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

(

);

(

);

(

);

: kTargetOnly(

),

kMembershipBits(

),

kCopyOnly(

)

arg_desc->SetUsageContext(

arg_desc->SetCurrentGroup(

);

arg_desc->AddDefaultKey(

,

arg_desc->AddDefaultKey(

,

arg_desc->SetConstraint(

arg_desc->SetCurrentGroup(

);

arg_desc->AddOptionalKey(

,

,

,

arg_desc->AddOptionalKey(

,

,

,

arg_desc->AddOptionalKey(

,

,

arg_desc->AddOptionalKey(

,

,

,

arg_desc->SetConstraint(

,

kSwissprot(

);

kPdb(

);

kRefseq(

);

arg_desc->SetConstraint(

arg_desc->SetCurrentGroup(

);

arg_desc->AddOptionalKey(

,

arg_desc->AddDefaultKey(

,

,

,

copy_membership_bits =

,

copy_leaf_taxids =

total_timer, bioseq_timer, memb_timer, leaf_timer;

total_timer.

();

(

= 0;

< numSeqs;

++) {

bioseq_timer.

();

(bs_nc.

()) {

bioseq_timer.

();

bioseq_timer.

();

(copy_membership_bits) {

memb_timer.

();

(bdl->CanGetMemberships() &&

!bdl->GetMemberships().empty()) {

memb_bits = bdl->GetMemberships().front();

(memb_bits == 0) {

bdl->GetSeqid().front()->AsFastaString();

(copy_leaf_taxids) {

leaf_timer.

();

bdl->GetSeqid().front()->AsFastaString();

total_timer.

();

<<

<<

<<

<<

<<

blastdb->

(elem.

, oid);

(bs_nc.

()) {

vector<string> file_paths;

retval =

;

* isam_extensions[] = {

,

,

,

,

,

};

(vector<string>,

, file_paths) {

(

= 0; isam_extensions[

] !=

;

++) {

oss << *

<<

<<

<< isam_extensions[

];

(

.Exists() &&

.GetLength() > 0) {

(vector<string>,

, file_paths) {

std::size_t found =

->find_last_of(

);

oss <<

->substr(0, found) <<

<<

<<

;

(

.Exists() &&

.GetLength() > 0) {

vector<string> file_paths;

(vector<string>,

, file_paths) {

oss << *

<<

<<

;

(

.Exists() &&

.GetLength() > 0)

args[

].AsString(),

args[

].AsString(),

mbitName = args[

].AsString();

kIsSparse =

;

kUseGiMask =

;

(args[

]) {

dbver =

(args[

].AsInteger());

kIsSparse, kParseSeqids, kUseGiMask,

? args[

].AsOutputFile() : cerr),

, dbver);

kIsSparse =

;

kUseGiMask =

;

(args[

]) {

dbver =

(args[

].AsInteger());

kIsSparse, kParseSeqids, kUseGiMask,

? args[

].AsOutputFile() : cerr),

, dbver);

(args[

]) {

time_t now = time(0);

(

<<

(72,

) <<

<<

<< ctime(&now) );

MAX_VOL_FILE_SIZE = 0x100000000;

(bytes >= MAX_VOL_FILE_SIZE) {

(

<<

);

(

argc,

* argv[])

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

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

Code to build a database given various sources of sequence data.

virtual int Run(void)

Run the application.

~BlastdbCopyApplication()

void x_CopyDB(const CArgs &args, CSeqDB::ESeqType seq_type, Uint8 bytes)

CBlastUsageReport m_UsageReport

bool x_ShouldCopyPIGs(const string &dbname, CSeqDB::ESeqType seq_type) const

const string kMembershipBits

void x_MakeDBwIDList(const CArgs &args, CSeqDB::ESeqType seq_type, Uint8 bytes)

virtual void Exit(void)

Cleanup on application exit.

bool x_ShouldParseSeqIds(const string &dbname, CSeqDB::ESeqType seq_type) const

virtual void Init(void)

Initialize the application.

TMemBitMap m_MembershipMap

map< string, ICriteria::EMembershipBit > TMemBitMap

CRef< CSeqDBExpert > m_BlastDb

virtual CConstRef< CBioseq > GetNext()

Get a Bioseq object if there are any more to get.

