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

void CMacroFunction_TaxLookup::TheFunction()

(m_DataIter->IsHugeDataMode()) {

rmv_ncbicleanup_userobj = !(m_DataIter->TopLevelObject());

& remote_updater = m_DataIter->RemoteUpdater();

update_fnc = remote_updater->GetUpdateFunc();

cleanup_tax_cmd =

(m_DataIter->GetSEH(),

,

, update_fnc, rmv_ncbicleanup_userobj);

cleanup_tax_cmd =

(m_DataIter->GetSEH(),

,

);

(cleanup_tax_cmd) {

m_DataIter->RunCommand(cleanup_tax_cmd, m_CmdComposite);

<<

;

CMacroFunction_TaxLookup::x_ValidArguments()

(m_Args.empty());

s_SpellingFixes(*entry,

);

(m_DataIter->IsSetSeqSubmit() && m_DataIter->GetSeqSubmit().IsSetSub()){

& submit_block = m_DataIter->GetSeqSubmit().GetSub();

edited_subblock->

(submit_block);

s_SpellingFixes(*edited_subblock, log_sblock);

->AddCommand(*chg_subblock);

m_DataIter->RunCommand(

, m_CmdComposite);

<< log_sblock.str();

m_DataIter->SetModified();

x_LogFunction(

);

(

.empty());

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

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{

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{

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{

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{

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{

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{

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{

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{

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{

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{

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{

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{

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{

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{

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},

{

,

},

{

,

},

{

,

},

oss <<

<< search.substr(2, search.length() - 4) <<

<<

[pat].second << endl;

m_QualsChangedCount = s_RemoveSingleItemSet(seh);

(m_QualsChangedCount) {

m_DataIter->SetModified();

<<

<< m_QualsChangedCount <<

;

x_LogFunction(

);

(!direct_child_ci) {

(direct_child_ci) {

(; annot_ci; ++annot_ci) {

(

.empty());

m_QualsChangedCount = 0;

s_RenormalizeNucProtSets(seh, m_QualsChangedCount);

(m_QualsChangedCount) {

m_DataIter->SetModified();

<<

<< m_QualsChangedCount <<

;

x_LogFunction(

);

(

.empty());

void CMacroFunction_DiscrepancyAutofix::TheFunction()

(m_DataIter->IsHugeDataMode()) {

m_DataIter->RunCommand(autofix_cmd, m_CmdComposite);

x_LogChangedQuals(fnc_log);

m_DataIter->RunCommand(autofix_cmd, m_CmdComposite);

CMacroFunction_DiscrepancyAutofix::x_ValidArguments()

(!entry && !(bseq && bseq->

())) {

feat_list = m_Args[0]->GetString();

m_Descr.append(feat_list +

);

misc_feat = m_Args[1]->GetString();

m_Descr.append(

+ misc_feat);

x_AddModifiersToOptions(options);

autodef_cmd = s_AutodefSeqEntryNoTitle(m_DataIter->GetSEH(), options);

(!m_DataIter->HasBeenCompleted()) {

feat_list = m_Args[0]->GetString();

m_Descr.append(feat_list +

);

misc_feat = m_Args[1]->GetString();

m_Descr.append(

+ misc_feat);

x_AddModifiersToOptions(options);

seq_iter->SetAutodefOptions() = options;

m_DataIter->SetCompleted();

options = seq_iter->GetAutodefOptions();

autodef_cmd = s_AutodefSequenceNoTitle(m_DataIter->GetSEH(), m_DataIter->GetBioseqHandle(), options);

m_DataIter->RunCommand(autodef_cmd, m_CmdComposite);

<< x_GetDescription();

x_LogFunction(

);

mod_combo->InitFromOptions(options);

mod_combo->SetUseModifierLabels(

);

mod_combo->SetKeepParen(

);

mod_combo->SetMaxModifiers(0);

(

b_iter(seh); b_iter; ++b_iter) {

(

->IsSet() &&

->GetSet().GetCompleteBioseq_set()->NeedsDocsumTitle()) {

mod_combo->InitFromOptions(options);

mod_combo->SetUseModifierLabels(

);

mod_combo->SetKeepParen(

);

mod_combo->SetMaxModifiers(0);

->AddCommand(*delcmd);

opts_desc->

(*autodef_opts);

has_autodef_opts =

;

has_autodef_opts =

;

(!has_autodef_opts) {

(

& it :

) {

(!it->IsString()) {

(

index = 2; index <

.size(); ++index) {

& mod_name =

[index]->GetString();

.append(

+ mod_name);

.append(

+ mod_name);

(

.size() < 3) {

src_combo->GetAvailableModifiers(modifiers);

(

= 0;

< modifiers.size();

++) {

(modifiers[

].IsOrgMod()) {

opts.

