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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/tax4blast_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/blast/seqdb_reader/demo/tax4blast.cpp Source File

37 #ifndef SKIP_DOXYGEN_PROCESSING 63

arg_desc->SetUsageContext(

GetArguments

().GetProgramBasename(),

64 "Taxonomy for BLAST demo program"

);

66

arg_desc->SetCurrentGroup(

"Input options"

);

67

arg_desc->AddOptionalKey(

"taxids"

"taxonomy_ids"

69

arg_desc->AddOptionalKey(

"taxidlist"

"input_file"

73

arg_desc->SetCurrentGroup(

"Database options"

);

74

arg_desc->AddOptionalKey(

"db"

"path_to_sqlite_db"

88

cout << taxid <<

": "

;

103 auto

dbpath = args[

"db"

].HasValue() ? args[

"db"

].AsString() :

kEmptyStr

;

107 if

(args[

"taxids"

HasValue

()) {

108 string input

= args[

"taxids"

].AsString();

111 for

(

auto id

: ids) {

113

tb->GetLeafNodeTaxids(taxid, desc);

121 if

( !line.empty() ) {

123

tb->GetLeafNodeTaxids(taxid, desc);

133

}

catch

(

const

exception& e) {

136

cerr <<

"Unknown exception!"

<< endl;

142 #ifndef SKIP_DOXYGEN_PROCESSING 143 int main

(

int

argc,

const char

* argv[]

)

CTax4BlastDemo()

@inheritDoc

virtual void Init()

@inheritDoc

virtual int Run()

@inheritDoc

Clas to retrieve taxonomic information for filtering BLASTDBs.

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

void HideStdArgs(THideStdArgs hide_mask)

Set the hide mask for the Hide Std Flags.

virtual const CArgs & GetArgs(void) const

Get parsed command line arguments.

int AppMain(int argc, const char *const *argv, const char *const *envp=0, EAppDiagStream diag=eDS_Default, const char *conf=NcbiEmptyCStr, const string &name=NcbiEmptyString)

Main function (entry point) for the NCBI application.

virtual void SetupArgDescriptions(CArgDescriptions *arg_desc)

Setup the command line argument descriptions.

const CNcbiArguments & GetArguments(void) const

Get the application's cached unprocessed command-line arguments.

@ fHideXmlHelp

Hide XML help description.

@ fHideLogfile

Hide log file description.

@ fHideFullVersion

Hide full version description.

@ fHideDryRun

Hide dryrun description.

@ fHideConffile

Hide configuration file description.

@ fHideVersion

Hide version description.

@ eExcludes

One argument excludes another.

@ eInputFile

Name of file (must exist and be readable)

@ eString

An arbitrary string.

#define ERR_POST(message)

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

void Error(CExceptionArgs_Base &args)

const string & GetMsg(void) const

Get message string.

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

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 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.

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

static void s_FormatResults(const int taxid, const vector< int > &desc)

int main(int argc, const char *argv[])

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