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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/molinfoedit__util_8cpp_source.html below:

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

71

objects::CSeq_inst::ETopology topology = objects::CSeq_inst::eTopology_not_set;

73

topology = objects::CSeq_inst::eTopology_circular;

75

topology = objects::CSeq_inst::eTopology_linear;

77

topology = objects::CSeq_inst::eTopology_other;

79

topology = objects::CSeq_inst::eTopology_tandem;

85 string s_GetBiomolName

(objects::CSeq_inst::EMol mol, objects::CMolInfo::TBiomol biomol)

89 case

objects::CMolInfo::eBiomol_genomic:

90 case

objects::CMolInfo::eBiomol_unknown:

91 if

(mol == objects::CSeq_inst::eMol_rna) {

92

name =

"Genomic RNA"

;

93

}

else if

(mol == objects::CSeq_inst::eMol_dna) {

97 case

objects::CMolInfo::eBiomol_pre_RNA:

98

name =

"Precursor RNA"

;

100 case

objects::CMolInfo::eBiomol_mRNA:

103 case

objects::CMolInfo::eBiomol_rRNA:

104

name =

"Ribosomal RNA"

;

106 case

objects::CMolInfo::eBiomol_tRNA:

107

name =

"Transfer RNA"

;

109 case

objects::CMolInfo::eBiomol_peptide:

112 case

objects::CMolInfo::eBiomol_other_genetic:

113

name =

"Other-Genetic"

;

115 case

objects::CMolInfo::eBiomol_genomic_mRNA:

116

name =

"Genomic-mRNA"

;

118 case

objects::CMolInfo::eBiomol_cRNA:

121 case

objects::CMolInfo::eBiomol_transcribed_RNA:

122

name =

"Transcribed RNA"

;

124 case

objects::CMolInfo::eBiomol_ncRNA:

125 case

objects::CMolInfo::eBiomol_scRNA:

126 case

objects::CMolInfo::eBiomol_snoRNA:

127 case

objects::CMolInfo::eBiomol_snRNA:

128 case

objects::CMolInfo::eBiomol_tmRNA:

129

name =

"Non-coding RNA"

;

131 case

objects::CMolInfo::eBiomol_other:

141

mol = objects::CSeq_inst::eMol_na;

142

biomol = objects::CMolInfo::eBiomol_unknown;

145

biomol = objects::CMolInfo::eBiomol_genomic;

146

mol = objects::CSeq_inst::eMol_rna;

148

biomol = objects::CMolInfo::eBiomol_genomic;

149

mol = objects::CSeq_inst::eMol_dna;

154

biomol = objects::CMolInfo::eBiomol_pre_RNA;

155

mol = objects::CSeq_inst::eMol_rna;

159

biomol = objects::CMolInfo::eBiomol_mRNA;

160

mol = objects::CSeq_inst::eMol_rna;

163

biomol = objects::CMolInfo::eBiomol_rRNA;

164

mol = objects::CSeq_inst::eMol_rna;

167

biomol = objects::CMolInfo::eBiomol_tRNA;

168

mol = objects::CSeq_inst::eMol_rna;

171

biomol = objects::CMolInfo::eBiomol_peptide;

172

mol = objects::CSeq_inst::eMol_aa;

174

biomol = objects::CMolInfo::eBiomol_other_genetic;

175

mol = objects::CSeq_inst::eMol_na;

178

biomol = objects::CMolInfo::eBiomol_genomic_mRNA;

179

mol = objects::CSeq_inst::eMol_rna;

181

biomol = objects::CMolInfo::eBiomol_cRNA;

182

mol = objects::CSeq_inst::eMol_rna;

184

biomol = objects::CMolInfo::eBiomol_transcribed_RNA;

185

mol = objects::CSeq_inst::eMol_rna;

192

biomol = objects::CMolInfo::eBiomol_ncRNA;

193

mol = objects::CSeq_inst::eMol_rna;

195

biomol = objects::CMolInfo::eBiomol_other;

196

mol = objects::CSeq_inst::eMol_na;

203

vector<string> mol_options;

