RetroSearch Browse

Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/seqdb__demo_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/blast/seqdb_reader/demo/seqdb_demo.cpp Source File

58 virtual void Run

() = 0;

73

cout <<

" GetSequence() provides a basic interface to fetch\n" 74

" a sequence from a SeqDB object given an OID.\n"

;

85 if

(

.GiToOid(gi, oid)) {

87 unsigned

length =

.GetSequence(oid, &

buffer

);

92 for

(

unsigned i

= 0;

<length;

++) {

98

cout <<

" Found "

<< count_a

99

" alanines in sequence with GI "

<< gi

104

cout <<

" Failed: could not find GI "

<< gi << endl;

121

cout <<

" CheckOrFindOID() provides a simple OID based iteration\n" 122

" over the database. The method works well as the test\n" 123

" clause of a for loop. This example counts the number\n" 124

" of sequences in the \"swissprot\" database, displaying\n" 125

" the count and the combined length of the first 1000.\n"

;

137 if

(oid_count++ < 1000) {

142 int

measured = (oid_count > 1000) ? 1000 : oid_count;

144

cout <<

" Number of swissprot sequences in (from iteration): " 145

<< oid_count << endl;

147

cout <<

" Number of sequences in swissprot (from index file): " 150

cout <<

" Combined length of the first "

<< measured

151

" sequences: "

<< length_1000 << endl;

167

cout <<

" GetNextOIDChunk() provides versatile iteration meant\n" 168

" for multithreaded applications. Each thread fetches\n" 169

" a set of OIDs to work with, only returning for more\n" 170

" when done with that set. SeqDB guarantees that all\n" 171

" OIDs will be assigned, and no OID will be returned\n" 172

" more than once.\n\n" 173

" The data will be returned in one of two forms, either\n" 174

" as a pair of numbers representing a range of OIDs, or\n" 175

" in a vector. The number of OIDs desired is indicated\n" 176

" by setting the size of the vector on input.\n"

;

191 int

at_a_time = 1000;

197 int

begin(0), end(0);

236 switch

(sp.

GetNextOIDChunk

(begin, end, at_a_time, oids, & local_state)) {

238 for

(

int

index = 0; index < (

int

)oids.size(); index++) {

239 x_UseOID

(sp, oids[index], oid_count, length_1000);

245 for

(

int

oid = begin; oid < end; oid++) {

246 x_UseOID

(sp, oid, oid_count, length_1000);

248 done

= (begin == end);

255 unsigned

measured = (oid_count > 1000) ? 1000 : oid_count;

257

cout <<

" Sequences in swissprot (counted during iteration): " 258

<< oid_count << endl;

259

cout <<

" Sequences in swissprot (from database index file): " 261

cout <<

" Combined length of the first "

<< measured

262

" sequences: "

<< length_1000 << endl;

274 if

(oid_count++ < 1000) {

290 virtual void

Main

(

void

);

291 virtual void OnExit

(

void

);

294 static void Init

(

CSeqDB

& db,

bool

oid_shuffle,

bool

use_ambigs)

329 static const int

kLoops = 1;

332 static char

* lets =

NULL

;

337 for

(

int i

= 0;

< 4; ++

) {

338 mask

[

] =

static_cast<char>

(0x03 << (

<< 1));

339

lets[

] =

static_cast<char>

((

letter

& 0x03) << (

<< 1));

354 for

(

int

loop = 0; loop < kLoops; ++loop) {

357 for

(

int i

= 0;

< length; ++

) {

375 for

(

int

loop = 0; loop < kLoops; ++loop) {

379 for

(

int i

= 0;

< length; ++

) {

385 int

nbytes = (length + 3) / 4;

386 for

(

int i

= 0;

< nbytes; ++

) {

388 for

(

int

j = 0; j < 4; ++j) {

389 if

((c &

mask

[j]) == lets[j]) {

416

) : m_Index(index), m_AtATime(at_a_time), m_MaxLength(max_length),

423 long

* retval =

new

long;

436 int

oid_begin(0), oid_end(0);

463 for

(

int

oid = oid_begin; oid < oid_end; ++oid) {

478 for

(

int

oid = oid_begin; oid < oid_end; ++oid) {

485

shuffle(oids.begin(), oids.end(), default_random_engine());

487 ITERATE

(vector<int>, oid, oids) {

494

std::ostringstream oss;

