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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/demo__contig__assembly_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/align/contig_assembly/demo/demo_contig_assembly.cpp Source File

);

arg_descr->AddPositional(

,

,

arg_descr->AddPositional(

,

,

arg_descr->AddDefaultKey(

,

,

,

arg_descr->AddDefaultKey(

,

,

,

arg_descr->AddDefaultKey(

,

,

,

arg_descr->AddDefaultKey(

,

,

,

id_str1 = args[

].AsString();

id_str2 = args[

].AsString();

blast_params = args[

].AsString();

min_frac_ident = args[

].AsDouble();

max_end_slop = args[

].AsInteger();

vector<CRef<CSeq_align> > alns;

vector<unsigned int> half_widths;

list<string> width_strings;

(list<string>, width_string, width_strings) {

max_end_slop, *scope, &ostr, half_widths);

annot.

().SetAlign().push_back(*aln);

annot.

().Set().push_back(desc);

uo->

(

);

uo->

().SetStr(

);

(list<string>, line, lines) {

uf.

().SetStrs().push_back(*line);

annot.

().Set().push_back(desc);

(

argc,

** argv)

User-defined methods of the data storage class.

User-defined methods of the data storage class.

static vector< CRef< objects::CSeq_align > > Align(const objects::CSeq_id &id0, const objects::CSeq_id &id1, const string &blast_params, double min_ident, unsigned int max_end_slop, objects::CScope &scope, CNcbiOstream *ostr=0, const vector< unsigned int > &band_halfwidths=vector< unsigned int >(1, 200), unsigned int diag_finding_window=200, unsigned int min_align_length=50, objects::ENa_strand strand0=objects::eNa_strand_unknown, objects::ENa_strand strand1=objects::eNa_strand_unknown)

Most users of the class need only to call this function.

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)

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

CUser_field & SetField(const string &str, const string &delim=".", const string &obj_subtype=kEmptyStr, NStr::ECase use_case=NStr::eCase)

Access a named field in this user object.

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 ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

const CNcbiArguments & GetArguments(void) const

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

@ eDouble

Convertible into a floating point number (double)

@ eString

An arbitrary string.

@ eInteger

Convertible into an integer number (int or Int8)

@ eDS_Default

Try standard log file (app.name + ".log") in /log/, use stderr on failure.

#define MSerial_AsnText

I/O stream manipulators –.

string GetSeqIdString(bool with_version=false) const

Return seqid string with optional version for text seqid type.

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.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

static unsigned int StringToUInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to unsigned int.

@ fSplit_Tokenize

All delimiters are merged and trimmed, to get non-empty tokens only.

void SetClass(const TClass &value)

Assign a value to Class data member.

void SetType(TType &value)

Assign a value to Type data member.

void SetData(TData &value)

Assign a value to Data data member.

TTitle & SetTitle(void)

Select the variant.

void SetData(TData &value)

Assign a value to Data data member.

void SetDesc(TDesc &value)

Assign a value to Desc data member.

TUser & SetUser(void)

Select the variant.

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

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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