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NCBI C++ ToolKit: src/gui/objutils/test_bm/test_bm.cpp Source File

(

);

(

);

(

* buff,

,

& fileName);

(

<<

<< dir );

(

);

arg_desc->SetUsageContext(

().GetProgramBasename(),

);

accession = args[

].AsString();

(args[

].

()) {

max_count = args[

].AsInteger();

cout <<

<< accession;

feat_it(*scope, *seqLoc, sel);

(; feat_it; ++feat_it) {

((index % 10000) == 0)

cout << index << endl;

(pVariation->CanGetPlacements()) {

(!VarPlacements.empty()) {

(pVariation->GetId().CanGetTag()) {

&

= pVariation->GetId().GetTag();

svRsId[index] = rsid;

cout <<

<< index << endl;

bpsnp = sv_lay.

()*8.0 / index;

cout <<

<< sv_lay.

() <<

<< bpsnp << endl;

bpsnp = sv_lay.

()*8.0 / index;

cout <<

<< sv_lay.

() <<

<< bpsnp << endl;

User-defined methods of the data storage class.

User-defined methods of the data storage class.

Compressed bit-vector bvector<> container, set algebraic methods, traversal iterators.

#define BM_DECLARE_TEMP_BLOCK(x)

Compressed sparse container rsc_sparse_vector<> for integer types.

Serialization for sparse_vector<>

Class for support low level input/output for files.

static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, CReader *reader=0, CObjectManager::EIsDefault is_default=CObjectManager::eDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

namespace ncbi::objects::

CConstRef< CDbtag > GetNamedDbxref(const CTempString &db) const

Return a specified DB xref.

void x_SetupArgDescriptions()

void x_Serialize(const unsigned char *buff, size_t size, const string &fileName)

virtual void Init(void)

Initialize the application.

virtual int Run(void)

Run the application.

static bool ConvertFeat(CVariation &Variation, const CSeq_feat &SrcFeat)

legacy SNP feature conversion into a variation object

succinct sparse vector with runtime compression using bit-slicing / transposition method

bvector_type::size_type size_type

void optimize(bm::word_t *temp_block=0, typename bvector_type::optmode opt_mode=bvector_type::opt_compress, typename sparse_vector< Val, BV >::statistics *stat=0)

run memory optimization for all vector planes

static const char location[]

const CNcbiEnvironment & GetEnvironment(void) const

Get the application's cached environment.

const string & GetProgramExecutablePath(EFollowLinks follow_links=eIgnoreLinks) const

Get the application's executable path.

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.

virtual void SetupArgDescriptions(CArgDescriptions *arg_desc)

Setup the command line argument descriptions.

const CNcbiArguments & GetArguments(void) const

Get the application's cached unprocessed command-line arguments.

@ eString

An arbitrary string.

@ eInteger

Convertible into an integer number (int or Int8)

#define LOG_POST(message)

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

#define STD_CATCH_ALL(message)

Standard handling of "exception"-derived exceptions; catches non-standard exceptions and generates "u...

void Info(CExceptionArgs_Base &args)

size_t Write(const void *buf, size_t count) const

Write file.

void Open(const string &filename, EOpenMode open_mode, EAccessMode access_mode, EShareMode share_mode=eShare)

Open file.

static string DeleteTrailingPathSeparator(const string &path)

Delete trailing path separator, if any.

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

Concatenate two parts of the path for the current OS.

static void SplitPath(const string &path, string *dir=0, string *base=0, string *ext=0)

Split a path string into its basic components.

@ eWrite

File can be written.

@ eCreate

Create a new file, or truncate an existing one.

static objects::SAnnotSelector GetAnnotSelector(TAnnotFlags flags=0)

request an annotation selector for a given type

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Optimized implementation of CSerialObject::Assign, which is not so efficient.

CConstRef< CSeq_id > GetSeqId(void) const

static void LoadAccessionGuide(const string &filename)

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

TRange GetTotalRange(void) const

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

CConstRef< CSeq_feat > GetBestOverlapForSNP(const CSeq_feat &snp_feat, CSeqFeatData::E_Choice type, CScope &scope, bool search_both_strands=true)

Get the best overlapping feature for a SNP (variation) feature.

@ eGetId_Best

return the "best" gi (uses FindBestScore(), with CSeq_id::CalculateScore() as the score function

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

void AddDefaults(TPriority pri=kPriority_Default)

Add default data loaders from object manager.

const CSeq_feat & GetOriginalFeature(void) const

Get original feature with unmapped location/product.

SAnnotSelector & SetExcludeExternal(bool exclude=true)

External annotations for the Object Manger are annotations located in top level Seq-entry different f...

SAnnotSelector & SetMaxSize(TMaxSize max_size)

Set maximum number of annotations to find.

SAnnotSelector & AddNamedAnnots(const CAnnotName &name)

Add named annot to set of annots names to look for.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

@ use_null

support "non-assigned" or "NULL" logic

TFrom GetFrom(void) const

Get the From member data.

list< CRef< CVariantPlacement > > TPlacements

bool CanGetLoc(void) const

Check if it is safe to call GetLoc method.

const TLoc & GetLoc(void) const

Get the Loc member data.

void sparse_vector_serialize(const SV &sv, sparse_vector_serial_layout< SV > &sv_layout, bm::word_t *temp_block=0)

Serialize sparse vector into a memory buffer(s) structure.

const TYPE & Get(const CNamedParameterList *param)

const struct ncbi::grid::netcache::search::fields::SIZE size

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

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines command line argument related classes.

Defines unified interface to application:

layout class for serialization buffer structure

const unsigned char * buf() const noexcept

Return serialization buffer pointer.

size_t size() const noexcept

return current serialized size

int NcbiSys_main(int argc, ncbi::TXChar *argv[])

bm::sparse_vector< unsigned, bm::bvector<> > svector

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