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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/blast__sample_8cpp_source.html below:

NCBI C++ ToolKit: src/sample/app/blast/blast_sample.cpp Source File

57 virtual void Init

(

void

);

58 virtual int Run

(

void

);

59 virtual void Exit

(

void

);

85 return new

blast::SSeqLoc(seqloc, scope);

100

arg_desc->SetUsageContext(

GetArguments

().GetProgramBasename(),

101 "CBl2Seq demo to compare 2 sequences using BLAST"

);

105

arg_desc->SetConstraint

107 "blastp"

"blastn"

"blastx"

"tblastn"

"tblastx"

));

110

arg_desc->AddKey(

"query"

"QuerySequenceID"

111 "GI of the query sequence"

115

arg_desc->AddKey(

"subject"

"SubjectSequenceID"

116 "GI of the subject sequence"

120

arg_desc->AddDefaultKey(

"out"

"OutputFile"

121 "File name for writing the Seq-align results in ASN.1 form"

149 for

(

const auto

& it : alignments)

173 #ifndef SKIP_DOXYGEN_PROCESSING

Declares the CBl2Seq (BLAST 2 Sequences) class.

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

vector< CRef< objects::CSeq_align_set > > TSeqAlignVector

Vector of Seq-align-sets.

EProgram

This enumeration is to evolve into a task/program specific list that specifies sets of default parame...

virtual int Run(void)

Run the application.

blast::SSeqLoc * x_CreateSSeqLoc(ESeqType st)

virtual void Init(void)

Initialize the application.

virtual void Exit(void)

Cleanup on application exit.

static CRef< CScope > NewScope(bool with_defaults=true)

Return a new scope, possibly (by default) with default loaders, which will include the Genbank loader...

std::ofstream out("events_result.xml")

main entry point for tests

EProgram ProgramNameToEnum(const std::string &program_name)

Map a string into an element of the ncbi::blast::EProgram enumeration (except eBlastProgramMax).

void HideStdArgs(THideStdArgs hide_mask)

Set the hide mask for the Hide Std Flags.

#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.

@ fHideXmlHelp

Hide XML help description.

@ fHideLogfile

Hide log file description.

@ fHideFullVersion

Hide full version description.

@ fHideConffile

Hide configuration file description.

@ fHideVersion

Hide version description.

@ fPreOpen

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

@ eIntId

Convertible to TIntId (int or Int8 depending on NCBI_INT8_GI)

@ eString

An arbitrary string.

@ eOutputFile

Name of file (must be writable)

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

#define MSerial_AsnText

I/O stream manipulators â.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

static SLJIT_INLINE sljit_ins st(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

Definition of SSeqLoc structure.

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