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NCBI C++ ToolKit: src/gui/widgets/edit/macro_editor_context.cpp Source File

.insert(TPos(

,

));

(vector<const CFeatListItem *>, feat_it, featlist) {

feat_type = item.

();

(existing.

(desc) == existing.

()) {

left_it = str_bimap.left.find(

);

(left_it != str_bimap.left.end()) {

left_it->second;

right_it = str_bimap.right.find(

);

(right_it != str_bimap.right.end()) {

right_it->second;

allow_other =

;

{

,

};

vector<string>();

vector<string> fieldnames;

fieldnames.push_back((qual_name));

(

exception&) {

fieldnames.push_back(

);

fieldnames.push_back(qual_name);

(

exception&) {

fieldnames.push_back(

);

(fieldnames.begin(), fieldnames.end());

{

,

,

,

};

fieldnames.reserve(fieldnames.size() + text_names.size() + 2);

move(text_names.begin(), text_names.end(), inserter(fieldnames, fieldnames.end()));

fieldnames.push_back(

);

fieldnames.push_back(

);

{

,

,

};

vector<string> fieldnames;

fieldnames.push_back(it.first);

(fieldnames.begin(), fieldnames.end());

,

,

vector<string> fieldnames;

(

& it : values) {

(it.first ==

|| it.first ==

) {

((

)it.first[0]);

fieldnames.push_back(it.first);

(

&& it : fieldnames) {

((

)it[0]);

vector<string> feat_list;

feat_list.push_back(

);

feat_list.push_back(

);

feat_list.push_back(

);

feat_list.push_back(it);

feat_list.push_back(it);

vector<string> qual_names;

(

it : quals) {

vector<string>

;

vector<string>

{

};

.reserve(class_types.size() + 1);

(class_types.begin(), class_types.end(), back_inserter(

));

,

,

,

,

,

,

,

,

,

,

,

,

};

vector<string> bond_list;

(

it = list->

(); it != list->

(); ++it) {

bond_list.push_back(it->first);

vector<string> site_list;

(

it = list->

(); it != list->

(); ++it) {

site_list.push_back(it->first);

qual_name(qual);

(qual_name ==

) {

path =

;

}

(qual_name ==

) {

path =

;

path =

;

path =

;

}

(qual_name ==

) {

path =

;

(qual_name ==

|| qual_name ==

) {

path =

;

}

(qual_name ==

) {

path =

;

}

(qual_name ==

) {

path =

;

path =

;

(qual_name ==

) {

(feat.find(

) !=

) {

path =

;

path =

;

(qual_name ==

) {

path =

;

}

(qual_name ==

) {

path =

;

path =

;

path =

;

(qual_name ==

|| qual_name ==

) {

(qual_name ==

) {

path =

;

path =

;

path =

+ qual_name;

asn_path_to_feature;

asn_path_to_feature;

;

;

macro::CMacroFunction_SeqID::GetFuncName() +

;

path =

;

path =

;

path =

;

path =

;

path =

;

path =

;

path =

;

path =

;

path =

;

path =

;

path =

;

path =

+

;

;

field_name =

;

field_name =

;

(field_name.empty()) {

(!field_name.empty()) {

(!field_name.empty()) {

(!field_name.empty()) {

(!field_name.empty()) {

(!field_name.empty()) {

(!field_name.empty()) {

(!field_name.empty()) {

field_name =

+ field_name;

(!field_name.empty()) {

(field_name.empty() && macro::CMacroBioData::s_IsFeatSelector(target)) {

field_name =

;

field_name =

;

(field_name.empty()) {

pos =

.find(

);

(!field_name.empty()) {

(!field_name.empty())

(!field_name.empty()) {

(!field_name.empty()) {

field_name =

+ field_name;

(!field_name.empty()) {

(!field_name.empty());

(macro_field ==

) {

field_name =

;

(macro_field ==

) {

field_name =

;