206 switch

(wizard_type) {

208

mol_options.push_back(

"genomic RNA"

);

209

mol_options.push_back(

"cRNA"

);

210

mol_options.push_back(

"mRNA"

);

213

mol_options.push_back(

"mRNA"

);

219

mol_options.push_back(

"genomic RNA"

);

220

mol_options.push_back(

"cRNA"

);

221

mol_options.push_back(

"mRNA"

);

222

mol_options.push_back(

"Precursor RNA"

);

223

mol_options.push_back(

"Ribosomal RNA"

);

224

mol_options.push_back(

"Transfer RNA"

);

225

mol_options.push_back(

"Other-Genetic"

);

226

mol_options.push_back(

"Transcribed RNA"

);

227

mol_options.push_back(

"Transfer-messenger RNA"

);

228

mol_options.push_back(

"ncRNA"

);

237

vector<string> genome_options;

238

genome_options.clear();

240

genome_options.push_back(

"genomic"

);

241

genome_options.push_back(

"mitochondrion"

);

242

genome_options.push_back(

"chloroplast"

);

243

genome_options.push_back(

"plastid"

);

245

genome_options.push_back(

"genomic"

);

249

genome_options.push_back(

"mitochondrion"

);

253

genome_options.push_back(

"chloroplast"

);

254

genome_options.push_back(

"chromoplast"

);

255

genome_options.push_back(

"kinetoplast"

);

256

genome_options.push_back(

"plastid"

);

257

genome_options.push_back(

"macronuclear"

);

258

genome_options.push_back(

"cyanelle"

);

259

genome_options.push_back(

"nucleomorph"

);

260

genome_options.push_back(

"apicoplast"

);

261

genome_options.push_back(

"leucoplast"

);

262

genome_options.push_back(

"proplastid"

);

263

genome_options.push_back(

"hydrogenosome"

);

264

genome_options.push_back(

"chromatophore"

);

265

genome_options.push_back(

"extrachromosomal"

);

266

genome_options.push_back(

"plasmid"

);

267

genome_options.push_back(

"proviral"

);

268

genome_options.push_back(

"virion"

);

269

genome_options.push_back(

"endogenous-virus"

);

273 return

genome_options;

281

id_col->SetHeader().SetField_id(objects::CSeqTable_column_info::eField_id_location_id);

283 table

->SetColumns().push_back(id_col);

289

moltype_col =

new

objects::CSeqTable_column();

291

moltype_col->SetHeader().SetField_name(

"biomol"

);

292

moltype_col->SetData().SetString();

293 table

->SetColumns().push_back(moltype_col);

294

topology_col =

new

objects::CSeqTable_column();

295

topology_col->SetHeader().SetTitle(

"Topology"

);

296

topology_col->SetHeader().SetField_name(

"topology"

);

297

topology_col->SetData().SetString();

298 table

->SetColumns().push_back(topology_col);

301

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

302 for

( ; b_iter ; ++b_iter ) {

303

objects::CSeqdesc_CI it (*b_iter, objects::CSeqdesc::e_Molinfo);

305 id

->Assign (*(b_iter->GetSeqId()));

306

id_col->SetData().SetId().push_back(

id

);

308

objects::CSeq_inst::ETopology topology = objects::CSeq_inst::eTopology_not_set;

309 if

(b_iter->IsSetInst_Topology()) {

310

topology = b_iter->GetInst_Topology();

315

objects::CSeq_inst::EMol mol = objects::CSeq_inst::eMol_na;

316 if

(b_iter->IsSetInst_Mol()) {

317

mol = b_iter->GetInst_Mol();

319

objects::CMolInfo::TBiomol biomol = objects::CMolInfo::eBiomol_unknown;

320 if

(it && it->GetMolinfo().IsSetBiomol()) {

321

biomol = it->GetMolinfo().GetBiomol();

323

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

s_GetBiomolName

(mol, biomol));

344 if

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

348 for

(

int row

= 0;

row

< values_table->GetNum_rows() && (

unsigned int

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

row

++) {

349

objects::CBioseq_Handle bsh = seh.GetBioseqHandle(*(id_col->GetData().GetId()[

row

]));

