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

void CMacroFunction_RemoveDescriptor::TheFunction()

(!m_DataIter->IsDescriptor()) {

m_DataIter->SetToDelete(

);

report[

] = 1;

x_LogChangedQuals(fnc_log);

CMacroFunction_RemoveDescriptor::x_ValidArguments()

(m_Args.empty());

CMacroFunction_RemoveSequence::TheFunction()

m_DataIter->SetToDelete(

);

<< m_DataIter->GetBestDescr() <<

;

CMacroFunction_RemoveSequence::x_ValidArguments()

(m_Args.empty());

CMacroFunction_RemoveAlignment::TheFunction()

m_DataIter->SetToDelete(

);

<< m_DataIter->GetBestDescr() <<

;

CMacroFunction_RemoveAlignment::x_ValidArguments()

(m_Args.empty());

CMacroFunction_TrimStringQual::TheFunction()

nr_chars = (

)(m_Args[1]->GetInt());

(res_oi.empty() || nr_chars == 0) {

.erase(0, nr_chars);

SetQualStringValue(obj,

);

(m_QualsChangedCount) {

m_DataIter->SetModified();

<< m_DataIter->GetBestDescr() <<

<< nr_chars <<

<< m_QualsChangedCount <<

;

CMacroFunction_TrimStringQual::x_ValidArguments()

(m_Args.size() != 2) {

CMacroFunction_CorrectGeneticCodes::TheFunction()

scope = m_DataIter->GetScopedObject().scope;

(!

||

->GetId() == cds_gc) {

edit_feat->

().SetCdregion().SetCode(*

);

m_DataIter->SetModified();

<< m_DataIter->GetBestDescr() <<

;

CMacroFunction_CorrectGeneticCodes::x_ValidArguments()

(m_Args.empty());

res_oi =

[0]->GetObjects();

(res_oi.empty()) {

vector<CTempString> taxname_words;

vector<CTempString> words;

(

& it : taxname_words) {

words.erase(

(words.begin(), words.end(), it), words.end());

(new_field != field) {

(

.size() != 1)

;

vector<string> orig_seq, new_seq;

orig_seq.push_back(seq);

new_seq.push_back(seq);

new_seq.push_back(seq);

(

= 0;

< new_seq.size(); ++

) {

<<

<< orig_seq[

];

<<

<< new_seq[

];

CMacroFunction_FixUSAandStatesAbbrev::TheFunction()

* const_pubdesc =

*

(

.GetPointer());

modified =

;

(const_block) {

m_DataIter->SetModified();

<< m_DataIter->GetBestDescr() <<

;

CMacroFunction_FixUSAandStatesAbbrev::x_ValidArguments()

(m_Args.empty());

void CMacroFunction_FixSourceQualCaps::TheFunction()

x_GetObjectsFromRef(res_oi, 0);

(res_oi.empty()) {

vector<string>

, fixed;

is_subsrc(

);

field_name = (is_subsrc) ?

:

;

capitalize_after_colon(

);

SetQualStringValue(oi_field, new_value);

fixed.push_back(new_value);

(m_QualsChangedCount) {

m_DataIter->SetModified();

<< m_DataIter->GetBestDescr() <<

;

(

= 0;

< fixed.size(); ++

) {

<<

<<

[

] <<

<< fixed[

];

CMacroFunction_FixSourceQualCaps::x_ValidArguments()

CMacroFunction_FixMouseStrain::TheFunction()

x_GetObjectsFromRef(res_oi, 0);

(res_oi.empty()) {

vector<string>

, fixed;

orig_value =

;

new_value = orig_value;

SetQualStringValue(oi_field, new_value);

fixed.push_back(new_value);

(m_QualsChangedCount) {

m_DataIter->SetModified();

<< m_DataIter->GetBestDescr() <<

;

(

= 0;

< fixed.size(); ++

) {

<<

<<

[

] <<

<< fixed[

];

CMacroFunction_FixMouseStrain::x_ValidArguments()

CMacroFunction_FixAuthorCaps::TheFunction()

vector<string>

, fixed;

newValue(orig_value);

fix_abbrev(

), fix_short_words(

);

cap_after_apostrophe(

);

s_FixCapitalizationInElement(newValue, fix_abbrev, fix_short_words, cap_after_apostrophe)) {

.push_back(orig_value);

SetQualStringValue(oi, newValue);

fixed.push_back(newValue);

(m_QualsChangedCount) {

m_DataIter->SetModified();

<< m_DataIter->GetBestDescr() <<

;

(

= 0;

< fixed.size(); ++

) {

<<

<<

[

] <<

<< fixed[

] <<

;

CMacroFunction_FixAuthorCaps::x_ValidArguments()

punct_only = (++index <

.size()) ?

