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

(feat_it->IsSetProduct()

&& feat_it->GetProduct().Equals(product_loc)

&& feat_it->GetOriginalSeq_feat().GetPointer() != orig_feat.

()) {

(

.IsPub()) {

->AddCommand(*cit_cmd);

->AddCommand(*del_feat);

->AddCommand(*del_product);

product_to_cds.clear();

(

tse : tses)

(feat_it->IsSetProduct())

product_to_cds[product].insert(fh);

(

.IsPub()) {

->AddCommand(*cit_cmd);

->AddCommand(*del_feat);

product_to_cds[product].erase(fh);

(product && product.

() && product_to_cds[product].empty()) {

->AddCommand(*del_product);

->AddCommand(*delSet);

->AddCommand(*scmd);

(!bsh || !bsh.

())

delete_features_cmd;

(

it(new_seh); it; ++it) {

(

.IsPub()) {

(prot_bsh && prot_bsh.

()) {

proteins.

(prot_bsh);

& feat_list = annoth.GetSeq_annotCore()->GetData().GetFtable();

(feat_list.empty()) {

(

it : proteins) {

(proteins.

(bsh) == proteins.

()) {

->AddCommand(*swap_cmd);

((*it)->IsSource() && (*it)->GetSource().IsSetOrg()) {

src_descs.emplace_back(*it, &se);

->Assign(*entry);

->AddCommand(*clean);

->Assign(*entry);

(rmv_user_object) {

changes =

.ExtendedCleanup(new_seh, cleanup_flags);

->AddCommand(*clean);

validator::CTaxValidationAndCleanup tval;

vector<CRef<COrg_ref> > original_orgs = tval.GetTaxonomyLookupRequest();

(original_orgs.empty())

vector< CRef<COrg_ref> > edited_orgs;

(

< original_orgs.size())

vector< CRef<COrg_ref> > tmp_original_orgs(original_orgs.begin() +

, original_orgs.begin() +

+

);

vector< CRef<COrg_ref> > tmp_edited_orgs;

tmp_edited_orgs.push_back(cpy);

(tmp_lookup_reply) {

error_message;

tval.AdjustOrgRefsWithTaxLookupReply(*tmp_lookup_reply, tmp_edited_orgs, error_message);

edited_orgs.insert(edited_orgs.end(), tmp_edited_orgs.begin(), tmp_edited_orgs.end());

vector< CRef<COrg_ref> > spec_host_rq = tval.GetSpecificHostLookupRequest(

);

(

< spec_host_rq.size())

vector< CRef<COrg_ref> > tmp_spec_host_rq(spec_host_rq.begin() +

, spec_host_rq.begin() +

+

);

error_message = tval.IncrementalSpecificHostMapUpdate(tmp_spec_host_rq, *tmp_spec_host_reply);

tval.AdjustOrgRefsForSpecificHosts(edited_orgs);

num_descs = tval.NumDescs();

num_updated_descs = 0;

(

= 0;

< num_descs;

++) {

(!original_orgs[

]->

(*(edited_orgs[

]))) {

(original_desc && orig_entry) {

new_desc->

(*original_desc);

->AddCommand(*subcmd);

num_updated_feats = 0;

(

= 0;

< tval.NumFeats();

++) {

(!original_orgs[

+ num_descs]->

(*edited_orgs[

+ num_descs])) {

new_feat->

(*feat);

new_feat->

().SetBiosrc().SetOrg().Assign(*(edited_orgs[

+ num_descs]));

->AddCommand(*chgFeat);

validator::CTaxValidationAndCleanup tval;

vector<CRef<COrg_ref> > original_orgs = tval.GetTaxonomyLookupRequest();

(original_orgs.empty()) {

vector< CRef<COrg_ref> > edited_orgs;

(

< original_orgs.size())

vector< CRef<COrg_ref> > tmp_original_orgs(original_orgs.begin() +

, original_orgs.begin() +

+

);

vector< CRef<COrg_ref> > tmp_edited_orgs;

tmp_edited_orgs.push_back(cpy);

(tmp_lookup_reply) {

error_message;

tval.AdjustOrgRefsWithTaxLookupReply(*tmp_lookup_reply, tmp_edited_orgs, error_message);

edited_orgs.insert(edited_orgs.end(), tmp_edited_orgs.begin(), tmp_edited_orgs.end());

vector< CRef<COrg_ref> > spec_host_rq = tval.GetSpecificHostLookupRequest(

);