(macro_field ==

) {

field_name =

;

field ==

||

field ==

||

(!field_name.empty()) {

TBimapStrings::relation bsrc_tax_bm[] = {

{

,

},

{

,

},

{

,

},

{

,

} };

(!field_name.empty()) {

TBimapStrings::relation bsrc_text_bm[] = {

{

,

},

pos =

.find(

);

sv_part =

+

.substr(pos + 1,

);

=

.substr(0, pos);

ret = ret + sv_part;

TBimapStrings::relation struct_comm_bm[] = {

(!field_name.empty()) {

field_name =

+ field_name;

path =

;

((target == macro::CMacroBioData::sm_Seq ||

target == macro::CMacroBioData::sm_SeqNa ||

target == macro::CMacroBioData::sm_SeqAa) && !path.empty()) {

path =

+ path;

path =

;

path =

;

TBimapStrings::relation molinfo_descr_bm[] = {

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

} };

(!field_name.empty()) {

[

](

& elem) { return NStr::EqualNocase(elem, m_MacroField); });

(find(fields.begin(), fields.end(),

) != fields.end())

(!field_name.empty()) {

TBimapStrings::relation misc_descr_bm[] = {

(!field_name.empty()) {

path =

;

((target == macro::CMacroBioData::sm_Seq ||

target == macro::CMacroBioData::sm_SeqNa ||

target == macro::CMacroBioData::sm_SeqAa) && !path.empty()) {

path =

+ path;

(target == macro::CMacroBioData::sm_SeqNa) {

macro::CMacroFunction_GetDBLink::GetFuncName() +

+

+

;

;

;

CMacroEditorContext::TBimapStrings::relation gene_qual_bm[] = {

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

}

path =

+

.substr(pos + 1);

(gui_elem.empty()) {

gui_elem =

;

gui_elem =

;

path =

;

path =

;

gui_elem =

;

gui_elem =

;

gui_elem =

;

CMacroEditorContext::TBimapStrings::relation protein_qual_bm[] = {

{

,

},

{

,

},

{

,

},

{

,

},

{

,

}

vector<string> tokens;

(tokens.size() == 2) {

(field ==

|| field ==

) {

(field ==

) {

path =

;

path =

;

path = rna_type +

+ field;

path =

;

path =

;

path =

;

path =

;

path =

;

path =

+ field;

;

;

;

;

CMacroEditorContext::TBimapStrings::relation strand_bm[] = {

{

,

},

{

,

},

{

,

},

{

,

},

{

,

} };

(choice ==

) {

(field_type) {

(choice ==

)

(choice ==

)

(choice ==

)

(choice ==

)

(choice ==

)

(field_type) {

it = find_if(values.begin(), values.end(), [&choice](

pair<string, TEnumValueType>& elem)

{ return edit::CFieldHandler::QualifierNamesAreEquivalent(elem.first, choice); });

(it != values.end()) {

(

<< choice <<

);

(macro_field ==

|| macro_field ==

) {

(field_type) {

it = name_to_values.

(macro_field);

(it != name_to_values.

()) {

(field_type) {

User-defined methods of the data storage class.

User-defined methods of the data storage class.

const_iterator end() const

const_iterator begin() const

static vector< string > GetStrings()

static CRef< CConvertFeatureBase > Create(objects::CSeqFeatData::ESubtype subtype_from, objects::CSeqFeatData::ESubtype subtype_to)

virtual string GetDescription()

static vector< string > GetFieldNames()

CFeatListItem - basic configuration data for one "feature" type.

