueVec

list< CAlignModel > TAlignModelList

bool Include(TSignedSeqRange big, TSignedSeqRange small)

vector< CInDelInfo > TInDels

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

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

#define MSerial_AsnText

I/O stream manipulators –.

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

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

bool Match(const CSeq_id &sid2) const

Match() - TRUE if SeqIds are equivalent.

void SetPacked_int(TPacked_int &v)

TRange GetTotalRange(void) const

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

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

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)

void SetPartialStop(bool val, ESeqLocExtremes ext)

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

CSeq_entry_Handle AddTopLevelSeqEntry(CSeq_entry &top_entry, TPriority pri=kPriority_Default, EExist action=eExist_Default)

Add seq_entry, default priority is higher than for defaults or loaders Add object to the score with p...

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

void AddDefaults(TPriority pri=kPriority_Default)

Add default data loaders from object manager.

CSeq_annot_Handle GetSeq_annotHandle(const CSeq_annot &annot, EMissing action=eMissing_Default)

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

const CSeq_annot_Handle & GetAnnot(void) const

Get handle to seq-annot for this feature.

virtual CConstRef< CSeq_feat > GetSeq_feat(void) const

const CTSE_Handle & GetTSE_Handle(void) const

const CSeqFeatData & GetData(void) const

const CTSE_Handle & GetTSE_Handle(void) const

virtual const CSeq_loc & GetProduct(void) const

virtual const CSeq_loc & GetLocation(void) const

CScope & GetScope(void) const

Get scope this handle belongs to.

CConstRef< CSeq_feat > GetOriginalSeq_feat(void) const

CSeqFeatData::E_Choice GetFeatType(void) const

SAnnotSelector & SetFeatType(TFeatType type)

Set feature type (also set annotation type to feat)

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.

bool NotNull(void) const THROWS_NONE

Check if pointer is not null – same effect as NotEmpty().

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

bool NotEmpty(void) const THROWS_NONE

Check if CRef is not empty – pointing to an object and has a non-null value.

bool NotEmpty(void) const THROWS_NONE

Check if CConstRef is not empty – pointing to an object and has a non-null value.

int64_t Int8

8-byte (64-bit) signed integer

position_type GetLength(void) const

bool NotEmpty(void) const

bool IntersectingWith(const TThisType &r) const

CRange< TSignedSeqPos > TSignedSeqRange

static TThisType GetWhole(void)

#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 string DoubleToString(double value, int precision=-1, TNumToStringFlags flags=0)

Convert double to string.

static double StringToDouble(const CTempStringEx str, TStringToNumFlags flags=0)

Convert string to double.

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

Check if a string starts with a specified prefix value.

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.

void SetFrom(TFrom value)

Assign a value to From data member.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

void SetTo(TTo value)

Assign a value to To data member.

const TStr & GetStr(void) const

Get the variant data.

const TStrs & GetStrs(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

bool CanGetNum(void) const

Check if it is safe to call GetNum method.

const TClass & GetClass(void) const

Get the Class member data.

bool IsStr(void) const

Check if variant Str is selected.

void SetClass(const TClass &value)

Assign a value to Class data member.

TData & SetData(void)

Assign a value to Data data member.

const TStr & GetStr(void) const

Get the variant data.

void SetLabel(TLabel &value)

Assign a value to Label data member.

TStr & SetStr(void)

Select the variant.

const TData & GetData(void) const

Get the Data member data.

TReal GetReal(void) const

Get the variant data.

void SetType(TType &value)

Assign a value to Type data member.

void SetData(TData &value)

Assign a value to Data data member.

const TLabel & GetLabel(void) const

Get the Label member data.

const TType & GetType(void) const

Get the Type member data.

vector< CStringUTF8 > TStrs

vector< CRef< CUser_field > > TData

TNum GetNum(void) const

Get the Num member data.

const TId & GetId(void) const

Get the Id member data.

TModifiers & SetModifiers(void)

Assign a value to Modifiers data member.