(

< spec_host_rq.size()) {

vector< CRef<COrg_ref> > tmp_spec_host_rq(spec_host_rq.begin() +

, spec_host_rq.begin() +

+

);

error_message = tval.IncrementalSpecificHostMapUpdate(tmp_spec_host_rq, *tmp_spec_host_reply);

tval.AdjustOrgRefsForSpecificHosts(edited_orgs);

num_descs = tval.NumDescs();

num_updated_descs = 0;

(

= 0;

< num_descs;

++) {

(!original_orgs[

]->

(*(edited_orgs[

]))) {

(original_desc && orig_entry) {

new_desc->

(*original_desc);

->AddCommand(*subcmd);

num_updated_feats = 0;

(

= 0;

< tval.NumFeats();

++) {

(!original_orgs[

+ num_descs]->

(*edited_orgs[

+ num_descs])) {

new_feat->

(*feat);

new_feat->

().SetBiosrc().SetOrg().Assign(*(edited_orgs[

+ num_descs]));

->AddCommand(*chgFeat);

validator::CTaxValidationAndCleanup tval;

vector<CRef<COrg_ref> > original_orgs = tval.GetTaxonomyLookupRequest();

(original_orgs.empty())

vector< CRef<COrg_ref> > edited_orgs;

(

< original_orgs.size())

vector< CRef<COrg_ref> > tmp_original_orgs(original_orgs.begin() +

, original_orgs.begin() +

+

);

vector< CRef<COrg_ref> > tmp_edited_orgs;

tmp_edited_orgs.push_back(cpy);

error_message;

tval.AdjustOrgRefsWithTaxLookupReply(*tmp_lookup_reply, tmp_edited_orgs, error_message);

edited_orgs.insert(edited_orgs.end(), tmp_edited_orgs.begin(), tmp_edited_orgs.end());

vector< CRef<COrg_ref> > spec_host_rq = tval.GetSpecificHostLookupRequest(

);

(

< spec_host_rq.size())

vector< CRef<COrg_ref> > tmp_spec_host_rq(spec_host_rq.begin() +

, spec_host_rq.begin() +

+

);

error_message = tval.IncrementalSpecificHostMapUpdate(tmp_spec_host_rq, *tmp_spec_host_reply);

tval.AdjustOrgRefsForSpecificHosts(edited_orgs);

num_descs = tval.NumDescs();

num_updated_descs = 0;

(

= 0;

< num_descs;

++) {

(!original_orgs[

]->

(*(edited_orgs[

]))) {

(original_desc && orig_entry) {

new_desc->

(*original_desc);

->AddCommand(*subcmd);

num_updated_feats = 0;

(

= 0;

< tval.NumFeats();

++) {

(!original_orgs[

+ num_descs]->

(*edited_orgs[

+ num_descs])) {

new_feat->

(*feat);

new_feat->

().SetBiosrc().SetOrg().Assign(*(edited_orgs[

+ num_descs]));

->AddCommand(*chgFeat);

vector<pair<const CSeqdesc*, const CSeq_entry*>> src_descs;

vector<CConstRef<CSeq_feat> > src_feats;

(

&& desc_it : src_descs) {

& old_desc = *desc_it.first;

new_desc->

(old_desc);

->AddCommand(*subcmd);

new_feat->

(*old_feat);

new_feat->

().SetBiosrc().SetDisableStrainForwarding(disable);

->AddCommand(*chgFeat);

rq->SetOrg().Assign(org);

CTaxon3_reply::TReply::const_iterator reply_it = reply->GetReply().begin();

(reply_it != reply->GetReply().end()) {

((*reply_it)->IsData()

&& (*reply_it)->GetData().GetOrg().IsSetTaxname()) {

is_species_level =

, force_consult =

, has_nucleomorphs =

;

(*reply_it)->GetData().GetTaxFlags (is_species_level, force_consult, has_nucleomorphs);

(is_species_level) {

vector<pair<const CSeqdesc*, const CSeq_entry*>> src_descs;

vector<bool> is_species_level;

(

&& desc_it : src_descs) {

& desc = *desc_it.first;

is_species_level.push_back(

);

is_species_level.push_back(

);

CTaxon3_reply::TReply::const_iterator reply_it = reply->GetReply().begin();

(reply_it != reply->GetReply().end()) {

((*reply_it)->IsData()

&& (*reply_it)->GetData().GetOrg().IsSetTaxname()) {

species_level =

, force_consult =

, has_nucleomorphs =

;

(*reply_it)->GetData().GetTaxFlags (species_level, force_consult, has_nucleomorphs);

is_species_level[pos] =

;

(

&& desc_it : src_descs) {

& old_desc = *desc_it.first;

new_desc->

(old_desc);

->AddCommand(*subcmd);

new_feat->

(*old_feat);

new_feat->

().SetBiosrc().RemoveCultureNotes(is_species_level[pos]);

->AddCommand(*chgFeat);

(!product || (product && product.

