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

74 "Find overlap between closely related DNA Sequences"

75 "Generate an overlap alignment between " 76 "closely related DNA sequences, particularly for " 77 "exploring clone overlap relationships"

78 "https://www.ncbi.nlm.nih.gov/tools/gbench/tutorial5/"

79 "Alignment Creation"

86 return "find_overlap_tool"

;

92 return "Find Overlap Tool"

;

138 if

( !gui_seq_info.

IsNull

() && gui_seq_info->IsDNA() ){

200 if

(&scope1 != &scope2) {

201 LOG_POST

(

Error

"Inconsistent scopes - results may not be viewable"

);

218 LOG_POST

(

Info

"Find Overlap Alignments: \n"

" "

<< name1 <<

" x "

<< name2

220

" blast_params='"

<< blast_params <<

"'"

" " 226

vector<CRef<CSeq_align> > alns;

250 if

( sas && sas->

IsSet

() ){

251

alns.insert( alns.end(), sas->

Set

().begin(), sas->

Set

().end() );

260

annot->

SetData

().SetAlign().push_back(*iter);

267

name +=

": Overlap Alignment"

;

274

item->

SetItem

().SetAnnot(*annot);

281 LOG_POST

(

Info

"No acceptable overlaps are found."

);

283 x_SetTextResult

(

"No overlaps are found according to the settings desired."

);

292

opts->SetTraditionalBlastnDefaults();

293

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

307 if

( !blast_params.empty() ){

308 static const string

s_whitespace(

" \n\t\r"

);

314 for

(

unsigned int i

= 0;

< argv.size();

++ ){

315 string

& name = argv[

];

319

name =

"-word_size"

;

320

}

else if

(name ==

"-r"

) {

323

}

else if

(name ==

"-q"

) {

326

}

else if

(name ==

"-e"

) {

329

}

else if

(name ==

"-Z"

) {

331

name =

"-xdrop_gap_final"

;

332

}

else if

(name ==

"-F"

) {

336 string

value

= argv[

+ 1];

339

}

else if

(name ==

"-G"

) {

342

}

else if

(name ==

"-E"

) {

344

name =

"-gapextend"

;

382

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

383

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

388

blast::CGenericSearchArgs search_args(

false

391

search_args.ExtractAlgorithmOptions(*args, options);

393

blast::CFilteringArgs filter_args(

false

);

394

filter_args.ExtractAlgorithmOptions(*args, options);

396

blast::CNuclArgs nucl_args;

397

nucl_args.ExtractAlgorithmOptions(*args, options);

399

blast::CGappedArgs gapped_args;

400

gapped_args.ExtractAlgorithmOptions(*args, options);

403

blast::CHspFilteringArgs cull_args;

404

cull_args.ExtractAlgorithmOptions(*args, options);

407

blast::CWindowSizeArg window_args;

408

window_args.ExtractAlgorithmOptions(*args, options);

413 "Cannot parse BLAST params, please edit them:\n"

+ ex.

GetMsg

()

431 string

perfect_dovetail =

" pct_identity_ungap >= 100 AND longest_gap < 50 AND full_dovetail = 1 "

;

432 string

near_perfect_dovetail =

" pct_identity_ungap >= 99.8 AND longest_gap < 50 AND full_dovetail = 1 "

;

433 string

super_green_contained =

" pct_identity_ungap >= 99.8 AND contained > -1 "

;

435 string

green_dovetail =

" pct_identity_ungap >= 99.6 AND longest_gap < 50 AND full_dovetail = 1 "

;

436 string

green_contained =

" pct_identity_ungap >= 99.6 AND contained > -1 "

;

438 string

yellow_dovetail =

" pct_identity_ungap >= 98.0 AND longest_gap < 500 AND full_dovetail = 1 "

;

439 string

yellow_contained =

" pct_identity_ungap >= 98.0 AND contained > -1 "

;

440 string

yellow_half_dovetail =

" pct_identity_ungap >= 98.0 AND longest_gap < 500 AND half_dovetail = 1 AND tail_length <= 50 "

;

442 string

red_dovetail =

" pct_identity_ungap >= 95.0 AND full_dovetail = 1 "

;

443 string

red_half_dovetail =

" pct_identity_ungap >= 95.0 AND half_dovetail = 1 AND tail_length <= 2000 AND tail_length <= align_length_ungap "

;

444 string

red_contained =

" pct_identity_ungap >= 95.0 AND contained > -1 "

;

446 string

super_red_half_dovetail =

" pct_identity_ungap >= 92.0 AND half_dovetail = 1 AND tail_length <= 5000 AND tail_length <= align_length_ungap "

