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NCBI C++ ToolKit: src/app/cn3d/cn3d_ba_interface.cpp Source File

48 #include <wx/msw/winundef.h> 51 #include <wx/numdlg.h> 86  void

OnCloseWindow(wxCloseEvent& event);

87  void

OnButton(wxCommandEvent& event);

111

BlockMultipleAlignment::UngappedAlignedBlockList::const_iterator

112

m, me = multipleABlocks.end(), p, pe = pairwiseABlocks.end();

113  const Block::Range

*multipleRangeMaster, *pairwiseRangeMaster, *pairwiseRangeDependent;

115  for

(

i

=0, m=multipleABlocks.begin(); m!=me; ++

i

, ++m) {

116

multipleRangeMaster = (*m)->GetRangeOfRow(0);

117  for

(p=pairwiseABlocks.begin(); p!=pe; ++p) {

118

pairwiseRangeMaster = (*p)->GetRangeOfRow(0);

119  if

(pairwiseRangeMaster->

from

<= multipleRangeMaster->

from

&&

120

pairwiseRangeMaster->

to

>= multipleRangeMaster->

to

) {

121

pairwiseRangeDependent = (*p)->GetRangeOfRow(1);

123

(multipleRangeMaster->

from

- pairwiseRangeMaster->

from

);

148  ERRORMSG

(

"dpScoreFunction() - bad parameters: block "

<< block <<

" queryPos "

<< queryPos <<

170

unique_ptr<BlockMultipleAlignment>

175  int

s, blockScoreSum = 0;

176  for

(

unsigned int b

=0;

b

<

result

->nBlocks; ++

b

) {

185

bma->AddAlignedBlockAtEnd(newBlock);

188

<<

" position: "

<< (

result

->blockPositions[

b

] + 1)

192  if

(blockScoreSum !=

result

->score)

193  ERRORMSG

(

"block aligner reported score doesn't match sum of block scores"

);

196  if

(!bma->AddUnalignedBlocks() || !bma->UpdateBlockMapAndColors(

false

)) {

197  ERRORMSG

(

"Error finalizing new alignment!"

);

203

score.Printf(

" raw score: %i"

,

result

->score);

204

bma->SetRowStatusLine(0,

WX_TO_STD

(score));

205

bma->SetRowStatusLine(1,

WX_TO_STD

(score));

208  return

bma.release();

215

newAlignments->clear();

216

*nRowsAddedToMultiple = 0;

221  ERRORMSG

(

"merge selected but NULL sequenceViewer"

);

225  unsigned int

nAln = toRealign.size(),

a

= 0;

229  if

(

blocks

.size() == 0) {

230  ERRORMSG

(

"Must have at least one aligned block to use the block aligner"

);

236

unique_ptr < ProgressMeter > progress;

238  long

u = wxGetNumberFromUser(

"How many sequences do you want to realign?"

,

"Max:"

,

"Alignments..."

, nAln, 1, nAln,

NULL

);

241

nAln = (

unsigned int

) u;

243

progress.reset(

new ProgressMeter

(

NULL

,

"Running block alignment..."

,

"Working"

, nAln));

246

BlockMultipleAlignment::UngappedAlignedBlockList::const_iterator

b

, be =

blocks

.end();

251  unsigned int

*loopLengths =

new unsigned int

[multiple->

NRows

()];

252

BlockMultipleAlignment::UngappedAlignedBlockList::const_iterator

n

;

254  for

(

i

=0,

b

=

blocks

.begin();

b

!=be; ++

i

, ++

b

) {

255

range = (*b)->GetRangeOfRow(0);

263  for

(

unsigned int r

=0;

r

<multiple->

NRows

(); ++

r

) {

264

range = (*b)->GetRangeOfRow(

r

);

265

nextRange = (*n)->GetRangeOfRow(

r

);

266

loopLengths[

r

] = nextRange->

from

- range->

to

- 1;

278  bool

errorsEncountered =

false

;

280

AlignmentList::const_iterator s, se = toRealign.end();

281  for

(s=toRealign.begin(); s!=se; ++s, ++

a

) {

283  ERRORMSG

(

"master sequence mismatch"

);

291

newAlignments->push_back(newAlignment);

296

progress->SetValue(

a

);

299  dpQuery

= (*s)->GetSequenceOfRow(1);

300  int

startQueryPosition =

301

((*s)->alignDependentFrom >= 0 && (*s)->alignDependentFrom < (

int

)

dpQuery

->

Length

()) ?

302

(*s)->alignDependentFrom : 0;

303  int

endQueryPosition =

304

((*s)->alignDependentTo >= 0 && (*s)->alignDependentTo < (

int

)

dpQuery

->

Length

()) ?

306  TRACEMSG

(

"query region: "

<< (startQueryPosition+1) <<

" to "

<< (endQueryPosition+1));

323

startQueryPosition, endQueryPosition, &dpResult);

326

startQueryPosition, endQueryPosition, &dpResult);

335  ERRORMSG

(

"Couldn't create BlockMultipleAlignment from DP result"

);

348

++(*nRowsAddedToMultiple);

355

newAlignments->push_back(dpAlignment);

362  WARNINGMSG

(

"block aligner found no significant alignment - current alignment unchanged"

);

363

status =

"alignment unchanged"

;

365  WARNINGMSG

(

"block aligner encountered a problem - current alignment unchanged"

);

366

errorsEncountered =

true

;

367

status =

"block aligner error!"

