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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/macro__engine_8cpp_source.html below:

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

(!line_reader->

()) {

(

(

) + filename);

macro_list.resize(0);

(parser.

(

)) {

macro_list.push_back(mr);

macro_list.resize(0);

: m_SynFiles(&syn_fnames), m_MacroRep(

(&macro_rep)), m_Engine(engine) {}

found_boolargs =

;

(subnode != endnode && !found) {

arg = (*subnode)->GetValue();

m_MacroRep->GetNodeValue(arg.GetStrValue(),

);

= arg.GetStrValue();

(

.IsString()) {

m_SynFiles->push_back(

);

m_SynFiles->push_back(

);

(

.IsBool()) {

found_boolargs =

;

vector<string>* m_SynFiles{

};

CSynFileReader fnc(fnames, macro_rep, engine);

has_synonym =

;

(

& macro_it : macro_list) {

has_synonym =

;

where_tree = macro_it->GetWhereClause();

vector<string> fnames;

SearchForSynonymFile(*where_tree, *macro_it, fnames,

);

(

& f_it : fnames) {

do_where_trees = macro_it->GetAssignmentWhereClauses();

(

& wh_it : do_where_trees) {

vector<string> fnames;

SearchForSynonymFile(*wh_it, *macro_it, fnames,

);

(

& f_it : fnames) {

(!found && has_synonym) {

(

<<

<< macro_it->GetSource());

(

<<

<<

<<

);

vector<string> file_names(syn_files.

(), syn_files.

());

(!line_reader->

()) {

(

(

) + filename);

vector<CRef<CMacroRep>> parsed_vec;

(parser.

(

)) {

parsed_vec.push_back(mr);

lib.reserve(lib.size() + parsed_vec.size());

lib.insert(lib.end(), parsed_vec.begin(), parsed_vec.end());

(macro_text.empty()) {

=

;

(throw_on_error) {

=

;

=

;

,

->GetQueryTree());

nr_nonmatched = 0;

=

->GetUnMatchedTableEntries(nr_nonmatched);

(

<< identifier);

(

<<

);

(

);

(

);

(

<<

);

(

);

(

);

(

<< res);

+ name +

, &qnode);

+ name +

, &qnode);

message(

);

message +=

;

(

std::exception& e) {

(

<<

<< name <<

<< e.

());

name = iter.first;

do_funcs.push_back(name);

where_funcs.push_back(name);

do_funcs.push_back(name);

where_funcs.push_back(name);

(

<< name);

(

<< name);

(

<< name);

(

<< identifier);

sRTVarRoot, sRTVarFields;

(

<< rt_var <<

<< &v);

(

);

(

<< rt_var <<

<< &v);

(

<< rt_var <<

<< &v);

(

);

(

);

(

<< isOK);

(

);

(lookup_synonym_file) {

(!report.empty()) {

(!report.empty() &&

> 0) {

found =

;

found = (*it)->Merge(*

);

s =

;

s +=

;

s =

;

s +=

;

s += ((status) ?

:

);

s +=

;

s +=

;

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

The following asn-selectors are defined to be used in the FOR EACH statement:

class CMacroExecException

class CMacroExecException

Subclass of CQueryExec that adds: 1) Macro identifiers resolution 2) Where clause evaluation.

Class provides macro language interface for bulk bio-editing.

Class for parsed macro representation.

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

Query tree and associated utility methods.

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

definition of a Culling tree

Base class for any user function that performs editing operations on ASN.1 data.

container_type::iterator iterator

const_iterator begin() const

const_iterator end() const

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

const_iterator begin() const

const_iterator end() const

static const char * column

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define DIAG_COMPILE_INFO

Make compile time diagnostic information object to use in CNcbiDiag and CException.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

#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.

const string & GetMsg(void) const

Get message string.

string ReportAll(TDiagPostFlags flags=eDPF_Exception) const

Report all exceptions.

