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NCBI C++ ToolKit: src/sample/app/serial/hooks_highest_se_objs.cpp Source File

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75

cout <<

label

<< endl;

101  for

( ; isc; ++isc ) {

130  for

( ; isc; ++isc ) {

144  virtual void Init

(

void

);

145  virtual int Run

(

void

);

155

arg_desc->SetUsageContext(

GetArguments

().GetProgramBasename(),

156  "Bioseq-set info extractor"

);

159

arg_desc->AddKey(

"type"

,

"InputType"

,

"type of input data object"

,

161

arg_desc->SetConstraint(

"type"

,

176  string

type_str =

GetArgs

()[

"type"

].AsString();

177  if

(type_str ==

"Bioseq-set"

) {

178  in

->SetPathSkipMemberHook(

"Bioseq-set.seq-set"

,

180

}

else if

(type_str ==

"Seq-submit"

) {

181  in

->SetPathSkipVariantHook(

"Seq-submit.data.entrys"

,

186  while

( !

in

->EndOfData()) {

187  if

(type_str ==

"Bioseq-set"

) {

189

}

else if

(type_str ==

"Seq-submit"

) {

191

}

else if

(type_str ==

"Seq-entry"

) {

203 int main

(

int

argc,

const char

* argv[])

User-defined methods of the data storage class.

Reading (iterating through) elements of containers (SET OF, SEQUENCE OF).

virtual void Init(void)

Initialize the application.

virtual int Run(void)

Run the application.

void GetLabel(string *label, ELabelType type) const

Skip hook for a choice variant (CHOICE)

Skip hook for data member of a containing object (eg, SEQUENCE)

virtual void SkipClassMember(CObjectIStream &stream, const CObjectTypeInfoMI &passed_info)

virtual void SkipChoiceVariant(CObjectIStream &stream, const CObjectTypeInfoCV &passed_info)

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.

@ eSerial_AsnText

ASN.1 text.

CObjectTypeInfo GetVariantType(void) const

Get variant data type.

CObjectTypeInfo GetMemberType(void) const

Get data type information.

static CObjectIStream * Open(ESerialDataFormat format, CNcbiIstream &inStream, bool deleteInStream)

Create serial object reader and attach it to an input stream.

static const char label[]

static void s_Process(const CSeq_entry &entry)

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

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines command line argument related classes.

std::istream & in(std::istream &in_, double &x_)

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