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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/demo__gene__model_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/sequence/demo/demo_gene_model.cpp Source File

55  virtual void Init

(

void

);

56  virtual int Run

(

void

);

65

arg_desc->AddDefaultKey(

"i"

,

"InputFile"

,

66  "File containing seq-align to use"

,

70

arg_desc->AddDefaultKey(

"o"

,

"OutputFile"

,

71  "File containing seq-annot for gene model"

,

74

arg_desc->AddDefaultKey(

"ofmt"

,

"OutputFormat"

,

78

arg_desc->SetConstraint(

"ofmt"

,

80  "seq-annot"

,

"seq-feat"

));

91  string

ofmt = args[

"ofmt"

].AsString();

110  gen

.ConvertAlignToAnnot(align, annot, seqs);

122  if

(ofmt ==

"seq-annot"

) {

125  else if

(ofmt ==

"seq-feat"

) {

137 int main

(

int

argc,

char

** argv)

User-defined methods of the data storage class.

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

virtual int Run(void)

Run the application.

virtual void Init(void)

Initialize the application.

void SetNameDesc(const string &name)

void SetTitleDesc(const string &title)

int main(int argc, char **argv)

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.

void DisableArgDescriptions(TDisableArgDesc disable=fDisableStdArgs)

@ eInputFile

Name of file (must exist and be readable)

@ eString

An arbitrary string.

@ eOutputFile

Name of file (must be writable)

@ eDS_Default

Try standard log file (app.name + ".log") in /log/, use stderr on failure.

#define MSerial_AsnText

I/O stream manipulators –.

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.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

const TFtable & GetFtable(void) const

Get the variant data.

list< CRef< CSeq_feat > > TFtable

const TData & GetData(void) const

Get the Data member data.

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines command line argument related classes.

Defines unified interface to application:

CRef< objects::CObjectManager > om

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