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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/srceditdialog_8cpp_source.html below:

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

108

wxWindowID

id

,

const

wxString& caption,

const

wxPoint& pos,

const

wxSize&

size

,

long

style )

114  CBioseq_CI

b_iter(seh, objects::CSeq_inst::eMol_na);

115  for

( ; b_iter ; ++b_iter )

121  Create

(parent,

id

, caption, pos,

size

, style);

125

wxWindowID

id

,

const

wxString& caption,

const

wxPoint& pos,

const

wxSize&

size

,

long

style )

126

: m_BioseqHandles(bioseq_handles),

130  if

(!bioseq_handles.empty()) {

131  m_SEH

= bioseq_handles.front().GetTopLevelEntry();

134  Create

(parent,

id

, caption, pos,

size

, style);

142 bool SrcEditDialog::Create

( wxWindow* parent, wxWindowID

id

,

const

wxString& caption,

const

wxPoint& pos,

const

wxSize&

size

,

long

style )

145 

SetExtraStyle(wxWS_EX_BLOCK_EVENTS);

146

SetLayoutAdaptationMode(wxDIALOG_ADAPTATION_MODE_ENABLED);

147

wxDialog::Create( parent,

id

, caption, pos,

size

, style );

152

GetSizer()->SetSizeHints(

this

);

194

wxBoxSizer* itemBoxSizer2 =

new

wxBoxSizer(wxVERTICAL);

195

itemDialog1->SetSizer(itemBoxSizer2);

197

wxBoxSizer* itemBoxSizer3 =

new

wxBoxSizer(wxHORIZONTAL);

198

itemBoxSizer2->Add(itemBoxSizer3, 0, wxGROW|wxALL, 5);

200

wxArrayString itemChoiceStrings, itemChoiceStringsWritable;

208  if

(seqTable->GetNum_rows() < 1)

210

wxMessageBox(

wxT

(

"No Source records found"

),

wxT

(

"Error"

), wxOK | wxICON_ERROR);

221  m_Grid

->SetTable(gridAdapter,

true

);

223  m_Grid

->AutoSizeColumns();

224  int

l_height =

m_Grid

->GetColLabelSize();

225  m_Grid

->SetColLabelSize( 2 * l_height );

227  m_Grid

->SetRowLabelSize(wxGRID_AUTOSIZE);

238  if

((*it)->IsSetHeader() && (*it)->GetHeader().IsSetTitle() )

240  string

title = (*it)->GetHeader().GetTitle();

243

itemChoiceStrings.Add(wxString(title));

245

itemChoiceStringsWritable.Add(wxString(title));

254  if

(glyph_col >= 0 && glyph_col+1 <

m_Grid

->GetNumberCols())

259

wxBoxSizer* itemBoxSizer4 =

new

wxBoxSizer(wxHORIZONTAL);

260

itemBoxSizer2->Add(itemBoxSizer4, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 2);

262

wxArrayString m_QualListStrings;

263  m_QualList

=

new

wxChoice( itemDialog1,

ID_QUALCHOICE

, wxDefaultPosition, wxDefaultSize, m_QualListStrings, 0 );

264

itemBoxSizer4->Add(

m_QualList

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

270

itemChoiceStringsWritable.Add(

m_QualList

->GetString(

i

));

275

itemBoxSizer4->Add(

m_AddQualBtn

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

277

wxBoxSizer* itemBoxSizer7 =

new

wxBoxSizer(wxHORIZONTAL);

278

itemBoxSizer2->Add(itemBoxSizer7, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 2);

280

wxButton* itemButton8 =

new

wxButton( itemDialog1,

ID_LOADQUALS

,

_

(

"Import Qualifier Table"

), wxDefaultPosition, wxDefaultSize, 0 );

281

itemBoxSizer7->Add(itemButton8, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

283

wxButton* itemButton9 =

new

wxButton( itemDialog1,

ID_EXPORT_QUALS

,

_

(

"Export Qualifier Table"

), wxDefaultPosition, wxDefaultSize, 0 );

284

itemBoxSizer7->Add(itemButton9, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

293

wxBoxSizer* itemBoxSizer13 =

new

wxBoxSizer(wxHORIZONTAL);

