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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/taxid__set_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/blast/seqdb_writer/taxid_set.cpp Source File

(

&& (!

.eof())) {

vector<string> tokens;

gi_str = tokens.front();

(tokens.size() == 2) {

tx_str = tokens.back();

(gi_str.size() && tx_str.size()) {

retval = item->second;

retval = item->second;

}

(defline.IsSetTaxid()) {

retval = defline.GetTaxid();

void FixTaxId(CRef< objects::CBlast_def_line_set > deflines)

Check that each defline has the specified taxid; if not, replace the defline and set the taxid.

static const TTaxId kTaxIdNotSet

void AddTaxId(const objects::CSeq_id &seqid, const TTaxId &taxid)

map< string, TTaxId > m_TaxIdMap

TTaxId x_SelectBestTaxid(const objects::CBlast_def_line &defline)

Selects the most suitable tax id for the input passed in, checking the global taxid first,...

void SetMappingFromFile(CNcbiIstream &f)

const_iterator end() const

const_iterator find(const key_type &key) const

#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.

SStrictId_Tax::TId TTaxId

Taxon id type.

const string AsFastaString(void) const

#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.

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 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 string TruncateSpaces(const string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string.

@ fAllowLeadingSpaces

Ignore leading whitespace characters in converted string.

list< CRef< CBlast_def_line > > Tdata

string AccessionToKey(const string &acc)

void GetDeflineKeys(const objects::CBlast_def_line &defline, vector< string > &keys)

Get all keys for a defline.

const string version

version string

const struct ncbi::grid::netcache::search::fields::KEY key

Class which defines sequence id to taxid mapping.

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