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NCBI C++ ToolKit: src/app/cn3d/update_viewer_window.cpp Source File

41 #include <wx/msw/winundef.h> 44 #include <wx/stattext.h> 79

updateViewer(thisUpdateViewer)

84

editMenu->AppendSeparator();

85

wxMenu *subMenu =

new

wxMenu;

86

subMenu->Append(MID_SORT_UPDATES_IDENTIFIER,

"By &Identifier"

);

87

subMenu->Append(MID_SORT_UPDATES_PSSM,

"By &PSSM Score"

);

88

editMenu->Append(MID_SORT_UPDATES,

"So&rt Imports..."

, subMenu);

89

editMenu->AppendSeparator();

90

editMenu->Append(MID_IMPORT_SEQUENCES,

"&Import Sequences"

);

91

editMenu->Append(MID_IMPORT_STRUCTURE,

"Import S&tructure"

);

93

editMenu->Insert(8, MID_DELETE_ALL_BLOCKS,

"Delete A&ll Blocks"

""

true

);

94

editMenu->Insert(9, MID_DELETE_BLOCKS_ALL_ROWS,

"Delete All Blocks in All Ali&gnments"

);

97

menuBar->Enable(MID_SELECT_COLS,

false

);

98

menuBar->Enable(MID_SELECT_BLOCKS,

false

);

101

wxMenu *menu =

new

wxMenu;

102

menu->Append(MID_BLOCKALIGN_ONE,

"B&lock Align Single"

""

true

);

103

menu->Append(MID_BLOCKALIGN_ALL,

"Bloc&k Align N"

);

104

menu->AppendSeparator();

105

menu->Append(MID_BLAST_ONE,

"&BLAST Single"

""

true

);

106

menu->Append(MID_BLAST_PSSM_ONE,

"BLAST/&PSSM Single"

""

true

);

107

menu->Append(MID_BLAST_NEIGHBOR,

"BLAST &Neighbor"

""

true

);

108

menu->AppendSeparator();

109

menu->Append(MID_THREAD_ONE,

"Thread &Single"

""

true

);

110

menu->Append(MID_THREAD_ALL,

"Thread &All"

);

111

menu->AppendSeparator();

112

menu->Append(MID_EXTEND_ONE,

"&Extend Single"

""

true

);

113

menu->Append(MID_EXTEND_ALL,

"E&xtend All"

);

114

menu->AppendSeparator();

115

menu->Append(MID_SET_REGION,

"Set &Region"

""

true

);

116

menu->Append(MID_RESET_REGIONS,

"Reset All Re&gions"

);

117

menuBar->Append(menu,

"Al&gorithms"

);

121

menu->Append(MID_MERGE_ONE,

"&Merge Single"

""

true

);

122

menu->Append(MID_MERGE_NEIGHBOR,

"Merge to &Neighbor"

""

true

);

123

menu->Append(MID_MERGE_ALL,

"Merge &All"

);

124

menu->AppendSeparator();

125

menu->Append(MID_DELETE_ONE,

"&Delete Single"

""

true

);

126

menu->Append(MID_DELETE_ALL,

"Delete A&ll"

);

127

menuBar->Append(menu,

"&Alignments"

);

130

EnableBaseEditorMenuItems(

true

);

131

menuBar->Check(MID_ENABLE_EDIT,

true

);

132

menuBar->Enable(MID_ENABLE_EDIT,

false

);

136

menuBar->Check(MID_DRAG_HORIZ,

true

);

137

menuBar->Check(MID_SELECT_RECT,

false

);

149 if

(event.CanVeto()) {

172 switch

(event.GetId()) {

176

SetCursor(*wxCROSS_CURSOR);

182 ERRORMSG

(

"Can't run threader without existing core alignment"

);

192 if

(optDialog.ShowModal() == wxCANCEL)

return

;

195 ERRORMSG

(

"Error retrieving options values from dialog"

);

200

SetCursor(*wxHOURGLASS_CURSOR);

202

SetCursor(wxNullCursor);

210 switch

(event.GetId()) {

214

SetCursor(*wxCROSS_CURSOR);

221

SetCursor(*wxCROSS_CURSOR);

229 if

(currentUpdates.size() > 0) {

230

ViewerBase::AlignmentList::const_iterator u, ue = currentUpdates.end();

231 for

(u=currentUpdates.begin(); u!=ue; ++u)

all

[*u] =

true

;

241 switch

(event.GetId()) {

245

SetCursor(*wxCROSS_CURSOR);

251 if

(currentUpdates.size() > 0) {

253

ViewerBase::AlignmentList::const_iterator u, ue = currentUpdates.end();

254 for

(u=currentUpdates.begin(); u!=ue; ++u) {

257

newAlignments.push_back(newAlignment);

266

SetCursor(*wxCROSS_CURSOR);

286 option

= wxYES_NO | wxYES_DEFAULT | wxICON_EXCLAMATION | wxCENTRE;

287 if

(canCancel)

option

|= wxCANCEL;

289

wxMessageDialog dialog(

NULL

"Do you want to keep the changes to these updates?"