352

inst->Assign(bsh.GetInst());

353 bool

inst_changed =

false

;

356

objects::CSeq_inst::ETopology new_topology =

s_TopologyFromName

(*topology_col->GetStringPtr(

row

) );

357 if

(inst->IsSetTopology()) {

358 if

(new_topology != inst->GetTopology()) {

359

inst->SetTopology(new_topology);

360

inst_changed =

true

;

363 if

(new_topology != objects::CSeq_inst::eTopology_not_set) {

364

inst->SetTopology(new_topology);

365

inst_changed =

true

;

371

objects::CMolInfo & molinfo = new_molinfo_desc->SetMolinfo();

372 bool

molinfo_changed =

false

;

373

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

375

molinfo.Assign(desc_ci->GetMolinfo());

377

molinfo_changed =

true

;

381

objects::CSeq_inst::EMol new_mol;

382

objects::CMolInfo::EBiomol new_biomol;

384 if

(inst->IsSetMol()) {

385 if

(new_mol != inst->GetMol()) {

386

inst->SetMol(new_mol);

387

inst_changed =

true

;

390 if

(new_mol != objects::CSeq_inst::eMol_not_set) {

391

inst->SetMol(new_mol);

392

inst_changed =

true

;

396 if

(molinfo.IsSetBiomol()) {

397 if

(new_biomol != molinfo.GetBiomol()) {

398

molinfo.SetBiomol(new_biomol);

399

molinfo_changed =

true

;

402 if

(new_biomol != objects::CMolInfo::eBiomol_unknown) {

403

molinfo.SetBiomol(new_biomol);

404

molinfo_changed =

true

;

411 cmd

->AddCommand(*scmd);

413 if

(molinfo_changed) {

416 cmd

->AddCommand (*ecmd);

421 if

(add_confirmed && (inst_changed || molinfo_changed)) {

435

id_col->SetHeader().SetField_id(objects::CSeqTable_column_info::eField_id_location_id);

437 table

->SetColumns().push_back(id_col);

440

comment_col->SetHeader().SetTitle(

label

);

441

comment_col->SetHeader().SetField_name(

"comment"

);

442

comment_col->SetData().SetString();

443 table

->SetColumns().push_back(comment_col);

446

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

447 for

( ; b_iter ; ++b_iter ) {

448

objects::CSeqdesc_CI it (*b_iter, objects::CSeqdesc::e_Comment);

450 id

->Assign (*(b_iter->GetSeqId()));

451

id_col->SetData().SetId().push_back(

id

);

452 string

comment =

""

;

454

comment = it->GetComment();

456

comment_col->SetData().SetString().push_back(comment);

475 if

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

479 for

(

int row

= 0;

row

< values_table->GetNum_rows() && (

unsigned int

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

row

++) {

480

objects::CBioseq_Handle bsh = seh.GetBioseqHandle(*(id_col->GetData().GetId()[

row

]));

481 string

new_comment =

""

;

482 if

((

unsigned int

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

483

new_comment = comment_col->GetData().GetString()[

row

];

485 string

old_comment =

""

;

486

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

488

old_comment = desc_ci->GetComment();

492

new_desc->SetComment(new_comment);

495 cmd

->AddCommand (*ecmd);

512 if

(src.IsSetGenome() && src.GetGenome() == objects::CBioSource::eGenome_mitochondrion) {

514

}

else if

(src.IsSetOrg() && src.GetOrg().IsSetOrgname() && src.GetOrg().GetOrgname().IsSetLineage()) {

515 const string

& lineage = src.GetOrg().GetOrgname().GetLineage();

535

id_col->SetHeader().SetField_id(objects::CSeqTable_column_info::eField_id_location_id);

537 table

->SetColumns().push_back(id_col);

540

comment_col->SetHeader().SetTitle(

label

);

541

comment_col->SetHeader().SetField_name(

"comment"

);

542

comment_col->SetData().SetString();