())) {

molinfo_changed =

;

molinfo_changed =

;

(molinfo_changed) {

->AddCommand(*ecmd);

->AddCommand(*ecmd);

any_cmd =

;

->AddCommand(*synch_molinfo);

new_prot->

(*(

->GetSeq_feat()));

.SetData().SetProt();

->Assign(*(product.

().front().GetSeqId()));

.SetLocation().SetInt().SetId(*

);

.SetLocation().SetInt().SetFrom(0);

.SetPartial(partial5 || partial3);

((*it)->IsSetData() && (*it)->GetData().IsProt()) {

.SetData().SetProt().Assign((*it)->GetData().GetProt());

(cds.

().size() == 0) {

->Assign(*((*existing).GetSeq_feat()));

cds_change =

;

(!new_product->

()) {

cds.

().SetWhole().Assign(*product_id);

new_product->

().push_back(product_id);

prot_entry->

(*new_product);

((*it)->IsSetData() && (*it)->GetData().IsProt()) {

->SetData().SetProt().Assign((*it)->GetData().GetProt());

(cds.

().size() == 0) {

->AddCommand(*subcmd);

cds_change =

;

(new_protein_bioseq && new_protein_bioseq->

())

( !new_protein_bioseq ) {

(prot_seq.empty()) {

prot_seq = prot_seq.substr(0, prot_seq.length() - 1);

new_protein_bioseq->

().SetSeq_data().SetNcbieaa().Set(prot_seq);

new_protein_bioseq->

().SetLength(

(prot_seq.length()));

->AddCommand(*chgInst);

(synch_molinfo) {

->AddCommand(*synch_molinfo);

new_feat->

(prot_feat_ci->GetOriginalFeature());

->Assign(*prot_bsh.

());

sub->

(*

);

->AddCommand(*chgFeat);

cds_change =

;

->AddCommand(*chgFeat);

->AddCommand(*chgFeat);

(adjust_gene && gene) {

(gene_stop > cds_stop) {

diff = gene_stop - cds_stop;

(gene_stop < cds_stop) {

diff = cds_stop - gene_stop;

new_gene->

(*gene);

->AddCommand(*chgGene);

->AddCommand(*flip);

(!product || !product.

()) {

modified =

;

prot_seq.erase(prot_seq.end() - 1);

new_inst->

().SetIupacaa().Set(prot_seq);

new_inst->

().SetNcbieaa().Set(prot_seq);

->AddCommand(*chgInst);

( ; feat_ci; ++feat_ci ) {

(feat_stop > new_inst->

() -1 ) {

->AddCommand(*chgFeat);

fname = reg_view.

(

);

->Assign(*entry);

scope2.AddDefaults();

(suspect_rules.empty()) {

discrSet->SetSuspectRules(suspect_rules);

product = discrSet->RunTests({

}, *

,

);

product->Summarize();

report = discrSet->Autofix();

(report.empty()) {

(

: report) {

->AddCommand(*clean);

->Assign(*entry);

(suspect_rules.empty()) {

discrSet->SetSuspectRules(suspect_rules);

discrSet->Parse(*

.GetNCPointer());

discrSet->Summarize();

(

.size() != 1) {

(

it : reports) {

(

obj : it->GetDetails()) {

(obj->CanAutofix()) {

(tofix.empty()) {

discrSet->Autofix(tofix,

);

->AddCommand(*clean);

->Assign(*entry);

(suspect_rules.empty()) {

discrSet->SetSuspectRules(suspect_rules);

lcl_product = discrSet->RunTests({

}, *

,

);

lcl_product->Summarize();

lcl_report = discrSet->Autofix();

(lcl_report.empty()) {

report = lcl_report;