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

void Info(CExceptionArgs_Base &args)

static const char * sm_BsrcForSeq

static CTempString GetFuncName()

static const char * sm_Stop

vector< CRef< CMacroRep > > TMacroLibrary

static CTempString GetFuncName()

static const char * sm_Contain

static CTempString GetFuncName()

static CTempString GetFuncName()

static const char * sm_Lower

static CTempString GetFuncName()

static CTempString GetFuncName()

bool Parse(bool bSingleMacroMode=true, CQueryExec *exec=NULL)

Parse the macro and build its representation Function throws CMacroException if parsing is unsuccessf...

static const char * sm_BsrcForSeqdesc

void SetName(const string &name)

static const char * sm_PubIssue

static const char * sm_SeqNa

class CMacroFunction_LocationSeqType IS_SEQ_AA(["location"]) - returns true if the sequence identifie...

static CTempString GetFuncName()

EScopeEnum GetFuncScope()

bool GetNodeValue(const string &name, IQueryMacroUserObject &v) const

Function fills in IQueryMacroUserObject-derived node out of stored variable.

void AddToReport(const string &report)

function gradually builds the log report

void GatherUnMatchedTableEntries(const string &report, const int count)

Used when applying a table to the entry: it stores the values and number of table entries that were n...

static CTempString GetFuncName()

static const char * sm_SeqForFeat

static CTempString GetFuncName()

shared_ptr< CISOJTALookupWithCache > m_ISOJTAUpdater

void ThrowCMacroExecException(const CDiagCompileInfo &info, CMacroExecException::EErrCode code, const string &message, const CQueryParseTree::TNode *treeNode, const CException *previous=nullptr)

Throws CMacroExecException with the specified message and error location from the TNode.

void SetSource(const char *sMacroText)

Reset the parser and sets macro text to be parsed.

void x_ResetStatus(void)

Reset status and error related private data.

static CTempString GetFuncName()

static CTempString GetFuncName()

CIRef< IMacroBioDataIter > m_DataIter

static const char * sm_FunctionName

class CMacroFunction_SetPubField SetPub_Date(year, month, day, season, hour, minute,...

static CTempString GetFuncName()

static CTempString GetFuncName()

static CTempString GetFuncName()

const string & GetForEachString() const

Return "for each" string.

static CTempString GetFuncName()

static const char * sm_FunctionName

class CMacroFunction_ApplyPublication SetPub_Sub(author_field_name, author_field_value) Apply new pub...

static CTempString GetFuncName()

static CTempString GetFuncName()

void EvaluateTree(CQueryParseTree &Qtree, IResolver &resolver, bool query_tree, bool case_sensitive=false)

Evaluates tree.

static const char * sm_InList

static CTempString GetFuncName()

static CTempString GetFuncName()

static CTempString GetFuncName()

static const char * sm_PubJournal

void AddDataChanged(bool change)

function to collect whether any data was changed during the execution of the macro

static const char * sm_Equal

static const char * sm_Last

const string & GetErrorReport() const

static const char * sm_SeqForDescr

class CMacroFunction_Sequence_For_Seqdesc SEQUENCE_FOR_SEQDESC(field_name) SEQUENCE_FOR_SEQFEAT(field...

bool m_Status

execution status of most recent command

static CTempString GetFuncName()

virtual CRef< CMQueryNodeValue > GetOrCreateRTVar(const string &name)

Gets or creates run-time vars (used in assignment in Do clause)

static CTempString GetFuncName()

static CTempString GetFuncName()

static CTempString GetFuncName()

static CTempString GetFuncName()

CMacroRep * DetachMacroRep()

Detach macro representation for futher processing Caller is responsible for deletion of returned obje...

static const char * sm_PartialStart

class CMacroFunction_LocPartialTest - tests whether the location is 5'/3' partial ISPARTIALSTART() - ...

list< SResolvedField > TObs

static CTempString GetFuncName()

static const char * sm_SeqAa

bool x_AppendToLibrary(const string &filename, CMacroLib::TMacroLibrary &lib)

virtual bool GetTmpRTVarObject(const string &name, CObjectInfo &oi)

static CTempString GetFuncName()

static const char * sm_PubSerialNumber

static CTempString GetFuncName()

static CTempString GetFuncName()

static CTempString GetFuncName()

static CTempString GetFuncName()

static const char * sm_MolinfoForFeat

bool GetSimpleTypeValue(CObjectInfo &oi, const string &field_name, CMQueryNodeValue &value)