[index]->GetBool() :

;

first_is_upper(

);

as =

.size();

(as < 1 || as > 2) {

new_country = country;

(cap_after_apostrophe) {

(fix_short_words) {

fixed_title(title);

cap_after_apostrophe(

);

fix_abbrev(

), fix_short_words(

);

affiliation = affil_std.

();

div = affil_std.

();

city = affil_std.

();

(

.length() == 2) {

(!affil.

()) {

(!affil.

()) {

vector<string>

, fixed;

.push_back(orig_value);

fixed.push_back(newValue);

ambiguous =

, day_first =

;

month_ambiguous =

;

(desc_it && ambiguous) {

((*subsrc)->IsSetName() && !

(orig_value, (*subsrc)->GetName())) {

month_ambiguous =

;

fixed.push_back(newValue);

.push_back(orig_value);

fixed.push_back(newValue);

(

= 0;

< fixed.size(); ++

) {

<<

<<

[

] <<

<< fixed[

];

additional(

+

);

modified(

);

((*subsrc)->IsSetName()) {

new_note = (*subsrc)->GetName() +

+ additional;

(*subsrc)->SetName() = new_note;

(lat_lon.empty())

format_correct =

, precision_correct =

, lat_in_range =

, lon_in_range =

;

lat_value = 0.0, lon_value = 0.0;

orig_value(lat_lon);

(!format_correct) {

fix = fix.substr(0, pos);

extra_text = fix.substr(pos + 2,

);

CMacroFunction_Resolve::TheFunction()

m_Result->SetNotSet();

m_Result->SetObjects(m_Args[0]->

());

x_GetObjectsFromRef(objs, 0);

m_Result->SetNotSet();

m_Result->SetObjects(objs);

CMacroFunction_Resolve::x_ValidArguments()

(m_Args.size() != 1)

CMacroFunction_ResolveBioSourceQuals::TheFunction()

vector<string> field_names;

field_names.push_back(

);

field_names.push_back(

);

field_names.push_back(

);

field_names.push_back(

);

field_names.push_back(

);

field_names.push_back(

);

field_names.push_back(

);

field_names.push_back(

);

(vector<string>, it, field_names) {

objs.push_back(res_oi.front());

(!objs.empty()) {

m_Result->SetObjects(objs);

CMacroFunction_ResolveBioSourceQuals::x_ValidArguments()

(m_Args.empty());

CMacroFunction_ResolveNASeq::TheFunction()

CMacroFunction_ResolveNASeq::x_ValidArguments()

CMacroFunction_ChangeSeqInst::TheFunction()

scope = m_DataIter->GetScopedObject().scope;

(!orig_molinfo || !scope) {

new_inst->Assign(bseq->

());

objInfo(new_inst.GetPointer(), new_inst->GetTypeInfo());

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

m_QualsChangedCount++;

(m_QualsChangedCount) {

->AddCommand(*chgInst);

m_DataIter->RunCommand(

, m_CmdComposite);

<<

<< field <<

<< m_Args[1]->GetString() <<

<< best_seqid;

CMacroFunction_ChangeSeqInst::x_ValidArguments()

arg_size = m_Args.size();

(arg_size != 2) {

(

= 0;

< arg_size; ++

) {

CMacroFunction_RemoveLineageSourceNotes::TheFunction()

vector<string> orig_value;

((*orgmod)->IsSetSubname()) {

orig_value.push_back((*orgmod)->GetSubname());

((*subsrc)->IsSetName()) {

orig_value.push_back((*subsrc)->GetName());

vector<string> new_value;

((*orgmod)->IsSetSubname()) {

new_value.push_back((*orgmod)->GetSubname());

((*subsrc)->IsSetName()) {

new_value.push_back((*subsrc)->GetName());

(

< orig_value.size()) {

(j < new_value.size()) {

.append(

+ orig_value[

] +

+ bsrc->

());

.append(

+ orig_value[

] +

+ bsrc->

());

m_DataIter->SetModified();

<< m_DataIter->GetBestDescr() <<

<<

;

CMacroFunction_RemoveLineageSourceNotes::x_ValidArguments()

(m_Args.empty());

<<

;

orig_denseg.

(denseg);

(!denseg.

(orig_denseg)) {

(

.empty());

CMacroFunction_RmvDuplStructComments::TheFunction()

scope = m_DataIter->GetScopedObject().scope;

(!bseq || !scope)

vector<CConstRef<CSeqdesc> > struct_comments;

(struct_comments.size() < 2)

vector<CConstRef<CSeqdesc> >::const_iterator it1 = struct_comments.begin();

vector<CConstRef<CSeqdesc> >::const_iterator it2(it1);

(it1 != struct_comments.end()) {

(it2 != struct_comments.end()) {

((*it2)->Equals((**it1))) {

duplicates[seh1].

