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NCBI C++ ToolKit: src/algo/seqqa/demo/demo_seqtest.cpp Source File

);

arg_descr->AddDefaultKey(

,

,

,

arg_descr->AddDefaultKey(

,

,

,

arg_descr->AddFlag(

,

);

arg_descr->AddFlag(

,

);

arg_descr->AddFlag(

,

);

arg_descr->AddExtra(0, 100,

,

(

arg_num = 1; arg_num <= args.

(); arg_num += 2) {

(line ==

|| line[0] ==

) {

results_container->SetSource().SetSeq_id(*

);

results_container->SetResults(*

);

(args[

]) {

uo->

().SetStr(

);

vector<CRef<CUser_object > > results_vector;

results_vector.push_back(result_uo);

uo->

(

, results_vector);

aln.

().push_back(uo);

(

argc,

** argv)

void Init()

Initialize the application.

int Run()

Run the application.

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

CSeqTestContext defines any contextual information that a derived class might need.

virtual void RegisterStandardTests()

Provide a standard battery of quality checks that should always be run.

virtual CRef< objects::CSeq_test_result_set > RunTests(const CSerialObject &obj, const CSeqTestContext *ctx=NULL)

Run tests for a given serial object.

void SetNamedScore(const string &id, int score)

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

CUser_object & AddField(const string &label, const string &value, EParseField parse=eParse_String)

add a data field to the user object that holds a given value

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 NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

const CNcbiArguments & GetArguments(void) const

Get the application's cached unprocessed command-line arguments.

size_t GetNExtra(void) const

Get the number of unnamed positional (a.k.a. extra) args.

@ fPreOpen

Open file right away; for eInputFile, eOutputFile, eIOFile.

@ 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_AsnBinary

#define MSerial_AsnText

I/O stream manipulators –.

CBeginInfo Begin(C &obj)

Get starting point of object hierarchy.

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.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

const TData & GetData(void) const

Get the Data member data.

TBool GetBool(void) const

Get the variant data.

bool IsInt(void) const

Check if variant Int is selected.

void SetClass(const TClass &value)

Assign a value to Class data member.

const TStr & GetStr(void) const

Get the variant data.

TInt GetInt(void) const

Get the variant data.

TReal GetReal(void) const

Get the variant data.

void SetType(TType &value)

Assign a value to Type data member.

bool IsReal(void) const

Check if variant Real is selected.

const TLabel & GetLabel(void) const

Get the Label member data.

bool IsBool(void) const

Check if variant Bool is selected.

list< CRef< CSeq_test_result > > Tdata

TExt & SetExt(void)

Assign a value to Ext data member.

const struct ncbi::grid::netcache::search::fields::KEY key

Magic spell ;-) needed for some weird compilers... very empiric.

const GenericPointer< typename T::ValueType > T2 value

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines command line argument related classes.

Defines unified interface to application:

#define GetProgramName

Avoid name clash with the NCBI C Toolkit.

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