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NCBI C++ ToolKit: include/objtools/format/flat_file_config.hpp Source File

1 #ifndef OBJTOOLS_FORMAT___FLAT_FILE_CONFIG__HPP 2 #define OBJTOOLS_FORMAT___FLAT_FILE_CONFIG__HPP 103  void

FormatProteinId(

string

&

str

,

const CSeq_id

& seq_id,

const string

& prot_id)

const override

;

104  void

FormatTranscriptId(

string

&

str

,

const CSeq_id

& seq_id,

const string

& nuc_id)

const override

;

105  void

FormatNucSearch(ostream& os,

const string

&

id

)

const override

;

106  void

FormatNucId(

string

&

str

,

const CSeq_id

& seq_id,

TIntId

gi,

const string

& acc_id)

const override

;

107  void

FormatTaxid(

string

&

str

,

const TTaxId

taxid,

const string

& taxname)

const override

;

108  void

FormatLocation(

string

&

str

,

const CSeq_loc

& loc,

TIntId

gi,

const string

& visible_text)

const override

;

109  void

FormatModelEvidence(

string

&

str

,

const SModelEvidance

& me)

const override

;

110  void

FormatTranscript(

string

&

str

,

const string

& name)

const override

;

111  void

FormatGeneralId(ostream& os,

const string

&

id

)

const override

;

112  void

FormatGapLink(ostream& os,

TSeqPos

gap_size,

const string

&

id

,

bool

is_prot)

const override

;

113  void

FormatUniProtId(

string

&

str

,

const string

& prot_id)

const override

;

