A RetroSearch Logo

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

Search Query:

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/cdd__ibis__annot__dialog_8cpp_source.html below:

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

67 #include <wx/artprov.h> 69 #include <wx/imaglist.h> 70 #include <wx/statline.h> 71 #include <wx/spinbutt.h> 72 #include <wx/spinctrl.h> 73 #include <wx/splitter.h> 74 #include <wx/listctrl.h> 75 #include <wx/treectrl.h> 76 #include <wx/notebook.h> 78 #include <wx/toolbar.h> 79 #include <wx/tglbtn.h> 84 #define ID_TEXT_INT 10000 85 #define ID_C_TYPE 10001 86 #define ID_LC_INT 10002 87 #define ID_B_ADD_INT 10003 88 #define ID_B_LAUNCH_INT 10004 89 #define ID_B_HIGHLIGHT_INT 10005 90 #define ID_LB_ANNOT 10006 91 #define ID_B_DELETE_ANNOT 10007 92 #define ID_B_HIGHLIGHT_ANNOT 10008 93 #define ID_B_HIGHLIGHT_OLAP 10009 94 #define ID_B_HIGHLIGHT_NONOLAP_ANNOT 10010 95 #define ID_B_HIGHLIGHT_NONOLAP_INTN 10011 117

m_queryMolecule =

NULL

;

118

m_querySequence = querySequence;

119  if

(m_querySequence) m_queryMolecule = m_querySequence->identifier;

162  INFOMSG

(

"type "

<< integer <<

" is not a valid Ibis interaction type"

);

167  if

(

result

&& ibisType) {

176  string result

=

"Unknown"

;

233  INFOMSG

(

"IBIS interaction type "

<< ibisType <<

" not mapped to a Cdd interaction type"

);

262  INFOMSG

(

"Cdd interaction type "

<< cddType <<

" not mapped to an IBIS interaction type"

);

295  bool

inRange =

true

;

299

from =

location

.SetInt().SetFrom();

306

}

else if

(

location

.IsPacked_int()) {

307

CPacked_seqint::Tdata::iterator s, se =

location

.SetPacked_int().Set().end();

308  for

(s =

location

.SetPacked_int().Set().begin(); s!=se; ++s) {

309

from = (**s).SetFrom();

317  ERRORMSG

(

"interaction '"

<<

m_desc

<<

"' has unexpected location type"

);

321  ERRORMSG

(

"interaction '"

<<

m_desc

<<

"' has out-of-range positions"

);

344  int

intType =

m_seqfeat

.GetExt().GetType().GetId();

369  WARNINGMSG

(

"IBIS feature data with unexpected type "

<< intType);

374

CSeq_feat::TExt::TData::const_iterator uoCit = userObjectData.begin();

375

CSeq_feat::TExt::TData::const_iterator uoEnd = userObjectData.end();

376  for

(; uoCit != uoEnd; ++uoCit) {

378  if

((*uoCit)->GetLabel().IsStr()) {

379  label

= (*uoCit)->GetLabel().GetStr();

381  ERRORMSG

(

"IBIS feature data with non-string label is skipped"

);

385  if

((*uoCit)->GetData().IsInt()) {

386

intValue = (*uoCit)->GetData().GetInt();

388  ERRORMSG

(

"IBIS feature data with non-integral type and label '"

<<

label

<<

"' is skipped"

);

392  if

(

label

==

"mmdbId"

) {

394

}

else if

(

label

==

"sdiId"

) {

396

}

else if

(

label

==

"nMembers"

) {

398

}

else if

(

label

==

"nInterfaceRes"

) {

400

}

else if

(

label

==

"nUniqueChemicals"

) {

402

}

else if

(

label

==

"nUniqueIons"

) {

404

}

else if

(

label

==

"comb_scr"

) {

406

}

else if

(

label

==

"avgIdent"

) {

407  m_pid

= (double) intValue/1000000.0;

408

}

else if

(

label

==

"isObserverd"

) {

411  ERRORMSG

(

"IBIS feature data with unexpected label '"

<<

label

<<

"' is skipped"

);

419  bool

isLocOK =

false

;

423

annot->SetDescription(

m_desc

);

426  const

ncbi::objects::CSeq_loc& loc =

GetLocation

(isLocOK);

429

packedInt->Assign(loc.GetPacked_int());

430

annot->SetLocation().SetPacked_int(*packedInt);

444

boilerplateEvidence->SetComment(commentEvid);

445

evidence.push_back(boilerplateEvidence);

458  ERRORMSG

(

"error converting interaction '"

<<

m_desc

<<

"' to an annotation!"

);

469  if

(!

m_seqfeat

.GetLocation().IsPacked_int()) {

471  ERRORMSG

(

"IBIS feature has unexpected location type"

);

474  ERRORMSG

(

"could not extract IBIS feature location"

);

488

from =

location

.GetInt().GetFrom();

490  for

(pos = from; pos <= to; ++pos) {

493

}

else if

(isOK &&

location

.IsPacked_int()) {

494

CPacked_seqint::Tdata::const_iterator s, se =

location

.GetPacked_int().Get().end();

495  for

(s =

location

.GetPacked_int().Get().begin(); s!=se; ++s) {

496

from = (**s).GetFrom();

498  for

(pos = from; pos <= to; ++pos) {

516  if

(intervals.size() > 0) {

517

from = (

int

) intervals.front()->GetFrom();

518

to = (

int

) intervals.back()->GetTo();

521  ERRORMSG

(

"IBIS feature has no defined intervals"

);

535

CPacked_seqint::Tdata::const_iterator it = intervals.begin(), itEnd = intervals.end();

538  const CSeq_id

& firstId = (*it)->GetId();

543  for

(; idsMatch && it != itEnd; ++it) {

544

idsMatch = firstId.