543 table

->SetColumns().push_back(comment_col);

546

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

547 for

( ; b_iter ; ++b_iter ) {

548

objects::CSeqdesc_CI desc (*b_iter, objects::CSeqdesc::e_Source);

555

objects::CFeat_CI fit (*b_iter);

556 while

(fit && this_count < 2) {

558 if

(fit->IsSetData() && fit->GetData().IsRna()

559

&& fit->GetData().GetRna().IsSetType()

560

&& fit->GetData().GetRna().GetType() == objects::CRNA_ref::eType_rRNA

561

&& fit->GetData().GetRna().IsSetExt()

562

&& fit->GetData().GetRna().GetExt().IsName()

563

NStr::Equal

(fit->GetData().GetRna().GetExt().GetName(),

"16S ribosomal RNA"

)) {

570 if

(this_count == 1 && any) {

572 id

->Assign (*(b_iter->GetSeqId()));

573

id_col->SetData().SetId().push_back(

id

);

574

objects::CSeqdesc_CI it (*b_iter, objects::CSeqdesc::e_Comment);

578 string

prog_ver =

""

;

582

comment_col->SetData().SetString().push_back(prog_ver);

606 if

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

610 for

(

int row

= 0;

row

< values_table->GetNum_rows() && (

unsigned int

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

row

++) {

611

objects::CBioseq_Handle bsh = seh.GetBioseqHandle(*(id_col->GetData().GetId()[

row

]));

612 string

new_comment = comment_col->GetData().GetString()[

row

];

616 string

old_comment =

""

;

617

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

622

old_comment = desc_ci->GetComment();

626

new_desc->SetComment(new_comment);

629 cmd

->AddCommand (*ecmd);

647

id_col->SetHeader().SetField_id(objects::CSeqTable_column_info::eField_id_location_id);

649 table

->SetColumns().push_back(id_col);

654

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

655 for

( ; b_iter ; ++b_iter ) {

657 id

->Assign (*(b_iter->GetSeqId()));

658

id_col->SetData().SetId().push_back(

id

);

660

objects::CSeqdesc_CI it (*b_iter, objects::CSeqdesc::e_User);

662 if

(it->GetUser().IsSetType()

663

&& it->GetUser().GetType().IsStr()

665 ITERATE

(objects::CUser_object::TData, field_it, it->GetUser().GetData()) {

666 if

((*field_it)->IsSetLabel()

667

&& (*field_it)->GetLabel().IsStr()

668

&& (*field_it)->IsSetData()) {

669 string

existing_val =

""

;

670 if

((*field_it)->GetData().IsStr()) {

671

existing_val = (*field_it)->GetData().GetStr();

672

}

else if

((*field_it)->GetData().IsStrs()) {

673 for

(vector<CStringUTF8>::const_iterator str_it = (*field_it)->GetData().GetStrs().begin();

674

str_it != (*field_it)->GetData().GetStrs().end();

676

existing_val +=

", "

+ *str_it;

679

existing_val = existing_val.substr(2);

706 const

objects::CSeq_table::TColumns &

columns

= values_table->GetColumns();

707 size_t

num_cols =

columns

.size();

709 for

(

int row

= 0;

row

< values_table->GetNum_rows() && (

size_t

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

row

++) {

710

objects::CBioseq_Handle bsh = seh.GetBioseqHandle(*(id_col->GetData().GetId()[

row

]));

713

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

715 while

(desc_ci && !found) {

716 if

(desc_ci->GetUser().IsSetType()

717

&& desc_ci->GetUser().GetType().IsStr()

720

new_desc->SetUser().Assign(desc_ci->GetUser());

726 bool

any_change =

false

;

727 for

(

size_t i

= 1;

< num_cols;

++) {

728 string

col_name = values_table->GetColumns()[

]->GetHeader().GetTitle();

730

objects::CUser_field& field = new_desc->SetUser().SetField(col_name);

731 if

(!field.IsSetLabel() || !field.GetLabel().IsStr() ||

NStr::IsBlank

(field.GetLabel().GetStr())) {

732

field.SetLabel().SetStr(col_name);