(modifiers[

].GetOrgModType());

+

;

s_ConfigureAutodefOptionsForID(modifiers, m_DataIter->GetSEH());

(

= 0;

< modifiers.size();

++) {

(modifiers[

].IsRequested()) {

(modifiers[

].IsOrgMod()) {

opts.

(modifiers[

].GetOrgModType());

m_DataIter->RunCommand(autodef_cmd, m_CmdComposite);

<<

;

x_LogFunction(

);

(

.empty());

(

= 0;

< modifiers.size();

++) {

(modifiers[

].IsOrgMod() && is_org_mod) {

(modifiers[

].GetOrgModType() == subtype) {

(modifiers[

].AllPresent()) {

(modifiers[

].AnyPresent() && !require_all) {

modifiers[

].SetRequested(

);

(!modifiers[

].IsOrgMod() && !is_org_mod) {

(modifiers[

].GetSubSourceType() == subtype) {

(modifiers[

].AllPresent()) {

(modifiers[

].AnyPresent() && !require_all) {

modifiers[

].SetRequested(

);

vector<string> clause_list;

clause_list.push_back(clause);

(clause_list.size() < 2) {

(clause_list.begin(), clause_list.end());

vector<string>::iterator it = clause_list.begin();

(it != clause_list.end()) {

src_combo->GetAvailableModifiers(modifiers);

is_orgmod[] = {

,

,

,

,

,

,

,

,

,

};

num_subtypes =

(subtypes) /

(

);

(

= 0;

< num_subtypes && !found;

++) {

(

= 0;

< num_subtypes && !found;

++) {

(

= 0;

< modifiers.size();

++) {

(modifiers[

].AnyPresent()) {

(modifiers[

].IsOrgMod()) {

(src_combo->HasOrgMod(modifiers[

].GetOrgModType())) {

modifiers[

].SetRequested(

);

(src_combo->HasSubSource(modifiers[

].GetSubSourceType())) {

modifiers[

].SetRequested(

);

m_DataIter->RunCommand(refresh_cmd, m_CmdComposite);

<<

;

x_LogFunction(

);

(

b_iter(se, objects::CSeq_inst::eMol_na); b_iter; ++b_iter) {

defline = autodef.

(&mod_combo, *b_iter);

found_existing =

;

((*it)->IsTitle()) {

->AddCommand(*ecmd);

found_existing =

;

(!found_existing) {

(

&& !options) {

found_existing =

;

((*it)->IsTitle()) {

->AddCommand(*ecmd);

found_existing =

;

(!found_existing) {

(

.empty());

misc_feat = m_Args[0]->GetString();

m_Descr.append(

+ misc_feat);

x_AddModifiersToOptions(options);

autodef_complete.

(m_DataIter->GetSEH());

mod_combo->InitFromOptions(options);

mod_combo->SetUseModifierLabels(

);

mod_combo->SetKeepParen(

);

mod_combo->SetMaxModifiers(0);

(

b_iter(seh); b_iter; ++b_iter) {

is_complete = x_IsComplete(*b_iter);

->AddCommand(*delcmd);

m_QualsChangedCount++;

m_QualsChangedCount++;

(m_QualsChangedCount > 0) {

m_DataIter->RunCommand(

, m_CmdComposite);

<<

+ m_Descr;

x_LogFunction(

);

(

.size() < 2) {

src_combo->GetAvailableModifiers(modifiers);

(

= 0;

< modifiers.size();

++) {

(modifiers[

].IsOrgMod()) {

opts.

(modifiers[

].GetOrgModType());

(

index = 1; index <

.size(); ++index) {

& mod_name =

[index]->GetString();

.append(

+ mod_name);

.append(

+ mod_name);

is_complete =

;

(

.size() < 1) {

(

& it :

) {

(!it->IsString()) {

scope = m_DataIter->GetScopedObject().scope;

(!scope || !entry)

(!m_DataIter->HasBeenCompleted()) {

m_ProductToCds.clear();

m_DataIter->SetCompleted();

(

& it : m_ProductToCds) {

(cds_set.