154

fShowContigFeatures = 1 << 1,

155

fShowContigSources = 1 << 2,

156

fShowFarTranslations = 1 << 3,

157

fTranslateIfNoProduct = 1 << 4,

158

fAlwaysTranslateCDS = 1 << 5,

159

fOnlyNearFeatures = 1 << 6,

160

fFavorFarFeatures = 1 << 7,

161

fCopyCDSFromCDNA = 1 << 8,

162

fCopyGeneToCDNA = 1 << 9,

163

fShowContigInMaster = 1 << 10,

164

fHideImpFeatures = 1 << 11,

165

fHideRemoteImpFeatures = 1 << 12,

166

fHideSNPFeatures = 1 << 13,

167

fHideExonFeatures = 1 << 14,

168

fHideIntronFeatures = 1 << 15,

169

fHideMiscFeatures = 1 << 16,

170

fHideCDSProdFeatures = 1 << 17,

171

fHideCDDFeatures = 1 << 18,

172

fShowTranscript = 1 << 19,

173

fShowPeptides = 1 << 20,

174

fHideGeneRIFs = 1 << 21,

175

fOnlyGeneRIFs = 1 << 22,

176

fLatestGeneRIFs = 1 << 23,

177

fShowContigAndSeq = 1 << 24,

178

fHideSourceFeatures = 1 << 25,

179

fShowFtableRefs = 1 << 26,

180

fOldFeaturesOrder = 1 << 27,

181

fHideGapFeatures = 1 << 28,

182

fNeverTranslateCDS = 1 << 29,

183

fShowSeqSpans = 1 << 30

190

fLongLocusNames = 1 << 2,

191

fExpandGaps = 1 << 3,

192

fShowSNPFeatures = 1 << 6,

193

fShowCDDFeatures = 1 << 7,

194

fShowDebugTiming = 1 << 8,

195

fFasterReleaseSets = 1 << 9,

196

fDisableAnnotRefs = 1 << 10,

197

fUseSeqEntryIndexer = 1 << 11,

198

fUseAutoDef = 1 << 12,

199

fIgnoreExistingTitle = 1 << 13,

200

fGeneRNACDSFeatures = 1 << 14,

201

fShowFtablePeptides = 1 << 15,

202

fDisableReferenceCache = 1 << 16,

203

fShowDeflineModifiers = 1 << 17,

204

fDoNotUseAutoDef = 1 << 18,

205

fOldTpaDisplay = 1 << 19,

206

fDisableDefaultIndex = 1 << 20,

207

fGeoLocNameCountry = 1 << 21,

208

fLeavePrefixSuffix = 1 << 22

213

fViewNucleotides = 0x1,

215

fViewAll = (fViewNucleotides | fViewProteins),

221

ePolicy_Adaptive = 0,

222

ePolicy_Internal = 1,

223

ePolicy_External = 2,

224

ePolicy_Exhaustive = 3,

233

fGenbankBlocks_All = (~0u),

234

fGenbankBlocks_None = 0,

243

fGenbankBlocks_Head = (1u << 0),

244

fGenbankBlocks_Locus = (1u << 1),

245

fGenbankBlocks_Defline = (1u << 2),

246

fGenbankBlocks_Accession = (1u << 3),

247

fGenbankBlocks_Version = (1u << 4),

248

fGenbankBlocks_Project = (1u << 5),

249

fGenbankBlocks_Dbsource = (1u << 6),

250

fGenbankBlocks_Keywords = (1u << 7),

251

fGenbankBlocks_Segment = (1u << 8),

252

fGenbankBlocks_Source = (1u << 9),

253

fGenbankBlocks_Reference = (1u << 10),

254

fGenbankBlocks_Comment = (1u << 11),

255

fGenbankBlocks_Primary = (1u << 12),

256

fGenbankBlocks_Featheader = (1u << 13),

257

fGenbankBlocks_Sourcefeat = (1u << 14),

258

fGenbankBlocks_FeatAndGap = (1u << 15),

259

fGenbankBlocks_Basecount = (1u << 16),

260

fGenbankBlocks_Origin = (1u << 17),

261

fGenbankBlocks_Sequence = (1u << 18),

262

fGenbankBlocks_Contig = (1u << 19),

263

fGenbankBlocks_Wgs = (1u << 20),

264

fGenbankBlocks_Tsa = (1u << 21),

265

fGenbankBlocks_Slash = (1u << 22),

266

fGenbankBlocks_Cache = (1u << 23)

288 

eAction_HaltFlatfileGeneration

303  virtual

EAction notify(

string

& block_text,

306  virtual

EAction notify(

string

& block_text,

309  virtual

EAction notify(

string

& block_text,

312  virtual

EAction notify(

string

& block_text,

315  virtual

EAction notify(

string

& block_text,

318  virtual

EAction notify(

string

& block_text,

321  virtual

EAction notify(

string

& block_text,

324  virtual

EAction notify(

string

& block_text,

327  virtual

EAction notify(

string

& block_text,

330  virtual

EAction notify(

string

& block_text,

333  virtual

EAction notify(

string

& block_text,

336  virtual

EAction notify(

string

& block_text,

339  virtual

EAction notify(

string

& block_text,

342  virtual

EAction notify(

string

& block_text,

345  virtual

EAction notify(

string

& block_text,

348  virtual

EAction notify(

string

& block_text,

351  virtual

EAction notify(

string

& block_text,

354  virtual

EAction notify(

string

& block_text,

357  virtual

EAction notify(

string

& block_text,

360  virtual

EAction notify(

string

& block_text,

363  virtual

EAction notify(

string

& block_text,

366  virtual

EAction notify(

string

& block_text,

369  virtual

EAction notify(

string

& block_text,

372  virtual

EAction notify(

string

& block_text,

375  virtual

EAction notify(

string

& block_text,

378  virtual

EAction notify(

string

& block_text,

397

TMode

mode

= eMode_GBench,

398

TStyle style = eStyle_Normal,

400

TView view = fViewNucleotides,

401

TPolicy policy = ePolicy_Adaptive,

409

m_html_formatter = html_fmt;

413  return

*m_html_formatter;

425  bool IsFormatAGP

(

void

)

const

{

return

m_Format == eFormat_AGP; }

445  bool IsModeDump

(

void

)

const

{

return

m_Mode == eMode_Dump; }

470  bool IsViewNuc

(

void

)

const

{

return

(m_View & fViewNucleotides) != 0; }

471  bool IsViewProt

(

void

)

const

{

return

(m_View & fViewProteins) != 0; }

472  bool IsViewAll

(

void

)

const

{

return

IsViewNuc() && IsViewProt(); }

473  bool IsViewFirst

(

void

)

const

{

return

(m_View & fViewFirst) != 0; }

478

m_View = (m_View & ~fViewAll) | fViewNucleotides;

482

m_View = (m_View & ~fViewAll) | fViewProteins;

491

m_View |= fViewFirst;

493

m_View &= ~fViewFirst;

504  bool IsPolicyFtp

(

void

)

const

{

return

m_Policy == ePolicy_Ftp; }

505  bool IsPolicyWeb

(

void

)

const

{

return

m_Policy == ePolicy_Web; }

521  bool

DoHTML (

void

)

const

;

522  bool

HideImpFeatures (

void

)

const

;

523  bool

HideSNPFeatures (

void

)

const

;

524  bool

HideExonFeatures (

void

)

const

;

525  bool

HideIntronFeatures (

void

)

const

;