Match

((*it)->GetId());

548  if

(firstId.

IsGi

()) {

549

gi = firstId.

GetGi

();

552  ERRORMSG

(

"unexpected sequence identifier used for IBIS feature location (expected a GI)"

);

556  ERRORMSG

(

"inconsistent sequence ids used to give IBIS feature location"

);

560  ERRORMSG

(

"IBIS feature has no defined intervals"

);

570 #define DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR(var, id, type) \ 572  var = wxDynamicCast(FindWindow(id), type); \ 574  ERRORMSG("Can't find window with id "

<< id); \

578 #define DECLARE_AND_FIND_WINDOW_RETURN_FALSE_ON_ERR(var, id, type) \ 580  var = wxDynamicCast(FindWindow(id), type); \ 582  ERRORMSG("Can't find window with id "

<< id); \

595

wxDialog(parent, -1, "IBIS Annotations", wxPoint(400, 100), wxDefaultSize, wxDEFAULT_DIALOG_STYLE),

596

dialogHandle(handle), structureSet(

set

), annotSet(

set

->GetCDDAnnotSet()), m_images(

NULL

)

598  if

(annotSet.Empty()) {

604

PopulateInteractionData();

613  if

(sbs) sbs->GetStaticBox()->SetLabel(

buf

);

620

topSizer->Fit(

this

);

621

topSizer->SetSizeHints(

this

);

622

SetClientSize(topSizer->GetMinSize());

629  if

(vecIbisInteractions.size() > 0) {

631

choiceId = intTypeFilter->FindString(

wxT

(

"Protein-Protein"

));

632  if

(choiceId != wxNOT_FOUND) {

633

intTypeFilter->Delete(choiceId);

639

choiceId = intTypeFilter->FindString(

wxT

(

"Protein-NucAcid"

));

640  if

(choiceId != wxNOT_FOUND) {

641

intTypeFilter->Delete(choiceId);

645

choiceId = intTypeFilter->FindString(

wxT

(

"Protein-Chemical"

));

646  if

(choiceId != wxNOT_FOUND) {

647

intTypeFilter->Delete(choiceId);

651

choiceId = intTypeFilter->FindString(

wxT

(

"Protein-Peptide"

));

652  if

(choiceId != wxNOT_FOUND) {

653

intTypeFilter->Delete(choiceId);

657

choiceId = intTypeFilter->FindString(

wxT

(

"Protein-Ion"

));

658  if

(choiceId != wxNOT_FOUND) {

659

intTypeFilter->Delete(choiceId);

664

intTypeFilter->SetSelection(0);

669

wxIcon infoIcon = wxArtProvider::GetIcon(wxART_INFORMATION);

670

wxIcon warnIcon = wxArtProvider::GetIcon(wxART_WARNING);

671

wxIcon questionIcon = wxArtProvider::GetIcon(wxART_QUESTION);

672

wxIcon bookmarkIcon = wxArtProvider::GetIcon(wxART_ADD_BOOKMARK);

673

wxIcon tickMarkIcon = wxArtProvider::GetIcon(wxART_TICK_MARK);

674  if

(tickMarkIcon.Ok()) {

675

m_images =

new

wxImageList(16, 16,

true

);

676 

m_images->Add(infoIcon);

677

m_images->Add(warnIcon);

678

m_images->Add(questionIcon);

679

m_images->Add(bookmarkIcon);

680

m_images->Add(tickMarkIcon);

681

interactions->SetImageList(m_images, wxIMAGE_LIST_SMALL);

685  if

(interactions->GetWindowStyleFlag() & wxLC_REPORT) {

687

itemCol.SetText(

wxT

(

"Annot Overlap?"

));

688

itemCol.SetAlign(wxLIST_FORMAT_LEFT);

689

interactions->InsertColumn(0, itemCol);

691

itemCol.SetText(

wxT

(

"Type"

));

692

itemCol.SetAlign(wxLIST_FORMAT_LEFT);

693

interactions->InsertColumn(1, itemCol);

695

itemCol.SetText(

wxT

(

"Observed?"

));

696

itemCol.SetAlign(wxLIST_FORMAT_RIGHT);

697

interactions->InsertColumn(2, itemCol);

699

itemCol.SetText(

wxT

(

"Filtered on Web?"

));

700

itemCol.SetAlign(wxLIST_FORMAT_RIGHT);

701

interactions->InsertColumn(3, itemCol);

703

itemCol.SetText(

wxT

(

"Description"

));

704

itemCol.SetAlign(wxLIST_FORMAT_LEFT);

705

interactions->InsertColumn(4, itemCol);

707

itemCol.SetText(

wxT

(

"# Res. on Query"

));

708

itemCol.SetAlign(wxLIST_FORMAT_CENTER);

709

interactions->InsertColumn(5, itemCol);

711

itemCol.SetText(

wxT

(

"Clust. Size"

));

712

itemCol.SetAlign(wxLIST_FORMAT_CENTER);

713

interactions->InsertColumn(6, itemCol);

715

itemCol.SetText(

wxT

(

"Avg. Clust. %Id"

));

716

itemCol.SetAlign(wxLIST_FORMAT_CENTER);

717

interactions->InsertColumn(7, itemCol);

719

itemCol.SetText(

wxT

(

"IBIS Score"

));

720

itemCol.SetAlign(wxLIST_FORMAT_CENTER);

721

interactions->InsertColumn(8, itemCol);

726

SetupGUIControls(-1, -1);

739  TRACEMSG

(

"destroyed IBISAnnotateDialog"

);

752  return

listCtrl.GetNextItem(-1, wxLIST_NEXT_ALL, wxLIST_STATE_SELECTED);

759  long

item = listCtrl.GetNextItem(-1, wxLIST_NEXT_ALL, wxLIST_STATE_SELECTED);

762  while

( item != -1 ) {

764

item = listCtrl.GetNextItem(item, wxLIST_NEXT_ALL, wxLIST_STATE_SELECTED);

801  ERRORMSG

(

"Error calling ibis.cgi: from ("

<<

query

.from <<

") > to ("

<<

query

.to <<

")."

