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NCBI C++ ToolKit: src/sample/app/objmgr/objmgr_sample.cpp Source File

(

);

(

);

arg_desc->AddKey(

,

,

,

prog_description =

;

arg_desc->SetUsageContext(

().GetProgramBasename(), prog_description,

);

scope(*object_manager);

(

&

: ids) {

( &

!= &ids.front() ) {

cout <<

.AsString();

( !bioseq_handle ) {

cout <<

<< seq_vect.

();

desc_count = 0;

(

desc_it(bioseq_handle); desc_it; ++desc_it) {

cout <<

<< desc_count << endl;

cout <<

<< endl;

feat_count = 0;

(

feat_it(scope, seq_loc, sel); feat_it; ++feat_it) {

cout <<

<< feat_count << endl;

gene_count = 0;

(

feat_it(scope, seq_loc, sel); feat_it; ++feat_it) {

cout <<

<< gene_count << endl;

seq_loc.

().SetId().SetGi(gi);

seq_loc.

().SetFrom(0);

seq_loc.

().SetTo(9);

ranged_feat_count = 0;

(

feat_it(scope, seq_loc, sel); feat_it; ++feat_it) {

cout <<

<< ranged_feat_count << endl;

ranged_tse_feat_count = 0;

ranged_tse_feat_count++;

cout <<

<< ranged_tse_feat_count << endl;

cout <<

<< endl;

align_count = 0;

(

align_it(scope, seq_loc); align_it; ++align_it) {

cout <<

<< align_count << endl;

cout <<

<< endl;

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

virtual void Init(void)

Initialize the application.

virtual int Run(void)

Run the application.

Include a standard set of the NCBI C++ Toolkit most basic headers.

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

#define GI_FROM(T, value)

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.

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.

@ eIntId

Convertible to TIntId (int or Int8 depending on NCBI_INT8_GI)

#define ERR_POST(message)

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

void Fatal(CExceptionArgs_Base &args)

TIds GetIds(const CSeq_id &id, TGetFlags flags=0)

Get "native" bioseq ids without filtering and matching.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

void AddDefaults(TPriority pri=kPriority_Default)

Add default data loaders from object manager.

vector< CSeq_id_Handle > TId

CRef< CSeq_loc > GetRangeSeq_loc(TSeqPos start, TSeqPos stop, ENa_strand strand=eNa_strand_unknown) const

Return CSeq_loc referencing the given range and strand on the bioseq If start == 0,...

CSeq_entry_Handle GetTopLevelEntry(void) const

Get top level Seq-entry handle.

CSeqVector GetSeqVector(EVectorCoding coding, ENa_strand strand=eNa_strand_plus) const

Get sequence: Iupacna or Iupacaa if use_iupac_coding is true.

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

SAnnotSelector & SetFeatType(TFeatType type)

Set feature type (also set annotation type to feat)

SAnnotSelector & SetResolveAll(void)

SetResolveAll() is equivalent to SetResolveMethod(eResolve_All).

SAnnotSelector & SetLimitTSE(const CTSE_Handle &limit)

Limit annotations to those from the TSE only.

void GetSeqData(TSeqPos start, TSeqPos stop, string &buffer) const

Fill the buffer string with the sequence data for the interval [start, stop).

static string PrintableString(const CTempString str, TPrintableMode mode=fNewLine_Quote|fNonAscii_Passthru)

Get a printable version of the specified string.

void CONNECT_Init(const IRWRegistry *reg=0, CRWLock *lock=0, TConnectInitFlags flag=eConnectInit_OwnNothing, FSSLSetup ssl=0)

Init [X]CONNECT library with the specified "reg" and "lock" (ownership for either or both can be deta...

@ e_not_set

No variant selected.

TGi & SetGi(void)

Select the variant.

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines command line argument related classes.

Defines unified interface to application:

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

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