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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/blastdbcmd_8cpp_source.html below:

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

51 #include "../blast/blast_app_util.hpp" 55 #ifndef SKIP_DOXYGEN_PROCESSING 60 static const string NA

"N/A"

;

138 bool x_GetOids

(

const string

& acc, vector<int> & oids);

155 if

((

id

.find(

'|'

) !=

NPOS

) || (

id

.find(

'_'

) !=

NPOS

)) {

168 else if

(seqid->

IsPdb

()) {

170

rv =

tmp

.substr(0,4);

171

rv +=

tmp

.substr(4);

198

oids.push_back(gi_oid);

215 unsigned int

err_found = 0;

223

}

else if

(args[

"entry"

HasValue

()) {

224 static const string

kDelim(

","

);

225 const string

& entry = args[

"entry"

].AsString();

227

vector<string> queries;

228 if

(entry.find(kDelim[0]) != string::npos) {

234 for

(

unsigned int i

=0;

< queries.size();

++) {

235

vector<CSeqDB::TOID> oids;

237 for

(

unsigned int

j=0; j < oids.size(); j++) {

250 if

(err_found == queries.size()) {

252 "Entry or entries not found in BLAST database"

);

255 return

(err_found) ? 1:0;

261

vector<int> algo_id(1,

id

);

263 if

( !invalid_algo_ids.empty()) {

282 for

(

unsigned int i

=0;

tmp

.size();

++) {

283 if

(

tmp

[

].find(

'-'

)!= string::npos) {

306

vector<blastdb::TOid> oids;

308 if

(oids.size() == 0) {

309 ERR_POST

(

Error

"No seq found in db for taxonomy list"

);

312 for

(

unsigned i

=0;

< oids.size();

++) {

333 if

( !line.empty() ) {

339

unique_ptr<ITaxonomy4Blast> tb;

345 LOG_POST

(

Warning

"The -taxids command line option requires additional data files. Please see the section 'Taxonomic filtering for BLAST databases' in https://www.ncbi.nlm.nih.gov/books/NBK569839/ for details."

);

349 for

(

auto id

: ids) {

353

vector<int> descendants;

354

tb->GetLeafNodeTaxids(taxid, descendants);

355 for

(

auto

d: descendants)

380

vector<string> ids, formats;

381

vector<CSeqDB::TOID> oids;

385 if

( !line.empty() ) {

388 if

(

id

empty

()) {

392

formats.push_back(

format

);

397 for

(

unsigned int i

=0;

< ids.size();

++) {

405 if

(e.

GetMsg

().find(

"DB contains no accession info"

) ==

NPOS

){

409 for

(

unsigned i

=0;

< ids.size();

++) {

437 return

(err_found) ? 1 : 0;

450 if

( !line.empty() ) {

453 if

(

id

empty

()) {

469 for

(

unsigned int

j=0; j < oids.size(); j++) {

483 return

(err_found) ? 1 : 0;

497 if

( !line.empty() ) {

500 if

(

id

empty

()) {

520 return

(err_found) ? 1 : 0;

538 const string

kLetters =

m_DbIsProtein

"residues"

"bases"

;

548 if

(args[

"exact_length"

])

552 out

" total "

<< kLetters << endl << endl

554

"\tLongest sequence: " 556

<< kLetters << endl << endl;

560 #if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \ 561 (!defined(NCBI_COMPILER_MIPSPRO)) ) 567

vector<string> volumes;

569 out

<< endl <<

"Volumes:"

<< endl;

594

vector<string> fields;

596 for

(

unsigned int i

= 0;

< fmt.size();

++) {

597 if

(fmt[

] ==

'%'

) {

598 if

(fmt[

+1] ==

'%'

) {

653 "Invalid format options for tax_info."

);

658 for

(

unsigned int i

=0;

m_Fields

.size();

++) {

665 m_Out

.scientific_name;

681 "Invalid format options for tax_info."