734 string

new_val =

""

;

735 if

((

size_t

) row < values_table->GetColumns()[

]->GetData().GetSize()) {

736

new_val = values_table->GetColumns()[

]->GetData().GetString()[

row

];

738

vector<string> values;

741 for

(vector<string>::iterator str_it = values.begin(); str_it != values.end(); str_it++) {

742

field.SetData().SetStrs().push_back(*str_it);

744 if

(values.size() == 0) {

745

field.SetData().SetStrs().push_back(

" "

);

753 cmd

->AddCommand (*ecmd);

755

new_desc->SetUser().SetType().SetStr(

"DBLink"

);

776

inst = &(

->GetInst());

836

vector<string> rvals;

837

rvals.push_back(

GetVal

(

object

));

967

vector<CConstRef<CObject> > objs;

989

vector<CRef<edit::CApplyObject> > objs;

1000

new_desc->

Assign

(*desc_ci);

1004

objs.push_back(new_obj);

1014

objs.push_back(new_obj);

1029

objs.push_back(new_obj);

User-defined methods of the data storage class.

static string GetBiomolLabel(objects::CMolInfo::TBiomol biomol)

static objects::CSeq_inst::TStrand GetStrandFromLabel(const string &val)

static objects::CSeq_inst::TMol GetMolFromLabel(const string &val)

static string GetTechLabel(objects::CMolInfo::TTech tech)

static objects::CSeq_inst::TTopology GetTopologyFromLabel(const string &val)

static EMolInfoFieldType GetFieldType(const string &field_name)

static objects::CMolInfo::TTech GetTechFromLabel(const string &val)

static string GetStrandLabel(objects::CSeq_inst::TStrand val)

static string GetMolLabel(objects::CSeq_inst::TMol val)

static string GetTopologyLabel(objects::CSeq_inst::TTopology tech)

static objects::CMolInfo::TCompleteness GetCompletenessFromLabel(const string &val)

static objects::CMolInfo::TBiomol GetBiomolFromLabel(const string &val)

static string GetCompletenessLabel(objects::CMolInfo::TCompleteness tech)

virtual void SetConstraint(const string &field, CConstRef< objects::edit::CStringConstraint > string_constraint)

virtual bool SetVal(CObject &object, const string &val, objects::edit::EExistingText existing_text)

CMolInfoFieldType::EMolInfoFieldType m_FieldType

virtual vector< string > GetVals(const CObject &object)

virtual string GetVal(const CObject &object)

CMolInfoFieldType::EMolInfoFieldType m_ConstraintFieldType

virtual vector< CConstRef< CObject > > GetObjects(CBioseq_Handle bsh)

virtual vector< CRef< objects::edit::CApplyObject > > GetApplyObjects(CBioseq_Handle bsh)

virtual bool IsEmpty(const CObject &object) const

virtual void ClearVal(CObject &object)

CRef< objects::edit::CStringConstraint > m_StringConstraint

@ eWizardSrcType_bacteria_or_archaea

@ eWizardType_microsatellite

@ eWizardType_rrna_its_igs

static CRef< CCmdComposite > SetWizardFieldInSeqEntry(objects::CSeq_entry_Handle entry, string field_name, string value)

objects::CSeqdesc::E_Choice m_Subtype

virtual vector< CConstRef< CObject > > GetObjects(objects::CBioseq_Handle bsh)

const char * kMoleculeType

const char * kDefaultMoleculeType

const char * kSequenceIdColLabel

static const column_t columns[]

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

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

Set object to copy of another one.

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

CSeq_entry_Handle GetParentEntry(void) const

Get parent Seq-entry handle.

bool IsSetInst(void) const

const TInst & GetInst(void) const

TObjectType * GetPointer(void) const THROWS_NONE

Get pointer,.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

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 IsBlank(const CTempString str, SIZE_TYPE pos=0)

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

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 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 const char label[]

void SetCompleteness(TCompleteness value)

Assign a value to Completeness data member.

void ResetStrand(void)

Reset Strand data member.

bool IsSetCompleteness(void) const

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

bool IsMolinfo(void) const

Check if variant Molinfo is selected.