526  bool

HideMiscFeatures (

void

)

const

;

527  bool

HideRemoteImpFeatures (

void

)

const

;

528  bool

HideGeneRIFs (

void

)

const

;

529  bool

OnlyGeneRIFs (

void

)

const

;

530  bool

HideCDSProdFeatures (

void

)

const

;

531  bool

HideCDDFeatures (

void

)

const

;

532  bool

LatestGeneRIFs (

void

)

const

;

533  bool

ShowContigFeatures (

void

)

const

;

534  bool

ShowContigSources (

void

)

const

;

535  bool

ShowContigAndSeq (

void

)

const

;

536  bool

CopyGeneToCDNA (

void

)

const

;

537  bool

ShowContigInMaster (

void

)

const

;

538  bool

CopyCDSFromCDNA (

void

)

const

;

539  bool

HideSourceFeatures (

void

)

const

;

540  bool

AlwaysTranslateCDS (

void

)

const

;

541  bool

OnlyNearFeatures (

void

)

const

;

542  bool

FavorFarFeatures (

void

)

const

;

543  bool

ShowFarTranslations (

void

)

const

;

544  bool

TranslateIfNoProduct (

void

)

const

;

545  bool

ShowTranscript (

void

)

const

;

546  bool

ShowPeptides (

void

)

const

;

547  bool

ShowFtableRefs (

void

)

const

;

548  bool

OldFeaturesOrder (

void

)

const

;

549  bool

HideGapFeatures (

void

)

const

;

550  bool

NeverTranslateCDS (

void

)

const

;

551  bool

ShowSeqSpans (

void

)

const

;

553  bool

SuppressLocalId (

void

)

const

;

554  bool

ValidateFeatures (

void

)

const

;

555  bool

IgnorePatPubs (

void

)

const

;

556  bool

DropShortAA (

void

)

const

;

557  bool

AvoidLocusColl (

void

)

const

;

558  bool

IupacaaOnly (

void

)

const

;

559  bool

DropBadCitGens (

void

)

const

;

560  bool

NoAffilOnUnpub (

void

)

const

;

561  bool

DropIllegalQuals (

void

)

const

;

562  bool

CheckQualSyntax (

void

)

const

;

563  bool

NeedRequiredQuals (

void

)

const

;

564  bool

NeedOrganismQual (

void

)

const

;

565  bool

NeedAtLeastOneRef (

void

)

const

;

566  bool

CitArtIsoJta (

void

)

const

;

567  bool

DropBadDbxref (

void

)

const

;

568  bool

UseEmblMolType (

void

)

const

;

569  bool

HideBankItComment (

void

)

const

;

570  bool

CheckCDSProductId (

void

)

const

;

571  bool

FrequencyToNote (

void

)

const

;

572  bool

SrcQualsToNote (

void

)

const

;

573  bool

HideEmptySource (

void

)

const

;

574  bool

GoQualsToNote (

void

)

const

;

575  bool

SelenocysteineToNote(

void

)

const

;

576  bool

ForGBRelease (

void

)

const

;

577  bool

HideUnclassPartial (

void

)

const

;

578  bool

CodonRecognizedToNote(

void

)

const

;

579  bool

GoQualsEachMerge (

void

)

const

;

580  bool

ShowOutOfBoundsFeats(

void

)

const

;

581  bool

HideSpecificGeneMaps(

void

)

const

;

620  bool

HideProteinID (

void

)

const

;

621  bool

HideGI (

void

)

const

;

622  bool

LongLocusNames (

void

)

const

;

623  bool

ExpandGaps (

void

)

const

;

624  bool

ShowSNPFeatures (

void

)

const

;

625  bool

ShowCDDFeatures (

void

)

const

;

626  bool

ShowDebugTiming (

void

)

const

;

627  bool

FasterReleaseSets (

void

)

const

;

628  bool

DisableAnnotRefs (

void

)

const

;

629  bool

UseSeqEntryIndexer (

void

)

const

;

630  bool

UseAutoDef (

void

)

const

;

631  bool

IgnoreExistingTitle (

void

)

const

;

632  bool

GeneRNACDSFeatures (

void

)

const

;

633  bool

ShowFtablePeptides (

void

)

const

;

634  bool

DisableReferenceCache (

void

)

const

;

635  bool

ShowDeflineModifiers (

void

)

const

;

636  bool

DoNotUseAutoDef (

void

)

const

;

637  bool

OldTpaDisplay (

void

)

const

;

638  bool

DisableDefaultIndex (

void

)

const

;

639  bool

GeoLocNameCountry (

void

)

const

;