495

oss <<

"Thread "

m_Index

" says: " 496

count

" occurrences of A"

<< endl;

499

cout << oss.str() << flush;

584

cout <<

" GetNextOIDChunk() provides versatile iteration meant\n" 585

" for multithreaded applications. Each thread fetches\n" 586

" a set of OIDs to work with, only returning for more\n" 587

" when done with that set. SeqDB guarantees that all\n" 588

" OIDs will be assigned, and no OID will be returned\n" 589

" more than once.\n\n" 590

" The data will be returned in one of two forms, either\n" 591

" as a pair of numbers representing a range of OIDs, or\n" 592

" in a vector. The number of OIDs desired is indicated\n" 593

" by setting the size of the vector on input.\n"

;

603

cout <<

"Sequence type is PROTEIN"

<< endl;

605

cout <<

"Sequence type is NUCLEOTIDE"

<< endl;

613

vector<string> paths;

614 bool

recursive =

true

;

616

cout <<

"Volume paths:"

<< endl;

617 ITERATE

(vector<string>, path, paths) {

618

cout <<

"\t"

<< *path << endl;

640

vector<CSeqDBDemo_Thread*> threads;

650

threads.push_back(thread);

658

vector<CSeqDBDemo_Thread*>::iterator

thr

;

659 while

(!threads.empty()) {

662

vector<CSeqDBDemo_Thread*>,

667 if

->IsRunning()) {

675

(*thr)->Join(

reinterpret_cast<void

>

(&retval));

677

cout <<

"Thread "

<< (*thr)->GetIndex() <<

" returned " 680

threads.erase(

thr

);

686

cout <<

"Threads combined returned "

<< sumval << endl;

710

cout <<

" SeqidToBioseq() provides a basic interface to fetch\n" 711

" sequences from a SeqDB object. Given a Seq-id, the\n" 712

" method returns the first matching CBioseq found in\n" 713

" the database.\n"

;

721 string str

(

"gi|129295"

);

726 if

(! bs.

Empty

()) {

729

cout <<

" Length of sequence \""

str 732

cout <<

" Failed: could not get length from CSeq_inst." 736

cout <<

" Failed: could not get CSeq_inst from CBioseq." 740

cout <<

" Failed: could not get CBioseq from SeqDB."

<< endl;

748 int main

(

int

argc,

char

** argv)

772

list< CRef<ISeqDBDemoCase> > demo_list;

776 bool

display_help =

false

;

780 for

(

int

arg = 1; arg < argc; arg++) {

781 char

* args = argv[arg];

782 if

(

string

(args) ==

"-db"

) {

784

cout <<

"** No database name specified. **\n"

<< endl;

789

}

else if

(

string

(args) ==

"-num_threads"

) {

791

cout <<

"** Number of threads not given. **\n"

<< endl;

796

}

else if

(

string

(args) ==

"-oid_batch"

) {

798

cout <<

"** Number of oids not given. **\n"

<< endl;

803

}

else if

(

string

(args) ==

"-list_vols"

) {

805

}

else if

(

string

(args) ==

"-no_mmap"

) {

807

}

else if

(

string

(args) ==

"-shuffle_oids"

) {

809

}

else if

(

string

(args) ==

"-use_ambigs"

) {

812

TDemoSet::iterator it = demo_set.find(

string

(args));

813 if

(it == demo_set.end()) {

814

cout <<

"** Sorry, option ["

<< argv[arg]

815

"] was not found. **\n"

<< endl;

816

display_help =

true

;

818

cout <<

"Queueing test ["

<< argv[arg] <<

"]:"

<< endl;

819

demo_list.push_back(it->second);

825

cout <<

" This application is meant to be read (as source code),\n" 826

" stepped through in a debugger, or as a minimal test app.\n" 827

" It demonstrates use of the CSeqDB library API to perform\n" 828

" simple and/or common blast database operations.\n"

;

830

display_help =

true

;

836

cout <<

"\nAvailable options:\n\n"

;

839

cout << demo->first <<

":\n"

;

840

demo->second->DisplayHelp();

ncbi::TMaskedQueryRegions mask

Demo for chunk iteration methods (single-threaded).

void x_UseOID(CSeqDB &sp, int oid, int &oid_count, int &length_1000)

Use this OID as part of the set.

virtual void DisplayHelp()

Show description for this test case.

virtual void Run()

Run this test case.

virtual ~CSeqDBDemo_ChunkIteration()

Destructor.