(*it1);

duplicates[seh2].

(*it2);

(duplicates.

())

( ; it != duplicates.

(); ++it) {

->AddCommand(*del_cmd);

m_DataIter->RunCommand(

, m_CmdComposite);

<< m_DataIter->GetBestDescr() <<

<<

<<

;

CMacroFunction_RmvDuplStructComments::x_ValidArguments()

(m_Args.empty());

CMacroFunction_ReorderStructComment::TheFunction()

& rule = rules->FindCommentRule(prefix);

m_QualsChangedCount++;

m_DataIter->SetModified();

report[

] = m_QualsChangedCount;

x_LogChangedQuals(fnc_log);

<<

<< prefix;

(

<<

<< prefix);

CMacroFunction_ReorderStructComment::x_ValidArguments()

(m_Args.empty());

(!bseq || !scope) {

edited_desc->

(*desc_it);

->AddCommand(*edit_cmd);

<<

->GetBestDescr() <<

;

(

.empty());

& seqid = **seqid_it;

((*dbtag)->IsSetTag()) {

(*dbtag)->GetTag().AsString(ss_tag);

bold_xref->

().SetStr(barcode_id);

CMacroFunction_AddProteinTitles::TheFunction()

scope = m_DataIter->GetScopedObject().scope;

(!bseq || bseq->

() || !scope) {

defline = sequence::CDeflineGenerator().GenerateDefline(bsh, sequence::CDeflineGenerator::fAllProteinNames);

(!defline.empty()) {

new_desc->SetTitle(defline);

m_DataIter->RunCommand(

, m_CmdComposite);

m_QualsChangedCount++;

report[

] = m_QualsChangedCount;

x_LogChangedQuals(fnc_log);

CMacroFunction_AddProteinTitles::x_ValidArguments()

(m_Args.empty());

eTrimResult = trimmer.

( edited_bsh, from, to );

(

.empty());

void CMacroFunction_PrintCSV::TheFunction()

(!m_DataIter->IsSetOutputStream())

& del = (m_Args.size() == 2) ? m_Args[1]->GetString() :

;

(m_Args[0]->IsString()) {

(m_Args[0]->AreObjects()) {

res_oi = m_Args[0]->GetObjects();

(m_Args[0]->IsRef()) {

(

.AreObjects()) {

res_oi =

.GetObjects();

(

.IsInt()) {

(

.IsString()) {

(res_oi.empty()) {

(

& it : res_oi) {

(

& iter : objs) {

CMacroFunction_PrintCSV::x_ValidArguments()

(m_Args.empty() || m_Args.size() > 2)

first_ok = (m_Args[0]->IsString() || m_Args[0]->AreObjects() || m_Args[0]->IsRef());

(m_Args.size() == 2 && !m_Args[1]->IsString()) {

void CMacroFunction_PrintTSV::TheFunction()

(!m_DataIter->IsSetOutputStream())

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

(m_Args[index]->AreObjects()) {

res_oi = m_Args[index]->GetObjects();

(m_Args[index]->IsRef()) {

(

.AreObjects()) {

res_oi =

.GetObjects();

(

.IsInt()) {

(

.IsString()) {

(res_oi.empty()) {

(

& it : res_oi) {

(

& iter : objs) {

CMacroFunction_PrintTSV::x_ValidArguments()

(m_Args.empty() || m_Args.size() > 2)

first_ok = (m_Args[0]->IsString() || m_Args[0]->AreObjects() || m_Args[0]->IsRef());

(m_Args.size() == 2 && !m_Args[1]->IsString()) {

void CMacroFunction_PrintVerbatim::TheFunction()

(!m_DataIter->IsSetOutputStream())

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

(m_Args[index]->AreObjects()) {

res_oi = m_Args[index]->GetObjects();

(m_Args[index]->IsRef()) {

(

.AreObjects()) {

res_oi =

.GetObjects();

(

.IsInt()) {

(

.IsString()) {

ostr <<

.GetString();

(res_oi.empty()) {

(

& it : res_oi) {

(

& iter : objs) {

CMacroFunction_PrintVerbatim::x_ValidArguments()

(m_Args.empty() || m_Args.size() > 1)

first_ok = (m_Args[0]->IsString() || m_Args[0]->AreObjects() || m_Args[0]->IsRef());

modified_name = name;

(name ==

) {

modified_name =

;

(name ==

) {

modified_name =

;

(name ==

) {

modified_name =

;

(name ==

) {

modified_name =

;

(name ==

) {

modified_name =

;

(name ==

) {

modified_name =

;