""

option

);

290 option

= dialog.ShowModal();

292 if

(

option

== wxID_CANCEL)

return false

;

313 switch

(event.GetId()) {

317

SetCursor(*wxCROSS_CURSOR);

324

SetCursor(*wxCROSS_CURSOR);

331

SetCursor(*wxCROSS_CURSOR);

351

SetCursor(*wxCROSS_CURSOR);

359

(*a)->alignDependentFrom = -1;

360

(*a)->alignDependentTo = -1;

370

SetCursor(*wxCROSS_CURSOR);

385

SetCursor(*wxCROSS_CURSOR);

406

wxDialog(parent, -1, "Set

Threader

Options", wxDefaultPosition, wxDefaultSize, wxDEFAULT_DIALOG_STYLE)

409

wxPanel *panel =

new

wxPanel(

this

, -1);

410

wxBoxSizer *item0 =

new

wxBoxSizer(wxVERTICAL);

411

wxBoxSizer *item1 =

new

wxBoxSizer(wxVERTICAL);

412

wxStaticBox *item3 =

new

wxStaticBox(panel, -1,

"Threader Options"

);

413

wxStaticBoxSizer *item2 =

new

wxStaticBoxSizer(item3, wxHORIZONTAL);

414

wxFlexGridSizer *

grid

new

wxFlexGridSizer(2, 5, 0);

417

wxStaticText *item5 =

new

wxStaticText(panel, -1,

"Weighting of PSSM/Contact score? [0 .. 1], 1 = PSSM only"

, wxDefaultPosition, wxDefaultSize, 0);

418 grid

->Add(item5, 0, wxALIGN_RIGHT|wxALIGN_CENTER_VERTICAL|wxALL, 5);

420

0.0, 1.0, 0.05, initialOptions.weightPSSM,

421

wxDefaultPosition, wxSize(80, SPIN_CTRL_HEIGHT), 0,

422

wxDefaultPosition, wxSize(-1, SPIN_CTRL_HEIGHT));

423 grid

->Add(fpWeight->GetTextCtrl(), 0, wxALIGN_CENTRE|wxLEFT|wxTOP|wxBOTTOM, 5);

427

wxStaticText *item8 =

new

wxStaticText(panel, -1,

"Loop length multiplier? [0.1 .. 10]"

, wxDefaultPosition, wxDefaultSize, 0);

428 grid

->Add(item8, 0, wxALIGN_RIGHT|wxALIGN_CENTER_VERTICAL|wxALL, 5);

430

0.1, 10.0, 0.25, initialOptions.loopLengthMultiplier,

431

wxDefaultPosition, wxSize(80, SPIN_CTRL_HEIGHT), 0,

432

wxDefaultPosition, wxSize(-1, SPIN_CTRL_HEIGHT));

433 grid

->Add(fpLoops->GetTextCtrl(), 0, wxALIGN_CENTRE|wxLEFT|wxTOP|wxBOTTOM, 5);

437

wxStaticText *item11 =

new

wxStaticText(panel, -1,

"Number of random starts? [1 .. 1000]"

, wxDefaultPosition, wxDefaultSize, 0);

438 grid

->Add(item11, 0, wxALIGN_RIGHT|wxALIGN_CENTER_VERTICAL|wxALL, 5);

440

1, 1000, 5, initialOptions.nRandomStarts,

441

wxDefaultPosition, wxSize(80, SPIN_CTRL_HEIGHT), 0,

442

wxDefaultPosition, wxSize(-1, SPIN_CTRL_HEIGHT));

443 grid

->Add(iStarts->GetTextCtrl(), 0, wxALIGN_CENTRE|wxLEFT|wxTOP|wxBOTTOM, 5);

447

wxStaticText *item14 =

new

wxStaticText(panel, -1,

"Number of result alignments per row? [1 .. 20]"

, wxDefaultPosition, wxDefaultSize, 0);