);

700 const string

& kFmt = args[

"outfmt"

].AsString();

706 out

"# of Tax IDs in Database: "

<< tax_ids.

size

() << endl;

714 info

.scientific_name =

;

725

vector<blastdb::TOid> rv;

729

num_seqs = rv.size();

744 if

(args[

"outfmt"

HasValue

()) {

745

outfmt = args[

"outfmt"

].AsString();

749 if

((outfmt.find(

"%f"

) != string::npos &&

750

(outfmt.find(

"%b"

) != string::npos || outfmt.find(

"%d"

) != string::npos)) ||

751

(outfmt.find(

"%b"

) != string::npos && outfmt.find(

"%d"

) != string::npos)) {

753 "The %f, %b, %d output format options cannot be specified together."

);

756 if

(outfmt.find(

"%b"

) != string::npos) {

762 if

(outfmt.find(

"%f"

) != string::npos) {

767 if

(outfmt.find(

"%d"

) != string::npos) {

771 if

(outfmt.find(

"%m"

) != string::npos) {

773 size_t i

= outfmt.find(

"%m"

) + 2;

775 while

(

< outfmt.size() && outfmt[

] >=

'0'

&& outfmt[

] <=

'9'

) {

776

algo_id = algo_id * 10 + (outfmt[

] -

'0'

);

777

outfmt.erase(

, 1);

782 "The option '-outfmt %m' is not followed by a masking algo ID."

);

787 "Invalid filtering algorithm ID for outfmt %m."

);

793 if

(args[

"strand"

].AsString() ==

"plus"

) {

795

}

else if

(args[

"strand"

].AsString() ==

"minus"

) {

799 "Both strands is not supported"

);

803 if

(args[

"mask_sequence_with"

HasValue

()) {

811 "Invalid filtering algorithm ID for mask_sequence_with."

);

824 if

(args[

"entry"

HasValue

() && args[

"entry"

].AsString() ==

"all"

) {

827 else if

(args[

"entry_batch"

HasValue

()) {

838 else if

(args[

"ipg_batch"

HasValue

()) {

847 "Must specify query type: one of 'entry', 'entry_batch', or 'pig'"

);

855 if

(args[

"long_seqids"

].AsBoolean()) {

861 if

(

registry

Get

(

"BLAST"

"LONG_SEQID"

) ==

"1"

) {

908

arg_desc->SetUsageContext(

GetArguments

().GetProgramBasename(),

911

arg_desc->SetCurrentGroup(

"BLAST database options"

);

912

arg_desc->AddDefaultKey(

kArgDb

"dbname"

"BLAST database name"

915

arg_desc->AddDefaultKey(

kArgDbType

"molecule_type"

916 "Molecule type stored in BLAST database"

919 "nucl"

"prot"

"guess"

));

921

arg_desc->SetCurrentGroup(

"Retrieval options"

);

922

arg_desc->AddOptionalKey(

"entry"

"sequence_identifier"

923 "Comma-delimited search string(s) of sequence identifiers" 924 ":\n\te.g.: 555, AC147927, 'gnl|dbname|tag', or 'all' " 925 "to select all\n\tsequences in the database"

928

arg_desc->AddOptionalKey(

"entry_batch"

"input_file"

929 "Input file for batch processing (Format: one entry per line, seq id \n" 930 "followed by optional space-delimited specifier(s) [range|strand|mask_algo_id]"

937

arg_desc->AddOptionalKey(

"ipg"

"IPG"

"IPG to retrieve"

945

arg_desc->AddOptionalKey(

"ipg_batch"

"input_file"

946 "Input file for batch processing (Format: one entry per line, IPG \n" 947 "followed by optional space-delimited specifier(s) [range|strand|mask_algo_id]"

955

arg_desc->AddFlag(

"info"

"Print BLAST database information"

true

);

957 const char

* exclusions[] = {

"entry"

"entry_batch"

"outfmt"

"strand"

958 "target_only"

"ctrl_a"

"get_dups"

"pig"

"range"

959 "mask_sequence"

"list"

"remove_redundant_dbs"

"recursive"

962 for

(

size_t i

= 0;

sizeof

(exclusions)/

sizeof

(*exclusions);

