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

->SetVersionInfo(1, 0, 0);

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);

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);

=

;

arg_desc->SetUsageContext(

().GetProgramBasename(),

arg_desc->SetCurrentGroup(

);

arg_desc->AddDefaultKey(

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arg_desc->AddDefaultKey(

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arg_desc->AddDefaultKey(

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masker(args[

].AsInteger(),

args[

].AsDouble(),

args[

].AsDouble());

( (seq_entry = reader->GetNextSequence()).NotEmpty() ) {

unique_ptr<CSegMasker::TMaskList> masks(masker(sequence_data));

writer->Print(bioseq_handle, *masks,

()[

]);

cerr << e.

() << endl;

(

argc,

* argv[])

const double kSegLocut

Locut parameter for SEG.

const int kSegWindow

Window that SEG examines at once.

const double kSegHicut

Hicut parameter for SEG.

Class for reading sequences from BLAST databases.

Class for reading sequences from fasta files.

Virtual base class for all input readers.

Output filter to print masked sequence locations as Blast-db-mask-info objects.

Output filter to write masked data in fasta format.

Output filter to print masked sequences as sets of intervals.

Output filter to print masked sequence locations as NCBI Seq-loc objects.

A base class for winmasker output writers.

This class encapsulates the SEG filtering algorithm.

virtual void Init(void)

@inheritDoc

SegMaskerApplication()

Application constructor.

virtual int Run(void)

@inheritDoc

CMaskReader * x_GetReader()

Retrieves the sequence reader interface for the application.

CMaskWriter * x_GetWriter()

Retrieves the output writer interface for the application.

static const char *const USAGE_LINE

Contains the description of this application.

virtual void Exit(void)

@inheritDoc

static SQLCHAR output[256]

void SetFullVersion(CRef< CVersionAPI > version)

Set version data for the program.

void HideStdArgs(THideStdArgs hide_mask)

Set the hide mask for the Hide Std Flags.

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.

@ fHideLogfile

Hide log file description.

@ fHideDryRun

Hide dryrun description.

@ fHideConffile

Hide configuration file description.

@ fHideVersion

Hide version description.

CArgAllow_Strings * Allow(const string &value)

Add allowed string values.

@ eInputFile

Name of file (must exist and be readable)

@ eDouble

Convertible into a floating point number (double)

@ eString

An arbitrary string.

@ eOutputFile

Name of file (must be writable)

@ eInteger

Convertible into an integer number (int or Int8)

@ fBinary

Open file in binary mode.

void SetDiagStream(CNcbiOstream *os, bool quick_flush=true, FDiagCleanup cleanup=0, void *cleanup_data=0, const string &stream_name="")

Set diagnostic stream.

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

CSeq_entry_Handle AddTopLevelSeqEntry(CSeq_entry &top_entry, TPriority pri=kPriority_Default, EExist action=eExist_Default)

Add seq_entry, default priority is higher than for defaults or loaders Add object to the score with p...

CSeqVector GetSeqVector(EVectorCoding coding, ENa_strand strand=eNa_strand_plus) const

Get sequence: Iupacna or Iupacaa if use_iupac_coding is true.

@ eCoding_Ncbi

Set coding to binary coding (Ncbi4na or Ncbistdaa)

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

static string DoubleToString(double value, int precision=-1, TNumToStringFlags flags=0)

Convert double to string.

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

Convert int to string.

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

@ eBlast_filter_program_seg

E_Choice Which(void) const

Which variant is currently selected.

@ e_not_set

No variant selected.

The blob sat and sat key Both must be positive integers</td > n< td > Non empty string The interpretation of the blob id depends on a processor Cassandra n processor expects the following format

Contains the command line options common to filtering algorithms.

const size_t kNumInputFormats

Number of elements in kInputFormats.

const char * kOutputFormats[]

Output formats allowed, the first one is the default.

const size_t kNumOutputFormats

Number of elements in kOutputFormats.

const std::string kOutput

Command line flag to specify the output.

const std::string kOutputFormat

Command line flag to specify the output format.

const char * kInputFormats[]

Input formats allowed, the first one is the default.

const std::string kInput

Command line flag to specify the input.

const std::string kInputFormat

Command line flag to specify the input format.

string BuildAlgorithmParametersString(const CArgs &args)

Builds an algorithm options string for the filtering applications (segmasker, dustmasker) by examinin...

const string version

version string

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

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

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