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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/blastdb__path_8cpp_source.html below:

NCBI C++ ToolKit: src/app/blastdb/blastdb_path.cpp Source File

39 #include "../blast/blast_app_util.hpp" 43 #ifndef SKIP_DOXYGEN_PROCESSING 76

arg_desc->SetUsageContext(

GetArguments

().GetProgramBasename(),

79

arg_desc->SetCurrentGroup(

"BLAST database options"

);

80

arg_desc->AddDefaultKey(

kArgDb

"dbname"

"BLAST database name"

83

arg_desc->AddDefaultKey(

kArgDbType

"molecule_type"

84 "Molecule type stored in BLAST database"

88

arg_desc->AddFlag(

"getvolumespath"

"Get .[np]in adn .[np]sq volumes paths"

true

);

90

arg_desc->SetCurrentGroup(

"Output configuration options"

);

91

arg_desc->AddDefaultKey(

kArgOutput

"output_file"

"Output file name"

104 string

dbtype = args[

kArgDbType

].AsString();

106 if

(args[

"getvolumespath"

]) {

108

vector<string> paths;

111 for

(

size_t i

= 0;

< paths.size();

++) {

112 out

<< paths[

] <<

"."

<< dbtype.at(0) <<

"in "

<< paths[

] <<

"."

<< dbtype.at(0) <<

"sq"

;

113 if

(

< paths.size() - 1)

out

" "

;

118 if

(dbLocation.empty()) {

135 #ifndef SKIP_DOXYGEN_PROCESSING 136 int main

(

int

argc,

const char

* argv[]

)

Declares singleton objects to store the version and reference for the BLAST engine.

Interface for converting sources of sequence data into blast sequence input.

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

virtual void Init()

@inheritDoc

virtual int Run()

@inheritDoc

CBlastDBCmdApp()

@inheritDoc

Keeps track of the version of the BLAST engine in the NCBI C++ toolkit.

static void FindVolumePaths(const string &dbname, ESeqType seqtype, vector< string > &paths, vector< string > *alias_paths=NULL, bool recursive=true, bool expand_links=true)

Find volume paths.

ESeqType

Sequence types (eUnknown tries protein, then nucleotide).

const string kArgOutput

Output file name.

const string kArgDbType

BLAST database molecule type.

const string kArgDb

BLAST database name.

void Print(const CCompactSAMApplication::AlignInfo &ai)

std::ofstream out("events_result.xml")

main entry point for tests

void SetFullVersion(CRef< CVersionAPI > version)

Set version data for the program.

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.

@ fHideFullVersion

Hide full version description.

@ fHideDryRun

Hide dryrun description.

@ fHideConffile

Hide configuration file description.

@ eString

An arbitrary string.

@ eOutputFile

Name of file (must be writable)

#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.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

const string version

version string

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

string SeqDB_ResolveDbPathNoExtension(const string &filename, char dbtype='-')

Resolve a file path using SeqDB's path algorithms.

Defines `expert' version of CSeqDB interfaces.

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