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NCBI C++ ToolKit: src/app/asn_cache/asn_cache_test.cpp Source File

(vector<CSeq_id_Handle>, it, handles)

(ids1.size() != ids2.size())

((*it2)->Match(**it1)){

(

);

(

);

(

);

arg_desc->SetUsageContext(

().GetProgramBasename(),

);

arg_desc->AddKey(

,

,

,

arg_desc->AddDefaultKey(

,

,

,

arg_desc->AddDefaultKey(

,

,

,

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

readIndexOnly = args[

];

raw = args[

];

= !args[

];

verify_ids = args[

];

getIdOnly = args[

];

multiple = args[

];

vector< CConstRef<CSeq_entry> >

;

vector< CDataLoader::TIds > id_sets;

vector< CSeq_id_Handle > ids;

unique_ptr<CObjectOStream> os;

(line.empty() || line[0] ==

) {

<< line <<

<< e.

());

id_sets.reserve(ids.size());

(args[

]){

(args[

]){

cache_path = args[

].AsString();

num_cycles = args[

] ? 2 : 1;

count_failed = 0;

(

cycle = 0; cycle < num_cycles; cycle++){

(args[

]) {

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

(vector<CSeq_id_Handle>, id_it, ids){

( readIndexOnly ) {

vector<CAsnIndex::SIndexInfo>

;

(vector<CAsnIndex::SIndexInfo>, info_it,

) {

ostr << *info_it << endl;

vector<CAsnCache::TBuffer>

(multiple ? 0 : 1);

ostr.write((

*)&(*buf_it)[0],

<< id_it->GetSeqId()->AsFastaString());

}

(getIdOnly) {

loader->

(*id_it, id_set);

(id_set.empty()) {

<< id_it->GetSeqId()->AsFastaString());

id_sets.push_back(id_set);

vector< CRef<CSeq_entry> > entries_for_id;

entries_for_id.push_back(cache->

(*id_it));

(args[

]) {

loader->

(*id_it, id_set);

cout<<

<<

<<

<<

<< boolalpha << is_annotated << endl;

cout<<

<<

<< boolalpha << is_annotated << endl;

(entry && args[

]) {

cerr << *id_it << endl;

( desc->Which() ) {

(entry && args[

]) {

cerr << *id_it << endl;

=

;

(desc->GetQual() ==

||

desc->GetQual() ==

(

) { cout << *id_it << endl; }

=

;

(entry && args[

]) {

feat->IsSetProduct() ) {

( (*delta)->IsLoc() ) {

cout << *id_it <<

( ! args[

])

loader->

(*id_it, retrieved_ids);

cache->

(*id_it, retrieved_ids);

(retrieved_ids.empty()){

<< id_it->GetSeqId()->AsFastaString());

<< id_it->GetSeqId()->AsFastaString() <<

);

(vector<CSeq_id_Handle>, it, retrieved_ids)

(

<<

<< retrieved_ids.size()

<<

<< id_it->GetSeqId()->AsFastaString());

<< id_it->GetSeqId()->AsFastaString());

<< line <<

<< e.

());

(

<<

<< cycle+1 <<

<<

<<

<< e <<

<<

/ e <<

<< count_failed <<

);

(args[

]) {

(count_failed); }

(vector< CDataLoader::TIds >, it, id_sets){

(id_it != it->begin())

ostr << id_it->GetSeqId()->AsFastaString();

(args[

]) {

(

argc,

* argv[])

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

Contains the class definiton for CAsnCache, the main client class for accessing the ASN cache data.

static bool s_SameIds(const CBioseq::TId &ids1, const CBioseq::TId &ids2)

static const CBioseq::TId & s_GetSeqIds(const vector< CSeq_id_Handle > &handles)

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

CConstRef< objects::CBioseq > ExtractBioseq(CConstRef< objects::CSeq_entry > entry, const objects::CSeq_id_Handle &id)

virtual int Run(void)

Run the application.

virtual void Init(void)

Initialize the application.

bool x_FindAnnotated(const CSeq_entry &entry)

virtual void Exit(void)

Cleanup on application exit.