);

804  ERRORMSG

(

"Error calling ibis.cgi: mmdbId not set."

);

807  ERRORMSG

(

"Error calling ibis.cgi: molId not set.."

);

813

host =

"www.ncbi.nlm.nih.gov"

,

814

path =

"/Structure/ibis/ibis.cgi"

;

816

argstr <<

"sqat&range="

<< (

query

.from+1) <<

','

<< (

query

.to+1) <<

"&mmdbid="

<<

query

.mmdbId

817

<<

"&molid="

<<

query

.molId

828  INFOMSG

(

"try to load IBIS alignment data by mmdb-id from "

<< host << path <<

'?'

<< args);

831  ERRORMSG

(

"Error getting interaction data from ibis.cgi:\n"

<< err);

834

ibisSeqAnnot.

Reset

();

835  if

(

query

.pdb.length() > 0) {

838

argstrPdb <<

"sqat&range="

<< (

query

.from+1) <<

','

<< (

query

.to+1) <<

"&search="

<<

query

.pdb

842  INFOMSG

(

"try to load IBIS alignment data by pdb accession from "

<< host << path <<

'?'

<< args);

846  ERRORMSG

(

"Error getting interaction data by pdb accession from ibis.cgi:\n"

<< err);

849

ibisSeqAnnot.

Reset

();

850  INFOMSG

(

" ibis.cgi has no interaction data for MMDB-ID "

<<

query

.mmdbId <<

", molecule "

<<

query

.molId <<

" or PDB accession "

<<

query

.pdb);

852  INFOMSG

(

" successfully loaded interaction data from ibis.cgi for PDB accession "

<<

query

.pdb);

856  INFOMSG

(

" ibis.cgi has no interaction data for MMDB-ID "

<<

query

.mmdbId <<

", molecule "

<<

query

.molId <<

" (no known PDB accession)"

);

859  INFOMSG

(

" successfully loaded interaction data from ibis.cgi for MMDB-ID "

<<

query

.mmdbId);

882

ncbi::CRef< ncbi::objects::CSeq_annot > ibisInteractions(

new CSeq_annot

);

883  if

(ibisInteractions.NotEmpty()) {

911

ibisInteractions.Reset();

912

}

else if

(ibisInteractions.NotEmpty()&& ibisInteractions->GetData().IsFtable() && (ibisInteractions->GetData().GetFtable().size() > 0)) {

915

CSeq_annot::TData::TFtable::const_iterator fit = seqfeats.begin(), fend = seqfeats.end();

916  for

(; fit != fend; ++fit) {

917  if

(fit->NotEmpty()) {

925  ERRORMSG

(

"Error: allocation failure before trying to contact ibis.cgi."

);

940  for

(

unsigned i

= 0;

i

< num && !

result

; ++

i

) {

951  if

(positions.size() == 0)

return

0;

954

SeqPosSet::const_iterator pcit = positions.begin(), pend = positions.end();

958  while

(pcit != pend) {

961  if

(pcit != pend && (*pcit ==

last

+ 1)) {

969

intervals.push_back(interval);

977  return

positions.size();

983  int

eventId =

event

.GetId();

1028

wxString eventText =

event

.GetText();

1047  if

(ibisInt.

Empty

())

return

;

1051  buf

.Printf(

wxT

(

"(%d) %s [%d in cluster (%4.1f %%id); %d residues]"

), (

int

) ibisInt->GetType(),

1052

ibisInt->GetDesc().c_str(), ibisInt->GetNumMembers(), ibisInt->GetAverageIdentity(), ibisInt->GetNumInterfaceResidues());

1053

itemIndex = listCtrl.InsertItem(vecIndex,

buf

, -1);

1054  if

(itemIndex >= 0) {

1055

listCtrl.SetItemData(itemIndex, vecIndex);

1061  if

(ibisInt.

Empty

())

return

;

1068  long

itemIndex = listCtrl.InsertItem(vecIndex,

""

, -1);

1069  if

(itemIndex >= 0) {

1070

listCtrl.SetItemData(itemIndex, vecIndex);

1072

listCtrl.SetItem(itemIndex, 1,

buf

, -1);

1074  if

(ibisInt->IsObserved()) {

1075

listCtrl.SetItem(itemIndex, 2,

""

, 3);

1077  if

(ibisInt->IsFiltered()) {

1078

listCtrl.SetItem(itemIndex, 3,

""

, 2);

1081  buf

.Printf(

wxT

(

"%s"

), ibisInt->GetDesc().c_str());

1082

listCtrl.SetItem(itemIndex, 4,

buf

);

1090  buf

.Printf(

wxT

(

"%d"

), (

int

) ibisInt->GetPositions().size());

1091

listCtrl.SetItem(itemIndex, 5,

buf

);

1093  buf

.Printf(

wxT

(

"%d"

), ibisInt->GetNumMembers());

1094

listCtrl.SetItem(itemIndex, 6,

buf

);

