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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/feattree__sample_8cpp_source.html below:

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

78 virtual void Init

(

void

);

79 virtual int Run

(

void

);

80 virtual void Exit

(

void

);

103

arg_desc->SetUsageContext(

GetArguments

().GetProgramBasename(),

104 "Demonstrate CFeatTree class."

);

106

arg_desc->AddDefaultKey(

"gi"

107 "The gi for the Bioseq of interest, e.g. 455025."

110

arg_desc->AddDefaultKey(

"from"

111 "The starting position of the range."

114

arg_desc->AddDefaultKey(

"to"

115 "The ending position of the range."

143 CScope

scope(*object_manager);

154

cout <<

"Bioseq state: 0x" 160

cout <<

"Title: "

gen

.GenerateDefline(bioseq_handle) << endl;

166

cout <<

"Searching whole bioseq, gi|"

m_gi

" length = " 169

seq_loc.

SetInt

().SetId(seq_id);

172

cout <<

"Searching bioseq interval, gi|"

m_gi

":" 189

cout << feat_it.

GetSize

() <<

" features found."

<< endl;

193

feature::CFeatTree feat_tree;

194

feat_tree.AddFeatures(feat_it);

205 for

(feat_it.

Rewind

(); feat_it; ++feat_it) {

219

gene.

Reset

(seq_feat_ref);

236

feattree_map[feat_str] = gene_str;

237

gene_set.

insert

(gene_str);

242

cout << feattree_map.

size

() <<

" features mapped to genes."

<< endl;

243

cout << gene_set.

size

() <<

" unique genes found."

<< endl;

size_t GetSize(void) const

Class for computing sequences' titles ("definitions").

virtual void Exit(void)

Cleanup on application exit.

static string FeatString(CConstRef< CSeq_feat > seq_feat)

virtual void Init(void)

Initialize the application.

virtual int Run(void)

Run the application.

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

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

ESubtype GetSubtype(void) const

iterator_bool insert(const value_type &val)

The NCBI C++ standard methods for dealing with std::string.

API (CDeflineGenerator) for computing sequences' titles ("definitions").

USING_SCOPE(ncbi::objects)

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

#define GI_FROM(T, value)

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)

@ eInteger

Convertible into an integer number (int or Int8)

#define MSerial_AsnText

I/O stream manipulators â.

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.

TBioseqStateFlags GetState(void) const

Get state of the bioseq.

TSeqPos GetBioseqLength(void) const

SAnnotSelector & SetResolveAll(void)

SetResolveAll() is equivalent to SetResolveMethod(eResolve_All).

SAnnotSelector & SetAdaptiveDepth(bool value=true)

SetAdaptiveDepth() requests to restrict subsegment resolution depending on annotations found on lower...

SAnnotSelector & ExcludeNamedAnnots(const CAnnotName &name)

Add named annot to set of annots names to exclude.

CConstRef< CSeq_feat > GetSeq_feat(void) const

Get current seq-feat.

void Reset(void)

Reset reference object.

const TData & GetData(void) const

Get the Data member data.

TFrom GetFrom(void) const

Get the From member data.

TGi & SetGi(void)

Select the variant.

TTo GetTo(void) const

Get the To member data.

const TInt & GetInt(void) const

Get the variant data.

static void hex(unsigned char c)

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines command line argument related classes.

Miscellaneous common-use basic types and functionality.

NCBI C++ stream class wrappers for triggering between "new" and "old" C++ stream libraries.

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