294

itemBoxSizer2->Add(itemBoxSizer13, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 3);

296

wxButton* itemButton14 =

new

wxButton( itemDialog1, wxID_OK,

_

(

"Accept"

), wxDefaultPosition, wxDefaultSize, 0 );

297

itemBoxSizer13->Add(itemButton14, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

299

wxButton* itemButton15 =

new

wxButton( itemDialog1, wxID_CANCEL,

_

(

"Cancel"

), wxDefaultPosition, wxDefaultSize, 0 );

300

itemBoxSizer13->Add(itemButton15, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

308  return

(column_name ==

"location"

|| column_name.empty() || column_name ==

"expand"

);

314

vector<bool> tf_positions;

315  bool

any_tf =

false

;

317  ITERATE

( objects::CSeq_table::TColumns, col_iter, values->GetColumns() ) {

319  if

((*col_iter)->IsSetHeader() && (*col_iter)->GetHeader().IsSetTitle()) {

320  string label

= (*col_iter)->GetHeader().GetTitle();

322  if

(pos != string::npos) {

329

objects::CSubSource::TSubtype

st

= objects::CSubSource::GetSubtypeValue (

label

, objects::CSubSource::eVocabulary_insdc);

330  if

(objects::CSubSource::NeedsNoText(

st

)) {

334

}

catch

(exception &) {

339

tf_positions.push_back(is_tf);

347

vector<string> tf_strings;

348

tf_strings.push_back(

"true"

);

349

tf_strings.push_back(

""

);

351  for

(

size_t i

= 1;

i

< tf_positions.size();

i

++) {

353  if

(tf_positions[

i

]) {

354  for

(

size_t

j = 0; j < tf_strings.size(); j++) {

355

col->SetData().SetString().push_back(tf_strings[j]);

358

choices->SetColumns().push_back(col);

368  for

(

i

= 0;

i

<

m_Grid

->GetTable()->GetColsCount();

i

++) {

369

wxString col_name =

m_Grid

->GetTable()->GetColLabelValue(

i

);

380

wxArrayString srcModNameStrings;

384  ITERATE

(wxArrayString, it, srcModNameStrings) {

396

objects::CSubSource::TSubtype

st

= objects::CSubSource::GetSubtypeValue (qual_name, objects::CSubSource::eVocabulary_insdc);

397  if

(objects::CSubSource::NeedsNoText(

st

)) {

400

}

catch

(exception &) {

403

vector<string> new_choices;

405

new_choices.push_back(

"true"

);

406

new_choices.push_back(

""

);

478

wxMessageDialog dlg(

this

,

_

(

"Discard modifications?"

),

_

(

"Attention"

),wxOK|wxCANCEL|wxCENTRE);

479  if

(dlg.ShowModal() == wxID_OK)

495

wxString qual_name =

m_QualList

->GetStringSelection();

507

wxArrayString itemChoiceStrings, itemChoiceStringsWritable;

510  for

(

int i

= 0;

i

<

m_Grid

->GetTable()->GetColsCount();

i

++)

512

wxString title =

m_Grid

->GetTable()->GetColLabelValue(

i

);

513  if

(!title.IsEmpty())

515

itemChoiceStrings.Add(title);

517

itemChoiceStringsWritable.Add(title);

524

itemChoiceStringsWritable.Add(

m_QualList

->GetString(

i

));

532  int

num_cols =

m_Grid

->GetTable()->GetNumberCols();

533  m_Grid

->GetTable()->InsertCols(num_cols - 1);

534  m_Grid

->GetTable()->SetColLabelValue(num_cols - 1, new_col.ToStdString());

535  m_Grid

->AutoSizeColumns();

538  return

(num_cols - 1);

547  int

num_cols =

m_Grid

->GetTable()->GetNumberCols();

548  int

num_rows =

m_Grid

->GetTable()->GetNumberRows();

549  for

(

int

col = 0; col < num_cols; col++) {

550  for

(

int row

= 0;

row

< num_rows;

row

++) {

551  m_Grid

->GetTable()->SetValue(

row

, col,

""

);

563

vector<string> already_seen;

565  if

(!(*cit)->GetData().IsId()) {

567  if

((*cit)->IsSetHeader()