string GetDescription() const

static wxArrayString s_FillFeatQualList(objects::CSeqFeatData::ESubtype subtype)

static bool s_IsRarelyUsedOrDiscouragedFeatureType(int subtype)

static bool s_IsGeneQualifier(const string &field)

vector< string > m_GeneKeywords

string x_GetAsnPathToRna()

string x_GetAsnPathToCdsGeneProt()

string x_GetGUIFieldForGene()

vector< string > m_RnaKeywords

vector< string > m_DescrKeywords

string GetGUIFieldName(const string &macro_field, const string &target, EMacroFieldType &type, EMSection clause=EMSection::eDoSection)

vector< string > x_GetProteinFieldnames() const

string x_GetGUIFieldForRNA()

boost::bimap< boost::bimaps::set_of< string, PNocase >, boost::bimaps::set_of< string, PNocase > > TBimapStrings

vector< string > m_EmptyKeywords

static string s_GetGUIMappedMiscDescr(const string &value)

vector< string > GetFeatureTypes(bool for_removal=false, bool to_create=false, bool include_all=false) const

string GetGUIDateField(const string &macro_field)

string GetGUIPubField(CPubFieldType::EPubFieldType)

vector< string > m_ProteinKeywords

vector< string > x_GetStrCommFieldnames() const

vector< string > GetRNATypes() const

string x_GetAsnPathtoGene()

pair< int, int > GetFeatureType(const string &name) const

string GetAsnPathToFieldName(const string &field, EMacroFieldType type, const string &target=kEmptyStr)

vector< string > m_DBLinkKeywords

string x_GetAsnPathToMolinfo(const string &target)

string x_GetAsnPathToMiscDescr(const string &target)

string x_GetAsnPathToAllBsrc()

vector< string > m_FeatQualKeywords

static string s_GetGUIMappedStructCommField(const string &value)

vector< string > m_SourceTaxKeys

vector< string > m_Featuretypes

string x_GetAsnPathToMiscFields()

string x_GetGUIFieldForProtein()

string GetGUIMolinfoValue(const string &macro_field, const string &molinfo_field)

vector< string > m_BsrcAutodefWords

string x_GetAsnPathToDescriptors()

vector< string > m_MiscKeywordsToRmv

const vector< string > & GetKeywords(EMacroFieldType type) const

string x_GetAsnPathToBsrcTax()

string x_GetAsnPathToPub()

vector< string > GetncRNAClassTypes(bool include_any=true) const

TBimapStrings m_DescriptorMap

vector< string > m_SourceKeywords

bool x_GetGUIFieldForDBLink(string &field_name, EMacroFieldType &type)

vector< string > m_SourceTextKeys

bool x_GetGUIFieldForCdsGeneProtRna(string &field_name, EMacroFieldType &type)

string GetConversionDescr(const string &from_feat, const string &to_feat)

string GetGUIAuthorName(const string &author_part)

string x_GetGUIFieldForCDS()

string GetGUIFeatQualifier(const string &macro_field)

string GetGUIAffilField(const string &macro_field)

string x_GetAsnPathToCDS()

vector< string > x_GetBsrcTextFieldnames(bool complete=false) const

vector< string > x_GetDescriptorFieldnames() const

vector< string > GetFeatQualifiers() const

map< string, pair< int, int > > m_FeatureMap

bool x_GetGUIFieldForBsrcText(string &field_name, EMacroFieldType &type)

vector< string > m_PubdescKeywords

vector< string > m_MiscKeywords

vector< string > x_GetBsrcTaxFieldnames() const

string x_GetAsnPathToSet()

string x_GetAsnPathToBsrcText()

string x_GetAsnPathToDBLinkField(const string &target)

bool x_GetGUIFieldForPubdesc(string &field_name, EMacroFieldType &type)

string x_GetAsnPathToFeatQuals()

vector< string > m_CdsGeneProtKeywords

string x_GetAsnPathToAffilFields()

bool x_GetGUIFieldForMiscDescr(string &field_name, EMacroFieldType &type)

bool x_IsDescriptor(string &field_name, EMacroFieldType &type)

vector< string > x_GetAllBsrcFieldnames() const

string GetAsnPathToFeature(const string &feat_name) const

vector< string > m_MolinfoKeywords

bool x_GetGUIFieldForStructComm(string &field_name, EMacroFieldType &type, EMSection clause=EMSection::eDoSection)

