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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/ckblastindex_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/blast/proteinkmer/demo/ckblastindex.cpp Source File

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57 virtual void Init

(

void

);

58 virtual int Run

(

void

);

59 virtual void Exit

(

void

);

78

arg_desc->SetUsageContext(

GetArguments

().GetProgramBasename(),

79 "Runs sanity checks on KMER indices from mkkblastindex"

);

81

arg_desc->AddKey(

"db"

"database_name"

82 "BLAST database to check"

87

arg_desc->AddDefaultKey(

"logfile"

89 "File for logging errors"

111 string

error_msg=

""

;

114 CNcbiOstream

*logFile = & (args[

"logfile"

].AsOutputFile());

116

*logFile <<

"++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"

<< endl;

120

*logFile <<

"ERROR: "

database

" failed validation"

<< endl;

121 if

(error_msg !=

""

)

122

*logFile << error_msg << endl;

145 int main

(

int

argc,

const char

* argv[])

int BlastKmerVerifyIndex(CRef< CSeqDB > seqdb, string &error_msg)

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

virtual int Run(void)

Run the application.

virtual void Init(void)

Initialize the application.

virtual void Exit(void)

Cleanup on application exit.

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.

@ fAppend

Append to end-of-file; for eOutputFile or eIOFile.

@ eString

An arbitrary string.

@ eOutputFile

Name of file (must be writable)

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

string AsString(const CTimeFormat &format=kEmptyStr, TSeconds out_tz=eCurrentTimeZone) const

Transform time to string.

@ eCurrent

Use current time. See also CCurrentTime.

use only n Cassandra database for the lookups</td > n</tr > n< tr > n< td > yes</td > n< td > do not use tables BIOSEQ_INFO and BLOB_PROP in the Cassandra database

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines command line argument related classes.

Defines unified interface to application:

Defines BLAST database access classes.

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