568

&& (*cit)->GetHeader().IsSetTitle()) {

569  label

= (*cit)->GetHeader().GetTitle();

575  if

( (*cit)->IsSetHeader() && (*cit)->GetHeader().IsSetTitle() )

577  string

sTitle = (*cit)->GetHeader().GetTitle();

581  if

(new_name.empty()) {

584

(*cit)->SetHeader().SetTitle(new_name);

586  ITERATE

(vector<string>, sit, already_seen) {

590

+

" refer to the same field ("

+ new_name +

"); "

;

594

already_seen.push_back(new_name);

614

vector<string> format_ids;

615

format_ids.push_back(

"file_loader_table"

);

616

fileManager->LoadFormats(format_ids);

618

vector<CIRef<IOpenObjectsPanelClient> > loadManagers;

622

dlg.SetSize(710, 480);

627  if

(dlg.ShowModal() == wxID_OK) {

629  if

(!object_loader) {

630

wxMessageBox(

wxT

(

"Failed to get object loader"

),

wxT

(

"Error"

),

631

wxOK | wxICON_ERROR);

647  const CObject

& ptr = obj_it->GetObject();

648  const

objects::CSeq_annot* annot =

dynamic_cast<const

objects::CSeq_annot*

>

(&ptr);

649  if

(annot && annot->IsSeq_table()) {

651

input_table->Assign(annot->GetData().GetSeq_table());

659

wxOK | wxICON_ERROR,

this

);

673

wxOK | wxICON_ERROR,

this

);

678

wxMessageBox(

wxT

(

"New table conflicts with existing values"

),

wxT

(

"Error"

),

679

wxOK | wxICON_ERROR,

this

);

710

values_table->Assign(*grid_table);

712  NON_CONST_ITERATE

(objects::CSeq_table::TColumns, it, values_table->SetColumns()) {

713  if

((*it)->IsSetHeader() && (*it)->GetHeader().IsSetTitle()) {

714  string

title = (*it)->GetHeader().GetTitle();

716  if

(pos != string::npos) {

717

title = title.substr(0, pos);

719

(*it)->SetHeader().SetTitle(title);

733

wxString qual_name =

m_QualList

->GetStringSelection();

744  for

(

i

= 0;

i

< objects::CSubSource::eSubtype_other;

i

++) {

748

srcModNameStrings.push_back(

ToWxString

(qual_name));

750

}

catch

(exception &) {

753  for

(

i

= 0;

i

< objects::COrgMod::eSubtype_other;

i

++) {

760

srcModNameStrings.push_back(

ToWxString

(qual_name));

762

}

catch

(exception &) {

768  const

wxString s_DbXref =

_

(

kDbXref

);

771

srcModNameStrings.push_back(s_DbXref);

774

srcModNameStrings.Sort();

777

srcModNameStrings.push_back(s_OrgModNoteName);

780

srcModNameStrings.push_back(s_SubSourceNoteName);

795  if

( ! values_table->IsSetColumns() || values_table->GetColumns().empty() ) {

799  const

objects::CSeq_table::TColumns &

columns

= values_table->GetColumns();

800  size_t

num_cols =

columns

.size();

805

vector< CRef<CSrcTableColumnBase> > vecColEditFactories;

811

vector< CRef<CSrcTableColumnBase> > old_vecColEditFactories;

818  for

(

int row

= 0;

row

< values_table->GetNum_rows() && (

size_t

) row < id_col->GetData().GetSize();

row

++) {

824

objects::CSeqdesc_CI desc_ci( bsh, objects::CSeqdesc::e_Source);

826

new_source_desc->Assign(*desc_ci);

828

objects::CBioSource & bioSource = new_source_desc->SetSource();

830  if

(bioSource.IsSetOrg() && bioSource.GetOrg().IsSetTaxname()) {

831

old_taxname = bioSource.GetOrg().GetTaxname();

836  for

(

size_t

col = 1; col <

m_columns

.size(); ++col ) {

837  if

(old_vecColEditFactories[col])

838

old_vecColEditFactories[col]->ClearInBioSource(bioSource);