Get single node data from the node specified by parameter of type CObjectInfo and additionally field ...

static const char * sm_UpperAll

static const char * sm_FuncVolume

class CMacroFunction_SetPubVolIssuePages SetPubVolume(newValue, existing_text, delimiter,...

static CTempString GetFuncName()

static CTempString GetFuncName()

static CTempString GetFuncName()

const TObs & GetObjects() const

static const char * sm_PubAuthors

void AppendError(const string &errmsg)

void LogStart(const string &macro_name)

log start of macro execution

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

Resolve name to the list of objects.

static CTempString GetFuncName()

shared_ptr< objects::edit::CRemoteUpdater > m_RemoteUpdater

static CTempString GetFuncName()

string m_ErrorMessage

error message

void x_SetFunctions(CMacroParser &parser)

Initializes do/where lists of functions in parser.

static CTempString GetFuncName()

TBuiltInFunctionsMap m_BuiltInFunctions

Do section functions.

static const char * sm_FromStart

class CMacroFunction_LocationDistConstraint DISTFROMSTART() [>][=][<] distance DISTFROMSTOP()

static const char * sm_PartialStop

static CTempString GetFuncName()

void SetDataType(EType dt)

const string & GetName() const

shared_ptr< CHugeMacroContext > m_MacroContext

virtual ~CMacroEngine()

class CMacroEngine

unsigned GetColumnNo(void) const

Returns the column number where error occurred.

static CTempString GetFuncName()

static CTempString GetFuncName()

CRef< CMacroCmdComposite > m_CmdComposite

static const char * sm_PunctAll

const CMacroRep * m_MacroRep

temporary data available while Exec is working. It is used by resolver.

static const char * sm_Punct

static const char * sm_Upper

static CTempString GetFuncName()

IEditMacroFunction * x_ResolveFunctionName(const string &name) const

Locates function by name.

static CTempString GetFuncName()

static CTempString GetFuncName()

static CTempString GetFuncName()

void LogStop(bool status, const string &err_message)

log end of macro execution this includes time of execution, status, count of changed qualifiers and a...

CQueryParseTree * GetAssignmentWhereClause(int index) const

vector< CRef< IFunctionLog > > m_FunctionsLog

static CTempString GetFuncName()

static CTempString GetFuncName()

EType GetDataType() const

Uint4 m_Column

location of problem in macro text

static CTempString GetFuncName()

static const char * sm_First

CMacroFunction_FirstItem FIRSTOF(objects) - returns the first item from the list of objects LASTOF(ob...

void x_InitStringConstraints(bool lookup_synfile)

Define the list of functions used in string constraints.

CQueryParseTree::TFunctionNames TFunctionNamesList

Type for the list of functions in Where/Do clauses.

static const char * sm_FunctionName

void SetFunctionNames(const TFunctionNamesList &wh_funcs, const TFunctionNamesList &do_funcs)

initializes lists of known functions that should be recognized by the parser when going through WHERE...

void BuildReport(const string &rep)

static CTempString GetFuncName()

static CTempString GetFuncName()

const TSeqRange & GetSeqRange() const

Return sequence range.

static const char * sm_BsrcForFeat

const string & GetNamedAnnot() const

Return "from" named annotation.

static CTempString GetFuncName()

static CTempString GetFuncName()

static CTempString GetFuncName()

static CTempString GetFuncName()

static const char * sm_PubVolume

static CTempString GetFuncName()

static CTempString GetFuncName()

const string & GetName() const

Return macro name.

static CTempString GetFuncName()

virtual void ResetTmpRTVarObjects()

static CTempString GetFuncName()

shared_ptr< CDoiLookupWithCache > m_DOIUpdater

void SetRef(CRef< CMQueryNodeValue > node)

bool IsNotSetType() const

Check/get functions result from the top node after calculation.

virtual bool ResolveIdentifier(const string &identifier, CMQueryNodeValue &v, const CQueryParseTree::TNode *parent)

Function resolves identifiers.

static CTempString GetFuncName()

static CTempString GetFuncName()

static CTempString GetFuncName()

