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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/hgvsreader_8cpp_source.html below:

NCBI C++ ToolKit: src/app/hgvsreader/hgvsreader.cpp Source File

43 virtual void Init

(

void

);

44 virtual int Run

(

void

);

51

arg_desc->AddDefaultKey

54 "Text file containing hgvs expression"

59

arg_desc->AddDefaultKey

62 "Output file for seqfeat; used in conjunction with -out"

67

arg_desc->AddFlag(

"return-irep"

68 "Return intermediate representation as output"

);

71 string

prog_description =

"Convert hgvs expression to a Seq-feat\n"

;

72

arg_desc->SetUsageContext(

GetArguments

().GetProgramBasename(),

73

prog_description,

false

);

94 string

hgvs_expression;

96

istr >> hgvs_expression;

103 bool

success = hgvs_parser.

Apply

(hgvs_expression, irep);

109 if

(args[

"return-irep"

]) {

115 auto

seq_type = irep->GetSequence_variant().GetSeqtype();

118

seq_feat = irep_reader->CreateSeqfeat(*irep);

121

seq_feat = irep_reader->CreateSeqfeat(*irep);

134 int main

(

int

argc,

const char

* argv[])

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

bool Apply(const string &hgvs_expression, CRef< CVariantExpression > &varient_irep) const

virtual int Run(void)

Run the application.

virtual void Init(void)

Initialize the application.

virtual const char * GetErrCodeString(void) const

Get error code interpreted as text.

NCBI_EXCEPTION_DEFAULT(CHgvsVariantException, CException)

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.

@ fPreOpen

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

@ eInputFile

Name of file (must exist and be readable)

@ eOutputFile

Name of file (must be writable)

void SetDiagFilter(EDiagFilter what, const char *filter_str)

Set diagnostic filter.

EDiagSev SetDiagPostLevel(EDiagSev post_sev=eDiag_Error)

Set the threshold severity for posting the messages.

@ eDiag_Info

Informational message.

@ eDiag_Fatal

Fatal error â guarantees exit(or abort)

@ eDiagFilter_All

for all non-FATAL

TErrCode GetErrCode(void) const

Get error code.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

EErrCode

Error types that an application can generate.

virtual const char * GetErrCodeString(void) const

Get error code interpreted as text.

static void SetStackTraceLevel(EDiagSev level)

Set severity level for saving and printing stack trace.

#define MSerial_AsnText

I/O stream manipulators â.

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.

@ eVariantSeqType_p

protein

@ eVariantSeqType_c

coding

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

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines command line argument related classes.

Defines NCBI C++ exception handling.

void g_ValidateVariationSeqfeat(const CSeq_feat &feat, CScope *scope, bool IsCDS=false)

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