843  for

(

size_t

col = 1; col < num_cols; ++col ) {

844  if

(vecColEditFactories[col] &&

columns

[col]->GetData().GetSize() > (

size_t

)

row

) {

845

vecColEditFactories[col]->AddToBioSource(

852  if

(bioSource.IsSetOrg() && bioSource.GetOrg().IsSetTaxname()) {

853

new_taxname = bioSource.GetOrg().GetTaxname();

864  cmd

->AddCommand (*ecmd);

866

objects::CBioseq_set_Handle bssh = bsh.GetParentBioseq_set();

867  if

(bssh && bssh.IsSetClass() && bssh.GetClass() == objects::CBioseq_set::eClass_nuc_prot) {

882  if

(!

id

|| !id_col) {

888  while

(row < id_col->GetData().GetSize() && !found) {

890

objects::CSeq_id::E_SIC compare =

id

->Compare(*row_id);

891  if

(compare == objects::CSeq_id::e_YES) {

893

}

else if

(compare == objects::CSeq_id::e_DIFF) {

896  id

->Assign(*row_id);

910  return "No sequence ID column selected!"

;

915

vector<CRef<objects::CSeq_id> > already_seen;

916  while

(row < src_col->GetData().GetSize()) {

917  if

(!

OneRowOk

(src_col->GetData().GetId()[

row

], dst_col)) {

918  string

id_label =

""

;

924  if

((*sit)->Compare(*(src_col->GetData().GetId()[

row

])) == objects::CSeq_id::e_YES) {

927

+

" refer to the same sequence; "

;

931

already_seen.push_back(src_col->GetData().GetId()[

row

]);

972  ITERATE

(objects::CSeq_table::TColumns, cit,

table

.GetColumns()) {

973  if

((*cit)->IsSetData() && (*cit)->GetData().IsId()) {

986  for

(

i

= 0;

i

< src_id->GetData().GetSize() && i < src_col->GetData().GetSize();

i

++) {

989  while

(dst_col->SetData().SetString().size() < dst_id->GetData().GetSize()) {

990

dst_col->SetData().SetString().push_back (

""

);

993

dst_col->SetData().SetString()[

row

] = src_col->GetData().GetString()[

i

];

994

}

catch

(exception &) {

1010  ITERATE

(objects::CSeq_table::TColumns, cit, src.GetColumns()) {

1011  if

((*cit)->IsSetData() && !(*cit)->GetData().IsId()) {

1016

dst_col =

new

objects::CSeqTable_column();

1017

dst_col->SetHeader().Assign((*cit)->GetHeader());

1018  if

(!dst_col->GetHeader().IsSetTitle() && dst_col->GetHeader().IsSetField_name()) {

1019

dst_col->SetHeader().SetTitle(dst_col->GetHeader().GetField_name());

1021

dst->SetColumns().push_back(dst_col);

1033

wxFileDialog table_save_file(parent,

wxT

(

"Select a file"

), save_file_dir, save_file_name,

1036

wxFD_SAVE|wxFD_OVERWRITE_PROMPT);

1038  if

(table_save_file.ShowModal() == wxID_OK)

1040

wxString path = table_save_file.GetPath();

1041

wxString name = table_save_file.GetFilename();

1048

wxMessageBox(

wxT

(

"Please, select file name"

),

wxT

(

"Error"

),

1049

wxOK | wxICON_ERROR, parent);

1057

wxMessageBox(

wxT

(

"Cannot open file "

)+name,

wxT

(

"Error"

),

1058

wxOK | wxICON_ERROR, parent);

1063  ITERATE

(objects::CSeq_table::TColumns, cit, values_table->GetColumns()) {

1064

exporter.

Field

((*cit)->GetHeader().GetTitle());

1067  for

(

int i

= 0;

i

< values_table->GetNum_rows(); ++

i

) {

1068  ITERATE

(objects::CSeq_table::TColumns, cit, values_table->GetColumns()) {

1069  if

(

i

< (*cit)->GetData().GetSize()) {

1070  if

((*cit)->GetData().IsId()) {

1074

}

else if

((*cit)->GetData().IsString()) {

1075

exporter.

Field

((*cit)->GetData().GetString()[

i

]);

1079

exporter.