static string GetLoaderNameFromArgs(void)

static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, const string &db_path, CObjectManager::EIsDefault is_default=CObjectManager::eNonDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

CAsnCache is used by clients to access the ASN cache data.

vector< CRef< objects::CSeq_entry > > GetMultipleEntries(const objects::CSeq_id_Handle &id)

bool GetMultipleRaw(const objects::CSeq_id_Handle &id, vector< TBuffer > &buffer)

bool GetRaw(const objects::CSeq_id_Handle &id, TBuffer &buffer)

Return the raw blob in an unformatted buffer.

bool GetIndexEntry(const objects::CSeq_id_Handle &id, CAsnIndex::SIndexInfo &info)

Get the full ASN cache index entry.

CRef< objects::CSeq_entry > GetEntry(const objects::CSeq_id_Handle &id)

Return a blob as a CSeq_entry object.

bool GetMultipleIndexEntries(const objects::CSeq_id_Handle &id, vector< CAsnIndex::SIndexInfo > &info)

bool GetSeqIds(const objects::CSeq_id_Handle &id, vector< objects::CSeq_id_Handle > &all_ids, bool cheap_only=true)

Return the set of seq-ids associated with a given ID.

Template class for iteration on objects of class C (non-medifiable version)

const_iterator begin() const

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

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.

#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.

@ eExcludes

One argument excludes another.

@ eInputFile

Name of file (must exist and be readable)

@ eOutputFile

Name of file (must be writable)

#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.

void Error(CExceptionArgs_Base &args)

void Warning(CExceptionArgs_Base &args)

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

void Info(CExceptionArgs_Base &args)

#define MSerial_AsnText

I/O stream manipulators –.

@ eSerial_AsnText

ASN.1 text.

@ eSerial_AsnBinary

ASN.1 binary.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

static CObjectOStream * Open(ESerialDataFormat format, CNcbiOstream &outStream, bool deleteOutStream)

Create serial object writer and attach it to an output stream.

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,...

void AddDataLoader(const string &loader_name, TPriority pri=kPriority_Default)

Add data loader by name.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

vector< CSeq_id_Handle > TIds

string GetName(void) const

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

CDataLoader * FindDataLoader(const string &loader_name) const

Try to find a registered data loader by name.

virtual void GetIds(const CSeq_id_Handle &idh, TIds &ids)

Request for a list of all Seq-ids of a sequence.

virtual TTSE_LockSet GetRecords(const CSeq_id_Handle &idh, EChoice choice)

Request from a datasource using handles and ranges instead of seq-loc The TSEs loaded in this call wi...

@ eBioseq

main blob with complete bioseq

bool CanGetInst(void) const

const TInst & GetInst(void) const

void Reset(void)

Reset reference object.

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.

double Elapsed(void) const

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

void Start(void)

Start the timer.

size_t serialize(const BV &bv, unsigned char *buf, bm::word_t *temp_block=0, unsigned serialization_flags=0)

Saves bitvector into memory.

const TSeq & GetSeq(void) const

Get the variant data.

const TSet & GetSet(void) const

Get the variant data.

bool IsSeq(void) const

Check if variant Seq is selected.

bool IsSetAnnot(void) const

Check if a value has been assigned to Annot data member.

bool IsSet(void) const

Check if variant Set is selected.

bool IsSetAnnot(void) const

Check if a value has been assigned to Annot data member.

bool IsSetExt(void) const

extensions for special types Check if a value has been assigned to Ext data member.

list< CRef< CSeq_id > > TId

bool IsDelta(void) const

Check if variant Delta is selected.

const TExt & GetExt(void) const

Get the Ext member data.

const TDelta & GetDelta(void) const

Get the variant data.

const Tdata & Get(void) const

Get the member data.

list< CRef< CDelta_seq > > Tdata

@ e_User

user defined object

@ e_Comment

a more extensive comment

const CharType(& source)[N]

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines command line argument related classes.

Defines unified interface to application:

Defines classes: CDirEntry, CFile, CDir, CSymLink, CMemoryFile, CFileUtil, CFileLock,...

Int4 delta(size_t dimension_, const Int4 *score_)

static wxAcceleratorEntry entries[3]

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