++) {

964 string

(exclusions[

]));

967

arg_desc->AddFlag(

"metadata"

"Generate BLAST database metadata"

true

);

969 const char

* exclusions_m[] = {

"entry"

"entry_batch"

"outfmt"

"strand"

970 "target_only"

"ctrl_a"

"get_dups"

"pig"

"range"

971 "mask_sequence"

"list"

"remove_redundant_dbs"

"recursive"

974 for

(

size_t i

= 0;

sizeof

(exclusions_m)/

sizeof

(*exclusions_m);

++) {

976 string

(exclusions_m[

]));

979

arg_desc->AddOptionalKey(

"metadata_output_prefix"

""

983

arg_desc->AddFlag(

"tax_info"

984 "Print taxonomic information contained in this BLAST database.\n" 985 "Use -outfmt to customize output. Format specifiers supported are:\n" 986 "\t\t%T means taxid\n" 987 "\t\t%L means common taxonomic name\n" 988 "\t\t%S means scientific name\n" 989 "\t\t%K means taxonomic super kingdom\n" 990 "\t\t%B means BLAST name\n" 991 "\t\t%n means num of seqs\n" 992 "By default it prints: '%T %S %L %K %B'\n"

true

);

994 const char

* tax_info_exclusions[] = {

"info"

"entry"

"entry_batch"

"strand"

995 "target_only"

"ctrl_a"

"get_dups"

"pig"

"range"

996 "mask_sequence"

"list"

"remove_redundant_dbs"

"recursive"

999 for

(

size_t i

= 0;

sizeof

(tax_info_exclusions)/

sizeof

(*tax_info_exclusions);

++) {

1001 string

(tax_info_exclusions[

]));

1004

arg_desc->SetCurrentGroup(

"Sequence retrieval configuration options"

);

1005

arg_desc->AddOptionalKey(

"range"

"numbers"

1006 "Range of sequence to extract in 1-based offsets " 1007 "(Format: start-stop, for start to end of sequence use start - )"

1010

arg_desc->AddDefaultKey(

"strand"

1011 "Strand of nucleotide sequence to extract"

1016

arg_desc->AddOptionalKey(

"mask_sequence_with"

"mask_algo_id"

1017 "Produce lower-case masked FASTA using the " 1018 "algorithm ID specified"

1022

arg_desc->SetCurrentGroup(

"Taxonomic filtering options"

);

1037

arg_desc->AddFlag(

kArgNoTaxIdExpansion

"Do not expand the taxonomy IDs provided to their descendant taxonomy IDs "

true

);

1041

arg_desc->SetCurrentGroup(

"Output configuration options"

);

1042

arg_desc->AddDefaultKey(

kArgOutput

"output_file"

"Output file name"

1047

arg_desc->AddDefaultKey(

"outfmt"

"format"

1048 "Output format, where the available format specifiers are:\n" 1049 "\t\t%f means sequence in FASTA format\n" 1050 "\t\t%s means sequence data (without defline)\n" 1051 "\t\t%a means accession\n" 1053 "\t\t%o means ordinal id (OID)\n" 1054 "\t\t%i means sequence id\n" 1055 "\t\t%t means sequence title\n" 1056 "\t\t%l means sequence length\n" 1057 "\t\t%h means sequence hash value\n" 1058 "\t\t%T means taxid\n" 1059 "\t\t%X means leaf-node taxids\n" 1060 "\t\t%e means membership integer\n" 1061 "\t\t%L means common taxonomic name\n" 1062 "\t\t%C means common taxonomic names for leaf-node taxids\n" 1063 "\t\t%S means scientific name\n" 1064 "\t\t%N means scientific names for leaf-node taxids\n" 1065 "\t\t%B means BLAST name\n" 1067 "\t\t%n means a list of links integers separated by ';'\n" 1069 "\t\t%K means taxonomic super kingdom\n" 1070 "\t\t%P means PIG\n" 1072 "\t\t%d means defline in text ASN.1 format\n" 1073 "\t\t%b means Bioseq in text ASN.1 format\n" 1075 "\t\t%m means sequence masking data.\n" 1076 "\t\t Masking data will be displayed as a series of 'N-M' values\n" 1077 "\t\t separated by ';' or the word 'none' if none are available.\n" 1079 "\tIf '%f' or '%d' are specified, all other format specifiers are ignored.\n" 1080 "\tFor every format except '%f' and '%d', each line of output will " 1082 "\tIf '%f' is specified, all other format specifiers are ignored.\n" 1083 "\tFor every format except '%f', each line of output will " 1085 "correspond\n\tto a sequence.\n"