Field

(blank);

1085

save_file_dir = table_save_file.GetDirectory();

1086

save_file_name = table_save_file.GetFilename();

1095  if

(!id_col || !

id

|| !id_col->IsSetData() || !id_col->GetData().IsId()) {

1099  while

(row < id_col->GetData().GetSize()) {

1100  if

(id->Compare(*(id_col->GetData().GetId()[

row

])) == objects::CSeq_id::e_YES) {

1112  for

(

size_t i

= 0;

i

< src_id->GetData().GetSize() && i < src_col->GetData().GetSize();

i

++) {

1115  if

(dst_col->GetData().GetString().size() >

row 1117

&& !

NStr::Equal

(dst_col->GetData().GetString()[

row

], src_col->GetData().GetString()[

i

])) {

1130  int

conflicting_columns = 0;

1133  ITERATE

(objects::CSeq_table::TColumns, cit, src.GetColumns()) {

1134  if

((*cit)->IsSetData() && !(*cit)->GetData().IsId()) {

1138

conflicting_columns++;

1143  return

conflicting_columns;

1148  if

(!input_table || !input_table->IsSetColumns() || input_table->GetColumns().size() < 1) {

1152  bool

all_default =

true

;

1154  ITERATE

(objects::CSeq_table::TColumns, cit, input_table->SetColumns()) {

1156  if

(!(*cit)->IsSetHeader() || !(*cit)->GetHeader().IsSetTitle()

1157

|| !

NStr::Equal

(expected_title, (*cit)->GetHeader().GetTitle())) {

1158

all_default =

false

;

1164  bool

all_match =

true

;

1166  NON_CONST_ITERATE

(objects::CSeq_table::TColumns, cit, input_table->SetColumns()) {

1167  if

(!(*cit)->IsSetData() || (*cit)->GetData().GetSize() == 0) {

1171  string

first_val =

""

;

1172  if

((*cit)->GetData().IsString()) {

1173

first_val = (*cit)->GetData().GetString()[0];

1174

}

else if

((*cit)->GetData().IsId()) {

1178  if

(all_default || !(*cit)->IsSetHeader() || !(*cit)->GetHeader().IsSetTitle() ||

NStr::IsBlank

((*cit)->GetHeader().GetTitle())) {

1180

(*cit)->SetHeader().SetTitle(first_val);

1181

}

else if

(!

NStr::Equal

((*cit)->GetHeader().GetTitle(), first_val)) {

1195  NON_CONST_ITERATE

(objects::CSeq_table::TColumns, cit, input_table->SetColumns()) {

1196  if

(!(*cit)->IsSetData() || (*cit)->GetData().GetSize() == 0) {

1198

}

else if

((*cit)->GetData().IsString()) {

1199  string

title = (*cit)->GetHeader().GetTitle();

1205

vector<CRef<objects::CSeq_id> > new_ids;

1206  for

(

size_t

j = 0; j < (*cit)->GetData().GetString().

size

(); j++) {

1207  string val

= (*cit)->GetData().GetString()[j];

1210

new_ids.push_back(

id

);

1211

}

catch

(exception &) {

1213  id

->SetLocal().SetStr(

val

);

1214

new_ids.push_back(

id

);

1217  for

(

size_t

j = 0; j < new_ids.size(); j++) {

1218

(*cit)->SetData().SetId().push_back(new_ids[j]);

1228  NON_CONST_ITERATE

(objects::CSeq_table::TColumns, cit, input_table->SetColumns()) {

1229  if

(!(*cit)->IsSetData() || (*cit)->GetData().GetSize() == 0) {

1231

}

else if

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

1232

vector<string> values;

1233  for

(

size_t

j = 0; j < (*cit)->GetData().GetInt().

size

(); j++) {

1236  for

(

size_t

j = 0; j < values.size(); j++) {

1237

(*cit)->SetData().SetString().push_back(values[j]);

1239

}

else if

((*cit)->GetData().IsReal()) {

1240

vector<string> values;

1241  for

(

size_t

j = 0; j < (*cit)->GetData().GetInt().

size

(); j++) {

1244  for

(

size_t

j = 0; j < values.size(); j++) {

1245

(*cit)->SetData().SetString().push_back(values[j]);