448 grid

->Add(item14, 0, wxALIGN_RIGHT|wxALIGN_CENTER_VERTICAL|wxALL, 5);

450

1, 20, 1, initialOptions.nResultAlignments,

451

wxDefaultPosition, wxSize(80, SPIN_CTRL_HEIGHT), 0,

452

wxDefaultPosition, wxSize(-1, SPIN_CTRL_HEIGHT));

453 grid

->Add(iResults->GetTextCtrl(), 0, wxALIGN_CENTRE|wxLEFT|wxTOP|wxBOTTOM, 5);

457

wxStaticText *item16 =

new

wxStaticText(panel, -1,

"Terminal residue cutoff? [-1..N], -1 = unrestricted"

, wxDefaultPosition, wxDefaultSize, 0);

458 grid

->Add(item16, 0, wxALIGN_RIGHT|wxALIGN_CENTER_VERTICAL|wxALL, 5);

460

-1, 100000, 1, initialOptions.terminalResidueCutoff,

461

wxDefaultPosition, wxSize(80, SPIN_CTRL_HEIGHT), 0,

462

wxDefaultPosition, wxSize(-1, SPIN_CTRL_HEIGHT));

463 grid

->Add(iCutoff->GetTextCtrl(), 0, wxALIGN_CENTRE|wxLEFT|wxTOP|wxBOTTOM, 5);

467

wxStaticText *item17 =

new

wxStaticText(panel, -1,

"Merge results after each row is threaded?"

, wxDefaultPosition, wxDefaultSize, 0);

468 grid

->Add(item17, 0, wxALIGN_RIGHT|wxALIGN_CENTER_VERTICAL|wxALL, 5);

469

bMerge =

new

wxCheckBox(panel, -1,

""

, wxDefaultPosition, wxDefaultSize, 0);

470

bMerge->SetValue(initialOptions.mergeAfterEachSequence);

471 grid

->Add(bMerge, 0, wxALIGN_CENTRE|wxALL, 5);

472 grid

->Add(20, SPIN_CTRL_HEIGHT, 0, wxALIGN_CENTRE|wxRIGHT|wxTOP|wxBOTTOM, 5);

475

wxStaticText *item19 =

new

wxStaticText(panel, -1,

"Freeze isolated blocks?"

, wxDefaultPosition, wxDefaultSize, 0);

476 grid

->Add(item19, 0, wxALIGN_RIGHT|wxALIGN_CENTER_VERTICAL|wxALL, 5);

477

bFreeze =

new

wxCheckBox(panel, -1,

""

, wxDefaultPosition, wxDefaultSize, 0);

478

bFreeze->SetValue(initialOptions.freezeIsolatedBlocks);

479 grid

->Add(bFreeze, 0, wxALIGN_CENTRE|wxALL, 5);

480 grid

->Add(20, SPIN_CTRL_HEIGHT, 0, wxALIGN_CENTRE|wxRIGHT|wxTOP|wxBOTTOM, 5);

482

item2->Add(

grid

, 0, wxALIGN_CENTRE|wxALL, 5);

483

item1->Add(item2, 0, wxALIGN_CENTRE|wxALL, 5);

484

wxBoxSizer *item21 =

new

wxBoxSizer(wxHORIZONTAL);

486

bOK =

new

wxButton(panel, -1,

"OK"

, wxDefaultPosition, wxDefaultSize, 0);

488

item21->Add(bOK, 0, wxALIGN_CENTRE|wxALL, 5);

490

bCancel =

new

wxButton(panel, -1,

"Cancel"

, wxDefaultPosition, wxDefaultSize, 0);

491

item21->Add(bCancel, 0, wxALIGN_CENTRE|wxALL, 5);

493

item1->Add(item21, 0, wxALIGN_CENTRE|wxALL, 5);

494

item0->Add(item1, 0, wxALIGN_CENTRE|wxALL, 5);

495

panel->SetAutoLayout(

true

);

496

panel->SetSizer(item0);

499

item0->SetSizeHints(

this

);

531 if

(event.GetEventObject() ==

bOK

) {

537

}

else if

(event.GetEventObject() ==

bCancel

) {

547 #define ID_TEXT 10000 548 #define ID_T_TITLE 10001 549 #define ID_TEXTCTRL 10002 550 #define ID_SPINBUTTON 10003 551 #define ID_B_OK 10004 552 #define ID_B_CANCEL 10005 561

wxDialog(parentFrame, -1, "Set Alignment Region", wxDefaultPosition, wxDefaultSize, wxDEFAULT_DIALOG_STYLE)

