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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/mkindex__app_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/blast/dbindex/makeindex/mkindex_app.cpp Source File

43 #include "../libindexdb_new/sequence_istream_fasta.hpp" 44 #include "../libindexdb_new/sequence_istream_bdb.hpp" 45 #include "../libindexdb_new/dbindex.hpp" 62 "Create a BLAST database index."

;

68

arg_desc->SetUsageContext(

69

GetArguments().GetProgramBasename(), USAGE_LINE );

70

arg_desc->AddOptionalKey(

71 "input"

"input_file_name"

"input file name"

73

arg_desc->AddOptionalKey(

74 "output"

"output_file_name"

"output file name"

76

arg_desc->AddDefaultKey(

77 "verbosity"

"reporting_level"

"how much to report"

79

arg_desc->AddOptionalKey(

80 "iformat"

"input_format"

81 "type of input used (default is \"blastdb\" for new style index, " 82 "\"fasta\" for old style index)"

84

arg_desc->AddDefaultKey(

85 "legacy"

"use_legacy_index_format"

86 "use legacy (0-terminated offset lists) dbindex format"

88

arg_desc->AddDefaultKey(

89 "idmap"

"generate_idmap"

90 "generate id map for the sequences in the index"

92

arg_desc->AddOptionalKey(

93 "db_mask"

"filtering_algorithm"

94 "use the specified filtering algorithm from BLAST DB"

98 "show the info about available database filtering algorithms" 101

arg_desc->AddOptionalKey(

102 "nmer"

"nmer_size"

103 "length of the indexed words"

105

arg_desc->AddOptionalKey(

106 "ws_hint"

"word_size_hint"

107 "most likely word size used in searches"

109

arg_desc->AddOptionalKey(

110 "volsize"

"volume_size"

"size of an index volume in MB"

112

arg_desc->AddOptionalKey(

113 "stat"

"statistics_file"

114 "write index statistics into file with that name " 115 "(for testing and debugging purposes only)."

117

arg_desc->AddOptionalKey(

118 "stride"

"stride"

119 "distance between stored database positions"

121

arg_desc->AddDefaultKey(

122 "old_style_index"

"boolean"

123 "Use old style index (deprecated)"

125

arg_desc->SetConstraint(

128

arg_desc->SetConstraint(

131

arg_desc->SetConstraint(

134

arg_desc->SetConstraint(

137

arg_desc->SetConstraint(

140

arg_desc->SetConstraint(

143

arg_desc->SetDependency(

145

arg_desc->SetDependency(

147

SetupArgDescriptions( arg_desc.release() );

157 bool

old_style(

GetArgs

()[

"old_style_index"

].AsBoolean() );

165 if

(

GetArgs

()[

"volsize"

] ) {

180 if

(

GetArgs

()[

"stride"

] ) {

183 "legacy index creation"

);

188 if

(

GetArgs

()[

"ws_hint"

] ) {

191 "legacy index creation"

);

194 unsigned long

ws_hint =

GetArgs

()[

"ws_hint"

].AsInteger();

199 "to the minimum value of "

<< ws_hint );

206 unsigned int

vol_num = 0;

215 string

iformat(

GetArgs

()[

"iformat"

] ?

GetArgs

()[

"iformat"

].AsString()

216

: old_style ?

"fasta"

"blastdb"

);

218 if

( !old_style && iformat ==

"fasta"

) {

219 ERR_POST

(

Error

"new style index requires input format 'blastdb'"

);

223 if

( iformat ==

"fasta"

) {

224 if

(

GetArgs

()[

"db_mask"

] ) {

231

(

GetArgs

()[

"input"

].AsString() ) );

234

}

else if

( iformat ==

"blastdb"

) {

236 if

(

GetArgs

()[

"show_filters"

] ) {

238 GetArgs

()[

"input"

].AsString() ) << endl;

243 if

(

GetArgs

()[

"db_mask"

] ) {

245 GetArgs

()[

"input"

].AsString(),

true

246 GetArgs

()[

"db_mask"

].AsString() );

250 GetArgs

()[

"input"

].AsString(),

false

, 0 );

255 ERR_POST

(

Error

"input format 'blastdb' requires -input option"

);

262 if

( iformat !=

"blastdb"

264 GetArgs

()[

"db_mask"

].AsString() !=

""

) {

265 ERR_POST

(

Error

"option 'db_mask' requires input format 'blastdb'"

);

269 if

( !old_style && iformat ==

"blastdb"

) {

270 if

(

GetArgs

()[

"output"

] ) {

272 "option 'output' is ignored for new style indices"

);

275 typedef

std::vector< std::string > TStrVec;

285 bool

enable_mask(

GetArgs

()[

"db_mask"

] );

286 string

filter( enable_mask ?