1095  buf

.Printf(

wxT

(

"%4.1f"

), ibisInt->GetAverageIdentity());

1096

listCtrl.SetItem(itemIndex, 7,

buf

);

1098  buf

.Printf(

wxT

(

"%4.1f"

), (

double

) ibisInt->GetScore()/10000.0);

1102

listCtrl.SetItem(itemIndex, 8,

buf

);

1109  if

(choiceStr ==

wxT

(

"All"

)) {

1112

}

else if

(choiceStr.Contains(

wxT

(

"Protein-Protein"

))) {

1114

}

else if

(choiceStr.Contains(

wxT

(

"Protein-NucAcid"

))) {

1118

}

else if

(choiceStr.Contains(

wxT

(

"Protein-Chemical"

))) {

1120

}

else if

(choiceStr.Contains(

wxT

(

"Protein-Peptide"

))) {

1122

}

else if

(choiceStr.Contains(

wxT

(

"Protein-Ion"

))) {

1134

CPacked_seqint::Tdata::const_iterator s, se;

1136  offset

= (zeroBased) ? 0 : 1;

1138  if

(annotSeqLoc.

IsInt

()) {

1141  for

(pos = from; pos <= to; ++pos) {

1142

positions.insert(pos);

1147

from = (**s).GetFrom() +

offset

;

1148

to = (**s).GetTo() +

offset

;

1149  for

(pos = from; pos <= to; ++pos) {

1150

positions.insert(pos);

1159

intersection.clear();

1160  if

(set1.empty() || set2.empty())

return

0;

1162

set_intersection(set1.begin(), set1.end(),

1163

set2.begin(), set2.end(),

1164

inserter(intersection, intersection.begin()));

1166  return

intersection.size();

1173  if

(nInteractions == 0)

return

;

1175  SeqPosSet

annotPositions, overlapPositions;

1177

vector< SeqPosSet >& overlaps = annotInfo.

overlaps

;

1178

CAlign_annot_set::Tdata::const_iterator

a

, ae =

annotSet

->Get().end();

1181

overlaps.resize(nInteractions);

1182  for

(

a

=

annotSet

->Get().begin();

a

!=ae; ++

a

) {

1184

annotInfo.

ptr

= (

void

*)

a

->GetPointer();

1186

annotPositions.clear();

1187  if

(

a

->NotEmpty()) {

1190

annotInfo.

nRes

= annotPositions.size();

1192  for

(

i

= 0;

i

< nInteractions; ++

i

) {

1195

overlaps[

i

] = overlapPositions;

1214  SeqPosSet

annotPositions, annotPositionOverlaps;

1215

SeqPosSet::iterator setIt, setEnd;

1218

nonOverlaps.clear();

1224

nonOverlaps.insert(annotPositions.begin(), annotPositions.end());

1226

nonOverlaps.insert(interactionPositions.begin(), interactionPositions.end());

1229

setEnd = annotPositionOverlaps.end();

1230  for

(setIt = annotPositionOverlaps.begin(); setIt != setEnd; ++setIt) {

1231

nonOverlaps.erase(*setIt);

1237  static const double

overlapThreshold = 99.0;

1254  bool

readOnly, isIbisAnnot, isFullInteractionAnnotated;

1255  double

overlapPercentage;

1256  unsigned int i

, ibisIndex, nInteractions, nItems, nOverlaps, nRes, nResIntn;

1257  int

selectedVecIndex = -1;

1261

wxString annotDescStr, choiceSelectionStr;

1265

AnnotIbisOverlapMap::iterator olapIt, olapEnd;

1268

choiceSelectionStr = intTypeFilter->GetStringSelection();

1273

olapEnd = overlapMap.end();

1274  for

(olapIt = overlapMap.begin(); olapIt != olapEnd; ++olapIt) {

1276  if

(olapIt->second.nRes == 0)

continue

;

1278

vector< SeqPosSet >& olaps = olapIt->second.overlaps;

1279  for

(

i

= 0;

i

< olaps.size(); ++

i

) {

1280  if

(olaps[

i

].

size

() > 0) {

1281

ibisIndexWithOverlap.

insert

(

i

);

1285

ibisIndexEnd = ibisIndexWithOverlap.

end

();

1289  if

(selectInteraction >= 0) {

1290

selectedVecIndex = interactions->GetItemData(selectInteraction);

1291  if

(selectedVecIndex < 0 || selectedVecIndex >= (

int

) nInteractions) {

1292

selectedVecIndex = -1;

1293

selectInteraction = -1;

1295

selectedVecIndex = -1;

1296

selectInteraction = -1;

1302

selectInteraction = -1;

1310  if

(selectedVecIndex < 0) {

1320

interactions->Hide();

1323

interactions->DeleteAllItems();

1324  if

(interactions->GetWindowStyleFlag() & wxLC_LIST) {

1325  for

(

i

= 0;

i

< nInteractions; ++

i

) {

1330

}

else if

(interactions->GetWindowStyleFlag() & wxLC_REPORT) {

1332  for

(

i

= 0;

i

< nInteractions; ++

i

) {

1346  if

(selectedVecIndex >= 0) {

1347

this->SetEvtHandlerEnabled(

false

);

1348

nItems = interactions->GetItemCount();

1349  for

(

i

= 0;

i

< nItems; ++

i

) {

1350  if

((

int

) interactions->GetItemData(

i

) == selectedVecIndex) {

1351

selectInteraction =

i

;

1352

interactions->SetItemState(

i

, wxLIST_STATE_SELECTED, wxLIST_STATE_SELECTED);