1254  if

(!(*cit)->IsSetData() || (*cit)->GetData().GetSize() == 0) {

1257  int

num_vals =

static_cast<int>

((*cit)->GetData().GetSize());

1258  if

(

row

>= num_vals) {

1261  if

((*cit)->GetData().IsString()) {

1262  for

(

int

j =

row

; j < num_vals - 1; j++) {

1263

(*cit)->SetData().SetString()[j] = (*cit)->GetData().GetString()[j + 1];

1265

(*cit)->SetData().SetString().pop_back();

1266

}

else if

((*cit)->GetData().IsId()) {

1267  for

(

int

j =

row

; j < num_vals - 1; j++) {

1268

(*cit)->SetData().SetId()[j]->Assign(*((*cit)->GetData().GetId()[j + 1]));

1270

(*cit)->SetData().SetId().pop_back();

1271

}

else if

((*cit)->GetData().IsLoc()) {

1272  for

(

int

j =

row

; j < num_vals - 1; j++) {

1273

(*cit)->SetData().SetLoc()[j]->Assign(*((*cit)->GetData().GetLoc()[j + 1]));

1275

(*cit)->SetData().SetLoc().pop_back();

1276

}

else if

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

1277  for

(

int

j =

row

; j < num_vals - 1; j++) {

1278

(*cit)->SetData().SetInt()[j] = (*cit)->GetData().GetInt()[j + 1];

1280

(*cit)->SetData().SetInt().pop_back();

1281

}

else if

((*cit)->GetData().IsReal()) {

1282  for

(

int

j =

row

; j < num_vals - 1; j++) {

1283

(*cit)->SetData().SetReal()[j] = (*cit)->GetData().GetReal()[j + 1];

1285

(*cit)->SetData().SetReal().pop_back();

1286

}

else if

((*cit)->GetData().IsBit()) {

1287  for

(

int

j =

row

; j < num_vals - 1; j++) {

1288

(*cit)->SetData().SetBit()[j] = (*cit)->GetData().GetBit()[j + 1];

1290

(*cit)->SetData().SetBit().pop_back();

1291

}

else if

((*cit)->GetData().IsBytes()) {

1292  for

(

int

j =

row

; j < num_vals - 1; j++) {

1293

(*cit)->SetData().SetBytes()[j] = (*cit)->GetData().GetBytes()[j + 1];

1295

(*cit)->SetData().SetBytes().pop_back();

1304  if

( nl_pos !=

NPOS

) {

1305

sTitle = sTitle.substr(0, nl_pos);

1310  if

(desc_pos !=

NPOS

) {

1311

sTitle = sTitle.substr(0, desc_pos);

1312

}

if

(feat_pos !=

NPOS

) {

1313

sTitle = sTitle.substr(0, feat_pos);

1316  if

(sTitle.empty()) {

1329  return "Organism Name"

;

1331  return "Taxname after binomial"

;

1333  string

organelle = sTitle.substr(6,

NPOS

);

1348  return "fwd-primer-name"

;

1351  return "fwd-primer-seq"

;

1354  return "rev-primer-name"

;

1357  return "rev-primer-seq"

;

1378  if

( pos !=

NPOS

) {

1379  string

subtype = sTitle.substr(0, pos);

1383  string

epart = sTitle.substr(pos+1,

NPOS

);

1384  if

(!(epart ==

"coll"

|| epart ==

"inst"

|| epart ==

"specid"

))

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

bool GUI_AsyncExecUnit(IExecuteUnit &exec_unit, const wxString &msg)

static string GetSubtypeName(const CSubSource &qual)

void SetColumns(wxArrayString &columns)

static bool AutoFill(objects::COrg_ref &org)

void Field(const string &value)

virtual void SetRegistryPath(const string &path)

static wxString GetDialogFilter(EFileType fileType)

IObjectLoader * GetObjectLoader()

void SetManagers(vector< CIRef< IOpenObjectsPanelClient > > &managers)

static bool IsValidSubtypeName(const string &str, EVocabulary vocabulary=eVocabulary_raw)

static TSubtype GetSubtypeValue(const string &str, EVocabulary vocabulary=eVocabulary_raw)