1091

arg_desc->AddFlag(

"target_only"

1092 "Definition line should contain target entry only"

true

);

1097

arg_desc->AddFlag(

"get_dups"

"Retrieve duplicate accessions"

true

);

1101

arg_desc->SetCurrentGroup(

"Output configuration options for FASTA format"

);

1102

arg_desc->AddDefaultKey(

"line_length"

"number"

"Line length for output"

1105

arg_desc->SetConstraint(

"line_length"

1108

arg_desc->AddFlag(

"ctrl_a"

1109 "Use Ctrl-A as the non-redundant defline separator"

true

);

1111 const char

* exclusions_discovery[] = {

"entry"

"entry_batch"

"outfmt"

1112 "strand"

"target_only"

"ctrl_a"

"get_dups"

"pig"

"range"

kArgDb

.c_str(),

1113 "info"

"mask_sequence"

"line_length"

};

1114

arg_desc->SetCurrentGroup(

"BLAST database configuration and discovery options"

);

1115

arg_desc->AddFlag(

"show_blastdb_search_path"

1116 "Displays the default BLAST database search paths"

true

);

1117

arg_desc->AddOptionalKey(

"list"

"directory"

1118 "List BLAST databases in the specified directory"

1120

arg_desc->AddFlag(

"remove_redundant_dbs"

1121 "Remove the databases that are referenced by another " 1122 "alias file in the directory in question"

true

);

1123

arg_desc->AddFlag(

"recursive"

1124 "Recursively traverse the directory structure to list " 1125 "available BLAST databases"

true

);

1126

arg_desc->AddDefaultKey(

"list_outfmt"

"format"

1127 "Output format for the list option, where the available format specifiers are:\n" 1128 "\t\t%f means the BLAST database absolute file name path\n" 1129 "\t\t%p means the BLAST database molecule type\n" 1130 "\t\t%t means the BLAST database title\n" 1131 "\t\t%d means the date of last update of the BLAST database\n" 1132 "\t\t%l means the number of bases/residues in the BLAST database\n" 1133 "\t\t%n means the number of sequences in the BLAST database\n" 1134 "\t\t%U means the number of bytes used by the BLAST database\n" 1135 "\t\t%v means the BLAST database format version\n" 1136 "\tFor every format each line of output will " 1137 "correspond to a BLAST database.\n"

1139 for

(

size_t i

= 0;

1140 sizeof

(exclusions_discovery)/

sizeof

(*exclusions_discovery);

++) {

1142 string

(exclusions_discovery[

]));

1144 string

(exclusions_discovery[

]));

1146 string

(exclusions_discovery[

]));

1148 string

(exclusions_discovery[

]));

1150 string

(exclusions_discovery[

]));

1159 "remove_redundant_dbs"

);

1161

arg_desc->AddFlag(

"exact_length"

"Get exact length for db info"

true

);

1164

arg_desc->AddFlag(

"long_seqids"

"Use long seq id for fasta deflines"

true

);

1181 if

(args[

"show_blastdb_search_path"

]) {

1184

}

else if

(args[

"list"

]) {

1185 const string

& blastdb_dir = args[

"list"

].AsString();

1186 const bool

recurse = args[

"recursive"

];

1187 const bool

remove_redundant_dbs = args[

"remove_redundant_dbs"

];

1191 const string

& kOutFmt = args[

"list_outfmt"

].AsString();

1192 const

vector<SSeqDBInitInfo> dbs =

1194

remove_redundant_dbs);