563

wxPanel *parent =

new

wxPanel(

this

, -1);

564

wxBoxSizer *item0 =

new

wxBoxSizer( wxVERTICAL );

566

wxStaticBox *item2 =

new

wxStaticBox( parent, -1,

"Region"

);

567

wxStaticBoxSizer *item1 =

new

wxStaticBoxSizer( item2, wxVERTICAL );

569

wxFlexGridSizer *item3 =

new

wxFlexGridSizer( 1, 0, 0, 0 );

570

item3->AddGrowableCol( 1 );

572

wxStaticText *item4 =

new

wxStaticText( parent,

ID_TEXT

"Sequence:"

, wxDefaultPosition, wxDefaultSize, 0 );

573

item3->Add( item4, 0, wxALIGN_CENTRE|wxALL, 5 );

576

title.Printf(

"%s, length %i"

, sequence->identifier->ToString().c_str(), sequence->Length());

577

wxStaticText *item5 =

new

wxStaticText( parent,

ID_T_TITLE

, title, wxDefaultPosition, wxDefaultSize, 0 );

578

item3->Add( item5, 0, wxGROW|wxALIGN_CENTER_VERTICAL|wxALL, 5 );

580

item1->Add( item3, 0, wxGROW|wxALIGN_CENTER_VERTICAL|wxALL, 5 );

582

wxFlexGridSizer *item6 =

new

wxFlexGridSizer( 1, 0, 0, 0 );

583

item6->AddGrowableCol( 1 );

584

item6->AddGrowableRow( 4 );

586

wxStaticText *item7 =

new

wxStaticText( parent,

ID_TEXT

"From:"

, wxDefaultPosition, wxDefaultSize, 0 );

587

item6->Add( item7, 0, wxALIGN_CENTRE|wxALL, 5 );

589

iFrom =

new IntegerSpinCtrl

(parent, 0, sequence->Length(), 1, initialFrom,

590

wxDefaultPosition, wxSize(80, SPIN_CTRL_HEIGHT), 0,

591

wxDefaultPosition, wxSize(-1, SPIN_CTRL_HEIGHT));

592

item6->Add( iFrom->GetTextCtrl(), 0, wxALIGN_CENTRE|wxLEFT|wxTOP|wxBOTTOM, 5 );

595

wxStaticText *item10 =

new

wxStaticText( parent,

ID_TEXT

"To:"

, wxDefaultPosition, wxDefaultSize, 0 );

596

item6->Add( item10, 0, wxALIGN_CENTRE|wxALL, 5 );

598

iTo =

new IntegerSpinCtrl

(parent, 0, sequence->Length(), 1, initialTo,

599

wxDefaultPosition, wxSize(80, SPIN_CTRL_HEIGHT), 0,

600

wxDefaultPosition, wxSize(-1, SPIN_CTRL_HEIGHT));

601

item6->Add( iTo->GetTextCtrl(), 0, wxALIGN_CENTRE|wxLEFT|wxTOP|wxBOTTOM, 5 );

604

item1->Add( item6, 0, wxGROW|wxALIGN_CENTER_VERTICAL|wxALL, 5 );

606

item0->Add( item1, 0, wxALIGN_CENTRE|wxALL, 5 );

608

wxBoxSizer *item13 =

new

wxBoxSizer( wxHORIZONTAL );

610

wxButton *item14 =

new

wxButton( parent,

ID_B_OK

"OK"

, wxDefaultPosition, wxDefaultSize, 0 );

611

item14->SetDefault();

612

item13->Add( item14, 0, wxALIGN_CENTRE|wxALL, 5 );

614

wxButton *item15 =

new

wxButton( parent,

ID_B_CANCEL

"Cancel"

, wxDefaultPosition, wxDefaultSize, 0 );

615

item13->Add( item15, 0, wxALIGN_CENTRE|wxALL, 5 );

617

item0->Add( item13, 0, wxALIGN_CENTRE|wxALL, 5 );

619

parent->SetAutoLayout(

TRUE

);

620

parent->SetSizer( item0 );

622

item0->Fit( parent );

623

item0->SetSizeHints(

this

);

639 if

(event.GetId() ==

ID_B_OK

) {

654 return

(

iFrom

->GetInteger(from) &&

iTo

->GetInteger(to));

void ExtendAllUpdates(void)

void BlockAlignAllUpdates(void)

std::map< BlockMultipleAlignment *, bool > UpdateMap

const BlockMultipleAlignment * GetCurrentMultipleAlignment(void) const

void MergeUpdates(const UpdateMap &updates, bool mergeToNeighbor)

void ThreadAllUpdates(const ThreaderOptions &options)