CBlastDbAllBioseqSource(CRef< CSeqDBExpert > blastdb)

bool x_GetOidFromSeqID(CRef< CSeqDBExpert > blastdb, CRef< CSeqDBGiList > gilist, CSeqDBFileGiList::EIdType idtype, int ind, int &oid)

virtual CConstRef< CBioseq > GetNext()

Get a Bioseq object if there are any more to get.

const TIdToLeafs GetLeafTaxIds() const

CBlastDbBioseqSource(CRef< CSeqDBExpert > blastdb, CRef< CSeqDBGiList > gilist, CSeqDBFileGiList::EIdType idtype, bool copy_membership_bits=false, bool copy_leaf_taxids=true)

list< CConstRef< CBioseq > > TBioseqs

TLinkoutMap m_MembershipBits

const TLinkoutMap GetMembershipBits() const

void AddParam(EUsageParams p, int val)

Build BlastDB format databases from various data sources.

bool AddSequences(IBioseqSource &src, bool add_pig=false)

Add sequences from an IBioseqSource object.

void SetMembBits(const TLinkoutMap &membbits, bool keep_mbits)

Specify a membership bit lookup object.

void SetUseRemote(bool use_remote)

Specify whether to use remote fetching for locally absent IDs.

void SetSourceDb(const string &src_db_name)

Specify source database(s) via the database name(s).

void StartBuild()

Start building a new database.

bool EndBuild(bool erase=false)

Finish building a new database.

void SetMaxFileSize(Uint8 max_file_size)

Set the maximum size of database component files.

void SetSkipCopyingGis(bool v)

void SetLeafTaxIds(const TIdToLeafs &taxids, bool keep_taxids)

Specify a leaf-taxids object.

Defines user input exceptions.

Defines invalid user input exceptions.

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

int GetNumGis() const

Get the number of GIs in the array.

const SGiOid & GetGiOid(int index) const

Access an element of the array.

int GetNumSis() const

Get the number of Seq-ids in the array.

const SSiOid & GetSiOid(int index) const

Access an element of the array.

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.

const string & GetDBNameList() const

Get list of database names.

ESeqType

Sequence types (eUnknown tries protein, then nucleotide).

bool SeqidToOid(const CSeq_id &seqid, int &oid) const

Translate a Seq-id to any matching OID.

CRef< CBioseq > GetBioseq(int oid, TGi target_gi=ZERO_GI, const CSeq_id *target_seq_id=NULL) const

Get a CBioseq for a sequence.

void SetVolsMemBit(int mbit)

Set the membership of all volumes.

string GetTitle() const

Returns the database title.

bool CheckOrFindOID(int &next_oid) const

Find an included OID, incrementing next_oid if necessary.

EBlastDbVersion GetBlastDbVersion() const

Return blast db version.

static CRef< CBlast_def_line_set > ExtractBlastDefline(const CBioseq &bioseq)

Extract a Blast-def-line-set object from a Bioseq retrieved by CSeqDB.

bool GiToOid(TGi gi, int &oid) const

Translate a GI to an OID.

Interface to a source of Bioseq objects.

container_type::iterator iterator

const_iterator end() const

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

const_iterator begin() const

const_iterator end() const

Constant declarations for command line arguments for BLAST programs.

const string kArgDbTitle

Title for the BLAST database.

const string kArgOutput

Output file name.

const string kArgDbType

BLAST database molecule type.

const string kArgSeqIdList

seqid list file name to restrict BLAST database

const string kArgDb

BLAST database name.

const string kArgGiList

gi list file name to restrict BLAST database

void Print(const CCompactSAMApplication::AlignInfo &ai)

This is the header file for defining and working with criteria functions.

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.

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.

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.

bool Exist(const string &name) const

Check existence of argument description.

@ eExcludes

One argument excludes another.

@ eInputFile

Name of file (must exist and be readable)

@ eString

An arbitrary string.

@ eInteger

Convertible into an integer number (int or Int8)

void SetDiagPostFlag(EDiagPostFlag flag)

Set the specified flag (globally).

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...

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

Set diagnostic stream.

@ eDPF_All

All flags (except for the "unusual" ones!)

@ eDiag_Info

Informational message.

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.

void Info(CExceptionArgs_Base &args)

void Reset(void)

Reset reference object.

bool Empty(void) const THROWS_NONE

Check if CRef is empty – not pointing to any object, which means having a null value.

uint64_t Uint8

8-byte (64-bit) unsigned integer

bool IsEnabled(void)

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

static Uint8 StringToUInt8_DataSize(const CTempString str, TStringToNumFlags flags=0)

Convert string that can contain "software" qualifiers to Uint8.

double Elapsed(void) const

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

void Stop(void)

Suspend the timer.

string AsSmartString(CTimeSpan::ESmartStringPrecision precision, ERound rounding, CTimeSpan::ESmartStringZeroMode zero_mode=CTimeSpan::eSSZ_SkipZero) const

Transform elapsed time to "smart" string.

void Start(void)

Start the timer.

const Tdata & Get(void) const

Get the member data.

list< CRef< CBlast_def_line > > Tdata

char * dbname(DBPROCESS *dbproc)

Get name of current database.

const string version

version string

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

CSeqDB::ESeqType ParseMoleculeTypeString(const string &str)

Convert a string to a CSeqDB ESeqType object.

bool DeleteBlastDb(const string &dbpath, CSeqDB::ESeqType seq_type)

Deletes all files associated with a BLAST database.

EBlastDbVersion

BLAST database version.

Structure that holds GI,OID pairs.

TGi gi

The GI or 0 if unknown.

Structure that holds Seq-id,OID pairs.

string si

The String-id or "" if unknown.

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