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NCBI C++ ToolKit: src/gui/packages/pkg_sequence_edit/far_pointer_seq.cpp Source File

32 #include "wx/wxprec.h" 103 Create

(parent,

id

, caption, pos,

size

, style);

111 bool CFarPointerSeq::Create

( wxWindow* parent, wxWindowID

id

const

wxString& caption,

const

wxPoint& pos,

const

wxSize&

size

long

style )

114

SetExtraStyle(wxWS_EX_BLOCK_EVENTS);

115

wxDialog::Create( parent,

id

, caption, pos,

size

, style );

120

GetSizer()->SetSizeHints(

this

);

162

wxBoxSizer* itemBoxSizer2 =

new

wxBoxSizer(wxVERTICAL);

163

itemDialog1->SetSizer(itemBoxSizer2);

167

vector<bool> checked;

168

wxArrayString choices;

172 for

(

auto row

= 0;

row

< num_rows;

row

++)

174 const CSeq_id

id

= align_it->GetSeq_id(

row

);

177 bool check

(

false

);

178 bool

disable(

false

);

180 if

(!disable && !

msg

.empty())

182

checked.push_back(

check

);

185

msgs.push_back(

msg

);

186 if

(

label

.size() > label_max.size())

191

wxGraphicsContext *gc = wxGraphicsContext::Create();

192

gc->SetFont(GetFont(), *wxBLACK);

197

choices.Add(wxString(

label

+ msgs[

]));

201 if

(choices.IsEmpty())

206 for

(

size_t i

= 0;

< checked.size();

++)

210

wxBoxSizer* itemBoxSizer10 =

new

wxBoxSizer(wxHORIZONTAL);

211

itemBoxSizer2->Add(itemBoxSizer10, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

213

wxButton* itemButton11 =

new

wxButton( itemDialog1, wxID_OK,

(

"Replace Selected Sequences"

), wxDefaultPosition, wxDefaultSize, 0 );

214

itemBoxSizer10->Add(itemButton11, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

216

wxButton* itemButton12 =

new

wxButton( itemDialog1, wxID_CANCEL,

(

"Cancel"

), wxDefaultPosition, wxDefaultSize, 0 );

217

itemBoxSizer10->Add(itemButton12, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

219

wxButton* itemButton13 =

new

wxButton( itemDialog1,

ID_FARPOINTERSEQ_EXPORT

(

"Export FarPointer Error Messages"

), wxDefaultPosition, wxDefaultSize, 0 );

220

itemBoxSizer10->Add(itemButton13, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

230

wxDouble externalLeading;

231

gc->GetTextExtent(wxString(

str

), &width, &height, &descent, &externalLeading);

232

wxDouble space_width;

233

gc->GetTextExtent(

(

" "

), &space_width, &height, &descent, &externalLeading);

235

gc->GetTextExtent(wxString(label_max), &max_width, &height, &descent, &externalLeading);

236 if

(max_width >= width)

238 int

add_spaces =

int

((max_width - width) / space_width) + 1;

246 int i

event

.GetInt();

260 msg

->first +

"\t"

->second +

"\n"

;

265

report->SetTitle(

wxT

(

"FarPointer Errors"

));

279 if

(!align_it->IsSetSegs() || !align_it->GetSegs().IsDenseg() ||

280

!align_it->GetSegs().GetDenseg().IsSetIds())

284

new_align->

Assign

(align_it.GetOriginalSeq_align());

286 bool

modified(

false

);

288 for

(

size_t

j = 0; j < checked.GetCount(); j++)

290 int i

= checked.Item(j);

297 for

(

auto row

= 0;

row

< num_rows;

row

++)

299 const CSeq_id

id

= align_it->GetSeq_id(

row

);

315

new_align->

SetSegs

().SetDenseg().SetIds()[

row

]->Assign(*new_id);

323

new_align->

SetSegs

().SetDenseg().RemovePureGapSegs();

325

new_align->

SetSegs

().SetDenseg().Compact();

327 cmd

->AddCommand(*chgAlign);

331 for

(

size_t

j = 0; j < checked.GetCount(); j++)

333 int i

= checked.Item(j);

415 return "Not a far pointer"

;

417 string

orig_label(

label

);

427 catch

(

const CException

&) {}

catch

(

const

exception&) {}

444 catch

(

const CException

&) {}

catch

(

const

exception&) {}

454 if

(query_seqloc.

IsNull

() || subject_seqloc.