;

374

newAlignments->push_back(newAlignment);

387  if

(progress.get()) {

388

progress->Close(

true

);

394  if

(errorsEncountered)

395  ERRORMSG

(

"Block aligner encountered problem(s) - see message log for details"

);

409  bool ok

= (dialog.ShowModal() == wxOK);

411  ERRORMSG

(

"Error getting options from dialog!"

);

421 #define ID_TEXT 10000 422 #define ID_T_PERCENT 10001 423 #define ID_S_EXT 10002 424 #define ID_T_EXTENSION 10003 425 #define ID_S_PERCENT 10004 426 #define ID_T_CUTOFF 10005 427 #define ID_S_LAMBDA 10006 428 #define ID_C_GLOBAL 10007 429 #define ID_C_KEEP 10008 430 #define ID_C_MERGE 10009 431 #define ID_B_OK 10010 432 #define ID_B_CANCEL 10011 441

wxDialog(parent, -1, "Set

Block

Aligner Options", wxPoint(100,100), wxDefaultSize, wxDEFAULT_DIALOG_STYLE)

443

wxPanel *panel =

new

wxPanel(

this

, -1);

444

wxBoxSizer *item0 =

new

wxBoxSizer( wxVERTICAL );

445

wxStaticBox *item2 =

new

wxStaticBox( panel, -1,

wxT

(

"Block Aligner Options"

) );

446

wxStaticBoxSizer *item1 =

new

wxStaticBoxSizer( item2, wxVERTICAL );

447

wxFlexGridSizer *item3 =

new

wxFlexGridSizer( 2, 0, 0 );

448

item3->AddGrowableCol( 1 );

450

wxStaticText *item4 =

new

wxStaticText( panel,

ID_TEXT

,

wxT

(

"Loop percentile:"

), wxDefaultPosition, wxDefaultSize, 0 );

451

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

453

0.0, 100.0, 0.1,

init

.loopPercentile,

454

wxDefaultPosition, wxSize(80, SPIN_CTRL_HEIGHT), 0,

455

wxDefaultPosition, wxSize(-1, SPIN_CTRL_HEIGHT));

456

item3->Add(fpPercent->GetTextCtrl(), 0, wxALIGN_CENTRE|wxLEFT|wxTOP|wxBOTTOM, 5);

459

wxStaticText *item7 =

new

wxStaticText( panel,

ID_TEXT

,

wxT

(

"Loop extension:"

), wxDefaultPosition, wxDefaultSize, 0 );

460

item3->Add( item7, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5 );

462

0, 100000, 10,

init

.loopExtension,

463

wxDefaultPosition, wxSize(80, SPIN_CTRL_HEIGHT), 0,

464

wxDefaultPosition, wxSize(-1, SPIN_CTRL_HEIGHT));

465

item3->Add(iExtension->GetTextCtrl(), 0, wxALIGN_CENTRE|wxLEFT|wxTOP|wxBOTTOM, 5);

468

wxStaticText *item10 =

new

wxStaticText( panel,

ID_TEXT

,

wxT

(

"Loop cutoff (0=none):"

), wxDefaultPosition, wxDefaultSize, 0 );

469

item3->Add( item10, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5 );

471

0, 100000, 0,

init

.loopCutoff,

472

wxDefaultPosition, wxSize(80, SPIN_CTRL_HEIGHT), 0,

473

wxDefaultPosition, wxSize(-1, SPIN_CTRL_HEIGHT));

474

item3->Add(iCutoff->GetTextCtrl(), 0, wxALIGN_CENTRE|wxLEFT|wxTOP|wxBOTTOM, 5);

477

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

478

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

481

wxStaticText *item13 =

new

wxStaticText( panel,

ID_TEXT

,

wxT

(

"Global alignment:"

), wxDefaultPosition, wxDefaultSize, 0 );

482

item3->Add( item13, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5 );

483

cGlobal =

new

wxCheckBox( panel,

ID_C_GLOBAL

,

wxT

(

""

), wxDefaultPosition, wxDefaultSize, 0 );

484

cGlobal->SetValue(

init

.globalAlignment);

485

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

488

wxStaticText *item15 =

new

wxStaticText( panel,

ID_TEXT

,

wxT

(

"Keep existing blocks (global only):"

), wxDefaultPosition, wxDefaultSize, 0 );

489

item3->Add( item15, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5 );

490

cKeep =

new

wxCheckBox( panel,

ID_C_KEEP

,

wxT

(

""

), wxDefaultPosition, wxDefaultSize, 0 );

491

cKeep->SetValue(

init

.keepExistingBlocks);

492

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

495

wxStaticText *item17 =

new

wxStaticText( panel,

ID_TEXT

,

wxT

(

"When to merge new alignments:"

), wxDefaultPosition, wxDefaultSize, 0 );

