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NCBI C++ ToolKit: src/gui/packages/pkg_alignment/ngalign_job.cpp Source File

result_iter,

->Get()) {

assm_iter, result_iter->second->Get()) {

query_iter, assm_iter->second) {

query_iter->second->Set()) {

is_splittable_sequences =

(

blast::CBlastNucleotideOptionsHandle);

opts->SetTraditionalBlastnDefaults();

blast::CBlastOptions& options = opts->SetOptions();

options.SetWordSize (

(params.

()));

options.SetEvalueThreshold (params.

());

unique_ptr<CAutoEnvironmentVariable> p_wm_path;

options.SetWindowMaskerTaxId(params.

());

(

<<

);

options.SetBestHitScoreEdge(0.1);

options.SetBestHitOverhang(0.1);

(!advParams.empty()) {

s_whitespace(

);

unique_ptr<CArgDescriptions> arg_descs( blast_args->SetCommandLine() );

unique_ptr<CArgs> args( arg_descs->CreateArgs( argv.size(), argv ) );

blast::CGenericSearchArgs search_args(

,

search_args.ExtractAlgorithmOptions(*args, options);

blast::CFilteringArgs filter_args(

);

filter_args.ExtractAlgorithmOptions(*args, options);

blast::CNuclArgs nucl_args;

nucl_args.ExtractAlgorithmOptions(*args, options);

blast::CGappedArgs gapped_args;

gapped_args.ExtractAlgorithmOptions(*args, options);

blast::CHspFilteringArgs cull_args;

cull_args.ExtractAlgorithmOptions(*args, options);

blast::CWindowSizeArg window_args;

window_args.ExtractAlgorithmOptions(*args, options);

( aSplitter && is_splittable_sequences ){

(filterMode == 0 || filterMode == 1) {

));

));

));

));

));

));

));

));

aligner.

();

list< CRef<CSeq_loc> > subject_locs;

( seq_id !=

){

loc->

( *seq_id );

subject_locs.push_back( loc );

( seq_loc !=

){

(

<<

);

->SetLocList().insert(

->SetLocList().end(), subject_locs.begin(), subject_locs.end() );

list< CRef<CSeq_loc> > query_locs;

* seq_id =

*

( iter->object.GetPointer() );

( seq_id !=

){

loc->

( *seq_id );

query_locs.push_back( loc );

* seq_loc =

*

( iter->object.GetPointer() );

( seq_loc !=

){

(

<<

);

unique_ptr<CUnorderedSplitter> splitter;

queries->AddSeqLoc(*it);

( sas && sas->

() ){

alignments->Set().insert(

alignments->Set().end(),

sas->

().begin(),

queries->SetLocList().insert( queries->SetLocList().end(), query_locs.begin(), query_locs.end() );

( sas && sas->

() ){

alignments->Set().insert(

alignments->Set().end(),

sas->

().begin(),

(alignments && ! alignments->Get().empty()) {

TAlign& seqannot_align = annot->

().SetAlign();

seqannot_align.push_back(*align);

title +=

;

item->

().SetAnnot(*annot);

User-defined methods of the data storage class.

User-defined methods of the data storage class.

@ eBlastn

Nucl-Nucl (traditional blastn)

Main argument class for BLASTN application.

@ eSkipUnsupportedAlignments

void AddProjectItem(objects::CProjectItem &item)

void ScoreAlignments(TAlignResultsRef results, CScope &scope)

Base class to build jobs with cancel functionality.

void SetQuery(ISequenceSet *Set)

void SetSubject(ISequenceSet *Set)

void AddFilter(IAlignmentFilter *Filter)

void AddAligner(IAlignmentFactory *Aligner)

void AddScorer(IAlignmentScorer *Scorer)

int GetGapCount(const CSeq_align &align)

Compute the number of gaps in the alignment.

void AddScore(CScope &scope, CSeq_align &align, EScoreType score)

deprecated: use CSeq_align::EScoreType directly

@ eScore_PercentIdentity_GapOpeningOnly

@ eScore_PercentIdentity_Gapped

@ eScore_PercentIdentity_Ungapped

void SetNamedScore(const string &id, int score)

void SetNameDesc(const string &name)

void SetCreateDate(const CTime &dt)

void SetTitleDesc(const string &title)

Operators to edit gaps in sequences.

string EProgramToTaskName(EProgram p)

Convert a EProgram enumeration value to a task name (as those used in the BLAST command line binaries...

int WindowMaskerPathInit(const string &window_masker_path)

Initialize the path to the windowmasker data files.

#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 ERR_POST(message)

Error posting with file, line number information but without error codes.

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

void Error(CExceptionArgs_Base &args)

virtual void x_CreateProjectItems()

override this function in derived classes and populate m_Items.

CNGAlignJob(const CNGAlignParams &params)

CNGAlignJob.

TConstScopedObjects & SetQueries()

wxString GetAdvParams() const

int GetFilterMode() const

const SConstScopedObject & GetSubject() const

static void GetLabel(const CObject &obj, string *label, ELabelType type=eDefault)

CRef< objects::CScope > scope

string m_Descr

mutex to sync our internals

virtual bool IsCanceled() const override

CConstRef< CObject > object

vector< SConstScopedObject > TConstScopedObjects

void SetId(CSeq_id &id)

set the 'id' field in all parts of this location

TObjectType * GetPointer(void) const THROWS_NONE

Get pointer,.

#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.

CTime CurrentTime(CTime::ETimeZone tz=CTime::eLocal, CTime::ETimeZonePrecision tzp=CTime::eTZPrecisionDefault)

void SetLabel(const TLabel &value)

Assign a value to Label data member.

void SetItem(TItem &value)

Assign a value to Item data member.

Tdata & Set(void)

Assign a value to data member.

bool IsSet(void) const

Check if a value has been assigned to data member.

list< CRef< CSeq_align > > Tdata

void SetData(TData &value)

Assign a value to Data data member.

list< CRef< CSeq_align > > TAlign

Uint1 Boolean

bool replacment for C

#define TRUE

bool replacment for C indicating true.

#define FALSE

bool replacment for C indicating false.

Defines a portable execute class.

Defines classes: CDirEntry, CFile, CDir, CSymLink, CMemoryFile, CFileUtil, CFileLock,...

static Boolean s_BlastInterruptCallback(SBlastProgress *prog)

@ fScore_GapCount

add a 'gap_count' score

@ fScore_Identities

add BLAST-style 'num_ident' score

@ fScore_Default

default flags: everything

@ fScore_Mismatches

add a 'mismatch' core with a count of mismatches

@ fScore_PercentCoverage

add a score for percent coverage of query (sequence 0)

@ fScore_PercentIdentity

add scores for ungapped and gapped percent identity

static CRef< CSeq_align_set > s_CallAligner(CNGAlignParams &params, CNgAligner &aligner, CJobCancelable *job, CUnorderedSplitter *aSplitter=NULL, bool is_splittable_sequences=false)

void AddStandardAlignmentScores(CScope &scope, CSeq_align &align, TAlignScoreFlags flags=fScore_Default)

Progress monitoring structure.

Interface to retrieve list of available windowmasker filtering.

string ToStdString(const wxString &s)

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