1356

this->SetEvtHandlerEnabled(

true

);

1361

nItems = interactions->GetItemCount();

1362  for

(

i

= 0;

i

< nItems; ++

i

) {

1363

ibisIndex = (

unsigned int

) interactions->GetItemData(

i

);

1364  if

(ibisIndexWithOverlap.

find

(ibisIndex) != ibisIndexEnd) {

1365

interactions->SetItemImage(

i

, 4);

1369  for

(

i

= 0;

i

< (

unsigned int

) interactions->GetColumnCount(); ++

i

) {

1371

interactions->SetColumnWidth(

i

, wxLIST_AUTOSIZE);

1373

interactions->SetColumnWidth(

i

, wxLIST_AUTOSIZE_USEHEADER);

1377

interactions->Show();

1379  if

(selectInteraction >= 0) {

1380

interactions->EnsureVisible(selectInteraction);

1387

isFullInteractionAnnotated =

false

;

1391  if

(selectedVecIndex >= 0 && (ibisIndexWithOverlap.

find

(selectedVecIndex) != ibisIndexEnd)) {

1393  for

(olapIt = overlapMap.begin(); olapIt != olapEnd; ++olapIt) {

1394

nOverlaps = olapIt->second.overlaps[selectedVecIndex].size();

1395

nRes = olapIt->second.nRes;

1396

annotPtr =

reinterpret_cast<CAlign_annot

*

>

(olapIt->second.ptr);

1397  if

(nOverlaps > 0 && annotPtr) {

1399

overlapPercentage = (nRes > 0) ? (100.0*nOverlaps)/((double) nRes) : 0.0;

1400

isFullInteractionAnnotated = (overlapPercentage >= overlapThreshold);

1404

annotDescStr.Printf(

"%s (%d residues; %4.1f%% are overlapped)"

, annotPtr->

GetDescription

().c_str(), nRes, overlapPercentage);

1406

annotDescStr.Printf(

"<no description> (%d residues; %4.1f%% are overlapped)"

, nRes, overlapPercentage);

1408

annots->Append(annotDescStr, olapIt->second.ptr);

1414  if

(annots->GetCount() == 0) {

1420

isIbisAnnot =

false

;

1421  if

(selectAnnot >= 0) {

1422

annots->SetSelection(selectAnnot);

1423

annotPtr =

reinterpret_cast<CAlign_annot

*

>

(annots->GetClientData(selectAnnot));

1426

olapIt = overlapMap.find((

unsigned long

) annotPtr);

1427  if

(selectedVecIndex >= 0 && olapIt != olapEnd) {

1428

nOverlaps = olapIt->second.overlaps[selectedVecIndex].size();

1429

nRes = olapIt->second.nRes;

1433

annots->SetSelection(wxNOT_FOUND);

1445

bAddInt->Enable(selectInteraction >= 0 && !isFullInteractionAnnotated && !readOnly);

1446

bLaunchInt->Enable(selectInteraction >= 0);

1447

bHighlightInt->Enable(selectInteraction >= 0);

1449

bDelAnnot->Enable(selectAnnot >= 0 && isIbisAnnot && !readOnly);

1450

bHighlightAnnot->Enable(selectAnnot >= 0);

1451

bHighlightOlap->Enable(selectAnnot >= 0 && nOverlaps > 0 && (nOverlaps < nRes));

1454

bHighlightNoOlapA->Enable(selectAnnot >= 0 && nRes > 0 && (nOverlaps < nRes));

1455

bHighlightNoOlapI->Enable(selectAnnot >= 0 && nResIntn > 0 && (nOverlaps < nResIntn));

1457

interactions->SetFocus();

1464  bool

launchGeneralUrl =

false

;

1466

wxString url, pdbQuery;

1469  int

index = interactions->GetItemData(selectedItem);

1471  ERRORMSG

(

"IBISAnnotateDialog::LaunchIbisWebPage() - error getting IBIS interaction with index "

<< index);

1487

launchGeneralUrl =

true

;

1489

launchGeneralUrl =

true

;

1492  if

(launchGeneralUrl) {

1499

url.Printf(

"https://www.ncbi.nlm.nih.gov/Structure/ibis/ibis.cgi?search=%s"

, pdbQuery.c_str());

1502

url.Printf(

"https://www.ncbi.nlm.nih.gov/Structure/ibis/ibis.cgi?id=%d&type=%d&rowid=%d"

, ibisInt->GetSdiId(), (

int

) ibisInt->GetType(), ibisInt->GetRowId());

1506  if

(url.length() > 0) {

1509  ERRORMSG

(

"IBISAnnotateDialog::LaunchIbisWebPage() - problem building URL for IBIS interaction with index "

<< index);

1517  bool

okay =

true

, isLocationOK =

false

;

1523  if

(interactions->GetItemCount() == 0) {

1525

}

else if

(selectedItem < 0) {

1531  int

index = interactions->GetItemData(selectedItem);

1533  ERRORMSG

(

"IBISAnnotateDialog::HighlightAnnotation() - error getting IBIS interaction with index "

<< index);

1547

}

else if

(

location

.IsPacked_int()) {

1548

CPacked_seqint::Tdata::const_iterator s,

1549

se =

location

.GetPacked_int().Get().end();

1550  for

(s=

location

.GetPacked_int().Get().begin(); s!=se; ++s) {

1558

wxMessageBox(

"This interaction specifies master residues outside the aligned blocks;" 1559  " see the message log for details."