IsNull

())

460

blast::SSeqLoc query_sl(*query_seqloc, scope);

461

blast::SSeqLoc subject_sl(*subject_seqloc, scope);

463

blast::CBlastNucleotideOptionsHandle& opts =

dynamic_cast<

blast::CBlastNucleotideOptionsHandle&

>

(bl2seq.SetOptionsHandle());

464

opts.SetTraditionalMegablastDefaults();

466

opts.SetMaskAtHash(

true

);

467

opts.SetDustFiltering(

true

);

469

opts.SetMismatchPenalty(-3);

472

vector< CRef<objects::CSeq_align_set> > res = bl2seq.Run();

475 if

(align && align->

IsSet

() && !align->

Get

().empty())

476 return

(align->

Get

().front());

484 return

(

"No alignment found!"

);

490 int

num_rows = align->CheckNumRows();

500 bool

flip_strand = (align->GetSeqStrand(0) != align->GetSeqStrand(1));

503 if

(align->GetSeq_id(0).Match(*bsh1.

GetSeqId

()))

505

start1 = align->GetSeqStart(0);

506

stop1 = align->GetSeqStop(0);

507

start2 = align->GetSeqStart(1);

508

stop2 = align->GetSeqStop(1);

510 else if

(align->GetSeq_id(1).Match(*bsh1.

GetSeqId

()))

512

start1 = align->GetSeqStart(1);

513

stop1 = align->GetSeqStop(1);

514

start2 = align->GetSeqStart(0);

515

stop2 = align->GetSeqStop(0);

528

assem_len = stop1 - start1 + 1;

530

assem_len = start1 - stop1 + 1;

536 for

(

size_t i

= 0;

< seq1.size();

++)

538 if

(seq1[

] ==

'N'

)

544 for

(

int i

= length - 1;

>= 0;

--)

546 if

(seq1[

] ==

'N'

)

552 for

(

size_t i

= 0;

< seq1.size();

++)

554 if

(seq1[

] ==

'N'

)

560 if

(!align->IsSetSegs() || !align->GetSegs().IsDenseg() ||

561

!align->GetSegs().GetDenseg().IsSetStarts() || !align->GetSegs().GetDenseg().IsSetLens())

568

vector< TSignedSeqPos > starts(align->GetSegs().GetDenseg().GetStarts());

569

vector< TSeqPos > lens(align->GetSegs().GetDenseg().GetLens());

570 size_t

num_segs = lens.size();

576 for

(

size_t

seg = 0; seg < num_segs; ++seg)

582 if

(seg_start1 < 0 || seg_start2 < 0)

587 for

(

size_t i

= 0;

len

;

++)

589 char a

= seq1[

+ seg_start1];

590 char b

= seq2[

+ seg_start2];

593 if

(

'N'

)

602 tmp

[

+ seg_start1] =

'+'

;

606 int

uncovered_non_n = 0;

607 for

(

size_t i

= 0;

tmp

.size();

++)

609 if

(

tmp

[

] ==

'+'

)

611 if

(

tmp

[

] ==

'N'

)

617 if

(gaps>0 || mismatches>0 ||

> 0)

619 if

(beg > 0 || end > 0)

621

errors +=

"The local sequence has "

NStr::ULongToString

(beg + end) +

" terminal N"

+ (beg+end > 1 ?

"s. "

". "

);

625

errors +=

"The local sequence has "

NStr::ULongToString

(nctr) +

" internal N"

+ (nctr > 1 ?

"s. "

". "

);

630 if

(!errors.empty() && assem_len == length && gaps == 0 && mismatches == 0)

632

errors +=

"There are no other differences between the local and database sequences."

;

636 if

((

TSeqPos

)assem_len < length)

638

errors +=

"The alignment to the database sequence does not cover all of the local sequence. "

;

640 if

(uncovered_n != 0 && uncovered_non_n == 0)

642

errors +=

"The unaligned sequence consists only of Ns. "

;

644 if

(uncovered_non_n != 0)

646

errors +=

"There are non-N residues in the unaligned sequence. "

;

650 if

(gaps > 0 || mismatches > 0 ||

> 0)

652

errors +=

"The alignment to the database sequence has "

NStr::ULongToString

(gaps) +

" gap"

+ (gaps != 1 ?

"s, "

", "

)

Declares the CBl2Seq (BLAST 2 Sequences) class.

Declares the CBlastNucleotideOptionsHandle class.

Definitions of special type used in BLAST.

