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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/prosplign__demo_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/align/prosplign/demo/prosplign_demo.cpp Source File

50 virtual void Init

(

void

);

57

arg_desc->AddKey(

"protein"

"proteinSeqEntryID"

58 "Seq-id of the protein"

60

arg_desc->AddKey(

"genomic"

"genomicSeqEntryID"

61 "Seq-id of the genomic sequence"

63

arg_desc->AddKey(

"start"

64 "genomic region start"

66

arg_desc->AddKey(

"stop"

67 "genomic region stop"

70

arg_desc->AddFlag(

"t"

"produce alignment text"

);

73 string

prog_description =

"Example of the ProSplign usage\n"

;

74

arg_desc->SetUsageContext(

GetArguments

().GetProgramBasename(),

75

prog_description,

false

);

77

arg_desc->AddFlag(

"no_introns"

"alignment without introns"

);

107 CSeq_id

protein(args[

"protein"

].AsString());

108 CSeq_id

genomic(args[

"genomic"

].AsString());

129 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)

virtual int Run()

Run the application.

virtual void Init(void)

Initialize the application.

Output filtering parameters.

static void SetupArgDescriptions(CArgDescriptions *argdescr)

static void Output(const objects::CSeq_align &seqalign, objects::CScope &scope, ostream &out, int width, const string &matrix_name="BLOSUM62")

Outputs formatted text.

spliced protein to genomic alignment

CRef< objects::CSeq_align > FindAlignment(objects::CScope &scope, const objects::CSeq_id &protein, const objects::CSeq_loc &genomic, CProSplignOutputOptions output_options=CProSplignOutputOptions())

Aligns protein to a region on genomic sequence.

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.

@ eInteger

Convertible into an integer number (int or Int8)

#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.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define USING_SCOPE(ns)

Use the specified namespace.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

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

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