,

"IBIS Annotation Warning"

,

1560

wxOK | wxCENTRE | wxICON_WARNING,

this

);

1583  if

(itemId == -1)

return

;

1587

wxString defText = selectedInt->GetDesc().c_str();

1588

wxString descr = wxGetTextFromUser(

1589  "Enter a description for the new annotation:"

,

"Description"

, defText);

1590  if

(descr.size() == 0)

return

;

1594

annot = selectedInt->ToAlignAnnot();

1595

annot->SetDescription(

WX_TO_STD

(descr));

1620  if

(annots->GetCount() == 0 || annots->GetSelection() < 0)

return

;

1623  reinterpret_cast<CAlign_annot

*

>

(annots->GetClientData(annots->GetSelection()));

1624  if

(!selectedAnnot) {

1625  ERRORMSG

(

"IBISAnnotateDialog::DeleteAnnotation() - error getting annotation pointer"

);

1630  int

confirm = wxMessageBox(

"This will remove the selected (putatively IBIS-derived) annotation\n" 1631  "and all evidence associated with it.\nIs this correct?"

,

"Confirm"

, wxOK | wxCANCEL | wxCENTRE,

this

);

1632  if

(confirm != wxOK)

return

;

1635

CAlign_annot_set::Tdata::iterator

a

, ae =

annotSet

->Set().end();

1636  for

(

a

=

annotSet

->Set().begin();

a

!=ae; ++

a

) {

1637  if

(*

a

== selectedAnnot) {

1658  bool

highlightResult;

1659  bool

idMatchResult =

true

;

1662  WARNINGMSG

(

"interval Seq-id "

<< interval.GetId().GetSeqIdString() <<

" does not match master Seq-id"

);

1663

idMatchResult =

false

;

1667  return

(idMatchResult && highlightResult);

1676  if

(annots->GetCount() == 0 || annots->GetSelection() < 0)

return

;

1678  reinterpret_cast<CAlign_annot

*

>

(annots->GetClientData(annots->GetSelection()));

1679  if

(!selectedAnnot) {

1680  ERRORMSG

(

"IBISAnnotateDialog::HighlightAnnotation() - error getting annotation pointer"

);

1691

CPacked_seqint::Tdata::iterator s,

1692

se = selectedAnnot->

SetLocation

().SetPacked_int().Set().end();

1693  for

(s=selectedAnnot->

SetLocation

().SetPacked_int().Set().begin(); s!=se; ++s) {

1704  int

index = interactions->GetItemData(selectedItem);

1706  if

(selectedItem < 0) {

1709  ERRORMSG

(

"IBISAnnotateDialog::HighlightAnnotation() - error getting IBIS interaction "

<< index <<

" for overlap calculation"

);

1715

IntervalList::iterator intIt, intEnd;

1722

intEnd = intervals.end();

1723  for

(intIt = intervals.begin(); intIt != intEnd; ++intIt) {

1728  ERRORMSG

(

"IBISAnnotateDialog::HighlightAnnotation() - invalid event id "

<< eventId);

1732

wxMessageBox(

"WARNING: this annotation specifies master residues outside the aligned blocks;" 1733  " see the message log for details."

,

"Annotation Error"

,

1734

wxOK | wxCENTRE | wxICON_ERROR,

this

);

1747

wxBoxSizer *item0 =

new

wxBoxSizer( wxVERTICAL );

1749

wxFlexGridSizer *item1 =

new

wxFlexGridSizer( 1, 0, 0, 0 );

1750

item1->AddGrowableCol( 1 );

1752

wxStaticBox *item3 =

new

wxStaticBox( parent, -1,

wxT

(

"IBIS Interactions"

) );

1753

wxStaticBoxSizer *item2 =

new

wxStaticBoxSizer( item3, wxVERTICAL );

1756

wxFlexGridSizer *item4 =

new

wxFlexGridSizer( 1, 0, 0, 0 );

1758

wxStaticText *item5 =

new

wxStaticText( parent,

ID_TEXT_INT

,

wxT

(

"Interaction Type Filter"

), wxDefaultPosition, wxDefaultSize, 0 );

1759

item4->Add( item5, 0, wxALIGN_CENTER|wxALL, 5 );

1764  wxT

(

"Protein-Protein"

),

1765  wxT

(

"Protein-NucAcid"

),

1766  wxT

(

"Protein-Chemical"

),

1767  wxT

(

"Protein-Peptide"

),

1768  wxT

(

"Protein-Ion"

)

1770

wxChoice *item6 =

new

wxChoice( parent,

ID_C_TYPE

, wxDefaultPosition, wxSize(100,-1), 6, strs6, 0 );

1771

item4->Add( item6, 0, wxALIGN_CENTER|wxALL, 5 );

1773

item2->Add( item4, 0, wxALIGN_CENTER|wxALL, 5 );

1775

wxListCtrl *item7 =

new

wxListCtrl( parent,

ID_LC_INT

, wxDefaultPosition, wxSize(450,150), wxLC_REPORT|wxLC_SINGLE_SEL|wxSUNKEN_BORDER );

1776

item2->Add( item7, 0, wxALIGN_CENTER|wxALL, 5 );

1778

wxFlexGridSizer *item8 =

new

wxFlexGridSizer( 3, 0, 0 );

1780

wxButton *item9 =

new

wxButton( parent,

ID_B_ADD_INT

,

wxT

(

"Make IBIS Annotation"

), wxDefaultPosition, wxDefaultSize, 0 );

1781

item8->Add( item9, 0, wxALIGN_CENTER|wxALL, 5 );

1783

wxButton *item10 =

new

wxButton( parent,

ID_B_LAUNCH_INT

,

wxT

(

"Launch"

), wxDefaultPosition, wxDefaultSize, 0 );

