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NCBI C++ ToolKit: src/objtools/readers/idmapper_config.cpp Source File

:

(strContext, bInvert, pErrors), m_LocalOnly(localOnly)

<< e <<

);

strLine(

);

( !is.eof() ) {

(*iter ==

||

*iter ==

) {

(list<string>, id_iter, ids) {

id_from.

(*id_iter);

list<SMappingContext>& contexts)

list<string> sections;

(list<string>, iter, sections) {

.context = *iter;

.map_from = reg.

(*iter,

);

.map_to = reg.

(*iter,

);

contexts.push_back(

);

& strLine,

& strContext )

& strLine )

strLength =

[2];

( hSource && hTarget ) {

& strId )

& strId )

list< CRef< CSeq_id > > ids;

list< CRef< CSeq_id > >::iterator idit;

( idit = ids.begin(); idit != ids.end(); ++idit ) {

& current = **idit;

( current.

() ) {

IdMapper implementation using an external configuration file.

void AddMapEntry(const std::string &)

CSeq_id_Handle TargetHandle(const std::string &)

static void DescribeContexts(CNcbiIstream &istr, list< SMappingContext > &contexts)

void Initialize(CNcbiIstream &istr)

void SetCurrentContext(const std::string &, std::string &)

CSeq_id_Handle SourceHandle(const std::string &)

CIdMapperConfig(CNcbiIstream &istr, const std::string &strContext="", bool bInvert=false, ILineErrorListener *pErrors=0)

Constructor specifying the content of the mapping table, mapping context, direction,...

IdMapper base class implementation.

const std::string m_strContext

virtual void AddMapping(const CSeq_id_Handle &from, const CSeq_id_Handle &to)

Add a mapping to the internal mapping table.

static const column_t columns[]

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

#define ERR_POST(message)

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

void Warning(CExceptionArgs_Base &args)

static SIZE_TYPE ParseFastaIds(CBioseq::TId &ids, const CTempString &s, bool allow_partial_failure=false)

Parse an entire set of |-delimited FASTA-style IDs, appending the results to IDS.

CSeq_id & Set(const CTempString &the_id, TParseFlags flags=fParse_AnyRaw)

Reassign based on flat specifications; arguments interpreted as with constructors.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

@ fParse_AnyLocal

Treat otherwise unidentified strings as local accessions as long as they don't resemble FASTA-style I...

CRef< C > Ref(C *object)

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

virtual void EnumerateSections(list< string > *sections, TFlags flags=fAllLayers) const

Enumerate section names.

virtual const string & Get(const string &section, const string &name, TFlags flags=0) const

Get the parameter value.

virtual void EnumerateEntries(const string &section, list< string > *entries, TFlags flags=fAllLayers) const

Enumerate parameter names for a specified section.

IRWRegistry * Read(CNcbiIstream &is, TFlags flags=0, const string &path=kEmptyStr)

Read and parse the stream "is", and merge its content with current Registry entries.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

CNcbiIstream & NcbiGetlineEOL(CNcbiIstream &is, string &str, string::size_type *count=NULL)

Read from "is" to "str" the next line (taking into account platform specifics of End-of-Line)

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

bool NcbiStreamCopy(CNcbiOstream &os, CNcbiIstream &is)

Copy the entire contents of stream "is" to stream "os".

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

Truncate whitespace in a string (in-place)

static long StringToLong(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to long.

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

Check if a string starts with a specified prefix value.

@ fSplit_MergeDelimiters

Merge adjacent delimiters.

TStr & SetStr(void)

Select the variant.

E_Choice Which(void) const

Which variant is currently selected.

TLocal & SetLocal(void)

Select the variant.

@ e_Gi

GenInfo Integrated Database.

Process information in the NCBI Registry, including working with configuration files.

static wxAcceleratorEntry entries[3]

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