(name ==

) {

modified_name =

;

modified_name;

& append_del,

& multiple_del,

& ostr)

& class_name = res_oi.front().field.GetName();

all_the_same =

;

(

& it : res_oi) {

(it.field.GetName() != class_name) {

all_the_same =

;

unordered_map<string, vector<string>> qualifiers;

(

& it : res_oi) {

name_oi = it.field.GetClassMemberIterator(index).GetMember();

value_oi = it.field.GetClassMemberIterator(++index).GetMember();

(

& it : qualifiers) {

ostr << it.first <<

<<

(it.second, multiple_del) << append_del;

!qualifiers.empty();

void CMacroFunction_PrintBankit::TheFunction()

(!m_DataIter->IsSetOutputStream())

multiple_del = (index < m_Args.size()) ? m_Args[index]->GetString() :

;

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

(m_Args[index]->AreObjects()) {

res_oi = m_Args[index]->GetObjects();

(m_Args[index]->IsRef()) {

(

.AreObjects()) {

res_oi =

.GetObjects();

(

.IsInt()) {

(

.IsString()) {

ostr <<

.GetString() << append_del;

(

.AreStrings()) {

ostr <<

(

.GetStrings(), multiple_del) << append_del;

(res_oi.empty()) {

appended =

;

(

& it : res_oi) {

(

& iter : objs) {

(appended) ostr << multiple_del;

(appended) ostr << multiple_del;

(appended) ostr << multiple_del;

(appended) ostr << multiple_del;

CMacroFunction_PrintBankit::x_ValidArguments()

(m_Args.empty() || m_Args.size() > 3)

first_ok = (m_Args[0]->IsString() || m_Args[0]->AreObjects() || m_Args[0]->IsRef());

(

index = 1; index < m_Args.size(); ++index) {

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

void CMacroFunction_PrintLiteral::TheFunction()

(!m_DataIter->IsSetOutputStream())

= m_Args[0]->GetString();

print_once = (m_Args.size() == 2) ? m_Args[1]->GetBool() :

;

(!m_DataIter->HasBeenCompleted()) {

m_DataIter->SetCompleted();

(

<<

<<

);

CMacroFunction_PrintLiteral::x_ValidArguments()

(m_Args.empty() || m_Args.size() > 2)

(!m_Args[0]->IsString())

(m_Args.size() == 2 && !m_Args[1]->IsBool())

void CMacroFunction_ToUnknownLengthGap::TheFunction()

scope = m_DataIter->GetScopedObject().scope;

(!bseq || !bseq->

() || !scope) {

(m_Args[0]->GetInt() <= 0)

new_inst->Assign(bsh.

());

(new_inst->IsSetRepr() &&

new_inst->IsSetExt() &&

new_inst->GetExt().IsDelta()) {

literals = new_inst->SetExt().SetDelta().Set();

(

&& it : literals) {

(it->IsLiteral()) {

& lit = it->SetLiteral();

(lit.IsSetSeq_data() && lit.GetSeq_data().IsGap() &&

lit.IsSetLength() && lit.GetLength() == gap_len && !lit.IsSetFuzz()) {

m_QualsChangedCount++;

(m_QualsChangedCount) {

->AddCommand(*chgInst);

m_DataIter->RunCommand(

, m_CmdComposite);

<< m_DataIter->GetBestDescr() <<

<< m_QualsChangedCount <<

<< gap_len <<

;

CMacroFunction_ToUnknownLengthGap::x_ValidArguments()

(m_Args.size() == 1 && m_Args[0]->IsInt());

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

CRef< CGenetic_code > GetGeneticCodeForBioseq(CBioseq_Handle bh)

GetGeneticCodeForBioseq A function to construct the appropriate CGenetic_code object to use when cons...

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

const string & GetLineage(void) const

const string & GetTaxname(void) const

bool RemoveLineageSourceNotes()

bool IsSetTaxname(void) const

CConstRef< CSeqdesc > GetClosestDescriptor(CSeqdesc::E_Choice choice, int *level=NULL) const

void AddCommand(IEditCommand &command)

static string CountryFixupItem(const string &input, bool capitalize_after_colon)

void RemovePureGapSegs()

Remove any segments in which every row has a gap (these can arise when ExtractRows is used)

void Compact()

Join adjacent mergeable segments to create a more compact alignment.

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

overloaded Assign()

Subclass of the IQueryParseUserObject which is held as the user-defined object in each CQueryParseNod...

CMacroBioData_BioSourceIter - iterates over all biosource descriptors and features in the seq-entry.