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

Resolve name to simple types value.

static CTempString GetFuncName()

static CTempString GetFuncName()

static const char * sm_FuncPages

bool HasDataChanged() const

bool x_ResolveRTVar(const string &identifier, CMQueryNodeValue &v, const CQueryParseTree::TNode *parent)

Gets the value of RT variable.

static CTempString GetFuncName()

static const char * sm_PubStatus

static CTempString GetFuncName()

void SetNestedState(ENestedFunc type)

const string & GetFuncReport() const

Function extracts statistic from the object.

static CTempString GetFuncName()

static CTempString GetFuncName()

static CTempString GetFuncName()

void x_InitSetOfBuiltInFunctions(bool lookup_synfile)

Define the list of functions that is recognized by the engine.

static CTempString GetFuncName()

static const char * sm_PubTitle

class CMacroFunction_PubFields PUB_TITLE(), PUB_ISSUE(), PUB_AFFIL(subfield) - returns a list of CObj...

static const char * sm_PubDOI

static CTempString GetFuncName()

static CTempString GetFuncName()

virtual void AddTmpRTVarObject(const string &name, CObjectInfo &oi)

Temporary run-time variables used in evaluating subqueries in the DO section, used together with the ...

static CTempString GetFuncName()

static CTempString GetFuncName()

void x_SetError(const string &message, Uint4 line=0, Uint4 column=0)

Sets m_Status, error_message and its location.

TTempRTVarsMap m_TempRTVars

static CTempString GetFuncName()

static const char * sm_End

unsigned GetLineNo(void) const

Returns the line number where error occurred.

static CTempString GetFuncName()

static const char * sm_LowerAll

static const char * sm_PubPMID

static CTempString GetFuncName()

static CTempString GetFuncName()

static const char * sm_PubDate

virtual bool ExistRTVar(const string &name)

Returns true if the run-time variable, identified by its name, was defined.

static const char * sm_PubAffil

static CTempString GetFuncName()

bool m_EvalDo

Flag indicates if the work should be performed on the Do clause.

CQueryParseTree * GetDoTree() const

Return "do" clause.

static CTempString GetFuncName()

void AddFunctionName(const string &func_name)

function to collect DO function names to be used for processing reporting in huge file mode

static const char * sm_BsrcForMolinfo

class CMacroFunction_GetSeqdesc BIOSOURCE_FOR_MOLINFO(field_name) or BIOSOURCE_FOR_MOLINFO(container,...

static const char * sm_PubCit

static CTempString GetFuncName()

static CTempString GetFuncName()

static CTempString GetFuncName()

static CTempString GetFuncName()

static const char * sm_FromStop

bool ReadAndParseMacros(const string &filename, vector< CRef< CMacroRep >> &macro_list)

Parses a file containing macros and stores them in a list.

vector< pair< string, int > > m_UnmatchedList

static CTempString GetFuncName()

void Reset()

reset the macro name, qualifier and iteration counts

virtual void CallFunction(const string &name, CQueryParseTree::TNode &qnode)

Function call the function specified by name, passing args as parameters and it can update nv as a re...

static CTempString GetFuncName()

static CTempString GetFuncName()

const CRef< IFunctionLog > & GetFunctionLog() const

static CTempString GetFuncName()

static CTempString GetFuncName()

CRef< CMQueryNodeValue > x_LocateRTVar(const string &identifier)

Gets the pointer to RT variable.

static CTempString GetFuncName()

static const char * sm_Start

static const char * sm_FunctionName

EditRelatedFeatureQual(feat_type, field_name, find_text, repl_text, location, case_sensitive,...

bool GetBoolValue() const

static CTempString GetFuncName()

static const char * sm_PubPages

static CTempString GetFuncName()

vector< string > GetSynonymFilenames(const vector< CRef< CMacroRep >> &macro_list) const

Extracts synonym files present in the list of macros.

bool m_HugeFileMode

execution will take place in 'huge file mode'

bool AppendToLibrary(const string &filename, CMacroLib::TMacroLibrary &lib)

Parses a file containing macros and appends the results to a map.