@ eMegablast

Nucl-Nucl (traditional megablast)

wxIcon GetIconResource(const wxString &name)

Retrieves icon resources.

void AddSpaces(string &str, const string &label_max, wxGraphicsContext *gc)

map< CBioseq_Handle, int > m_offset

map< string, CBioseq_Handle > m_label_to_bsh1

void ReverseRow(CDense_seg &dense_seg, int offset, size_t row, CSeq_align::TDim num_rows)

string ValidateAlignment(CRef< objects::CSeq_align > align, CBioseq_Handle bsh1, CBioseq_Handle bsh2, bool &check)

string GetMessageForId(const CSeq_id &id, string label, bool &check, bool &disable)

bool Create(wxWindow *parent, wxWindowID id=wxID_ANY, const wxString &caption=_("Far Pointer Sequences"), const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL)

Creation.

CRef< objects::CSeq_align > RunBlast(const CBioseq_Handle &sh, const CBioseq_Handle &qh)

vector< string > m_labels

map< CBioseq_Handle, bool > m_flip_strand

void OnCheck(wxCommandEvent &event)

CFarPointerSeq()

Constructors.

void OnExport(wxCommandEvent &event)

~CFarPointerSeq()

Destructor.

map< string, string > m_errors

map< string, CBioseq_Handle > m_label_to_bsh2

CRef< CCmdComposite > GetCommand()

static bool ShowToolTips()

Should we show tooltips?

wxBitmap GetBitmapResource(const wxString &name)

Retrieves bitmap resources.

void CreateControls()

Creates the controls and sizers.

void Init()

Initialises member variables.

CSeq_entry_Handle m_TopSeqEntry

wxCheckListBox * m_CheckListBox

vector< bool > m_disabled

void SetText(const wxString &text)

void OffsetRow(TDim row, TSignedSeqPos offset)

Offset row's coords.

const_iterator begin() const

const_iterator end() const

#define ID_FARPOINTERSEQ_EXPORT

#define ID_FARPOINTERSEQ_CHECKLISTBOX

static const char * str(char *buf, int n)

unsigned int TSeqPos

Type for sequence locations and lengths.

int TSignedSeqPos

Type for signed sequence position.

void swap(NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair1, NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair2)

#define NCBI_THROW(exception_class, err_code, message)

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

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

Set object to copy of another one.

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

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

CConstRef< CSeq_id > GetSeqId(void) const

@ fParse_Default

By default in ParseIDs and IsValid, allow raw parsable non-numeric accessions and plausible local acc...

@ eContent

Untagged human-readable accession or the like.

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

@ eGetId_Best

return the "best" gi (uses FindBestScore(), with CSeq_id::CalculateScore() as the score function

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

TClass GetClass(void) const

CBioseq_set_Handle GetParentBioseq_set(void) const

Return a handle for the parent Bioseq-set, or null handle.

TSeqPos GetBioseqLength(void) const

CConstRef< CSeq_id > GetSeqId(void) const

Get id which can be used to access this bioseq handle Throws an exception if none is available.

bool IsSetClass(void) const

CScope & GetScope(void) const

Get scope this handle belongs to.

CScope & GetScope(void) const

Get scope this handle belongs to.

CRef< CSeq_loc > GetRangeSeq_loc(TSeqPos start, TSeqPos stop, ENa_strand strand=eNa_strand_unknown) const

Return CSeq_loc referencing the given range and strand on the bioseq If start == 0,...

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

Check if a string starts with a specified prefix value.

static string ULongToString(unsigned long value, TNumToStringFlags flags=0, int base=10)

Convert unsigned long to string.

static void TrimPrefixInPlace(string &str, const CTempString prefix, ECase use_case=eCase)

Trim prefix from a string (in-place)

static const char label[]

bool IsSetStrands(void) const

Check if a value has been assigned to Strands data member.

const TStarts & GetStarts(void) const

Get the Starts member data.

void SetSegs(TSegs &value)

Assign a value to Segs data member.

const TLens & GetLens(void) const

Get the Lens member data.

TStarts & SetStarts(void)

Assign a value to Starts data member.

TStrands & SetStrands(void)

Assign a value to Strands data member.

bool IsSet(void) const

Check if a value has been assigned to data member.

const TStrands & GetStrands(void) const

Get the Strands member data.

const Tdata & Get(void) const

Get the member data.

@ eClass_nuc_prot

nuc acid and coded proteins

unsigned int

A callback function used to compare two keys in a database.

const struct ncbi::grid::netcache::search::fields::SIZE size

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

Definition of SSeqLoc structure.

#define row(bind, expected)

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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/far__pointer__seq_8cpp_source.html below:

NCBI C++ ToolKit: src/gui/packages/pkg_sequence_edit/far_pointer_seq.cpp Source File

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/farpointerseq_8cpp_source.html below: