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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/table__reader__macro_8cpp_source.html below:

NCBI C++ ToolKit: src/gui/packages/pkg_sequence_edit/table_reader_macro.cpp Source File

(it.m_CreateProteins) {

macros.push_back(script);

(it->IsSetLabel() && it->GetLabel().IsStr()) {

= it->GetLabel().GetStr().substr(

(

).length(),

);

(it->IsSetData() && it->GetData().IsStr()) {

col_meta_info = it->GetData().GetStr();

(skipped ==

) {

(!qualifier_type.empty());

iterator =

(qualifier_type, field_type, qualifier,

);

[field_type, &iterator](

& elem){ return elem.m_Fieldtype == field_type; });

(it->m_Iterator.empty()) {

it->m_Iterator = iterator;

it->m_Values.emplace_back(qualifier,

);

it->m_ColumnInfo.push_back(col_meta_info);

macro_script =

;

macro_script +=

;

macro_script +=

(del_options, list_update_mrna) +

;

macro_script +=

+

.m_Iterator +

;

vector<string> pure_constraints;

pure_constraints.reserve(constraints.size());

(

p : constraints) {

pure_constraints.push_back(p.second);

macro_script +=

+

(pure_constraints,

) +

;

macro_script +=

+ do_function +

;

macro_script +=

;

macro_script =

;

macro_script +=

;

macro_script +=

+ macro::CMacroFunction_CreateProteinFeats::GetFuncName() +

;

macro_script +=

;

(list_update_mrna) {

& qualifier,

apply)

(qual_type.empty())

macro::CMacroBioData::sm_BioSource;

macro::CMacroBioData::sm_SeqNa;

macro::CMacroBioData::sm_Seq;

macro::CMacroBioData::sm_MolInfo;

macro::CMacroBioData::sm_StrComm;

macro::CMacroBioData::sm_Pubdesc;

macro::CMacroBioData::sm_SeqNa;

vector<string> tokens;

(tokens.size() == 2) {

macro::CMacroBioData::sm_SeqFeat;

rna_type, ncRNA_class, rna_qual;

(del ==

) del =

;

vector<string> tokens;

(tokens.size() == 2) {

rna_type, ncRNA_class, rna_qual;

(path.find(

) !=

) {

vector<string> tokens;

path =

+ tokens[0] +

+ tokens[1] +

;

(path.find(

) !=

) {

path =

+ path +

;

(

.m_Iterator == macro::CMacroBioData::sm_MolInfo) {

constraint = macro::CMacroFunction_GetSeqdesc::sm_BsrcForMolinfo +

(

) + path +

;

(

.m_Iterator == macro::CMacroBioData::sm_StrComm ||

.m_Iterator == macro::CMacroBioData::sm_Pubdesc) {

constraint = macro::CMacroFunction_GetSeqdesc::sm_BsrcForSeqdesc +

(

) + path +

;

(

.m_Iterator == macro::CMacroBioData::sm_Seq ||

.m_Iterator == macro::CMacroBioData::sm_SeqNa) {

constraint = macro::CMacroFunction_GetSeqdesc::sm_BsrcForSeq +

(

) + path +

;

constraint = macro::CMacroFunction_GetSeqdesc::sm_BsrcForFeat +

(

) + path +

;

(

.m_Iterator == macro::CMacroBioData::sm_BioSource) {

(

.m_Iterator == macro::CMacroBioData::sm_MolInfo) {

constraint =

(macro::CMacroFunction_GetSequence::sm_SeqForDescr) +

+ path +

;

(

.m_Iterator == macro::CMacroBioData::sm_Seqdesc) {

constraint =

(macro::CMacroFunction_GetSequence::sm_SeqForDescr) +

+ path +

;

constraint =

(macro::CMacroFunction_GetSequence::sm_SeqForFeat) +

+ path +

;

constraint =

(macro::CMacroFunction_GetSeqdesc::sm_MolinfoForFeat) +

+ path +

;

(

.m_Iterator == macro::CMacroBioData::sm_BioSource) {

constraint =

(macro::CMacroFunction_GetSequence::sm_SeqForDescr) +

+ path +

;

constraint =

(macro::CMacroFunction_GetSeqdesc::sm_MolinfoForBsrc) +

+ path +

;

(

.m_Iterator == macro::CMacroBioData::sm_Seq ||

.m_Iterator == macro::CMacroBioData::sm_SeqNa ||

.m_Iterator == macro::CMacroBioData::sm_SeqAa) {

constraint = macro::CMacroFunction_GetDBLink::GetFuncName() +

+

.