1196 ITERATE

(vector<SSeqDBInitInfo>, db, dbs) {

1202 if

(args[

"info"

]) {

1206 else if

(args[

"metadata"

]) {

1208 string

output_prefix = args[

"metadata_output_prefix"

]

1209

? args[

"metadata_output_prefix"

].AsString()

1216

json_out->PreserveKeyNames();

1218

json_out->WriteObject(obj_info);

1223 else if

(args[

"tax_info"

]) {

1247 if

(args[

"info"

]) {

1250 else if

(args[

"tax_info"

]) {

1259 else if

(args[

"entry"

HasValue

() || args[

"entry_batch"

HasValue

()) {

1261 if

(args[

"entry"

HasValue

() && args[

"entry"

].AsString() ==

"all"

) {

1268 if

(args[

"outfmt"

HasValue

()) {

1272

vector<string> db_list;

1277

(*itr).erase(0, off+1);

1284

db_name.erase(0, off+1);

1294 #ifndef SKIP_DOXYGEN_PROCESSING 1295 int main

(

int

argc,

const char

* argv[]

)

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

#define CATCH_ALL(exit_code)

Standard catch statement for all BLAST command line programs.

Declares the BLAST exception class.

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

Auxiliary classes/functions for BLAST input library.

TSeqRange ParseSequenceRangeOpenEnd(const string &range_str, const char *error_prefix=NULL)

Parse and extract a sequence range from argument provided to this function.

static const NStr::TNumToStringFlags kFlags

Definition of an identifier for a sequence in a BLAST database.

Definition of a customizable BLAST DB information formatter interface.

string s_PreProcessAccessionsForDBv5(const string &id)

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

bool s_IsMaskAlgoIdValid(CSeqDB &blastdb, int id)

Class to constrain the values of an argument to those greater than or equal to the value specified in...

void x_PrintBlastDatabaseInformation()

Prints the BLAST database information (e.g.

void x_InitBlastDB()

Initializes Blast DB.

int x_ProcessBatchEntry(CBlastDB_Formatter &seq_fmt)

Process batch entry with range, strand and filter id.

virtual void Init()

@inheritDoc

void x_PrintBlastDatabaseTaxInformation()

bool m_Asn1Bioseq

output is ASN.1 defline

int x_ProcessBatchEntry_NoDup(CBlastDB_Formatter &fmt)

bool x_GetOids(const string &acc, vector< int > &oids)

bool m_TargetOnly

should we output target sequence only?

virtual int Run()

@inheritDoc

string x_InitSearchRequest()

CBlastDBCmdApp()

@inheritDoc

virtual void Init()

@inheritDoc

bool m_DbIsProtein

Is the database protein.

CRef< CSeqDBExpert > m_BlastDb

Handle to BLAST database.

int x_ProcessSearchRequest()

Processes all requests except printing the BLAST database information.

bool m_FASTA

output is FASTA

int x_ProcessTaxIdList(CBlastDB_Formatter &fmt)

bool m_GetDuplicates

should we find duplicate entries?

int x_ProcessBatchPig(CBlastDB_Formatter &fmt)

int x_ProcessEntry(CBlastDB_Formatter &fmt)

Process entry with range, strand and filter id.

int x_ModifyConfigForBatchEntry(const string &config)

CBlastDB_FormatterConfig m_Config

CBlastUsageReport m_UsageReport

set< TTaxId > m_TaxIdList

void x_InitBlastDB_TaxIdList()

int x_ProcessSearchType(CBlastDB_Formatter &fmt)

virtual int Run()

@inheritDoc

Fasta formatter interface.

virtual int Write(CSeqDB::TOID oid, const CBlastDB_FormatterConfig &config, string target_id=kEmptyStr)=0

virtual void DumpAll(const CBlastDB_FormatterConfig &config)=0

Customizable sequence formatter interface.

Customizable BLAST DB information formatter interface.

void AddParam(EUsageParams p, int val)

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

Defines user input exceptions.