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

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

ostream & AsString(ostream &s) const

static bool TrimJunk(string &seq)

static bool Fixi(string &seq)

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

virtual EResult Trim(objects::CBioseq_Handle &bioseq_handle, TSignedSeqPos &left, TSignedSeqPos &right)

void TrimAlignments(CRef< CCmdComposite > command, objects::CBioseq_Handle bsh, const objects::CBioseq::TId &seqids, TSeqPos from, TSeqPos to)

void AdjustAndTranslate(objects::CBioseq_Handle bsh, int length, int from, int to, CRef< CCmdComposite > command, objects::CScope &scope, map< objects::CBioseq_Handle, set< objects::CSeq_feat_Handle > > &product_to_cds)

void TrimSeqGraphs(CRef< CCmdComposite > command, objects::CBioseq_Handle bsh, const objects::CBioseq::TId &seqids, TSeqPos from, TSeqPos to, int length)

namespace ncbi::objects::

bool HasExceptionText(const string &exception_text) const

Returns whether or not the given exception_text is set for this feature.

static string FixLatLonFormat(string orig_lat_lon, bool guess=false)

static string FixDateFormat(const string &orig_date)

Attempt to fix the format of the date Returns a blank if the format of the date cannot be determined.

static void IsCorrectLatLonFormat(string lat_lon, bool &format_correct, bool &precision_correct, bool &lat_in_range, bool &lon_in_range, double &lat_value, double &lon_value)

static string FixAltitude(const string &value)

static void DetectDateFormat(const string &orig_date, bool &ambiguous, bool &day_first)

static bool GetBestId(CSeq_id_Handle, CScope &, string &)

const_iterator begin() const

const_iterator end() const

iterator_bool insert(const value_type &val)

void FixAbbreviationsInElement(string &result, bool fix_end_of_sentence=true)

API (CDeflineGenerator) for computing sequences' titles ("definitions").

static auto & FixOrdinalNumbers

static auto & FixCapitalizationInElement

static auto & CapitalizeAfterApostrophe

static auto & FixUSAAbbreviationInAffil

static auto & FixKnownAbbreviationsInElement

static auto & ResetCapitalization

static auto & FixShortWordsInElement

static auto & FindReplaceString_CountryFixes

static auto & FixOrgNames

static auto & FixAffiliationShortWordsInElement

static auto & FixupMouseStrain

static auto & FixStateAbbreviationsInCitSub

static auto & FixCountryCapitalization

static auto & InsertMissingSpacesAfterNo

static auto & FixStateAbbreviationsInAffil

static auto & InsertMissingSpacesAfterCommas

vector< CConstRef< CObject > > GetObjects(CSeq_entry_Handle seh, const string &field, CFieldNamePanel::EFieldType field_type, int subtype, const string &ncRNA_class, CConstRef< objects::CSeq_submit > submit, CRef< CEditingActionConstraint > constraint, vector< CSeq_entry_Handle > *descr_context=nullptr)

static void DLIST_NAME() remove(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

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

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.

#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 TheFunction()

Function implementation.

bool StringsAreEquivalent(const string &name1, const string &name2)

static Int4 s_FixCapsInPubAffil_Affil(objects::CAffil &affil, bool punct_only)

map< objects::CBioseq_Handle, set< objects::CSeq_feat_Handle > > m_ProductToCds

bool SetQualStringValue(CObjectInfo &oi, const string &value)

Functions make the action and collect statistics.

virtual void TheFunction()

Function implementation.

static string s_GetBarcodeId(const objects::CBioseq &bseq)

virtual void TheFunction()

Function implementation.

static Int4 s_FixCapsInPubAffil_Country(objects::CAffil &affil, bool punct_only)

CRef< CMacroCmdComposite > m_CmdComposite

static Int4 s_FixCapsInPubAffil_NoAffilDiv(objects::CAffil &affil, bool punct_only)

static Int4 s_FixCapsInPubAffil_Street(objects::CAffil &affil, bool punct_only)

static Int4 s_FixCapsInPubAffil_Div(objects::CAffil &affil, bool punct_only)

static CRef< objects::CDbtag > s_MakeBarcodeDbXref(const string &barcode_id)

DEFINE_MACRO_FUNCNAME(CMacroFunction_RemoveSequence, "RemoveSequence")

class CMacroFunction_RemoveSequence RemoveSequence()

static Int4 s_FixCapsInPubAffil_Sub(objects::CAffil &affil, bool punct_only)

list< SResolvedField > TObs

static string s_ConvertAltitudeToMeters(const string &value)

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

virtual void TheFunction()

Function implementation.

void Dereference()

If it is a reference it is resolved to the first non reference type in the hierarchy.

const TObs & GetObjects() const

static Int4 s_FixCapitalizationInAuthor(objects::CName_std &auth_names)

bool ResolveIdentToObjects(const CObjectInfo &oi, const string &identifier, CMQueryNodeValue &v)