bool x_GetGUIFieldForMolinfo(string &field_name, EMacroFieldType &type)

string GetAsnPathToAuthorFieldName(const string &author_name)

static string FindInBimapOrEmpty(const string &type, const TBimapStrings &str_bimap)

string GetGUIDescriptor(const string &macro_field)

string GetAsnMolinfoValue(const string &molinfo_field, const string &choice)

vector< string > GetBondTypes() const

vector< string > GetRNAProductnames(const string &rna_type) const

bool x_GetGUIFieldForBsrcTax(string &field_name, EMacroFieldType &type)

string x_GetAsnPathToProtein()

vector< string > GetLegalQualifiers(const string &feat_name) const

vector< string > x_GetSetClassFieldnames(bool all=true) const

vector< string > GetFieldNames(EMacroFieldType type) const

vector< string > GetSiteTypes() const

string x_GetAsnPathToRnaFieldName(const string &rna_type, const string &field)

static string GetBiomolLabel(objects::CMolInfo::TBiomol biomol)

static vector< string > GetFieldNames()

static string GetTechLabel(objects::CMolInfo::TTech tech)

static EMolInfoFieldType GetFieldType(const string &field_name)

static string GetReprLabel(objects::CSeq_inst::TRepr val)

static string GetStrandLabel(objects::CSeq_inst::TStrand val)

static string GetMolLabel(objects::CSeq_inst::TMol val)

static string GetTopologyLabel(objects::CSeq_inst::TTopology tech)

static vector< string > GetChoicesForField(CMolInfoFieldType::EMolInfoFieldType field_type, bool &allow_other)

static string GetCompletenessLabel(objects::CMolInfo::TCompleteness tech)

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

static string GetSubtypeName(TSubtype stype, EVocabulary vocabulary=eVocabulary_raw)

static vector< string > GetFieldNamesWithoutDOI(bool extended=false)

@ ePubFieldType_AuthorLastName

@ ePubFieldType_AuthorFirstName

@ ePubFieldType_AffilDept

@ ePubFieldType_AffilState

@ ePubFieldType_AuthorConsortium

@ ePubFieldType_AuthorMiddleInitial

@ ePubFieldType_AuthorSuffix

@ ePubFieldType_AffilPostalCode

@ ePubFieldType_AffilAffil

static EPubFieldType GetTypeForLabel(string label)

static string NormalizePubFieldName(string orig_label)

static string GetLabelForType(EPubFieldType field_type)

static vector< string > GetFieldNames(bool extended=false)

static vector< string > GetChoicesForField(EPubFieldType field_type, bool &allow_other)

static string GetMacroLabelForType(EPubFieldType field_type)

static vector< string > GetRNAFields()

static vector< string > GetRNATypes()

static vector< string > GetncRNAClassList()

static const CSiteList * GetSiteList()

const TLegalQualifiers & GetLegalQualifiers(void) const

Get a list of all the legal qualifiers for the feature.

static E_Choice GetTypeFromSubtype(ESubtype subtype)

@ eSubtype_transit_peptide_aa

@ eSubtype_sig_peptide_aa

@ eSubtype_mat_peptide_aa

static EQualifier GetQualifierType(CTempString qual)

convert qual string to enumerated value

static const CBondList * GetBondList()

static CTempString GetQualifierAsString(EQualifier qual)

Convert a qualifier from an enumerated value to a string representation or empty if not found.

static ESubtype SubtypeNameToValue(CTempString sName)

Turn a string into its ESubtype which is NOT necessarily related to the identifier of the enum.

static CTempString SubtypeValueToName(ESubtype eSubtype)

Turns a ESubtype into its string value which is NOT necessarily related to the identifier of the enum...

static bool IsRegulatory(ESubtype subtype)

const_iterator begin() const

const_iterator end() const

static vector< string > s_GetSourceLocationOptions()

static vector< string > s_GetSourceOriginOptions()