;

447 string

mega_red_half_dovetail =

" pct_identity_ungap >= 92.0 AND half_dovetail = 1 AND tail_length <= 10000 "

;

448 string

ultra_red_half_dovetail =

" pct_identity_ungap >= 92.0 AND half_dovetail = 1 AND tail_length <= MUL(5, align_length_ungap) "

;

449 string

omega_red_half_dovetail =

" pct_identity_ungap >= 92.0 AND half_dovetail = 1 "

;

453 if

( filter_qty >= 0 ){

458 if

( filter_qty >= 1 ){

462 if

( filter_qty >= 2 ){

467 if

( filter_qty >= 3 ){

472 if

( filter_qty >= 4 ){

Declares the BLAST exception class.

@ eBlastn

Nucl-Nucl (traditional blastn)

Main argument class for BLASTN application.

void SetInterruptCallback(TInterruptFnPtr fnptr=NULL, void *user_data=NULL)

CDataLoadingAppJob - a base class for Jobs loading data into projects.

void AddProjectItem(objects::CProjectItem &item)

void x_SetTextResult(const string &result)

CFindOverlapJob(const CFindOverlapParams &params)

CFindOverlapJob.

void x_PrepareAligner(CNgAligner &aligner, CFindOverlapParams &params)

static Boolean x_BlastInterruptCallback(SBlastProgress *prog)

CFindOverlapParams m_Params

virtual void x_CreateProjectItems()

override this function in derived classes and populate m_Items.

void SetQuery(ISequenceSet *Set)

void SetSubject(ISequenceSet *Set)

void AddFilter(IAlignmentFilter *Filter)

void AddAligner(IAlignmentFactory *Aligner)

void AddScorer(IAlignmentScorer *Scorer)

void SetNameDesc(const string &name)

void SetCreateDate(const CTime &dt)

IRegSettings An interface for objects that save / restore settings using CGuiRegistry.

#define SYMBOL_CFINDOVERLAPPANEL_STYLE

string EProgramToTaskName(EProgram p)

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

#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 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)

#define NCBI_THROW(exception_class, err_code, message)

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

const string & GetMsg(void) const

Get message string.

void Info(CExceptionArgs_Base &args)

virtual CAlgoToolManagerParamsPanel * x_GetParamsPanel()

returns a pointer to the parameters panel, override in derived classes

void SetObjects(TConstScopedObjects *objects)

const SConstScopedObject & GetSeq1() const

virtual string GetExtensionLabel() const

returns a displayable label for this extension ( please capitalize the key words - "My Extension" )

virtual bool x_CreateParamsPanelIfNeeded()

returns / creates Parameters panel, override in derived classes see cpp file for example

wxString GetMaxSlop() const

virtual IRegSettings * x_GetParamsAsRegSetting()

return a pointer to Parameters object as IRegSettings interface

TConstScopedObjects m_SeqIds

int GetFilterQuality() const

CFindOverlapParams & GetData()

virtual void CleanUI()

override this function in a derived class and clean extra members

virtual void InitUI()

override this function in a derived class and initialize extra members

virtual void x_SelectCompatibleInputObjects()

select only Seq-ids

virtual void LoadSettings()

CFindOverlapParams m_Params

virtual CDataLoadingAppJob * x_CreateLoadingJob()

factory method for creating the job that executes the tool algorithm override in derived classes

virtual string GetExtensionIdentifier() const

returns the unique human-readable identifier for the extension the id should use lowercase letters se...

CFindOverlapTool()

CFindOverlapTool.

void SetData(const CFindOverlapParams &data)

virtual bool x_ValidateParams()

validates user input in Parameters panel, report errors if any

const SConstScopedObject & GetSeq2() const

wxString GetBlastParams() const

CFindOverlapPanel * m_Panel

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

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

void AddScope(CScope &scope, TPriority pri=kPriority_Default)

Add the scope's datasources as a single group with the given priority All data sources (data loaders ...

void Reset(void)

Reset reference object.

bool IsNull(void) const THROWS_NONE

Check if pointer is null â same effect as Empty().

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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

Convert string to int.

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.

@ eCurrent

Use current time. See also CCurrentTime.

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.

void SetData(TData &value)

Assign a value to Data data member.

const GenericPointer< typename T::ValueType > T2 value

Uint1 Boolean

bool replacment for C

#define TRUE

bool replacment for C indicating true.

#define FALSE

bool replacment for C indicating false.

Progress monitoring structure.

string ToStdString(const wxString &s)

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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/find__overlap__tool_8cpp_source.html below:

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

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