static CTempString GetFuncName()

static CTempString GetFuncName()

virtual CQueryParseTree * GetAssignmentWhereClause(int index) const

get one of the "where" sub-clauses which are indentified by an index in the main parsed tree

set< string > m_FuncNames

CQueryParseTree * GetWhereClause() const

Return "where" clause.

static bool s_IsStringMatching(const string &fn_name)

static CTempString GetFuncName()

static CTempString GetFuncName()

static const char * sm_FuncIssue

static CTempString GetFuncName()

bool Exec(const CMacroRep &macro_rep, const CMacroBioData &data, CRef< CMacroCmdComposite > CmdComposite, bool throw_on_error=false, CNcbiOstream *ostream=nullptr)

Executes a macro.

void AddToErrorReport(const string &error)

store encountered errors

void AddFunctionLog(const CRef< IFunctionLog > &log)

static CTempString GetFuncName()

static const char * sm_PubClass

static bool s_IsSynonymFile(const string &str)

static const char * sm_Start

class CMacroFunction_LocEnd Start() and Stop() - return the positional extremes of a location

static CTempString GetFuncName()

CMacroStat m_MacroStat

Most recent executed macro statistics.

static CTempString GetFuncName()

static CTempString GetFuncName()

static CTempString GetFuncName()

CMacroRep * Parse(const string &macro_text)

Parses macro script into its binary representation.

static const char * sm_MolinfoForBsrc

@ eFunctionNotImplemented

CTempString GetCurrentLine(void) const

static CRef< ILineReader > New(const string &filename)

Return a new ILineReader object corresponding to the given filename, taking "-" (but not "....

virtual bool AtEOF(void) const =0

Indicates (negatively) whether there is any more input.

TObjectType * GetNCPointerOrNull(void) const THROWS_NONE

Get pointer value.

CConstRef< C > ConstRef(const C *object)

Template function for conversion of const object pointer to CConstRef.

void Reset(void)

Reset reference object.

TObjectType * GetPointerOrNull(void) THROWS_NONE

Get pointer value.

TObjectType & GetNCObject(void) const

Get object.

uint32_t Uint4

4-byte (32-bit) unsigned integer

unsigned pos

Position in the src line.

unsigned line

Src line number.

const string & GetStrValue() const

@ eString

String ("free text")

#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.

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 string LongToString(long value, TNumToStringFlags flags=0, int base=10)

Convert Int to string.

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

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

static bool SplitInTwo(const CTempString str, const CTempString delim, string &str1, string &str2, TSplitFlags flags=0)

Split a string into two pieces using the specified delimiters.

static void GetCurrentTimeT(time_t *sec, long *nanosec=0)

Get current UTC time in time_t format (with nanoseconds).

Fun TreeDepthFirstTraverse(TTreeNode &tree_node, Fun func)

Depth-first tree traversal algorithm.

ETreeTraverseCode

Tree traverse code returned by the traverse predicate function.

TNodeList_CI SubNodeBegin(void) const

Return first const iterator on subnode list.

TNodeList_CI SubNodeEnd(void) const

Return last const iterator on subnode list.

const TValue & GetValue(void) const

Return node's value.

const TTreeType * GetParent(void) const

Get node's parent.

@ eTreeTraverse

Keep traversal.

@ eTreeTraverseStepOver

Do not traverse current node (pick the next one)

@ ePublication_field_affiliation

@ ePublication_field_pages

@ ePublication_field_pmid

@ ePublication_field_pub_class

@ ePublication_field_issue

@ ePublication_field_date

@ ePublication_field_title

@ ePublication_field_serial_number

@ ePublication_field_authors

@ ePublication_field_volume

@ ePublication_field_journal

@ eSeqtype_constraint_prot

@ eSeqtype_constraint_nuc

@ e_Molinfo

info on the molecule and techniques

@ e_Source

source of materials, includes Org-ref

Lightweight interface for getting lines of data with minimal memory copying.

Macro engine for macro execution.

Functions that resolve field names described in asn format.

Interface class for macro function implementation.

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

const GenericPointer< typename T::ValueType > T2 value

Int4 delta(size_t dimension_, const Int4 *score_)

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

Source location (points to the position in the original src) All positions are 0 based.

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