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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/lds2__indexer_8cpp_source.html below:

NCBI C++ ToolKit: src/app/lds2_indexer/lds2_indexer.cpp Source File

40 using namespace ncbi

;

53 virtual void Init

(

void

);

54 virtual int Run

(

void

);

61 #define GB_RELEASE_MODE_NONE "none" 62 #define GB_RELEASE_MODE_GUESS "guess" 63 #define GB_RELEASE_MODE_FORCE "force" 70

arg_desc->SetUsageContext(GetArguments().GetProgramBasename(),

71 "LDS2 Indexer"

false

);

73

arg_desc->AddKey(

"source"

"path_name"

74 "Paht to the directory with source data files"

77

arg_desc->AddOptionalKey(

"db"

"db_name"

78 "Path to the LDS2 database file"

81

arg_desc->AddFlag(

"norecursive"

82 "Do not search for source files recursively"

);

84

arg_desc->AddOptionalKey(

"gb_release"

"gb_release_mode"

85 "Mode of GB release file detection"

87

arg_desc->SetConstraint(

"gb_release"

103

arg_desc->AddOptionalKey(

"group_aligns"

"group_size"

104 "Group standalone seq-aligns into blobs"

107

arg_desc->AddOptionalKey(

"dump_table"

"table_name"

108 "Dump LDS2 table content"

110

arg_desc->AddDefaultKey(

"dump_file"

"file_name"

112

SetupArgDescriptions(arg_desc.release());

118 string

lds2_section_name =

"lds2"

;

120 string

db_path = reg.

Get

(lds2_section_name,

"Path"

122 string

source_path = reg.

Get

(lds2_section_name,

"Source"

126 if

(args[

"source"

]) {

127

source_path = args[

"source"

].AsString();

131

db_path = args[

"db"

].AsString();

139 if

( args[

"gb_release"

] ) {

140 string mode

= args[

"gb_release"

].AsString();

152 if

( args[

"group_aligns"

] ) {

156 if

( args[

"dump_table"

] ) {

157

mgr.

GetDatabase

()->

Dump

(args[

"dump_table"

].AsString(), args[

"dump_file"

].AsOutputFile());

160

mgr.

AddDataDir

(source_path, args[

"norecursive"

] ?

196 int main

(

int

argc,

const char

* argv[])

void Dump(const string &table, CNcbiOstream &out)

Dump the selected table (use empty string to dump table names or * to dump all tables.

Class for managing LDS2 database and related data files.

@ eGB_Force

Split all top-level bioseq-sets into seq-entries.

@ eGB_Guess

Try to autodetect and split GB release bioseq-sets.

@ eGB_Ignore

Do not split bioseq-sets (default)

void AddDataDir(const string &data_dir, EDirMode mode=eDir_Recurse)

Add data directory.

void SetSeqAlignGroupSize(int sz)

CLDS2_Database * GetDatabase(void)

Get the current database object.

void UpdateData(void)

Rescan all indexed files, check for modifications, update the database.

@ eDir_Recurse

Automatically scan sub-directories (default).

@ eDir_NoRecurse

Do not parse sub-dirs automatically.

void SetGBReleaseMode(EGBReleaseMode mode)

Include a standard set of the NCBI C++ Toolkit most basic headers.

@ eString

An arbitrary string.

@ eOutputFile

Name of file (must be writable)

@ eInteger

Convertible into an integer number (int or Int8)

static string ConcatPath(const string &first, const string &second)

Concatenate two parts of the path for the current OS.

virtual const string & Get(const string &section, const string &name, TFlags flags=0) const

Get the parameter value.

@ fTruncate

Leading, trailing blanks can be truncated.

void Run(void)

Enter the main loop.

#define GB_RELEASE_MODE_GUESS

#define GB_RELEASE_MODE_NONE

#define GB_RELEASE_MODE_FORCE

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

Magic spell ;-) needed for some weird compilers... very empiric.

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

#define GetArgs

Avoid preprocessor name clash with the NCBI C Toolkit.

Defines command line argument related classes.

Defines unified interface to application:

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