1784

item8->Add( item10, 0, wxALIGN_CENTER|wxALL, 5 );

1786

wxButton *item11 =

new

wxButton( parent,

ID_B_HIGHLIGHT_INT

,

wxT

(

"Highlight"

), wxDefaultPosition, wxDefaultSize, 0 );

1787

item8->Add( item11, 0, wxALIGN_CENTER|wxALL, 5 );

1789

item2->Add( item8, 0, wxALIGN_CENTER|wxALL, 5 );

1791

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

1793

wxStaticBox *item13 =

new

wxStaticBox( parent, -1,

wxT

(

"Overlapping Annotations"

) );

1794

wxStaticBoxSizer *item12 =

new

wxStaticBoxSizer( item13, wxVERTICAL );

1796

item12->Add( 20, 10, 0, wxALIGN_CENTER|wxALL, 5 );

1802

wxListBox *item14 =

new

wxListBox( parent,

ID_LB_ANNOT

, wxDefaultPosition, wxSize(275,100), 1, strs14, wxLB_SINGLE );

1803

item12->Add( item14, 0, wxALIGN_CENTER|wxALL, 5 );

1805

wxFlexGridSizer *item15 =

new

wxFlexGridSizer( 3, 0, 0 );

1809  wxT

(

"IBIS Annotation"

),

1810

wxDefaultPosition, wxDefaultSize, 0 );

1811

item15->Add( item16, 0, wxALIGN_CENTER|wxALL, 5 );

1814  wxT

(

"Highlight\n"

)

1815  wxT

(

"Annotation"

),

1816

wxDefaultPosition, wxDefaultSize, 0 );

1817

item15->Add( item17, 0, wxALIGN_CENTER|wxALL, 5 );

1820  wxT

(

"Highlight\n"

)

1822

wxDefaultPosition, wxDefaultSize, 0 );

1823

item15->Add( item18, 0, wxALIGN_CENTER|wxALL, 5 );

1825

item12->Add( item15, 0, wxALIGN_CENTER|wxALL, 5 );

1827

wxFlexGridSizer *item19 =

new

wxFlexGridSizer( 2, 0, 0 );

1830  wxT

(

"Highlight Non-Overlap\n"

)

1831  wxT

(

"of Annotation"

),

1832

wxDefaultPosition, wxDefaultSize, 0 );

1833

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

1836  wxT

(

"Highlight Non-Overlap\n"

)

1837  wxT

(

"of Interaction"

),

1838

wxDefaultPosition, wxDefaultSize, 0 );

1839

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

1841

item12->Add( item19, 0, wxALIGN_CENTER|wxALL, 5 );

1843

item1->Add( item12, 0, wxGROW|wxALIGN_CENTER_VERTICAL|wxALL, 5 );

1845

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

1849

parent->SetSizer( item0 );

1851

item0->SetSizeHints( parent );

User-defined methods of the data storage class.

User-defined methods of the data storage class.

bool GetAsnDataViaHTTPS(const std::string &host, const std::string &path, const std::string &args, ASNClass *asnObject, std::string *err, bool binaryData=true)

wxSizer * SetupIbisAnnotationDialog(wxWindow *parent, bool call_fit=TRUE, bool set_sizer=TRUE)

#define ID_B_HIGHLIGHT_NONOLAP_ANNOT

#define DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR(var, id, type)

bool DoesInteractionMatchChoice(const wxString &choiceStr, IBISInteraction::eIbisInteractionType ibisIntType)

static const string IBIS_EVIDENCE_COMMENT

long GetFirstSelectedListCtrlItemId(const wxListCtrl &listCtrl)

static unsigned int GetSetIntersection(const SeqPosSet &set1, const SeqPosSet &set2, SeqPosSet &intersection)

void GetPositionsForAlignAnnot(const CAlign_annot &annot, SeqPosSet &positions, bool zeroBased)

#define ID_B_HIGHLIGHT_INT

#define ID_B_DELETE_ANNOT

void InsertItemInListView(int vecIndex, const CRef< IBISInteraction > &ibisInt, wxListCtrl &listCtrl)

wxSizer * ibisIntStaticBoxSizer

static bool GetInteractionDataFromIbis(CSeq_annot &ibisSeqAnnot, IbisQuery &query)

unsigned int GetAllSelectedListCtrlItemIds(const wxListCtrl &listCtrl, vector< long > &ids)

void InsertItemInReportView(int vecIndex, const CRef< IBISInteraction > &ibisInt, wxListCtrl &listCtrl)

#define ID_B_HIGHLIGHT_OLAP

#define ID_B_HIGHLIGHT_NONOLAP_INTN

#define ID_B_HIGHLIGHT_ANNOT

std::set< ncbi::TSeqPos > SeqPosSet

const BlockMultipleAlignment * GetCurrentMultipleAlignment(void) const

const Sequence * GetMaster(void) const

bool HighlightAlignedColumnsOfMasterRange(unsigned int from, unsigned int to) const

bool IsAligned(unsigned int row, unsigned int seqIndex) const

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

~IBISAnnotateDialog(void)

void DeleteAnnotation(void)

void HighlightAnnotation(int eventId)

void LaunchIbisWebPage(void)

void OnListCtrlSelection(wxListEvent &event)

void PopulateInteractionData(void)

void OnListBoxSelection(wxCommandEvent &event)

void GetAnnotIbisNonOverlaps(const IBISInteraction &interaction, const ncbi::objects::CAlign_annot &annot, SeqPosSet &nonOverlaps, bool onAnnotation) const