CConstRef< objects::CSeq_submit > m_SeqSubmit

void MakeColumnReadOnly(int pos, bool val=true)

void CollapseByCol(int col)

int GetCollapseColAndExpand(void)

void UpdateColumnChoices(int pos, vector< string > choices)

void SetColumnSizesAndChoices()

void InitColumnCollapse(int col)

void SetValuesTable(CRef< objects::CSeq_table > table)

CRef< objects::CSeq_table > GetValuesTable()

static CRef< CSrcTableColumnBase > Create(const objects::CSeqTable_column &column)

void SetColumns(wxArrayString &columns)

static TSubtype GetSubtypeValue(const string &str, EVocabulary vocabulary=eVocabulary_raw)

static bool IsValidSubtypeName(const string &str, EVocabulary vocabulary=eVocabulary_raw)

virtual bool PreExecute()=0

virtual bool PostExecute()=0

vector< SObject > TObjects

IWorkbench is the central interface in the application framework.

string FindBadColumns(CRef< objects::CSeq_table > table)

int GetNewColumn(wxString new_col)

void OnAddQual(wxCommandEvent &event)

wxEVT_COMMAND_BUTTON_CLICKED event handler for ID_ADD_QUAL_BUTTON

CStringConstraintSelect * m_StringConstraintPanel

int CombineTables(CRef< objects::CSeq_table > dst, const objects::CSeq_table &src)

void DeleteTableRow(CRef< objects::CSeq_table > table, int row)

SrcEditDialog()

Constructors.

objects::CSeq_table::TColumns m_columns

bool Create(wxWindow *parent, wxWindowID id=10013, const wxString &caption=_("Source Editing"), const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxDefaultSize, long style=wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxMAXIMIZE_BOX|wxCLOSE_BOX|wxTAB_TRAVERSAL)

Creation.

int GetCollapsible() const

void GetQualChoices(wxArrayString &srcModNameStrings)

CRef< objects::CSeq_table > x_GetSourceTableChoices(CRef< objects::CSeq_table > values)

void OnQualchoiceSelected(wxCommandEvent &event)

wxEVT_COMMAND_CHOICE_SELECTED event handler for ID_QUALCHOICE

CSeqTableGridPanel * m_GridPanel

CRef< objects::CSeq_table > x_GetValuesTableFromGridPanel()

wxBitmap GetBitmapResource(const wxString &name)

Retrieves bitmap resources.

~SrcEditDialog()

Destructor.

void OnExportQualsClick(wxCommandEvent &event)

wxEVT_COMMAND_BUTTON_CLICKED event handler for ID_EXPORT_QUALS

int CountColumnRowConflicts(CRef< objects::CSeqTable_column > dst_id, CRef< objects::CSeqTable_column > dst_col, CRef< objects::CSeqTable_column > src_id, CRef< objects::CSeqTable_column > src_col)

void OnClickCancel(wxCommandEvent &event)

wxEVT_COMMAND_BUTTON_CLICKED event handler for wxID_CANCEL

void CombineColumns(CRef< objects::CSeqTable_column > dst_id, CRef< objects::CSeqTable_column > dst_col, CRef< objects::CSeqTable_column > src_id, CRef< objects::CSeqTable_column > src_col)

string GetLabelForTitle(string sTitle)

CApplyEditconvertPanel * m_AecrPanel

void Init()

Initialises member variables.

CBioseq_Handle GetBioseqHandle(int row)

CRef< CCmdComposite > ApplySrcTableToSeqEntry(CRef< objects::CSeq_table >values_table)

CRef< CCmdComposite > GetCommand()

virtual const CObject * RowToScopedObjects(int row, TConstScopedObjects &objects, CBioseq_Handle &bsh)

CRef< objects::CSeqTable_column > FindSeqIDColumn(const objects::CSeq_table &table)

int FindRowForSeqId(CRef< objects::CSeqTable_column > id_col, CRef< objects::CSeq_id > id)

void OnClearQuals(wxCommandEvent &event)

wxEVT_COMMAND_BUTTON_CLICKED event handler for ID_CLEAR_QUALS_BTN

static bool ShowToolTips()

Should we show tooltips?