+

;

constraint = macro::CMacroFunction_StructCommDatabase::GetFuncName() +

;

constraint = macro::CMacroFunction_StructCommFieldname::GetFuncName() +

;

constraint = macro::CMacroFunction_StructCommField::GetFuncName();

constraint +=

+ field_name +

;

(!constraint.empty()) {

field_in_macro;

(field_name_panel) {

field_name = field_name_panel->

(

);

(!str_constraint.empty()) {

constraints.emplace_back(field_in_macro, str_constraint);

first_field =

.m_Values.front().first;

feat_type, feat_qual;

update_mrna =

;

.m_Iterator, update_mrna,

.m_ColumnInfo);

first_field =

.m_Values.front().first;

vector<string> tokens;

(tokens.size() == 2) {

update_mrna =

;

.m_Iterator, update_mrna,

.m_ColumnInfo);

first_field =

.m_Values.front().first;

rna_type, ncRNA_class, rna_qual;

rna_type,

.m_ColumnInfo);

(

.m_Iterator == macro::CMacroBioData::sm_Protein &&

(

&& it :

.m_Values) {

.m_CreateProteins =

;

(macros.empty()) {

(

<<

);

apply_pmid =

;

(

& it : macros) {

(it.find(macro::CMacroFunction_SetPubPMID::GetFuncName()) !=

)

start = chrono::steady_clock::now();

macro::CMacroEngine macro_engine;

data_updated =

;

ignored_lines;

(

&& it : macros) {

(

<<

);

macro::CMacroBioData bio_data(entry);

macro_engine.Exec(*macro_rep, bio_data, macro_cmd,

);

(

macro::CMacroExecException& e) {

(e.GetErrCode() == macro::CMacroExecException::eMultipleEntries) {

= e.ReportAll();

pos =

.find(

);

end_pos =

.find(

);

(pos !=

&& end_pos !=

) {

=

.substr(pos, end_pos - pos);

report->SetTitle(

(

));

report->Show(

);

(

, eInvalid,

);

(

<<

<<

macro_rep->GetTitle() <<

<< err.

());

& macro_stat = macro_engine.GetStatistics();

& report = macro_stat.GetMacroReport();

(!report.GetLog().empty()) {

report_all += report.GetName() +

+ report.GetLog() +

;

& logs = macro_stat.GetFunctionsLog();

report_all += report.GetName() +

;

(

& it : logs) {

report_all += it->Print() +

;

(!report.GetErrorLog().empty()) {

report_all +=

+ report.GetErrorLog();

& unmatched = macro_stat.GetUnmatchedTableEntries();

(!unmatched.empty()) {

(unmatched.size() == 1);

temp = unmatched.front().first;

= unmatched.front().second;

nl_pos = temp.find(

);

temp = temp.substr(nl_pos + 1);

nl_pos = temp.find(

);

= temp.substr(0, nl_pos);

(!ignored_lines.empty()) {

ignored_lines +=

;

ignored_lines +=

;

data_updated |= macro_stat.HasDataUpdated();

cmd_processor->

(macro_cmd);

stop = chrono::steady_clock::now();

chrono::duration<double> elapsed = stop - start;

(

<<

<< elapsed.count() <<

);

(

);

(!ignored_lines.empty()) {

(

+ ignored_lines);

static string s_GetFunction(const TStringPairsVector &values, TConstraints &constraints, bool del_enabled, const string &target, bool update_mrna, const vector< string > &column_info={})

static string s_GetFunction(const TStringPairsVector &values, TConstraints &constraints, bool del_enabled, const vector< string > &column_info={})

static string s_GetFunction(const TStringPairsVector &values, TConstraints &constraints, bool del_enabled, const string &target, bool update_mrna, const vector< string > &column_info={})

static string s_GetFunction(const TStringPairsVector &values, TConstraints &constraints, bool del_enabled, const vector< string > &column_info={})

static string s_GetFunction(const TStringPairsVector &values, TConstraints &constraints, bool del_enabled, const vector< string > &column_info={})

static string s_GetFunction(const TStringPairsVector &values, TConstraints &constraints, bool del_enabled, const vector< string > &column_info={})

static string s_GetFunction(const TStringPairsVector &values, TConstraints &constraints, bool del_enabled, const string &target_rna_type, const vector< string > &column_info={})

static string s_GetFunction(const TStringPairsVector &values, TConstraints &constraints, bool del_enabled, const vector< string > &column_info={})

static string s_GetFunction(const TStringPairsVector &values, TConstraints &constraints, bool del_enabled, const vector< string > &column_info={})

static string s_GetMatchFieldConstraint(const SFieldFromTable &match_field, const string &delimiter, EMacroFieldType field_type, const string &target=kEmptyStr)

static string s_GetMacroFieldName(const string &field_name, const string &target, const string &selected_field=kEmptyStr)

void AddCommand(IEditCommand &command)

CFieldNamePanel * GetFieldNamePanel(void)

string GetMacroStringConstraint(const string &field_name)

static string s_GetMacroFieldName(const string &feature, const string &qualifier, const string &target, const string &selected_field=kEmptyStr)

static string AutoMatch(string field_name)

virtual string GetFieldName(const bool subfield=false)=0

Returns the name of the field as selected in the panel.

virtual string GetMacroFieldName(const string &target, const string &selected_field=kEmptyStr)

static bool IsFeature(const string &target)

void SetText(const wxString &text)

implements special composite command, which does not call to its internal commands when run the very ...