TStrand GetStrand(void) const

Get the Strand member data.

void ResetMol(void)

Reset Mol data member.

TTopology GetTopology(void) const

Get the Topology member data.

bool IsSetTechexp(void) const

explanation if tech not enough

bool IsSetMol(void) const

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

bool IsSetStrand(void) const

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

void ResetCompleteness(void)

Reset Completeness data member.

bool IsSetBiomol(void) const

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

TTech GetTech(void) const

Get the Tech member data.

void ResetTechexp(void)

Reset Techexp data member.

TMol GetMol(void) const

Get the Mol member data.

const TTechexp & GetTechexp(void) const

Get the Techexp member data.

void SetInst(TInst &value)

Assign a value to Inst data member.

void ResetTech(void)

Reset Tech data member.

void ResetTopology(void)

Reset Topology data member.

TBiomol GetBiomol(void) const

Get the Biomol member data.

void SetTopology(TTopology value)

Assign a value to Topology data member.

void ResetBiomol(void)

Reset Biomol data member.

void SetBiomol(TBiomol value)

Assign a value to Biomol data member.

bool IsSetTech(void) const

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

void SetTechexp(const TTechexp &value)

Assign a value to Techexp data member.

TCompleteness GetCompleteness(void) const

Get the Completeness member data.

void SetStrand(TStrand value)

Assign a value to Strand data member.

void SetTech(TTech value)

Assign a value to Tech data member.

const TMolinfo & GetMolinfo(void) const

Get the variant data.

TMolinfo & SetMolinfo(void)

Select the variant.

void SetMol(TMol value)

Assign a value to Mol data member.

bool IsSetTopology(void) const

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

@ eTech_other

use Source.techexp

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

CRef< CCmdComposite > ApplyCommentValuesTableToSeqEntry(CRef< objects::CSeq_table >values_table, objects::CSeq_entry_Handle seh, const string &label)

CRef< objects::CSeq_table > BuildCommentDescriptorValuesTableFromSeqEntry(objects::CSeq_entry_Handle seh, const string &label)

objects::CSeq_inst::ETopology s_TopologyFromName(string name)

static void s_GetBiomolValuesFromName(string name, objects::CSeq_inst::EMol &mol, objects::CMolInfo::EBiomol &biomol)

CRef< CCmdComposite > ApplyMolInfoValuesTableToSeqEntry(CRef< objects::CSeq_table >values_table, objects::CSeq_entry_Handle seh, bool add_confirmed)

vector< string > GetSrcGenomeOptions(CSourceRequirements::EWizardType wizard_type, CSourceRequirements::EWizardSrcType src_type)

vector< string > GetMoleculeTypeOptions(CSourceRequirements::EWizardType wizard_type)

string s_GetBiomolName(objects::CSeq_inst::EMol mol, objects::CMolInfo::TBiomol biomol)

CRef< objects::CSeq_table > BuildMolInfoValuesTableFromSeqEntry(objects::CSeq_entry_Handle seh, CSourceRequirements::EWizardType wizard_type)

CRef< objects::CSeq_table > BuildChimeraValuesTableFromSeqEntry(objects::CSeq_entry_Handle seh, const string &label, CSourceRequirements::EWizardSrcType src_type)

static bool s_WantChimeraForSource(const objects::CBioSource &src, CSourceRequirements::EWizardSrcType src_type)

CRef< CCmdComposite > ApplyDBLinkValuesTableToSeqEntry(CRef< objects::CSeq_table >values_table, objects::CSeq_entry_Handle seh)

CRef< CCmdComposite > ApplyChimeraValuesTableToSeqEntry(CRef< objects::CSeq_table >values_table, objects::CSeq_entry_Handle seh, const string &label)

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

const string kChimeraCommentStart

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

void AddValueToTable(CRef< CSeq_table > table, string subtype_name, string value, size_t row, edit::EExistingText existing_text=edit::eExistingText_replace_old)

#define row(bind, expected)

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