Resolve name to the list of objects.

bool SetSimpleTypeValue(CObjectInfo &oi, const CMQueryNodeValue &value, objects::edit::EExistingText existing_text=objects::edit::eExistingText_replace_old)

Set single node data to the node specified by parameter of type CObjectInfo.

static void s_FixCapitalizationInCountryString(string &country, bool punct_only)

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

static bool s_AddAltitudeToSubSourceNote(objects::CBioSource &bsrc, const string &value)

CObjectInfo GetPrimitiveObjInfo(const CObjectInfo &info)

void SetCollDateType(bool ambiguous)

static bool s_HasBarcodeDbXref(const objects::CBioseq &bseq, const string &barcode_id)

static string s_FixCapitalizationInTitle(const string &title, bool first_is_upper, const objects::CSeq_entry_Handle &seh)

EType GetDataType() const

static string s_GetModifierName(const string &name)

class CMacroFunction_PrintBankit PrintBankit(field_name|object, multiple_del, append_del) The last tw...

void GetPrimitiveObjectInfos(CMQueryNodeValue::TObs &objs, const CMQueryNodeValue::SResolvedField &info)

string TransformForCSV(const string &str)

Int4 m_QualsChangedCount

Number of changed qualifiers during the function call.

bool GetFieldsByName(CMQueryNodeValue::TObs *results, const CObjectInfo &oi_i, const string &field_name)

Resolve existing dot qualified ASN.1 name (field_name) starting from the object information instance ...

bool SetFieldsByName(CMQueryNodeValue::TObs *results, CObjectInfo &oi_i, const string &field_name)

Resolve not necessarily existing dot qualified ASN.1 name (field_name) starting from the object infor...

static Int4 s_FixCapsInPubAffil_City(objects::CAffil &affil, bool punct_only)

static bool s_PrintContainer(const CMQueryNodeValue::TObs &res_oi, const string &append_del, const string &multiple_del, CNcbiOstream &ostr)

static bool s_FixCapitalizationInElement(string &value, bool fix_abbrev, bool fix_short_words, bool cap_after_apostrophe)

void x_GetObjectsFromRef(CMQueryNodeValue::TObs &objects, const size_t &index)

virtual void TheFunction()

Function implementation.

static string s_FixLatLonFormat(objects::CBioSource &bsrc, const string &value)

virtual 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.

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

void x_LogFunction(CNcbiOstrstream &logstr)

ECollDateType GetCollDateType() const

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

virtual void TheFunction()

Function implementation.

virtual bool x_ValidArguments() const

Tests the number and the type of function arguments.

static const char * kBOLDDb

static bool s_RemoveOrgName(const objects::CBioSource &bsrc, string &field)

CIRef< IMacroBioDataIter > m_DataIter

static Int4 s_FixCapsInPubAffil(objects::CAffil &affil, bool punct_only)

static bool s_RemoveSegGaps(objects::CSeq_align &align)

void x_FixCapsInPubAffilCountry(objects::CAffil &affil, bool punct_only)

virtual void TheFunction()

Function implementation.

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

size_t TMemberIndex

Type used for indexing class members and choice variants.

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

Set object to copy of another one.

static const TObjectType * SafeCast(TTypeInfo type)

virtual bool Equals(const CSerialObject &object, ESerialRecursionMode how=eRecursive) const

Check if both objects contain the same values.

@ ePrimitiveValueString

string|char*|const char*

@ ePrimitiveValueInteger

(signed|unsigned) (char|short|int|long)

@ ePrimitiveValueEnum

enum

TObjectPtr GetObjectPtr(void) const

Get pointer to object.

ETypeFamily GetTypeFamily(void) const

Get data type family.

void GetPrimitiveValueString(string &value) const

Get string data.

CMemberIterator FindClassMember(const string &memberName) const

Find class member by its name.

Int4 GetPrimitiveValueInt4(void) const

Get data as Int4.

const string & GetName(void) const

Get type name.

EPrimitiveValueType GetPrimitiveValueType(void) const

Get type of primitive value.

Int8 GetPrimitiveValueInt8(void) const

Get data as Int8.

EResult

This indicates what happened with the trim.

vector< STrimRule > TTrimRuleVec

Multiple STrimRules are allowed, which are applied from smallest bases_to_check to largest bases_to_c...

@ eMeaningOfAmbig_OnlyCompletelyUnknown

Here, only N for nucleotides and X for amino acids is considered ambiguous.

@ eResult_NoTrimNeeded

Bioseq is left unchanged because it did not need to be trimmed at all.

@ eResult_SuccessfullyTrimmed

Bioseq is now trimmed.