Defines invalid user input exceptions.

static CNcbiApplication * Instance(void)

Singleton method.

void PrintEntry(const SSeqDBTaxInfo &t, int num_seqs)

CPrintTaxFields(CNcbiOstream &out, const string &fmt)

vector< string > m_Seperators

void AddTaxIds(const set< TTaxId > &tax_ids)

static bool GetTaxNames(TTaxId tax_id, SSeqDBTaxInfo &info)

Get the taxonomy names for a given tax id.

int TOID

Sequence type accepted and returned for OID indices.

void GetDBTaxIds(set< TTaxId > &tax_ids) const

Get all unique tax ids from db.

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.

void TaxIdsToOids(set< TTaxId > &tax_ids, vector< blastdb::TOid > &rv) const

Get Oid list for input tax ids.

bool GiToOidwFilterCheck(TGi gi, int &oid) const

Translate a GI To an OID with filter check.

Uint8 GetTotalLength() const

Returns the sum of the lengths of all available sequences.

bool PigToOid(int pig, int &oid) const

Translate a PIG to an OID.

static string GenerateSearchPath()

Returns the default BLAST database search path configured for this local installation of BLAST.

vector< int > ValidateMaskAlgorithms(const vector< int > &algorithm_ids)

Validates the algorithm IDs passed to this function, returning a vector of those algorithm IDs not pr...

const string & GetDBNameList() const

Get list of database names.

string GetAvailableMaskAlgorithmDescriptions()

Returns a formatted string with the list of available masking algorithms in this database for display...

int GetMaxLength() const

Returns the length of the largest sequence in the database.

ESeqType GetSequenceType() const

Returns the type of database opened - protein or nucleotide.

ESeqType

Sequence types (eUnknown tries protein, then nucleotide).

string GetTitle() const

Returns the database title.

int GetNumSeqs() const

Returns the number of sequences available.

CRef< CBlast_db_metadata > GetDBMetaData(string user_path=kEmptyStr)

void AccessionToOids(const string &acc, vector< int > &oids) const

Translate an Accession to a list of OIDs.

string GetDate() const

Returns the construction date of the database.

int GetMaskAlgorithmId(const string &algo_name) const

Get the numeric algorithm ID for a string.

EBlastDbVersion GetBlastDbVersion() const

Return blast db version.

Uint8 GetExactTotalLength()

Returns the exact sum of the lengths of all available sequences.

void AccessionsToOids(const vector< string > &accs, vector< blastdb::TOid > &oids) const

Clas to retrieve taxonomic information for filtering BLASTDBs.

iterator_bool insert(const value_type &val)

const string kArgOutput

Output file name.

const string kArgDbType

BLAST database molecule type.

const string kArgTaxIdListFile

Argument to specify file with taxonomy ids for filtering.

const string kArgNoTaxIdExpansion

Argument to not to resolve TaxId to descendant.

const string kArgDb

BLAST database name.

const string kArgTaxIdList

Argument to specify taxonomy ids for filtering.

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.

const CNcbiRegistry & GetConfig(void) const

Get the application's cached configuration parameters (read-only).

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.

CVersionInfo GetVersion(void) const

Get the program version information.

virtual void SetupArgDescriptions(CArgDescriptions *arg_desc)

Setup the command line argument descriptions.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

SStrictId_Tax::TId TTaxId

Taxon id type.

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.

@ eNoOwnership

No ownership is assumed.

@ eRequires

One argument requires another.

@ eExcludes

One argument excludes another.

@ eInputFile

Name of file (must exist and be readable)

@ eString

An arbitrary string.

@ eOutputFile

Name of file (must be writable)

@ eInteger

Convertible into an integer number (int or Int8)

void SetDiagFilter(EDiagFilter what, const char *filter_str)

Set diagnostic filter.

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.

#define ERR_POST(message)

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

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

@ eDiag_Warning

Warning message.

@ eDiagFilter_Post

for all non-TRACE, non-FATAL

void Error(CExceptionArgs_Base &args)

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

const string & GetMsg(void) const

Get message string.