BlockMultipleAlignment * Clone(void) const

bool DeleteAllBlocks(void)

void UnPostRedrawSequenceViewer(ViewerBase *viewer)

void OnButton(wxCommandEvent &event)

bool GetValues(int *from, int *to)

ncbi::IntegerSpinCtrl * iFrom

ncbi::IntegerSpinCtrl * iTo

void OnCloseWindow(wxCloseEvent &event)

bool GetValues(ThreaderOptions *options)

void OnCloseWindow(wxCloseEvent &event)

ncbi::IntegerSpinCtrl * iStarts

~ThreaderOptionsDialog(void)

ncbi::FloatingPointSpinCtrl * fpWeight

void OnButton(wxCommandEvent &event)

ncbi::FloatingPointSpinCtrl * fpLoops

ncbi::IntegerSpinCtrl * iResults

ncbi::IntegerSpinCtrl * iCutoff

bool mergeAfterEachSequence

int terminalResidueCutoff

bool freezeIsolatedBlocks

double loopLengthMultiplier

static unsigned int EstimateNRandomStarts(const BlockMultipleAlignment *coreAlignment, const BlockMultipleAlignment *toBeThreaded)

void OnImport(wxCommandEvent &event)

void OnRunThreader(wxCommandEvent &event)

void EnableDerivedEditorMenuItems(bool enabled)

bool DoThreadSingle(void) const

bool DoBlastSingle(void) const

void OnDelete(wxCommandEvent &event)

void OnExtend(wxCommandEvent &event)

bool DoBlastPSSMSingle(void) const

void OnBlockAlign(wxCommandEvent &event)

void BlastPSSMSingleOff(void)

bool SaveDialog(bool prompt, bool canCancel)

void MergeSingleOff(void)

bool DoMergeSingle(void) const

bool DoDeleteSingle(void) const

void OnSortUpdates(wxCommandEvent &event)

void BlockAlignSingleOff(void)

void DeleteAllBlocksOff(void)

void OnCloseWindow(wxCloseEvent &event)

bool DoExtendSingle(void) const

void BlastSingleOff(void)

bool DoBlockAlignSingle(void) const

UpdateViewer * updateViewer

void OnMerge(wxCommandEvent &event)

void OnRunBlast(wxCommandEvent &event)

bool DoSetRegion(void) const

bool DoBlastNeighborSingle(void) const

bool DoDeleteAllBlocks(void) const

bool DoMergeNeighbor(void) const

~UpdateViewerWindow(void)

void BlastNeighborSingleOff(void)

void ThreadSingleOff(void)

@ MID_DELETE_BLOCKS_ALL_ROWS

@ MID_SORT_UPDATES_IDENTIFIER

void MergeNeighborOff(void)

void ExtendSingleOff(void)

void SetWindowTitle(void)

void DeleteSingleOff(void)

void OnSetRegion(wxCommandEvent &event)

void ReplaceAlignments(const AlignmentList &alignmentList)

void ImportStructure(void)

void SaveAlignments(void)

std::list< BlockMultipleAlignment * > AlignmentList

void ImportSequences(void)

void SortByIdentifier(void)

std::list< BlockMultipleAlignment * > AlignmentList

AlignmentManager * alignmentManager

const AlignmentList & GetCurrentAlignments(void) const

void CancelAllSpecialModesExcept(int id)

void RaiseLogWindow(void)

ThreaderOptions globalThreaderOptions

Include a standard set of the NCBI C++ Toolkit most basic headers.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_SCOPE(ns)

Define a new scope.

Messenger * GlobalMessenger(void)

constexpr bool empty(list< Ts... >) noexcept

#define TRUE

bool replacment for C indicating true.

static void SetTitle(CRef< CSeq_entry > entry, string title)

EVT_MENU_RANGE(MID_SHOW_TITLES, MID_HIDE_TITLES, ViewerWindowBase::OnTitleView) EVT_MENU_RANGE(MID_ENABLE_EDIT

#define INCLUDE_VIEWER_WINDOW_BASE_EVENTS

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Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/update__viewer__window_8cpp_source.html below:

NCBI C++ ToolKit: src/app/cn3d/update_viewer_window.cpp Source File

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/updateviewerwindow_8cpp_source.html below: