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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/mkkblastindex_8cpp_source.html below:

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

52 virtual void Init

(

void

);

53 virtual int Run

(

void

);

54 virtual void Exit

(

void

);

67

arg_desc->AddKey(

"db"

"database_name"

68 "BLAST database to read and create"

71

arg_desc->AddDefaultKey(

"samples"

"buhler_samples"

72 "Number of samples to check"

76

arg_desc->AddDefaultKey(

"kmer"

"kmerNum"

79

arg_desc->AddDefaultKey(

"width"

"width_data"

80 "Width of data arrays. 4 for an int, 2 for short(recommmended), 1 for byte"

83

arg_desc->AddDefaultKey(

"threads"

"number_threads"

84 "Number of threads to use."

87

arg_desc->AddDefaultKey(

"hashes"

"number_hashes"

88 "Number of Hash functions to use."

91

arg_desc->AddDefaultKey(

"alphabet"

"alphabet_choice"

92 "0 (zero) for 15 letter alphabet, 1 for 10 letter alphabet"

95

arg_desc->AddDefaultKey(

"kversion"

"index_version"

96 "1 for older LSH, 2 for Buhler LSH, 3 for one hash method"

99

arg_desc->AddOptionalKey(

"output"

"Outputfile"

102

arg_desc->AddDefaultKey(

"logfile"

104 "File for logging errors"

106 "mkkblastindex.log"

109

arg_desc->SetUsageContext(

"mkkblastindex"

"Index for protein kmer search"

);

128 int

samples =

GetArgs

()[

"samples"

].AsInteger();

130 int

kmerNum =

GetArgs

()[

"kmer"

].AsInteger();

132 int

dataWidth =

GetArgs

()[

"width"

].AsInteger();

134 int

numThreads =

GetArgs

()[

"threads"

].AsInteger();

136 int

numHashes =

GetArgs

()[

"hashes"

].AsInteger();

138 int

alphabet =

GetArgs

()[

"alphabet"

].AsInteger();

143

GetArgs

()[

"logfile"

].AsOutputFile()

150

build_index.

Build

(numThreads);

153

*logFile <<

"CSeqDB Database error: "

<< e.

GetMsg

() << endl;

156 catch

(

const

blast::CMinHashException& e) {

157

*logFile <<

"CMinHash error: "

<< e.

GetMsg

() << endl;

161

*logFile <<

"File error: "

<< e.

GetMsg

() << endl;

165

*logFile <<

"mkkblastindex failed to write output"

<< endl;

168 catch

(

const

std::bad_alloc&) {

169

*logFile <<

"mkkblastindex ran out of memory"

<< endl;

173

*logFile <<

"Unknown error"

<< endl;

194 #ifndef SKIP_DOXYGEN_PROCESSING 195 int main

(

int

argc,

const char

* argv[])

virtual void Exit(void)

Cleanup on application exit.

virtual void Init(void)

Initialize the application.

virtual int Run(void)

Run the application.

void Build(int numThreads=1)

Build the index.

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.

@ fHideXmlHelp

Hide XML help description.

@ fHideFullVersion

Hide full version description.

@ fHideDryRun

Hide dryrun description.

@ fHideConffile

Hide configuration file description.

@ fHideVersion

Hide version description.

@ fAppend

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

@ eString

An arbitrary string.

@ eOutputFile

Name of file (must be writable)

@ eInteger

Convertible into an integer number (int or Int8)

void SetDiagPostPrefix(const char *prefix)

Specify a string to prefix all subsequent error postings with.

EDiagSev SetDiagPostLevel(EDiagSev post_sev=eDiag_Error)

Set the threshold severity for posting the messages.

void SetDiagStream(CNcbiOstream *os, bool quick_flush=true, FDiagCleanup cleanup=0, void *cleanup_data=0, const string &stream_name="")

Set diagnostic stream.

@ eDiag_Warning

Warning message.

const string & GetMsg(void) const

Get message string.

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.

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

const string version

version string

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

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