bool SaveTableFile(wxWindow *parent, wxString &save_file_dir, wxString &save_file_name, CRef< objects::CSeq_table > values_table)

vector< CBioseq_Handle > m_BioseqHandles

int x_FindColumn(const wxString &name)

bool IsReadOnlyColumn(string column_name) const

void ChangeColumnName(int col, string qual_name)

void OnLoadqualsClick(wxCommandEvent &event)

wxEVT_COMMAND_BUTTON_CLICKED event handler for ID_LOADQUALS

void FixTableAfterImport(CRef< objects::CSeq_table > input_table)

string FindBadRows(CRef< objects::CSeq_table > src, CRef< objects::CSeq_table > dst)

objects::CSeq_entry_Handle m_SEH

wxIcon GetIconResource(const wxString &name)

Retrieves icon resources.

void CreateControls()

Creates the controls and sizers.

int CountTableColumnConflicts(CRef< objects::CSeq_table > dst, const objects::CSeq_table &src)

void x_RepopulateAddQualList()

bool OneRowOk(CRef< objects::CSeq_id > id, CRef< objects::CSeqTable_column > id_col)

std::ofstream out("events_result.xml")

main entry point for tests

const char * kGenomeProjectID

const char * kSubSourceNote

const char * kSequenceIdColLabel

static const column_t columns[]

#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 NCBI_THROW(exception_class, err_code, message)

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

void CleanupForTaxnameChange(CObjectInfo oi)

vector< SConstScopedObject > TConstScopedObjects

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

Set object to copy of another one.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

bool IsSameBioseq(const CSeq_id_Handle &id1, const CSeq_id_Handle &id2, EGetBioseqFlag get_flag)

Check if two seq-ids are resolved to the same Bioseq.

@ eGetBioseq_Resolved

Search only in already resolved ids.

TBioseqCore GetBioseqCore(void) const

Get bioseq core structure.

CConstRef< CSeq_entry > GetCompleteSeq_entry(void) const

Complete and get const reference to the seq-entry.

CScope & GetScope(void) const

Get scope this handle belongs to.

CSeq_entry_Handle GetTopLevelEntry(void) const

Get top level Seq-entry handle.

TObjectType * GetPointer(void) const THROWS_NONE

Get pointer,.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ofstream CNcbiOfstream

Portable alias for ofstream.

NCBI_NS_STD::string::size_type SIZE_TYPE

static SIZE_TYPE FindNoCase(const CTempString str, const CTempString pattern, SIZE_TYPE start, SIZE_TYPE end, EOccurrence which=eFirst)

Find the pattern in the specified range of a string using a case insensitive search.

static bool EndsWith(const CTempString str, const CTempString end, ECase use_case=eCase)

Check if a string ends with a specified suffix value.

static bool IsBlank(const CTempString str, SIZE_TYPE pos=0)

Check if a string is blank (has no text).

static void TruncateSpacesInPlace(string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string (in-place)

static SIZE_TYPE Find(const CTempString str, const CTempString pattern, ECase use_case=eCase, EDirection direction=eForwardSearch, SIZE_TYPE occurrence=0)

Find the pattern in the string.

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

Check if a string starts with a specified prefix value.

static bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another string.

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

static bool Equal(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2, ECase use_case=eCase)

Test for equality of a substring with another string.

static string & ReplaceInPlace(string &src, const string &search, const string &replace, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a string.

static string TruncateSpaces(const string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string.

@ eReverseSearch

Search in a backward direction.

@ eNocase

Case insensitive compare.

@ eCase

Case sensitive compare.

static const char label[]

@ eSubtype_other

ASN5: old-name (254) will be added to next spec.

vector< CRef< CSeqTable_column > > TColumns

<!DOCTYPE HTML >< html > n< header > n< title > PubSeq Gateway Help Page</title > n< style > n table

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

CRef< CSeqTable_column > FindSeqTableColumnByName(CRef< objects::CSeq_table > values_table, string column_name)

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

CRef< objects::CSeq_table > GetSeqTableFromSeqEntry(objects::CSeq_entry_Handle seh)

#define ID_ADD_QUAL_BUTTON

#define row(bind, expected)

@ eExistingText_replace_old

wxString ToWxString(const string &s)

string ToStdString(const wxString &s)

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