GetArgs

()[

"db_mask"

].AsString() :

""

);

288 ITERATE

( TStrVec, dbvi, db_vols ) {

292 Uint4

vol_num_seq( 0 );

299 Uint4

num_seq( 0 ), num_vol( 0 );

311

os << dbv_name <<

"."

<< setfill(

'0'

) << setw( 2 )

312

<< vol_num++ <<

".idx"

;

313

cerr <<

"creating "

<< os.str() <<

"..."

<< flush;

315

*seqstream, os.str(), start, stop, options );

316

num_seq += (stop - start);

318 if

( start == stop ) cerr <<

"removed (empty)"

<< endl;

321

cerr <<

"done"

<< endl;

323 "generated index volume with OIDs: "

324

start <<

"--"

<< stop );

327 while

( start != stop );

329 if

( num_seq != vol_num_seq ) {

331 "number of sequence reported by BLAST database" 332 " volume ("

<< vol_num_seq <<

") is not the same" 333 " as in the index ("

<< num_seq <<

")"

);

340

shdr.Save( dbv_name +

".shd"

);

342 "index generated for BLAST database volume "

343

dbv_name <<

" with "

<< num_seq <<

" sequences"

);

350 Uint4

num_seq( 0 ), num_vol( 0 );

352 GetArgs

()[

"show_filters"

] ?

""

GetArgs

()[

"output"

].AsString();

358

os << ofname_base <<

"."

<< setfill(

'0'

) << setw( 2 )

359

<< vol_num++ <<

".idx"

;

360

cerr <<

"creating "

<< os.str() <<

"..."

<< flush;

363

os.str(), start, stop, options );

364

num_seq += (stop - start);

366 if

( start == stop ) cerr <<

"removed (empty)"

<< endl;

367 else

{ ++num_vol; cerr <<

"done"

<< endl; }

368

}

while

( start != stop );

374

shdr.Save( ofname_base +

".shd"

);

static SOptions DefaultSOptions()

Creates an SOptions instance initialized with default values.

static void MakeIndex(const std::string &fname, const std::string &oname, TSeqNum start, TSeqNum start_chunk, TSeqNum &stop, TSeqNum &stop_chunk, const SOptions &options)

Create an index object.

CSequenceIStream::TStreamPos TSeqNum

Type used to enumerate sequences in the index.

static const char *const USAGE_LINE

String containing program usage information.

virtual int Run()

Application main procedure.

virtual void Init()

Application initialization.

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.

int GetNumOIDs() const

Returns the size of the (possibly sparse) OID range.

Sequence stream that reads BLAST nucleotide databases.

static string ShowSupportedFilters(const string &dbname)

Report on supported subject filter algorithms.

Sequence stream for reading FASTA formatted files.

Class used to abstract reading nucleotide sequences from various sources.

const unsigned long REPORT_QUIET

No progress reporting.

const unsigned long REPORT_VERBOSE

Verbose reporting.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

@ eRequires

One argument requires another.

@ eExcludes

One argument excludes another.

@ eBoolean

{'true', 't', 'false', 'f'}, case-insensitive

@ eString

An arbitrary string.

@ eInteger

Convertible into an integer number (int or Int8)

EDiagSev SetDiagPostLevel(EDiagSev post_sev=eDiag_Error)

Set the threshold severity for posting the messages.

#define ERR_POST(message)

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

@ eDiag_Warning

Warning message.

void Error(CExceptionArgs_Base &args)

void Warning(CExceptionArgs_Base &args)

void Info(CExceptionArgs_Base &args)

uint32_t Uint4

4-byte (32-bit) unsigned integer

USING_SCOPE(blastdbindex)

#define ASSERT

macro for assert.

#define GetArgs

Avoid preprocessor name clash with the NCBI C Toolkit.

Simple record type used to specify index creation parameters.

bool legacy

Indicator of the legacy index format.

unsigned long report_level

Verbose index creation.

unsigned long max_index_size

Maximum index size in megabytes.

std::string stat_file_name

File to write index statistics into.

unsigned long ws_hint

Most likely word size to use for searches.

bool idmap

Indicator of the index map creation.

unsigned long hkey_width

Width of the hash key in bits.

unsigned long stride

Stride to use for stored database locations.

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