->AddCommand(*clean);

retranslate,

adjust_gene,

& orig_feat,

& scope,

&

,

create_general_only)

new_feat->

(orig_feat);

any_change = policy.ApplyPolicyToFeature(*new_feat, scope);

(adjust_gene_cmd) {

->AddCommand(*adjust_gene_cmd);

(retranslate_cmd) {

->AddCommand(*retranslate_cmd);

->AddCommand(*synch);

new_gene->

(*old_gene);

gene_change =

;

gene_change =

;

gene_change =

;

gene_change =

;

any_change =

;

(

copy_pair : cds_gene_pairs) {

new_cds->

(*(copy_pair.first.GetOriginalSeq_feat()));

new_gene->

(*(copy_pair.second.GetOriginalSeq_feat()));

->AddCommand(*chgGene);

->AddCommand(*chgCDS);

any_change =

;

cp->

(*(

->GetSeq_feat()));

->AddCommand(*chgFeat);

new_mrna->

(*mrna);

modified =

;

(product.empty()) {

message +=

;

(!

.IsSetExt() || (

.IsSetExt() && !

(

.GetExt().GetName(), product))) {

.SetExt().SetName(product);

message =

+ product +

;

.Reset(

(

));

->AddCommand(*chgFeat);

* seq_feat =

*

(

.GetPointer());

new_mrna->

(*orig_mrna);

modified =

;

new_mrna->

().SetRna().SetRnaProductName(prot_product, remainder);

->AddCommand(*chgFeat);

@ eExtreme_Positional

numerical value

@ eExtreme_Biological

5' and 3'

void ExtendStop(CSeq_loc &loc, TSeqPos len, CScope &scope)

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)

void RemoveCultureNotes(bool is_species_level=true)

void SetDisableStrainForwarding(bool val)

TSeqPos GetLength(void) const

static vector< TFeatGenePair > GetNormalizableGeneQualPairs(CBioseq_Handle bsh)

@ eClean_NoNcbiUserObjects

static bool NormalizeGeneQuals(CSeq_feat &cds, CSeq_feat &gene)

void AddCommand(IEditCommand &command)

virtual void Execute()

Do the editing action.

virtual void Execute()

Do the editing action.

static CIRef< IEditCommand > RemoveCitations(objects::CSeq_entry_Handle &seh, const objects::CPub_equiv &pubs)

static CGuiRegistry & GetInstance()

access the application-wide singleton

CRegistryReadView GetReadView(const string &section) const

get a read-only view at a particular level.

Base class for all object manager exceptions.

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

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

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

ESubtype GetSubtype(void) const

SeqMap related exceptions.

const CSeq_descr & GetDescr(void) const

bool IsSetDescr(void) const

CSeq_feat_EditHandle –.

namespace ncbi::objects::

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

virtual CRef< CTaxon3_reply > SendRequest(const CTaxon3_request &request)

virtual CRef< CTaxon3_reply > SendOrgRefList(const vector< CRef< COrg_ref > > &list, COrg_ref::fOrgref_parts result_parts=COrg_ref::eOrgref_default, fT3reply_parts t3result_parts=eT3reply_default)

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

const_iterator end() const

void SetMolinfoForProtein(CRef< objects::CSeq_entry > protein, bool partial5, bool partial3)

CRef< objects::CSeq_feat > AddEmptyProteinFeatureToProtein(CRef< objects::CSeq_entry > protein, bool partial5, bool partial3)

static const int chunk_size

vector< CRef< CReportItem > > TReportItemList

vector< CRef< CReportObj > > TReportObjectList

eTestNames GetDiscrepancyCaseName(string_view)

static void cleanup(void)

static SQLCHAR output[256]

static DbTestEntry * tests

static char test_name[128]

void ReverseComplement(const BidirectionalIterator &first, const BidirectionalIterator &last)

bool RemoveDuplicateGoTerms(CSeq_feat &feat)

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.

#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.

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

Set object to copy of another one.

C * SerialClone(const C &src)

Create on heap a clone of the source object.