#define NCBI_RETHROW_SAME(prev_exception, message)

Generic macro to re-throw the same exception.

void Warning(CExceptionArgs_Base &args)

static char GetPathSeparator(void)

Get path separator symbol specific for the current platform.

const string AsFastaString(void) const

string GetSeqIdString(bool with_version=false) const

Return seqid string with optional version for text seqid type.

@ fParse_RawText

Try to ID raw non-numeric accessions.

@ fParse_PartialOK

Warn rather than throwing an exception when a FASTA-style ID set contains unparsable portions,...

@ fParse_AnyLocal

Treat otherwise unidentified strings as local accessions as long as they don't resemble FASTA-style I...

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

bool NotEmpty(void) const THROWS_NONE

Check if CRef is not empty â pointing to an object and has a non-null value.

int64_t Int8

8-byte (64-bit) signed integer

static TThisType GetEmpty(void)

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

Get the parameter value.

bool IsEnabled(void)

Indicates whether application usage statistics collection is enabled for a current reporter instance.

CNcbiIstream & NcbiGetlineEOL(CNcbiIstream &is, string &str, string::size_type *count=NULL)

Read from "is" to "str" the next line (taking into account platform specifics of End-of-Line)

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

static int StringToNonNegativeInt(const CTempString str, TStringToNumFlags flags=0)

Convert string to non-negative integer value.

static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

int TNumToStringFlags

Bitwise OR of "ENumToStringFlags".

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

static string Join(const TContainer &arr, const CTempString &delim)

Join strings using the specified delimiter.

static bool SplitInTwo(const CTempString str, const CTempString delim, string &str1, string &str2, TSplitFlags flags=0)

Split a string into two pieces using the specified delimiters.

static bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another string.

static string & ToUpper(string &str)

Convert string to upper case â string& version.

static string UInt8ToString(Uint8 value, TNumToStringFlags flags=0, int base=10)

Convert UInt8 to string.

@ fAllowTrailingSpaces

Ignore trailing whitespace characters.

@ fConvErr_NoThrow

Do not throw an exception on error.

@ fAllowLeadingSpaces

Ignore leading whitespace characters in converted string.

@ fSplit_Tokenize

All delimiters are merged and trimmed, to get non-empty tokens only.

@ fSplit_MergeDelimiters

Merge adjacent delimiters.

@ fWithCommas

Use commas as thousands separator.

double Elapsed(void) const

Return time elapsed since first Start() or last Restart() call (in seconds).

void Start(void)

Start the timer.

bool IsPrf(void) const

Check if variant Prf is selected.

bool IsPdb(void) const

Check if variant Pdb is selected.

bool IsPir(void) const

Check if variant Pir is selected.

The blob sat and sat key Both must be positive integers</td > n< td > Non empty string The interpretation of the blob id depends on a processor Cassandra n processor expects the following format

constexpr bool empty(list< Ts... >) noexcept

const string version

version string

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Definition of a blastdb formatter interfaces.

CSeqDB::ESeqType ParseMoleculeTypeString(const string &str)

Convert a string to a CSeqDB ESeqType object.

vector< SSeqDBInitInfo > FindBlastDBs(const string &path, const string &dbtype, bool recurse, bool include_alias_files=false, bool remove_redundant_dbs=false)

Find BLAST DBs in the directory specified.

Defines exception class and several constants for SeqDB.

const blastdb::TOid kSeqDBEntryNotFound

Defines `expert' version of CSeqDB interfaces.

Defines database volume access classes.

Configuration object for CBlastDB_Formatter classes.

int m_FmtAlgoId

Filtering algorithm ID for outfmt m.

bool m_UseCtrlA

Determines whether Ctrl-A characters should be used as defline separators.

int m_FiltAlgoId

Filtering algorithm ID to mask the FASTA.

TSeqRange m_SeqRange

The range of the sequence to retrieve, if empty, the entire sequence will be retrived.

objects::ENa_strand m_Strand

All SeqLoc types will have this strand assigned; If set to 'other', the strand will be set to 'unknow...

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