TId & SetId(void)

Assign a value to Id data member.

void SetAmin(TAmin value)

Assign a value to Amin data member.

bool IsSetParts(void) const

basic seqments always are in biologic order Check if a value has been assigned to Parts data member.

void SetProduct_id(TProduct_id &value)

Assign a value to Product_id data member.

void SetSegs(TSegs &value)

Assign a value to Segs data member.

TExons & SetExons(void)

Assign a value to Exons data member.

void SetProduct_strand(TProduct_strand value)

Assign a value to Product_strand data member.

void SetProduct_length(TProduct_length value)

Assign a value to Product_length data member.

list< CRef< CUser_object > > TExt

void SetType(TType value)

Assign a value to Type data member.

TExt & SetExt(void)

Assign a value to Ext data member.

void SetProduct_type(TProduct_type value)

Assign a value to Product_type data member.

bool CanGetExt(void) const

Check if it is safe to call GetExt method.

list< CRef< CSpliced_exon > > TExons

void SetPoly_a(TPoly_a value)

Assign a value to Poly_a data member.

TProtpos & SetProtpos(void)

Select the variant.

TParts & SetParts(void)

Assign a value to Parts data member.

void SetGenomic_id(TGenomic_id &value)

Assign a value to Genomic_id data member.

const TExt & GetExt(void) const

Get the Ext member data.

void SetGenomic_strand(TGenomic_strand value)

Assign a value to Genomic_strand data member.

void SetFrame(TFrame value)

Assign a value to Frame data member.

@ eType_partial

mapping pieces together

@ eProduct_type_transcript

void SetAa(TAa &value)

Assign a value to Aa data member.

const TExts & GetExts(void) const

Get the Exts member data.

void SetLocation(TLocation &value)

Assign a value to Location data member.

const TIds & GetIds(void) const

Get the Ids member data.

bool IsCdregion(void) const

Check if variant Cdregion is selected.

TIds & SetIds(void)

Assign a value to Ids data member.

list< CRef< CUser_object > > TExts

void SetPartial(TPartial value)

Assign a value to Partial data member.

void SetProduct(TProduct &value)

Assign a value to Product data member.

TExts & SetExts(void)

Assign a value to Exts data member.

TLocal & SetLocal(void)

Select the variant.

list< CRef< CCode_break > > TCode_break

TFrame GetFrame(void) const

Get the Frame member data.

const TData & GetData(void) const

Get the Data member data.

void SetData(TData &value)

Assign a value to Data data member.

const TCdregion & GetCdregion(void) const

Get the variant data.

void SetLoc(TLoc &value)

Assign a value to Loc data member.

bool CanGetFrame(void) const

Check if it is safe to call GetFrame method.

@ eFrame_not_set

not set, code uses one

@ eFrame_three

reading frame

ENa_strand

strand of nucleic acid

void SetFuzz_to(TFuzz_to &value)

Assign a value to Fuzz_to data member.

void SetFuzz_from(TFuzz_from &value)

Assign a value to Fuzz_from data member.

TSet & SetSet(void)

Select the variant.

TAnnot & SetAnnot(void)

Assign a value to Annot data member.

list< CRef< CSeq_annot > > TAnnot

list< CRef< CSeq_entry > > TSeq_set

TSeq_set & SetSeq_set(void)

Assign a value to Seq_set data member.

void SetData(TData &value)

Assign a value to Data data member.

const TInst & GetInst(void) const

Get the Inst member data.

void SetDesc(TDesc &value)

Assign a value to Desc data member.

list< CRef< CSeq_align > > TAlign

const TAssembly & GetAssembly(void) const

Get the Assembly member data.

TRegion & SetRegion(void)

Select the variant.

const THist & GetHist(void) const

Get the Hist member data.

list< CRef< CSeq_feat > > TFtable

TId & SetId(void)

Assign a value to Id data member.

unsigned int

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

const TYPE & Get(const CNamedParameterList *param)

constexpr auto sort(_Init &&init)

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

Magic spell ;-) needed for some weird compilers... very empiric.

void copy(Njn::Matrix< S > *matrix_, const Njn::Matrix< T > &matrix0_)

SModelData(const CAlignModel &model, const CEResidueVec &contig_seq, int shift)

const value_slice::CValueConvert< value_slice::SRunTimeCP, FROM > Convert(const FROM &value)

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