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

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

CConstRef< CSeq_id > GetSeqId(void) const

bool IsPartialStart(ESeqLocExtremes ext) const

check start or stop of location for e_Lim fuzz

ENa_strand GetStrand(void) const

Get the location's strand.

void SetId(CSeq_id &id)

set the 'id' field in all parts of this location

TSeqPos GetStart(ESeqLocExtremes ext) const

Return start and stop positions of the seq-loc.

const CSeq_id * GetId(void) const

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

bool IsPartialStop(ESeqLocExtremes ext) const

TSeqPos GetStop(ESeqLocExtremes ext) const

bool AdjustProteinMolInfoToMatchCDS(CMolInfo &molinfo, const CSeq_feat &cds)

AdjustProteinMolInfoToMatchCDS A function to change an existing MolInfo to match a coding region.

const CSeq_feat * GetCDSForProduct(const CBioseq &product, CScope *scope)

Get the encoding CDS feature of a given protein sequence.

static CRef< CBioseq > TranslateToProtein(const CSeq_feat &cds, CScope &scope)

CConstRef< CSeq_feat > GetOverlappingGene(const CSeq_loc &loc, CScope &scope, ETransSplicing eTransSplicing=eTransSplicing_Auto)

CConstRef< CSeq_feat > GetmRNAforCDS(const CSeq_feat &cds, CScope &scope)

GetmRNAforCDS A function to find a CSeq_feat representing the appropriate mRNA for a given CDS.

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.

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...

CSeq_entry_Handle GetSeq_entryHandle(CDataLoader *loader, const TBlobId &blob_id, EMissing action=eMissing_Default)

Get Seq-entry handle by its blob-id, with possible loading.

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.

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

CSeq_feat_Handle GetSeq_featHandle(const CSeq_feat &feat, EMissing action=eMissing_Default)

vector< CSeq_entry_Handle > TTSE_Handles

virtual CSeq_id_Handle GetLocationId(void) const

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

TClass GetClass(void) const

const CSeq_annot_Handle & GetAnnot(void) const

Get handle to seq-annot for this feature.

CBioseq_set_Handle GetParentBioseq_set(void) const

Return a handle for the parent Bioseq-set, or null handle.

CSeq_entry_Handle GetParentEntry(void) const

Get parent Seq-entry handle.

const CSeqFeatData & GetData(void) const

CSeq_entry_Handle GetSeq_entry_Handle(void) const

Get parent Seq-entry handle.

void Remove(void) const

Remove the feature from Seq-annot.

virtual const CSeq_loc & GetProduct(void) const

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.

virtual const CSeq_loc & GetLocation(void) const

CBioseq_set_Handle GetParentBioseq_set(void) const

Get parent bioseq-set handle.

bool IsProtein(void) const

CSeq_entry_Handle GetParentEntry(void) const

Return a handle for the parent seq-entry of the bioseq.

TInst_Length GetInst_Length(void) const

bool IsSetClass(void) const

CSeq_annot_EditHandle GetEditHandle(void) const

Get 'edit' version of handle.

CConstRef< CSeq_entry > GetCompleteSeq_entry(void) const

Complete and get const reference to the seq-entry.

CScope & GetScope(void) const

Get scope this handle belongs to.

CScope & GetScope(void) const

Get scope this handle belongs to.

const TInst_Seq_data & GetInst_Seq_data(void) const

CScope & GetScope(void) const

Get scope this handle belongs to.

CConstRef< CSeq_feat > GetOriginalSeq_feat(void) const

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.

const TId & GetId(void) const

virtual CSeq_id_Handle GetProductId(void) const

CSeqVector GetSeqVector(EVectorCoding coding, ENa_strand strand=eNa_strand_plus) const

Get sequence: Iupacna or Iupacaa if use_iupac_coding is true.

const TInst & GetInst(void) const

@ eCoding_Ncbi

Set coding to binary coding (Ncbi4na or Ncbistdaa)

const CSeq_loc & GetLocation(void) const

const CSeq_feat & GetOriginalFeature(void) const

Get original feature with unmapped location/product.

CConstRef< CSeq_feat > GetSeq_feat(void) const

Get current seq-feat.

CSeq_entry_Handle GetSeq_entry_Handle(void) const

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

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

void SetCoding(TCoding coding)

TObjectType * GetPointer(void) const THROWS_NONE

Get pointer,.

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.

uint32_t Uint4

4-byte (32-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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 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.

const TOrg & GetOrg(void) const

Get the Org member data.

void SetOrg(TOrg &value)

Assign a value to Org data member.

const TName & GetName(void) const

Get the Name member data.

bool IsSetName(void) const

protein name Check if a value has been assigned to Name data member.

TType GetType(void) const

Get the Type member data.