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

static CMacroEditorContext & GetInstance()

static CRef< CCmdComposite > GetPropagateUpCommand(objects::CSeq_entry_Handle seh)

static CRef< CCmdComposite > GetPropagateDownCommand(objects::CSeq_entry_Handle seh)

static string s_GetMacroFieldName(const string &rna_type, const string &qual_field, const string &target, const string &selected_field=kEmptyStr)

TVecMacroNames CreateMacros(const wxString &filename, CRef< objects::CUser_object > column_properties, const SColumnDelimiters &del_options, CConstraintPanel *panel=nullptr, bool test=false)

CMacroWorker::TVecMacroNames TVecMacroNames

SFieldFromTable m_MatchField

TStringPairsVector x_GetStringConstraint(const string &target)

static bool s_LooksLikeHeader(const string &value)

vector< SOneMacroData > m_MacroVec

string x_GetFunction(SOneMacroData &data, TStringPairsVector &constraints)

CConstraintPanel * m_ConstraintPnl

void x_GatherValuesAndMatchField()

void x_GetMatchFieldConstraint(const SOneMacroData &data, const string &delimiter, TStringPairsVector &constraints)

string x_GetVariables(const SColumnDelimiters &del_options, bool list_update_mrna=false) const

string x_GetCreateProtFeatsMacro()

EMacroFieldType m_MatchFieldType

CConstRef< objects::CUser_object > m_ColProperties

string x_GetIterator(const string &qual_type, EMacroFieldType &field_type, const string &qualifier, bool apply=false)

string x_GetMacro(SOneMacroData &data, const SColumnDelimiters &del_options)

bool RunMacro(const TVecMacroNames &macros, objects::CSeq_entry_Handle entry, ICommandProccessor *cmd_processor)

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

Undo/Redo interface for editing operations.

virtual void Execute(IEditCommand *command, wxWindow *window=0)=0

const char * kStructCommFieldName

const char * kFieldTypeSeqId

const char * kStructCommDBName

const char * kStructCommFieldValuePair

#define test(a, b, c, d, e)

static const char * column

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

string ReportAll(TDiagPostFlags flags=eDPF_Exception) const

Report all exceptions.

void Info(CExceptionArgs_Base &args)

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

virtual void Execute()

Do the editing action.

virtual void Unexecute()

Undo (opposite to Execute())

EDialogReturnValue NcbiInfoBox(const string &message, const string &title="Info")

specialized Message Box function for reporting general information messages

#define MSerial_AsnText

I/O stream manipulators –.

void Reset(void)

Reset reference object.

TObjectType & GetObject(void) const

Get object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static bool StringToBool(const CTempString str)

Convert string to bool.

vector< pair< string, string > > TStringPairsVector

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 const string BoolToString(bool value)

Convert bool to string.

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

Truncate whitespace in a string (in-place)

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

Join strings using the specified delimiter.

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.

@ eNocase

Case insensitive compare.

Macro engine for macro execution.

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

void UpdateConstraintsForDualCdsGeneProt(TConstraints &constraints, const string &src_feat)

CTempString UpdateTargetForFeatures(const string &feature, const string &qualifier, bool for_removal=false)

void UpdateConstraintsForFeatures(TConstraints &constraints, const string &feature)

void GetRNASpecificFieldsForTableReader(const string &field_name, string &rna_type, string &ncRNA_type, string &rna_qual)

CTempString UpdateTargetForRnas(const string &rna_type)

void UpdateConstraintsForRnas(TConstraints &constraints, const CArgumentList &arg_list)

CTempString UpdateTargetForCdsGeneProt(const string &fieldname)

void GetFeatureAndField(const string &field_name, string &feature, string &field)

string GetPropertyFromInfo(const string &info, const string &property)

const string kConvertMulti

const string kMultipleSpsOnly

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

const GenericPointer< typename T::ValueType > T2 value

static const char delimiter[]

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

bool m_Merge_first_two_cols

bool m_Multiple_spaces_only

EMacroFieldType m_Fieldtype

TStringPairsVector m_Values

vector< string > m_ColumnInfo

wxString GetAbsolutePath(const wxString &localpath)

string ToStdString(const wxString &s)

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