496

item3->Add( item17, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5 );

497

wxString choices[3] = {

"No Merge"

,

"After Each"

,

"After All"

};

498

cMerge =

new

wxChoice( panel,

ID_C_MERGE

, wxDefaultPosition, wxDefaultSize, 3, choices );

499

cMerge->SetSelection(

init

.mergeType);

500

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

503

item1->Add( item3, 0, wxALIGN_CENTRE, 5 );

504

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

505

wxBoxSizer *item19 =

new

wxBoxSizer( wxHORIZONTAL );

506

wxButton *item20 =

new

wxButton( panel,

ID_B_OK

,

wxT

(

"OK"

), wxDefaultPosition, wxDefaultSize, 0 );

507

item19->Add( item20, 0, wxALIGN_CENTRE|wxALL, 5 );

508

item19->Add( 20, 20, 0, wxALIGN_CENTRE|wxALL, 5 );

509

wxButton *item21 =

new

wxButton( panel,

ID_B_CANCEL

,

wxT

(

"Cancel"

), wxDefaultPosition, wxDefaultSize, 0 );

510

item19->Add( item21, 0, wxALIGN_CENTRE|wxALL, 5 );

511

item0->Add( item19, 0, wxALIGN_CENTRE|wxALL, 5 );

513

panel->SetAutoLayout(

true

);

514

panel->SetSizer(item0);

517

item0->SetSizeHints(

this

);

546  if

(event.GetId() ==

ID_B_OK

) {

User-defined methods of the data storage class.

FloatingPointSpinCtrl * fpPercent

void OnCloseWindow(wxCloseEvent &event)

IntegerSpinCtrl * iExtension

IntegerSpinCtrl * iCutoff

bool GetValues(BlockAligner::BlockAlignerOptions *options)

~BlockAlignerOptionsDialog(void)

void OnButton(wxCommandEvent &event)

bool CreateNewPairwiseAlignmentsByBlockAlignment(BlockMultipleAlignment *multiple, const AlignmentList &toRealign, AlignmentList *newAlignments, int *nRowsAddedToMultiple, SequenceViewer *sequenceViewer)

std::list< BlockMultipleAlignment * > AlignmentList

BlockAlignerOptions currentOptions

bool SetOptions(wxWindow *parent)

BlockMultipleAlignment * Clone(void) const

std::vector< const Sequence * > SequenceList

void SetRowDouble(unsigned int row, double value) const

void SetRowStatusLine(unsigned int row, const std::string &value) const

const Sequence * GetMaster(void) const

std::vector< const UngappedAlignedBlock * > UngappedAlignedBlockList

void GetUngappedAlignedBlocks(UngappedAlignedBlockList *blocks) const

unsigned int NRows(void) const

bool MergeAlignment(const BlockMultipleAlignment *newAlignment)

void SetRangeOfRow(unsigned int row, int from, int to)

bool GetDouble(double *value) const

bool GetUnsignedInteger(unsigned int *value) const

std::string ToString(void) const

const MoleculeIdentifier * identifier

unsigned int Length(void) const

AlignmentManager * alignmentManager

bool EditorIsOn(void) const

void SetDialogSevereErrors(bool status)

unique_ptr< BlockMultipleAlignment > dpMultiple

static void FreezeBlocks(const BlockMultipleAlignment *multiple, const BlockMultipleAlignment *pairwise, DP_BlockInfo *blockInfo)

int dpScoreFunction(unsigned int block, unsigned int queryPos)

static BlockMultipleAlignment * UnpackDPResult(DP_BlockInfo *blocks, DP_AlignmentResult *result, const Sequence *master, const Sequence *query)

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

static void DLIST_NAME() init(DLIST_LIST_TYPE *list)

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_SCOPE(ns)

Define a new scope.

unsigned int

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

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

unsigned int loopExtension

unsigned int * freezeBlocks

unsigned int * blockPositions

unsigned int * blockSizes

int DP_LocalBlockAlign(const DP_BlockInfo *blocks, DP_BlockScoreFunction BlockScore, unsigned int queryFrom, unsigned int queryTo, DP_AlignmentResult **alignment)

void DP_DestroyBlockInfo(DP_BlockInfo *blocks)

unsigned int DP_CalculateMaxLoopLength(unsigned int nLoops, const unsigned int *loopLengths, double percentile, unsigned int extension, unsigned int cutoff)

#define STRUCT_DP_FOUND_ALIGNMENT

int DP_GlobalBlockAlign(const DP_BlockInfo *blocks, DP_BlockScoreFunction BlockScore, unsigned int queryFrom, unsigned int queryTo, DP_AlignmentResult **alignment)

static const int DP_NEGATIVE_INFINITY

static const unsigned int DP_UNFROZEN_BLOCK

#define STRUCT_DP_NO_ALIGNMENT

void DP_DestroyAlignmentResult(DP_AlignmentResult *alignment)

DP_BlockInfo * DP_CreateBlockInfo(unsigned int nBlocks)

static DP_BlockInfo * blocks

unsigned char LookupNCBIStdaaNumberFromCharacter(char r)

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