() == 1) {

new_cds->

(*cds_set.

()->GetOriginalSeq_feat());

cds_change =

;

m_QualsChangedCount++;

(m_QualsChangedCount) {

m_DataIter->RunCommand(

, m_CmdComposite);

<<

<< m_QualsChangedCount <<

;

x_LogFunction(

);

(

.empty());

void CMacroFunction_ConvertRawToDeltabyNs::TheFunction()

scope = m_DataIter->GetScopedObject().scope;

(!entry || !scope)

NRawToDeltaSeq::SGapRequestInfo request;

request.min_unknown = (long)m_Args[index]->GetInt();

request.max_unknown = (long)m_Args[++index]->GetInt();

request.min_known = (long)m_Args[++index]->GetInt();

request.max_known = (long)m_Args[++index]->GetInt();

request.adjust_cds = m_Args[++index]->GetBool();

request.keep_gap_length = m_Args[++index]->GetBool();

linkage_evidence = -1;

(!m_Args[++index]->GetString().empty()) {

(!m_Args[++index]->GetString().empty()) {

request.linkage = linkage;

request.linkage_evidence = linkage_evidence;

request.is_assembly_gap =

;

remove_alignments =

;

(m_DataIter->IsHugeDataMode()) {

request, m_DataIter->MaxFeatureId(), remove_alignments,

);

request, remove_alignments,

);

m_DataIter->RunCommand(convert_cmd, m_CmdComposite);

<<

<<

<<

;

(remove_alignments) {

<<

;

CMacroFunction_ConvertRawToDeltabyNs::x_ValidArguments()

(m_Args.size() != 9)

(; index < 4; ++index) {

(!m_Args[index]->IsInt())

(!m_Args[index]->IsBool())

(!m_Args[++index]->IsBool())

(;index < m_Args.size(); ++index) {

(!m_Args[index]->IsString())

void CMacroFunction_AddGapFeaturesByNs::TheFunction()

scope = m_DataIter->GetScopedObject().scope;

(!entry || !scope)

NRawToDeltaSeq::SGapRequestInfo request;

request.min_unknown = (long)m_Args[index]->GetInt();

request.max_unknown = (long)m_Args[++index]->GetInt();

request.min_known = (long)m_Args[++index]->GetInt();

request.max_known = (long)m_Args[++index]->GetInt();

request.adjust_cds = m_Args[++index]->GetBool();

request.keep_gap_length = m_Args[++index]->GetBool();

remove_alignments =

;

(m_DataIter->IsHugeDataMode()) {

request, m_DataIter->MaxFeatureId(), remove_alignments,

);

request, remove_alignments,

);

m_DataIter->RunCommand(convert_cmd, m_CmdComposite);

<<

<<

<<

;

(remove_alignments) {

<<

;

CMacroFunction_AddGapFeaturesByNs::x_ValidArguments()

(m_Args.size() != 6)

(; index < 4; ++index) {

(!m_Args[index]->IsInt())

(m_Args[index]->IsBool() && m_Args[++index]->IsBool());

scope = m_DataIter->GetScopedObject().scope;

(!entry || !scope)

delta_to_raw = s_ConvertDeltaToRaw(m_DataIter->GetSEH(), m_QualsChangedCount);

(m_QualsChangedCount) {

m_DataIter->RunCommand(delta_to_raw, m_CmdComposite);

<<

<< m_QualsChangedCount <<

;

x_LogFunction(

);

(

.empty());

new_inst->

(b_iter->GetInst());

composite.

();

scope = m_DataIter->GetScopedObject().scope;

(!entry || !scope)

& filename = m_Args[0]->GetString();

(filename.empty()) {

<<

;

<<

<< filename;

x_ReadUpdateSeqs(in_str);

<<

<< filename <<

;

(m_Proteins.empty()) {

<<

<< filename <<

;

(

== eMatchId) {

(

index = 0; index < m_Proteins.size(); ++index) {

& prot_ids = m_Proteins[index]->GetSeq().GetId();

(

&

: prot_ids) {

inserted = id_to_index.emplace(idh, index);

(!inserted.second) {

<<

<< idh.AsString() <<

;

prot_ids = prot_iter->GetCompleteBioseq()->GetId();

(

&

: prot_ids) {

inserted = orig_proteins.emplace(idh, *prot_iter);

m_QualsChangedCount = 0;

(

& upd_it : id_to_index) {

orig_it = orig_proteins.

(upd_it.first);

(orig_it == orig_proteins.

()) {

& prot_seq = m_Proteins[upd_it.second]->GetSeq();

new_inst->

(prot_seq.GetInst());

m_QualsChangedCount++;

(m_QualsChangedCount) {

m_DataIter->RunCommand(composite, m_CmdComposite);

<<

<< m_QualsChangedCount <<

;

x_LogFunction(

);

(

== eMatchName) {

(!fasta_reader.

()) {

&

=

[1]->GetString();

(

.size() == 2) ? (

[0]->IsString() &&

[1]->IsString()) :

;

COrgMod::ESubtype GetOrgModType() const

CSubSource::ESubtype GetSubSourceType() const

void SetOptions(const CAutoDefOptions &options)

void AddOrgMod(COrgMod::TSubtype subtype)

unsigned int TMiscFeatRule

void InitFromUserObject(const CUser_object &obj)

void SetMiscFeatRule(TMiscFeatRule rule)

TFeatureListType GetFeatureListType() const

TMiscFeatRule GetMiscFeatRule() const

void SetFeatureListType(EFeatureListType list_type)

void SetUseLabels(bool val=true)

void AddSubSource(CSubSource::TSubtype subtype)

unsigned int TFeatureListType

vector< CAutoDefAvailableModifier > TAvailableModifierVector

string GetDocsumDefLine(CSeq_entry_Handle se)

void SetOptionsObject(const CUser_object &user)

void AddSources(CSeq_entry_Handle se)

CRef< CUser_object > GetOptionsObject() const

void SetOptions(const CAutoDefModifierCombo &mod_combo)

void SetFeatureListType(CAutoDefOptions::EFeatureListType feature_list_type)

string GetOneDefLine(CAutoDefModifierCombo *mod_combo, const CBioseq_Handle &bh, CRef< feature::CFeatTree > featTree=null)

CRef< CAutoDefModifierCombo > FindBestModifierCombo()

void SetMiscFeatRule(CAutoDefOptions::EMiscFeatRule misc_feat_rule)

CAutoDefModifierCombo * GetEmptyCombo()

string GetOneFeatureClauseList(CBioseq_Handle bh, unsigned int genome_val)

bool NeedsDocsumTitle() const

void Add(CObject *obj, const CObject *new_obj)

void AddCommand(IEditCommand &command)

Base class for reading FASTA sequences.

CFormatHints & AddPreferredFormat(TFormat fmt)

Mark the format as preferred.

CFormatHints & DisableAllNonpreferred(void)

Disable all formats not marked as preferred.

Class implements different ad-hoc unreliable file format identifications.

CFormatHints & GetFormatHints(void)

Get format hints.

EFormat

The formats are checked in the same order as declared here.

@ eFasta

FASTA format sequence record, CFastaReader.

@ eUnknown

unknown format

EFormat GuessFormat(EMode)

static bool IsValidSubtypeName(const string &str, EVocabulary vocabulary=eVocabulary_raw)

static TSubtype GetSubtypeValue(const string &str, EVocabulary vocabulary=eVocabulary_raw)

namespace ncbi::objects::

Base class for all serializable objects.

Simple implementation of ILineReader for i(o)streams.

static TSubtype GetSubtypeValue(const string &str, EVocabulary vocabulary=eVocabulary_raw)

static bool IsValidSubtypeName(const string &str, EVocabulary vocabulary=eVocabulary_raw)

Template class for iteration on objects of class C.

@ eObjectType_AutodefOptions

EObjectType GetObjectType() const

const_iterator end() const

const_iterator find(const key_type &key) const

const_iterator begin() const

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

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

static const char si[8][64]

CChangeUnindexedObjectCommand< objects::CSubmit_block > CChangeSubmitBlockCommand

Operators to edit gaps in sequences.

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

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

static SQLCHAR output[256]

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

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#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.

void x_ReadUpdateSeqs(CNcbiIstream &istr)

bool x_ValidArguments() const

Tests the number and the type of function arguments.

bool x_ValidArguments() const

Tests the number and the type of function arguments.

static void s_ConfigureAutodefOptionsForID(TModifiers &modifiers, objects::CSeq_entry_Handle seh)

static void s_AutodefSetsNoTitle(const objects::CSeq_entry_Handle &seh, objects::CAutoDefWithTaxonomy &autodef, CRef< CCmdComposite > composite_cmd)

static const SStaticPair< const char *, const char * > macro_spell_fixes[]

static void s_AddAutodefOptions(const objects::CAutoDef &autodef, const objects::CBioseq_Handle &bsh, CRef< CCmdComposite > composite_cmd)

bool x_ValidArguments() const

Tests the number and the type of function arguments.

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

string x_GetDescription()

static CRef< CCmdComposite > s_RefreshDeflineCommand(const objects::CSeq_entry_Handle &seh)

static CRef< CCmdComposite > s_AutodefSequenceNoTitle(const objects::CSeq_entry_Handle &seh, const objects::CBioseq_Handle &target, const objects::CAutoDefOptions &options)

bool x_ValidArguments() const

Tests the number and the type of function arguments.

bool x_IsComplete(const objects::CBioseq_Handle bsh)

void x_AddModifiersToOptions(objects::CAutoDefOptions &opts)

static void s_SelectModifiersforAutodefID(objects::CAutoDef &autodef, TModifiers &modifiers, objects::CSeq_entry_Handle seh)

bool x_IsRequested(const objects::CAutoDefAvailableModifier &modifier)

static bool s_ChooseModInModList(bool is_org_mod, int subtype, bool require_all, CAutoDefSourceDescription::TAvailableModifierVector &modifiers)

bool x_ValidArguments() const

Tests the number and the type of function arguments.

static CRef< CCmdComposite > s_ConvertDeltaToRaw(objects::CSeq_entry_Handle seh, Int4 &count)

static short s_RemoveSingleItemSet(objects::CSeq_entry_Handle &seh)

bool x_ValidArguments() const

Tests the number and the type of function arguments.

bool x_ValidArguments() const

Tests the number and the type of function arguments.

const string & GetSuspectRules() const

static bool s_AreFeatureClausesUnique(CSeq_entry_Handle seh, CAutoDef &autodef)

void x_AddModifiersToOptions(objects::CAutoDefOptions &opts)

#define DEFINE_MACRO_FUNCNAME(CL_NAME, FN_NAME)

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

vector< CRef< objects::CSeq_entry > > m_Proteins

bool x_IsRequested(const objects::CAutoDefAvailableModifier &modifier)

static CMacroLib & GetInstance()

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

static CRef< CCmdComposite > s_AutodefSeqEntryNoTitle(const objects::CSeq_entry_Handle &seh, const objects::CAutoDefOptions &options)

static void s_SpellingFixes(CSerialObject &object, CNcbiOstrstream &oss)

static bool s_IsSingletonSet(const objects::CBioseq_set_Handle &bioseq_set)

static void s_AutodefBioseqsNoTitle(const objects::CSeq_entry_Handle &seh, objects::CAutoDefWithTaxonomy &autodef, objects::CAutoDefModifierCombo *mod_combo, CRef< CCmdComposite > composite_cmd)

CIRef< IMacroBioDataIter > m_DataIter

void s_RenormalizeNucProtSets(objects::CSeq_entry_Handle seh, Int4 &count)

objects::CAutoDefSourceDescription::TAvailableModifierVector TModifiers

@ eMatchId

match protein by protein_id

@ eMatchName

match protein by protein name

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

Set object to copy of another one.

#define ENUM_METHOD_NAME(EnumName)

static const TObjectType * SafeCast(TTypeInfo type)

virtual CRef< CSeq_entry > ReadOneSeq(ILineErrorListener *pMessageListener=nullptr)

Read a single effective sequence, which may turn out to be a segmented set.

long TFlags

binary OR of EFlags

bool AtEOF(void) const

Indicates (negatively) whether there is any more input.

@ fForceType

Force specified type regardless of accession.

@ fAssumeProt

Assume prots unless accns indicate otherwise.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

TObjectPtr GetObjectPtr(void) const

Get pointer to object.

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

Get the encoding CDS feature of a given protein sequence.

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.

void AddDefaults(TPriority pri=kPriority_Default)

Add default data loaders from object manager.

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

TSeq ConvertSetToSeq(void) const

Do the same as CollapseSet() when sub-entry is of type bioseq.

TClass GetClass(void) const

CRef< CSeqdesc > RemoveSeqdesc(const CSeqdesc &v) const

bool IsEmptySeq_set(void) const

Check if the bioseq set is empty.

CSeq_entry_Handle GetSeq_entry_Handle(void) const

Get parent Seq-entry handle.

CSeq_entry_EditHandle GetEditHandle(void) const

Get 'edit' version of handle.

CSeq_entry_Handle GetParentEntry(void) const

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

bool IsSetClass(void) const

const TDescr & GetDescr(void) const

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.

void CollapseSet(void) const

Collapse one level of Bioseq-set.

CSeq_entry_Handle GetSeq_entry_Handle(void) const

@ eNonRecursive

Deprecated.

@ fIncludeGivenEntry

Include the top (given) entry.

@ fRecursive

Iterate recursively.

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.

bool IsNull(void) const THROWS_NONE

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

int32_t Int4

4-byte (32-bit) signed integer

size_t Replace(CTempStringEx search, CTempString replace, CRegexp::TCompile compile_flags=CRegexp::fCompile_default, CRegexp::TMatch match_flags=CRegexp::fMatch_default, size_t max_replace=0)

Replace occurrences of a substring within a string by pattern.

string GetResult(void)

Get result string.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define USING_SCOPE(ns)

Use the specified namespace.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

bool IsOssEmpty(CNcbiOstrstream &oss)

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

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 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.

static string & ToLower(string &str)

Convert string to lower case – string& version.

@ eSubtype_specimen_voucher

@ eSubtype_culture_collection

void SetExcept(TExcept value)

Assign a value to Except data member.

void SetExcept_text(const TExcept_text &value)

Assign a value to Except_text data member.

const TSeq & GetSeq(void) const

Get the variant data.

const TSet & GetSet(void) const

Get the variant data.

bool IsSeq(void) const

Check if variant Seq is selected.

const TSeq_set & GetSeq_set(void) const

Get the Seq_set member data.

list< CRef< CSeq_entry > > TSeq_set

@ eClass_pop_set

population study

@ eClass_phy_set

phylogenetic study

@ eClass_wgs_set

whole genome shotgun project

@ eClass_mut_set

set of mutations

@ eClass_eco_set

ecological sample study

@ eClass_nuc_prot

nuc acid and coded proteins

@ eClass_gen_prod_set

genomic products, chrom+mRNA+protein

@ eClass_genbank

converted genbank

@ eClass_small_genome_set

viral segments or mitochondrial minicircles

bool IsSetCompleteness(void) const

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

list< CRef< CSeqdesc > > Tdata

const TUser & GetUser(void) const

Get the variant data.

TTitle & SetTitle(void)

Select the variant.

const Tdata & Get(void) const

Get the member data.

TUser & SetUser(void)

Select the variant.

TCompleteness GetCompleteness(void) const

Get the Completeness member data.

const TMolinfo & GetMolinfo(void) const

Get the variant data.

@ eCompleteness_complete

complete biological entity

@ e_User

user defined object

@ e_Molinfo

info on the molecule and techniques

@ e_Title

a title for this sequence

@ eMol_na

just a nucleic acid

The blob sat and sat key Both must be positive integers</td > n< td > Non empty string The interpretation of the blob id depends on a processor Cassandra n processor expects the following format

Functions used in the DO/DONE section affecting the top seq-entry.

Macro library for storing parsed macros.

constexpr auto sort(_Init &&init)

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 SLJIT_INLINE sljit_ins st(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

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

C++ wrappers for the Perl-compatible regular expression (PCRE) library.

CRef< CCmdComposite > AutofixCommand(objects::CSeq_entry_Handle seh, const string &test_name, string *output, const string &suspect_rules=kEmptyStr)

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

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

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

CRef< CCmdComposite > AutofixCommandHugeMode(objects::CSeq_entry_Handle seh, const string &test_name, map< string, size_t > &report, const string &suspect_rules=kEmptyStr)

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

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