CBioseq_Handle AddBioseq(CBioseq &bioseq, TPriority pri=kPriority_Default, EExist action=eExist_Throw)

Add bioseq, return bioseq handle.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

CSeq_id_Handle GetAccessSeq_id_Handle(void) const

Get any CSeq_id_Handle handle that can be used to access this bioseq Use GetSeq_id_Handle() if it's n...

CSeq_entry_Handle GetSeq_entry_Handle(void) const

Get parent Seq-entry handle.

void SetInst(TInst &v) const

CBioseq_EditHandle GetEditHandle(void) const

Get 'edit' version of handle.

TInst_Length GetInst_Length(void) const

CScope & GetScope(void) const

Get scope this handle belongs to.

const TInst & GetInst(void) const

CSeq_entry_Handle GetSeq_entry_Handle(void) const

TObjectType * GetPointer(void) const THROWS_NONE

Get pointer,.

CRef< C > Ref(C *object)

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

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

TObjectType & GetObject(void) const

Get object.

int32_t Int4

4-byte (32-bit) signed integer

#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.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

NCBI_NS_STD::string::size_type SIZE_TYPE

static string Int8ToString(Int8 value, TNumToStringFlags flags=0, int base=10)

Convert Int8 to string.

static string PrintableString(const CTempString str, TPrintableMode mode=fNewLine_Quote|fNonAscii_Passthru)

Get a printable version of the specified string.

int TPrintableMode

Bitwise OR of EPrintableMode flags.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

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

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

static void TruncateSpacesInPlace(string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string (in-place)

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

Convert int to string.

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 string Join(const TContainer &arr, const CTempString &delim)

Join strings using the specified delimiter.

static string ParseEscapes(const CTempString str, EEscSeqRange mode=eEscSeqRange_Standard, char user_char='?')

Parse C-style escape sequences in the specified string.

static bool EqualCase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-sensitive equality of a substring with another string.

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

Check if a string starts with a specified prefix value.

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 string & ReplaceInPlace(string &src, const string &search, const string &replace, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a string.

static string & ToUpper(string &str)

Convert string to upper case – string& version.

@ fNonAscii_Passthru

Allow non-ASCII but printable characters.

@ fNewLine_Quote

Display "\n" instead of actual linebreak.

@ fSplit_Tokenize

All delimiters are merged and trimmed, to get non-empty tokens only.

@ eNocase

Case insensitive compare.

void SetAffil(const TAffil &value)

Assign a value to Affil data member.

void SetCountry(const TCountry &value)

Assign a value to Country data member.

void SetSub(const TSub &value)

Assign a value to Sub data member.

bool IsSetStreet(void) const

street address, not ANSI Check if a value has been assigned to Street data member.

bool IsSetCity(void) const

Author Affiliation, City Check if a value has been assigned to City data member.

bool IsSetAffil(void) const

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

const TStreet & GetStreet(void) const

Get the Street member data.

const TAffil & GetAffil(void) const

Get the Affil member data.

const TSub & GetSub(void) const

Get the Sub member data.

bool IsSetDiv(void) const

Author Affiliation, Division Check if a value has been assigned to Div data member.

const TCountry & GetCountry(void) const

Get the Country member data.

const TStd & GetStd(void) const

Get the variant data.

void SetCity(const TCity &value)

Assign a value to City data member.

void SetStreet(const TStreet &value)

Assign a value to Street data member.

void SetDiv(const TDiv &value)

Assign a value to Div data member.

bool IsStd(void) const

Check if variant Std is selected.

bool IsSetCountry(void) const

Author Affiliation, Country Check if a value has been assigned to Country data member.

const TCity & GetCity(void) const

Get the City member data.

bool IsSetAffil(void) const

Author Affiliation, Name Check if a value has been assigned to Affil data member.

const TDiv & GetDiv(void) const

Get the Div member data.

TStd & SetStd(void)

Select the variant.

bool IsSetSub(void) const

Author Affiliation, County Sub Check if a value has been assigned to Sub data member.

bool IsSetOrg(void) const

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

const TOrg & GetOrg(void) const

Get the Org member data.

void SetOrg(TOrg &value)

Assign a value to Org data member.

TSubtype & SetSubtype(void)

Assign a value to Subtype data member.

@ eSubtype_collection_date

DD-MMM-YYYY format.