std::list< ncbi::CRef< ncbi::objects::CSeq_interval > > IntervalList

void MakeAnnotationFromInteraction(void)

void GetAnnotIbisOverlaps(AnnotIbisOverlapMap &aioMap) const

IBISAnnotateDialog ** dialogHandle

void HighlightInteraction(void)

void OnButton(wxCommandEvent &event)

std::vector< ncbi::CRef< IBISInteraction > > vecIbisInteractions

void SetupGUIControls(int selectInteraction, int selectAnnot, unsigned int updateFlags=eRemakeListCtrl|eRemakeListBox)

bool HighlightInterval(const ncbi::objects::CSeq_interval &interval)

bool HasInteractionData(void) const

std::map< unsigned long, AlignAnnotInfo > AnnotIbisOverlapMap

StructureSet * structureSet

unsigned int GetIntervalsForSet(const SeqPosSet &positions, IntervalList &intervals)

ncbi::CRef< ncbi::objects::CAlign_annot_set > annotSet

void OnChoice(wxCommandEvent &event)

void OnCloseWindow(wxCloseEvent &event)

static const MoleculeIdentifier * GetQueryMolecule()

IBISInteraction(const ncbi::objects::CSeq_feat &seqfeat)

eIbisInteractionType m_type

bool GetGi(TGi &gi) const

static std::string IbisIntTypeToString(eIbisInteractionType ibisType)

static bool QueryMoleculeHasChain()

static const Sequence * m_querySequence

static const MoleculeIdentifier * m_queryMolecule

static void SetQuerySequence(const Sequence *querySequence)

ncbi::objects::CSeq_feat m_seqfeat

const ncbi::objects::CSeq_loc & GetLocation(bool &isOK) const

static eIbisInteractionType CddIntTypeToIbisIntType(eCddInteractionType cddType)

static const int NOT_ASSIGNED

ncbi::CRef< ncbi::objects::CAlign_annot > ToAlignAnnot(void) const

static bool IsIbisIntType(int integer, eIbisInteractionType *ibisType=NULL)

@ eIbisProteinCombo_DNA_RNA

const SeqPosSet & GetPositions(void) const

bool GetFootprint(int &from, int &to) const

static const TGi GI_NOT_ASSIGNED

static eCddInteractionType IbisIntTypeToCddIntType(eIbisInteractionType ibisType)

bool RemoveAllHighlights(bool postRedraws)

bool MatchesSeqId(const ncbi::objects::CSeq_id &sid) const

static const int VALUE_NOT_SET

bool HasStructure(void) const

std::string ToString(void) const

void FillOutSeqId(ncbi::objects::CSeq_id *sid) const

const MoleculeIdentifier * identifier

unsigned int Length(void) const

static const unsigned int eUserAnnotationData

AlignmentManager * alignmentManager

void SetDataChanged(unsigned int what) const

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

const_iterator end() const

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

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

static DLIST_TYPE *DLIST_NAME() last(DLIST_LIST_TYPE *list)

static const char location[]

unsigned int TSeqPos

Type for sequence locations and lengths.

bool Match(const CSeq_id &sid2) const

Match() - TRUE if SeqIds are equivalent.

void Reset(void)

Reset reference object.

bool NotEmpty(void) const THROWS_NONE

Check if CRef is not empty – pointing to an object and has a non-null value.

bool Empty(void) const THROWS_NONE

Check if CRef is empty – not pointing to any object, which means having a null value.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_SCOPE(ns)

Define a new scope.

string AsString(const CTimeFormat &format=kEmptyStr, TSeconds out_tz=eCurrentTimeZone) const

Transform time to string.

static CTimeFormat GetPredefined(EPredefined fmt, TFlags flags=fDefault)

Get predefined format.

@ eCurrent

Use current time. See also CCurrentTime.

@ eISO8601_DateTimeMin

Y-M-DTh:m (eg 1997-07-16T19:20)

static const char label[]

const TDescription & GetDescription(void) const

Get the Description member data.

list< CRef< CFeature_evidence > > TEvidence

bool IsSetType(void) const

for typing annotated features 0 .

void SetLocation(TLocation &value)

Assign a value to Location data member.

const TLocation & GetLocation(void) const

Get the Location member data.

bool IsSetDescription(void) const

to hold descriptions/names like "Heme binding site" or "catalytic triad" etc., something that should ...

vector< CRef< CUser_field > > TData

void SetTo(TTo value)

Assign a value to To data member.

list< CRef< CSeq_interval > > Tdata

const Tdata & Get(void) const

Get the member data.

void SetId(TId &value)

Assign a value to Id data member.

TFrom GetFrom(void) const

Get the From member data.

void SetFrom(TFrom value)

Assign a value to From data member.

TGi GetGi(void) const

Get the variant data.

bool IsPacked_int(void) const

Check if variant Packed_int is selected.

bool IsGi(void) const

Check if variant Gi is selected.

TTo GetTo(void) const

Get the To member data.

bool IsInt(void) const

Check if variant Int is selected.

const TInt & GetInt(void) const

Get the variant data.

const TPacked_int & GetPacked_int(void) const

Get the variant data.

virtual void Reset(void)

Reset the whole object.

const TFtable & GetFtable(void) const

Get the variant data.

list< CRef< CSeq_feat > > TFtable

bool IsFtable(void) const

Check if variant Ftable is selected.

const TData & GetData(void) const

Get the Data member data.

unsigned int

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

Messenger * GlobalMessenger(void)

double value_type

The numeric datatype used by the parser.

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

#define TRUE

bool replacment for C indicating true.

std::vector< SeqPosSet > overlaps

string ToString(const wxRect &rc)

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4