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

static string GetSubtypeName(CSubSource::TSubtype stype, EVocabulary vocabulary=eVocabulary_raw)

static bool IsDiscouraged(const TSubtype subtype)

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

const_iterator end() const

iterator_bool insert(const value_type &val)

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

const char * kDefinitionLineLabel

const char * kFwdPrimerSeq

const char * kFwdPrimerName

const char * kSubSourceNote

const char * kCommentDescriptorLabel

const char * kRevPrimerName

const char * kGenbankBlockKeyword

const char * kRevPrimerSeq

static const struct name_t names[]

static const struct type types[]

#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)

list< pair< string, TEnumValueType > > TValues

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

const char * kColl_suffix

objects::CSeqFeatData::ESubtype GetFeatSubtype(const string &feat_type)

const char * kStrCommFieldValue

bool IsStructVoucherPart(const string &field)

const char * kStrCommFieldName

const char * kInst_suffix

bool IsSatelliteSubfield(const string &field)

bool IsMobileElementTSubfield(const string &field)

const char * kSpecid_suffix

const char * kStrCommDbname

vector< const objects::CFeatListItem * > GetSortedFeatList(objects::CSeq_entry_Handle seh, size_t max=numeric_limits< size_t >::max())

#define ENUM_METHOD_NAME(EnumName)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

NCBI_NS_STD::string::size_type SIZE_TYPE

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 SIZE_TYPE FindNoCase(const CTempString str, const CTempString pattern, SIZE_TYPE start, SIZE_TYPE end, EOccurrence which=eFirst)

Find the pattern in the specified range of a string using a case insensitive search.

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 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.

@ eNocase

Case insensitive compare.

@ eSubtype_other

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

@ eSubtype_specimen_voucher

@ eSubtype_culture_collection

E_Choice

Choice variants.

@ 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_genbank

converted genbank

@ eClass_small_genome_set

viral segments or mitochondrial minicircles

ERepr

representation class

ETopology

topology of molecule

EMol

molecule class in living organism

EStrand

strandedness in living organism

static string SelectionName(E_Choice index)

Retrieve selection name (for diagnostic purposes).

@ e_Embl

EMBL specific information.

@ e_Het

cofactor, etc associated but not bound

@ e_Num

a numbering system

@ e_Update_date

date of last update

@ e_Pir

PIR specific info.

@ e_Genbank

GenBank specific info.

@ e_Prf

PRF specific information.

@ e_Sp

SWISSPROT specific info.

@ e_Dbxref

xref to other databases

@ e_Comment

a more extensive comment

@ e_Region

overall region (globin locus)

@ e_Maploc

map location of this sequence

@ e_Create_date

date entry first created/released

@ e_Title

a title for this sequence

@ e_Pdb

PDB specific information.

@ e_Name

a name for this sequence

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 smart and slim</td> n<td> orig</td> n</tr> n<tr> n<td> last_modified</td> n<td> optional</td> n<td> Integer</td> n<td class=\"description\"> The blob last modification If provided then the exact match will be requested with n the Cassandra storage corresponding field value</td> n<td> Positive integer Not provided means that the most recent match will be selected</td> n<td></td> n</tr> n<tr> n<td> use_cache</td> n<td> optional</td> n<td> String</td> n<td class=\"description\"> The option controls if the Cassandra LMDB cache and or database should be used It n affects the seq id resolution step and the blob properties lookup step The following n options are BIOSEQ_INFO and BLOB_PROP at all

static string s_MapStrandValues(const string &value)

static string s_GetGeneField(const string &value)

static string s_GetProteinField(const string &value)

constexpr auto sort(_Init &&init)

double value_type

The numeric datatype used by the parser.

const GenericPointer< typename T::ValueType > T2 value

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

bool QualifierNamesAreEquivalent(string name1, string name2)

void FromArrayString(const wxArrayString &in, vector< string > &out)

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