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NCBI C++ ToolKit: src/algo/blast/api/winmask_filter.cpp Source File

arg_window_size = 0;

arg_window_step = 1;

arg_unit_step = 1;

arg_textend = 0;

arg_cutoff_score = 0;

arg_max_score = 0;

arg_min_score = 0;

arg_set_max_score = 0;

arg_set_min_score = 0;

arg_merge_pass =

;

arg_merge_cutoff_score = 0;

arg_abs_merge_cutoff_dist = 0;

arg_mean_merge_cutoff_dist = 0;

arg_merge_unit_step = 0;

& arg_trigger =

;

tmin_count = 0;

arg_discontig =

;

arg_pattern = 0;

arg_use_ba =

;

arg_merge_cutoff_score,

arg_abs_merge_cutoff_dist,

arg_mean_merge_cutoff_dist,

ival->

(query_start + start);

ival->

(query_start + end);

ival->

(query_id);

mqr->push_back(info_plus);

mqr->push_back(info_minus);

(**psl).SetPacked_int().Set().push_back(ival);

(psl && !psl->Empty())

(*psl)->ChangeToPackedInt();

<

TQueries>

<

TQueries>

(

j = 0; j < queries.

(); j++) {

.SetMaskedRegions(mqr);

(

j = 0; j < queries.size(); j++) {

& queries[j].

);

( queries[0].

) {

queries[0].mask->SetPacked_int().Set();

((*itr)->CanGetStrand()) {

((*itr)->GetStrand()) {

(*itr)->ResetStrand();

( !retval.empty() ) {

kEnvVar(

);

(

);

path = window_masker_path;

supported_taxids.

();

path->erase(0, wmpath.size() + 1);

supported_taxids.

(taxid);

supported_taxids.

();

path->erase(0, wmpath.size() + 1);

supported_taxids.

(taxid);

(supported_taxids.

()) {

@ eExtreme_Positional

numerical value

Contains C++ wrapper classes to structures in algo/blast/core as well as some auxiliary functions to ...

BLAST filtering functions.

Structures and API used for saving BLAST hits.

Declares the CBlastNucleotideOptionsHandle class.

Declaration of ADT to retrieve sequences for the BLAST engine.

Internal auxiliary setup classes/functions for C++ BLAST APIs.

Definitions of special type used in BLAST.

ncbi::TMaskedQueryRegions mask

Defines BLAST error codes (user errors included)

Handle to the options to the BLAST algorithm.

Encapsulates ALL the BLAST algorithm's options.

CRef< objects::CScope > GetScope(size_type i) const

Get the scope containing a query by index.

size_type Size() const

Returns the number of queries found in this query vector.

CRef< CBlastSearchQuery > GetBlastSearchQuery(size_type i) const

Get the CBlastSearchQuery object at index i.

CEnvironmentRegistry –.

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

structure for seqloc info

Main interface to window based masker functionality.

vector< TMaskedInterval > TMaskList

A type representing the total of masking information about a sequence.

Collection of masked regions for a single query sequence.

iterator_bool insert(const value_type &val)

Classes to support using environment variables as a backend for the registry framework.

void Blast_FindWindowMaskerLoc_Fwd(TQueries &query, const CBlastOptions *opts)

int GetWindowMaskerTaxId() const

Returns the tax id used for the windowmasker database to use, if set via SetWindowMaskerTaxId (otherw...

DEFINE_STATIC_MUTEX(InitMutex)

string WindowMaskerTaxidToDb(int taxid)

Get the windowmasker file path for a given taxid.

static string s_FindPathToWM(void)

Find the path to the window masker files, first checking the (optionally set) value passed to the Win...

void WindowMaskerPathReset()

Resets the path to the windowmasker data files.

void GetTaxIdWithWindowMaskerSupport(set< int > &supported_taxids)

This function returns a list of NCBI taxonomy IDs for which there exists windowmasker masking data to...

CSeqMasker * s_BuildSeqMasker(const string &lstat)

void Blast_FindWindowMaskerLoc(CBlastQueryVector &query, const CBlastOptions *opts)

Find Window Masker filtered locations using a BlastOptions.

const CBlastOptions & GetOptions() const

Return the object which this object is a handle for.

static string s_WINDOW_MASKER_STAT_FILE_NAME("wmasker.obinary")

void s_BuildMaskedRanges(CSeqMasker::TMaskList &masks, const CSeq_loc &seqloc, CSeq_id &query_id, TMaskedQueryRegions *mqr, CRef< CSeq_loc > *psl)

static void s_OldGetTaxIdWithWindowMaskerSupport(set< int > &supported_taxids)

const char * GetWindowMaskerDatabase() const

Return the name of the windowmasker database to use.

static string s_WINDOW_MASKER_PATH(kEmptyStr)

string WindowMaskerPathGet()

Retrieves the path to the windowmasker data files.

int WindowMaskerPathInit(const string &window_masker_path)

Initialize the path to the windowmasker data files.

void Blast_FindWindowMaskerLocTaxId(CBlastQueryVector &queries, int taxid)

Find Window Masker filtered locations by taxonomic ID.

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

void FindFiles(TPathIterator path_begin, TPathIterator path_end, const vector< string > &masks, TFindFunc &find_func, TFindFiles flags=fFF_Default)

Generic algorithm for file search.

static char GetPathSeparator(void)

Get path separator symbol specific for the current platform.

static string GetCwd(void)

Get the current working directory.

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Optimized implementation of CSerialObject::Assign, which is not so efficient.

TSeqPos GetStart(ESeqLocExtremes ext) const

Return start and stop positions of the seq-loc.

const CSeq_id * GetId(void) const

Get the id of the location return NULL if has multiple ids or no id at all.

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

uint8_t Uint1

1-byte (8-bit) unsigned integer

uint32_t Uint4

4-byte (32-bit) unsigned integer

virtual const string & Get(const string &section, const string &name, TFlags flags=0) const

Get the parameter value.

void Add(const IRegistry &reg, TPriority prio=ePriority_Default, const string &name=kEmptyStr)

Non-empty names must be unique within each compound registry, but there is no limit to the number of ...

void AddMapper(const IEnvRegMapper &mapper, TPriority prio=ePriority_Default)

@ fWithNcbirc

Include .ncbirc (used only by CNcbiReg.)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define USING_SCOPE(ns)

Use the specified namespace.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

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

Convert string to int.

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.

static string & ReplaceInPlace(string &src, const string &search, const string &replace, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a string.

@ fConvErr_NoThrow

Do not throw an exception on error.

void SetTo(TTo value)

Assign a value to To data member.

list< CRef< CSeq_interval > > Tdata

void SetId(TId &value)

Assign a value to Id data member.

void SetFrom(TFrom value)

Assign a value to From data member.

virtual void Reset(void)

Reset the whole object.

void SetStrand(TStrand value)

Assign a value to Strand data member.

@ eNa_strand_both

in forward orientation

Main class to perform a BLAST search on the local machine.

NOTE: This file contains work in progress and the APIs are likely to change, please do not rely on th...

Implementation of the BlastSeqSrc interface using the C++ BLAST databases API.

const char *const kSection

vector< SSeqLoc > TSeqLocVector

Vector of sequence locations.

Interface to retrieve list of available windowmasker filtering.

Blast wrappers for WindowMasker filtering.

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