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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/taxon__cache_8cpp_source.html below:

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

57

}

catch

(std::exception& ex) {

58 LOG_POST

(

Error

"Exception in CTaxonCache::CTaxonCache() : "

<< ex.what());

67

}

catch

(std::exception& ex) {

68 LOG_POST

(

Error

"Exception in CTaxonCache::~CTaxonCache() : "

<< ex.what());

78 for

(

auto

&tax_it :

m_Map

) {

79

ostr << tax_it.first <<

'\t'

<< tax_it.second.Label <<

'\t'

<< tax_it.second.TaxName <<

'\t'

<< tax_it.second.CommonName <<

'\t'

<< tax_it.second.BlastName <<

'\n'

;

89 string

str_id,

label

;

91 while

( !line_reader->

AtEOF

() ) {

108 m_Map

[tax_id] = tax_info;

129

vector<int> to_initialize;

130 ITERATE

(vector<int>, it, tax_ids) {

132

to_initialize.push_back(*it);

135 if

(to_initialize.empty())

142 ITERATE

(vector<int>, it, to_initialize) {

143 bool

is_species =

false

;

144 bool

is_uncultured =

false

;

151

org_ref->GetLabel(&tax_info.

Label

);

152 if

(org_ref->CanGetTaxname())

153

tax_info.

TaxName

= org_ref->GetTaxname();

154 if

(org_ref->CanGetCommon())

158 m_Map

[*it] = tax_info;

162 catch

(

const

exception& ex) {

163 LOG_POST

(

Error

"CTaxonCache::Initialize: "

<< ex.what());

178 if

(conn_res !=

true

) {

186 bool

is_species =

false

;

187 bool

is_uncultured =

false

;

194

org_ref->GetLabel(&tax_info.

Label

);

195 if

(org_ref->CanGetTaxname())

196

tax_info.

TaxName

= org_ref->GetTaxname();

197 if

(org_ref->CanGetCommon())

201 m_Map

[tax_id] = tax_info;

213 catch

(

const

exception& ex) {

220 catch

(

const

exception& ex)

222 LOG_POST

(

Error

"Second try of CTaxonCache::GetLabel: "

<< ex.what());

236 return

it->second.Label;

246 return

it->second.TaxName;

256 return

it->second.CommonName;

266 return

it->second.BlastName;

CConstRef< COrg_ref > GetOrgRef(TTaxId tax_id, bool &is_species, bool &is_uncultured, string &blast_name, bool *is_specified=NULL)

void Initialize(const vector< int > &tax_ids)

void ResetConnection()

Drop connection to NCBI taxon service.

static void InitStorage(const char *cache_path)

TMap::const_iterator x_GetItem(int tax_id)

string GetTaxname(int tax_id)

static CTaxonCache & GetInstance()

string GetCommon(int tax_id)

string GetLabel(int tax_id)

void x_QueryTaxonService(int tax_id)

string GetBlastName(int tax_id)

void x_SaveTaxonCache() const

unique_ptr< objects::CTaxon1 > m_TaxonClient

static string m_CachePath

container_type::const_iterator const_iterator

const_iterator end() const

const_iterator find(const key_type &key) const

static const char *const strings[]

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define TAX_ID_FROM(T, value)

#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)

void Info(CExceptionArgs_Base &args)

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.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ofstream CNcbiOfstream

Portable alias for ofstream.

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

Convert string to int.

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 char label[]

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

Multi-threading â mutexes; rw-locks; semaphore.

DEFINE_STATIC_MUTEX(s_Mutex)

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