@ eSubtype_lat_lon

+/- decimal degrees

bool IsSetDb(void) const

name of database or system Check if a value has been assigned to Db data member.

void SetInitials(const TInitials &value)

Assign a value to Initials data member.

const TTag & GetTag(void) const

Get the Tag member data.

void SetTag(TTag &value)

Assign a value to Tag data member.

bool IsSetTag(void) const

appropriate tag Check if a value has been assigned to Tag data member.

const TInitials & GetInitials(void) const

Get the Initials member data.

void SetLast(const TLast &value)

Assign a value to Last data member.

const TDb & GetDb(void) const

Get the Db member data.

void SetFirst(const TFirst &value)

Assign a value to First data member.

bool IsSetInitials(void) const

first + middle initials Check if a value has been assigned to Initials data member.

bool IsSetLast(void) const

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

void SetDb(const TDb &value)

Assign a value to Db data member.

bool IsSetFirst(void) const

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

@ eSubtype_other

ASN5: old-name (254) will be added to next spec.

TSub & SetSub(void)

Select the variant.

bool IsSub(void) const

Check if variant Sub is selected.

bool IsSetLens(void) const

lengths in ids order within segs Check if a value has been assigned to Lens data member.

bool IsSetDim(void) const

dimensionality Check if a value has been assigned to Dim data member.

bool IsSetNumseg(void) const

number of segments here Check if a value has been assigned to Numseg data member.

void SetSegs(TSegs &value)

Assign a value to Segs data member.

bool IsSetSegs(void) const

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

bool IsSetStarts(void) const

start OFFSETS in ids order within segs Check if a value has been assigned to Starts data member.

const TSegs & GetSegs(void) const

Get the Segs member data.

bool IsDenseg(void) const

Check if variant Denseg is selected.

bool IsSetIds(void) const

sequences in order Check if a value has been assigned to Ids data member.

bool IsSetData(void) const

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

bool IsSetCode(void) const

genetic code used Check if a value has been assigned to Code data member.

bool IsCdregion(void) const

Check if variant Cdregion is selected.

const TData & GetData(void) const

Get the Data member data.

const TCode & GetCode(void) const

Get the Code member data.

void SetData(TData &value)

Assign a value to Data data member.

const TCdregion & GetCdregion(void) const

Get the variant data.

bool IsGeneral(void) const

Check if variant General is selected.

const TGeneral & GetGeneral(void) const

Get the variant data.

void SetPub(TPub &value)

Assign a value to Pub data member.

const TInst & GetInst(void) const

Get the Inst member data.

const TSource & GetSource(void) const

Get the variant data.

const TId & GetId(void) const

Get the Id member data.

void SetInst(TInst &value)

Assign a value to Inst data member.

TSource & SetSource(void)

Select the variant.

bool IsSetId(void) const

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

@ eRepr_delta

sequence made by changes (delta) to others

@ e_User

user defined object

@ e_Title

a title for this sequence

@ e_Source

source of materials, includes Org-ref

@ eMol_na

just a nucleic acid

const TContact & GetContact(void) const

Get the Contact member data.

void SetContact(TContact &value)

Assign a value to Contact data member.

void SetCit(TCit &value)

Assign a value to Cit data member.

bool IsSetCit(void) const

citation for this submission Check if a value has been assigned to Cit data member.

bool IsSetContact(void) const

who to contact Check if a value has been assigned to Contact data member.

void SetContact(TContact &value)

Assign a value to Contact data member.

bool IsSetContact(void) const

WARNING: this will replace the above Check if a value has been assigned to Contact data member.

unsigned int

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

where boath are integers</td > n< td ></td > n</tr > n< tr > n< td > tse</td > n< td > optional</td > n< td > String</td > n< td class=\"description\"> TSE option controls what blob is orig

Functions that resolve field names described in asn format.

const GenericPointer< typename T::ValueType > T2 value

#define EDIT_EACH_PUB_ON_PUBEQUIV(Itr, Var)

#define FOR_EACH_SEQID_ON_BIOSEQ(Itr, Var)

FOR_EACH_SEQID_ON_BIOSEQ EDIT_EACH_SEQID_ON_BIOSEQ.

#define FOR_EACH_DBXREF_ON_ORGREF(Itr, Var)

FOR_EACH_DBXREF_ON_ORGREF EDIT_EACH_DBXREF_ON_ORGREF.

#define FOR_EACH_ORGMOD_ON_BIOSOURCE(Itr, Var)

FOR_EACH_ORGMOD_ON_BIOSOURCE EDIT_EACH_ORGMOD_ON_BIOSOURCE.

#define FOR_EACH_SUBSOURCE_ON_BIOSOURCE(Itr, Var)

FOR_EACH_SUBSOURCE_ON_BIOSOURCE EDIT_EACH_SUBSOURCE_ON_BIOSOURCE.

#define EDIT_EACH_SUBSOURCE_ON_BIOSOURCE(Itr, Var)

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

For example, if bases_to_check is 10 and max_bases_allowed_to_be_ambig is 5, then on each iteration w...

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

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