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

=

;

arg_desc->SetUsageContext(

().GetProgramBasename(),

arg_desc->AddDefaultKey(

,

,

arg_desc->AddDefaultKey(

,

,

arg_desc->AddDefaultKey(

,

,

,

arg_desc->AddDefaultKey(

,

,

,

arg_desc->AddDefaultKey(

,

,

,

arg_desc->AddDefaultKey(

,

,

,

arg_desc->AddFlag (

,

,

);

arg_desc->AddFlag (

,

,

);

strings_allowed->

(

);

(args[

].AsBoolean() && (

!=

)) {

runtime_error(

);

(

==

) {

}

(

==

) {

}

(

==

) {

hard_masking = args[

].AsBoolean();

runtime_error(

);

(

==

) {

input_stream,

, args[

] );

(

==

) {

runtime_error(

);

pos = 0;

(objects::CSeqVector_CI itr=seq.begin();itr!=seq.end(); ++itr) {

((Ns > MAX_Ns ) || (pos == 0)) {

NsRange.push_back(

);

NsRange.push_back(

);

((!list.empty()) && (list.back().second + linker == new_mask.first)) {

list.back().second = new_mask.second;

list.push_back(new_mask);

std::unique_ptr< CSymDustMasker::TMaskList >

(NsRange.empty()){

(itr->first == 0) {

seq_start = itr->second + 1;

std::unique_ptr< CSymDustMasker::TMaskList > s_mask = duster(seq, seq_start, itr->first -1);

(s_mask->size() > 0) {

( s_mask->size() > 1) {

rv->insert(rv->end(), ++(s_mask->begin()), s_mask->end());

seq_start = itr->second + 1;

(seq_start < seq.size()){

std::unique_ptr< CSymDustMasker::TMaskList > s_mask = duster(seq, seq_start, seq.size() -1);

(s_mask->size() > 0) {

( s_mask->size() > 1) {

rv->insert(rv->end(), ++(s_mask->begin()), s_mask->end());

( ; bs_iter; ++bs_iter)

writer->Print(bsh, *res,

()[

] );

output_stream << flush;

User-defined methods of the data storage class.

virtual int Run(void)

Run the application.

CMaskReader * x_GetReader()

CMaskWriter * x_GetWriter()

virtual void Init(void)

Initialize the application.

static const char *const USAGE_LINE

Class for reading sequences from BLAST databases.

Class for reading sequences from fasta files.

Virtual base class for all input readers.

virtual CRef< objects::CSeq_entry > GetNextSequence()=0

Read the next sequence from the source stream.

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.

Output filter to print masked sequences as sets of intervals one per line.

A base class for winmasker output writers.

Looks for low complexity parts of sequences according to the symmetric version of DUST algorithm.

std::pair< size_type, size_type > TMaskedInterval

Type respresenting an interval selected for masking.

sequence_type::size_type size_type

Integer size type corresponding to sequence_type.

std::vector< TMaskedInterval > TMaskList

Type representing a list of masked intervals.

std::unique_ptr< CSymDustMasker::TMaskList > GetDustMasks_SkipNs(objects::CSeqVector &seq, Uint4 level, Uint4 window, Uint4 linker)

void s_InsertMerge(CSymDustMasker::TMaskList &list, CSymDustMasker::TMaskedInterval &new_mask, Uint4 linker)

CSymDustMasker::TMaskList s_FindSegmentWithLongNs(const unsigned int MAX_Ns, objects::CSeqVector &seq)

Operators to edit gaps in sequences.

static SQLCHAR output[256]

void HideStdArgs(THideStdArgs hide_mask)

Set the hide mask for the Hide Std Flags.

unsigned int TSeqPos

Type for sequence locations and lengths.

virtual const CArgs & GetArgs(void) const

Get parsed command line arguments.

virtual void SetupArgDescriptions(CArgDescriptions *arg_desc)

Setup the command line argument descriptions.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

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)

@ 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.

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...

TSeqPos GetBioseqLength(void) const

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

Get sequence: Iupacna or Iupacaa if use_iupac_coding is true.

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

uint32_t Uint4

4-byte (32-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

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_dust

@ eMol_na

just a nucleic acid

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

Lightweight interface for getting lines of data with minimal memory copying.

Contains the command line options common to filtering algorithms.

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...

NCBI C++ auxiliary debug macros.

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

CRef< objects::CObjectManager > om

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