TXref & SetXref(void)

Assign a value to Xref data member.

bool IsSetData(void) const

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

void SetLocation(TLocation &value)

Assign a value to Location data member.

bool IsCdregion(void) const

Check if variant Cdregion is selected.

void SetPartial(TPartial value)

Assign a value to Partial data member.

void SetProduct(TProduct &value)

Assign a value to Product data member.

bool IsSetXref(void) const

cite other relevant features Check if a value has been assigned to Xref data member.

const TLocation & GetLocation(void) const

Get the Location member data.

const TData & GetData(void) const

Get the Data member data.

void SetData(TData &value)

Assign a value to Data data member.

bool CanGetLocation(void) const

Check if it is safe to call GetLocation method.

const TBiosrc & GetBiosrc(void) const

Get the variant data.

const TProduct & GetProduct(void) const

Get the Product member data.

const TProt & GetProt(void) const

Get the variant data.

const TXref & GetXref(void) const

Get the Xref member data.

vector< CRef< CSeqFeatXref > > TXref

void ResetXref(void)

Reset Xref data member.

const TRna & GetRna(void) const

Get the variant 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 IsSetLocation(void) const

feature made from Check if a value has been assigned to Location data member.

bool CanGetTo(void) const

Check if it is safe to call GetTo method.

TTo GetTo(void) const

Get the To member data.

bool IsInt(void) const

Check if variant Int is selected.

const TInt & GetInt(void) const

Get the variant data.

const TSet & GetSet(void) const

Get the variant data.

bool IsSetSeq_set(void) const

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

bool IsSet(void) const

Check if variant Set is selected.

const TSeq_set & GetSeq_set(void) const

Get the Seq_set member data.

list< CRef< CSeq_entry > > TSeq_set

TSeq & SetSeq(void)

Select the variant.

@ eClass_nuc_prot

nuc acid and coded proteins

list< CRef< CSeqdesc > > Tdata

TId & SetId(void)

Assign a value to Id data member.

bool IsSetSeq_data(void) const

the sequence Check if a value has been assigned to Seq_data data member.

bool IsNcbieaa(void) const

Check if variant Ncbieaa is selected.

const TInst & GetInst(void) const

Get the Inst member data.

bool IsIupacaa(void) const

Check if variant Iupacaa is selected.

const TSource & GetSource(void) const

Get the variant data.

const Tdata & Get(void) const

Get the member data.

bool IsSetInst(void) const

the sequence data Check if a value has been assigned to Inst data member.

TLength GetLength(void) const

Get the Length member data.

void SetInst(TInst &value)

Assign a value to Inst data member.

TSource & SetSource(void)

Select the variant.

void SetBiomol(TBiomol value)

Assign a value to Biomol data member.

bool IsSetId(void) const

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

void SetLength(TLength value)

Assign a value to Length data member.

void ResetInst(void)

Reset Inst data member.

void SetSeq_data(TSeq_data &value)

Assign a value to Seq_data data member.

const TMolinfo & GetMolinfo(void) const

Get the variant data.

TMolinfo & SetMolinfo(void)

Select the variant.

@ eRepr_raw

continuous sequence

@ e_Ncbieaa

extended ASCII 1 letter aa codes

@ e_Molinfo

info on the molecule and techniques

@ eMol_na

just a nucleic acid

TRequest & SetRequest(void)

Assign a value to Request data member.

function< CRef< CTaxon3_reply >(const vector< CRef< COrg_ref > > &list)> taxupdate_func_t

void ReverseComplementFeature(CSeq_feat &feat, CScope &scope)

CRef< CSeq_loc > SeqLocExtend(const CSeq_loc &loc, size_t pos, CScope *scope)

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

static bool Equals(const CVariation::TPlacements &p1, const CVariation::TPlacements &p2)

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

CRef< CCmdComposite > GetDeleteAllFeaturesCommand(CSeq_entry_Handle seh, size_t &count, bool remove_proteins)

CRef< CCmdComposite > TrimStopsFromCompleteCDS(const CSeq_feat &cds, CScope &scope)

TrimStopsFromCompleteCDS If the CDS is 3' complete and the protein sequence ends with a stop codon,...

static bool s_IsNucLocation(CSeq_feat_Handle fh)

void SetProteinFeature(CSeq_feat &prot, CBioseq_Handle product, const CSeq_feat &cds)