Demo for GetSequence() methods.

virtual ~CSeqDBDemo_GetSequence()

Destructor.

virtual void Run()

Run this test case.

virtual void DisplayHelp()

Show description for this test case.

Demo for fetching a bioseq from a seqid methods.

virtual void DisplayHelp()

Show description for this test case.

virtual ~CSeqDBDemo_SeqidToBioseq()

Destructor.

virtual void Run()

Run this test case.

Demo for simple (single threaded) iteration methods.

virtual void Run()

Run this test case.

virtual void DisplayHelp()

Show description for this test case.

virtual ~CSeqDBDemo_SimpleIteration()

Destructor.

virtual void * Main(void)

Derived (user-created) class must provide a real thread function.

const int GetIndex(void) const

long x_UseOID(int letter, int oid)

Use this OID as part of the set.

static bool sm_oid_shuffle

static bool sm_is_protein

bool IsRunning(void) const

static void Init(CSeqDB &db, bool oid_shuffle, bool use_ambigs)

static bool sm_use_ambigs

CSeqDBDemo_Thread(int index, int at_a_time, int max_length)

virtual void OnExit(void)

Override this to execute finalization code.

Demo for chunk iteration methods (multi-threaded).

static void SetListVols(void)

static int sm_OidBatchSize

static void SetUseAmbigs(void)

static void SetNoMmap(void)

virtual ~CSeqDBDemo_Threaded()

Destructor.

virtual void Run()

Run this test case.

static bool sm_OidShuffle

static void SetNumThreads(const int nthreads)

virtual void DisplayHelp()

Show description for this test case.

static void SetDbName(const string &dbname)

static void SetOidShuffle(void)

static void SetOidBatchSize(const int num)

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 GetMaxLength() const

Returns the length of the largest sequence in the database.

int GetSeqLength(int oid) const

Returns the sequence length in base pairs or residues.

ESeqType GetSequenceType() const

Returns the type of database opened - protein or nucleotide.

void RetAmbigSeq(const char **buffer) const

Returns any resources associated with the sequence.

void RetSequence(const char **buffer) const

Returns any resources associated with the sequence.

int GetNumSeqs() const

Returns the number of sequences available.

EOidListType GetNextOIDChunk(int &begin_chunk, int &end_chunk, int oid_size, vector< int > &oid_list, int *oid_state=NULL)

Return a chunk of OIDs, and update the OID bookmark.

int GetSequence(int oid, const char **buffer) const

Get a pointer to raw sequence data.

bool CheckOrFindOID(int &next_oid) const

Find an included OID, incrementing next_oid if necessary.

void SetNumberOfThreads(int num_threads, bool force_mt=false)

Setting the number of threads.

CRef< CBioseq > SeqidToBioseq(const CSeq_id &seqid) const

Get a CBioseq for a given Seq-id.

int GetAmbigSeq(int oid, const char **buffer, int nucl_code) const

Get a pointer to sequence data with ambiguities.

virtual void DisplayHelp()=0

Show description for this test case.

virtual ~ISeqDBDemoCase()

Destructor.

virtual void Run()=0

Run this test case.

static const char * str(char *buf, int n)

#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.

bool Empty(void) const THROWS_NONE

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

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

const TInst & GetInst(void) const

Get the Inst member data.

bool CanGetLength(void) const

Check if it is safe to call GetLength method.

TLength GetLength(void) const

Get the Length member data.

bool CanGetInst(void) const

Check if it is safe to call GetInst method.

char * dbname(DBPROCESS *dbproc)

Get name of current database.

unsigned int

A callback function used to compare two keys in a database.

<!DOCTYPE HTML >< html > n< header > n< title > PubSeq Gateway Help Page</title > n< style > n th

void SleepMilliSec(unsigned long ml_sec, EInterruptOnSignal onsignal=eRestartOnSignal)

Multi-threading â mutexes; rw-locks; semaphore.

Defines BLAST database access classes.

int main(int argc, char **argv)

Run one or more test cases.

DEFINE_STATIC_MUTEX(s_mutex)

const int kSeqDBNuclNcbiNA8

Used to request ambiguities in Ncbi/NA8 format.

static SLJIT_INLINE sljit_ins nr(sljit_gpr dst, sljit_gpr src)

CRef< CTestThread > thr[k_NumThreadsMax]

static Uint4 letter(char c)

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4