CRef< CCmdComposite > TranslateCDSCommand(CScope &scope, CSeq_feat &cds, bool &cds_change, int &offset, bool create_general_only)

bool GetRemoveDuplicateGOTermsCommand(CBioseq_Handle bsh, CRef< CCmdComposite > cmd)

CRef< CCmdComposite > CleanupCommand(CSeq_entry_Handle orig_seh, bool extended, bool do_tax)

static bool s_IsFarLocation(CSeq_feat_Handle fh)

CRef< CCmdComposite > GetDeleteFeatureCommand(const CSeq_feat_Handle &fh, bool remove_proteins)

static const char * kDiscrepancyEdit

CRef< CCmdComposite > GetEditLocationCommand(const edit::CLocationEditPolicy &policy, bool retranslate, bool adjust_gene, const CSeq_feat &orig_feat, CScope &scope, int &offset, bool create_general_only)

GetEditLocationCommand Changes the location properties of a feature according to a location policy.

static bool s_AreThereOtherCDSForThisProduct(const CSeq_feat_Handle &fh)

CRef< CCmdComposite > GetSynchronizeProductMolInfoCommand(CScope &scope, const CSeq_feat &cds)

CRef< CCmdComposite > TaxonomyLookupCommand(CSeq_entry_Handle seh)

bool s_IsSpeciesLevel(const COrg_ref &org)

CRef< CCmdComposite > GetEnableStrainForwardingCommand(CSeq_entry_Handle seh)

CRef< CCmdComposite > GetRetranslateCDSCommand(CScope &scope, CSeq_feat &cds, bool &cds_change, bool create_general_only)

CRef< CCmdComposite > GetSynchronizeProteinPartialsCommand(CScope &scope, const CSeq_feat &cds)

CRef< CCmdComposite > GetChangeStrainForwardingCommand(CSeq_entry_Handle seh, bool disable)

CRef< CCmdComposite > CreateOrAdjustProteinFeature(CBioseq_Handle product, CSeq_feat &cds, bool &cds_change)

CRef< CCmdComposite > GetDeleteSequenceCommand(CBioseq_Handle bsh)

CRef< CCmdComposite > GetDeleteAllFeaturesCommand_Ex(CSeq_entry_Handle seh, size_t &count, bool remove_proteins)

CRef< CCmdChangeSeq_feat > AdjustGene(const CSeq_feat &orig_feat, const CSeq_feat &new_feat, CScope &scope)

CRef< CCmdComposite > SpecificHostCleanupCommand(CSeq_entry_Handle seh)

bool GetNormalizeGeneQualsCommand(CBioseq_Handle bsh, CRef< CCmdComposite > cmd)

void GetProductToCDSMap(CScope &scope, map< CBioseq_Handle, set< CSeq_feat_Handle > > &product_to_cds)

CRef< CCmdComposite > AutofixCommand(CSeq_entry_Handle orig_seh, const string &test_name, string *output, const string &suspect_rules)

CRef< CCmdComposite > GetRmCultureNotesCommand(CSeq_entry_Handle seh)

static void s_GetSourceDescriptors(const CSeq_entry &se, vector< pair< const CSeqdesc *, const CSeq_entry * >> &src_descs)

CRef< CCmdComposite > CleanupHugeFileCommand(CSeq_entry_Handle orig_seh, bool extended, bool do_tax, objects::taxupdate_func_t &updater, bool rmv_user_object)

CRef< CCmdComposite > GetDisableStrainForwardingCommand(CSeq_entry_Handle seh)

CRef< CCmdComposite > SetTranslExcept(CSeq_entry_Handle seh, const string &comment, bool strict, bool extend, bool adjust_gene)

SetTranslExcept A function to set a code break at the 3' end of coding regions in a Seq-entry to indi...

CRef< CCmdComposite > AutofixCommandHugeMode(CSeq_entry_Handle orig_seh, const string &str_test_name, map< string, size_t > &report, const string &suspect_rules)

CRef< CCmdComposite > GetReverseComplimentSequenceCommand(CBioseq_Handle bsh)

CRef< CCmdComposite > UpdatemRNAProduct(const CSeq_feat &protein, CScope &scope, string &message)

void AdjustProteinFeature(CSeq_feat &prot, CBioseq_Handle product, CSeq_feat &cds, bool &cds_change)

static string s_GetProductRules()

CRef< CCmdComposite > CachedTaxonomyLookupCommand(CSeq_entry_Handle seh, objects::taxupdate_func_t &updater)

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