640  bool

LeavePrefixSuffix (

void

)

const

;

667  void

SetRefSeqConventions(

void

);

682

m_fGenbankBlocks = genbank_blocks;

688  return

m_fGenbankBlocks & fTGenbankBlocksMask;

694

m_fGenbankBlocks |= (fTGenbankBlocksMask);

701

m_fGenbankBlocks &= (~fTGenbankBlocksMask);

705  static

FGenbankBlocks StringToGenbankBlock(

const string

&

str

);

708  static const

vector<string> & GetAllGenbankStrings(

void

);

712  return

m_GenbankBlockCallback; }

714

m_GenbankBlockCallback = pGenbankBlockCallback;

718  return

m_pCanceledCallback;

721

m_pCanceledCallback = pCallback;

733  if

( m_pCanceledCallback && m_pCanceledCallback->IsCanceled() ) {

741  void

FromArguments(

const CArgs

& args);

744  static const size_t

SMARTFEATLIMIT = 1000000;

748  static const bool

sm_ModeFlags[4][32];

750  void

x_ThrowHaltNow(

void

)

const

;

776 #define FLAG_ARG_GET(x) \ 778 bool CFlatFileConfig::x(void) const \ 780  return (m_Flags & f##x) != 0; \ 783 #define FLAG_ARG_SET(x) inline \ 784 CFlatFileConfig& CFlatFileConfig::Set##x(bool val) \ 794 #define FLAG_ARG_IMP(x) \ 831 #define CUSTOM_ARG_GET(x) \ 833 bool CFlatFileConfig::x(void) const \ 835  return (m_Custom & f##x) != 0; \ 838 #define CUSTOM_ARG_SET(x) inline \ 839 CFlatFileConfig& CFlatFileConfig::Set##x(bool val) \ 849 #define CUSTOM_ARG_IMP(x) \ 879 #undef CUSTOM_ARG_IMP 880 #undef CUSTOM_ARG_GET 881 #undef CUSTOM_ARG_SET

@ eAction_Default

the normal case

@ eAction_Skip

skip this block (i.e. don't print it)

virtual EAction unified_notify(string &, const CBioseqContext &, const IFlatItem &, FGenbankBlocks)

virtual ~CGenbankBlockCallback(void)

bool IsFormatDDBJ(void) const

void SetFormatGenbank(void)

void SetFlags(const TFlags &flags)

const TCustom & GetCustom(void) const

void SetSingleAccession(const string &accn)

void SetStyleMaster(void)

void SkipGenbankBlock(FGenbankBlocks fTGenbankBlocksMask)

bool IsModeGBench(void) const

const TFormat & GetFormat(void) const

const TStyle & GetStyle(void) const

const IHTMLFormatter & GetHTMLFormatter() const

bool IsPolicyInternal(void) const

bool IsFormatGBSeq(void) const

const ICanceled * GetCanceledCallback(void) const

bool IsStyleSegment(void) const

bool IsPolicyExhaustive(void) const

bool IsPolicyExternal(void) const

void SetViewFirst(bool enabled)

void SetRefSeqConventions(void)

void SetPolicyGenomes(void)

void SetFeatDepth(const int featDepth)

const TMode & GetMode(void) const

void SetFormat(const TFormat &format)

void SetHTMLFormatter(CRef< IHTMLFormatter > html_fmt)

void BasicCleanup(bool clean)

bool IsPolicyAdaptive(void) const

void SetStyleNormal(void)

void SetCustom(const TCustom &custom)

void SetGapDepth(const int gapDepth)

void ShowGenbankBlock(FGenbankBlocks fTGenbankBlocksMask)

void SetGenbankBlocks(const TGenbankBlocks &genbank_blocks)

bool IsPolicyFtp(void) const

bool IsPolicyWeb(void) const

void SetPolicyInternal(void)

int GetGapDepth(void) const

void SetPolicyExternal(void)

bool IsViewNuc(void) const

bool IsViewFirst(void) const

bool IsStyleMaster(void) const

const ICanceled * m_pCanceledCallback

void SetPolicy(const TPolicy &Policy)

bool IsFormatINSDSeq(void) const

bool IsPolicyGenomes(void) const

bool IsFormatGenbank(void) const

void SetMode(const TMode &mode)

bool IsFormatFTable(void) const

const TPolicy & GetPolicy(void) const

void SetStyle(const TStyle &style)

int GetFeatDepth(void) const

void SetFormatINSDSeq(void)

void SetCanceledCallback(ICanceled *pCallback)

void SetGenbankBlockCallback(CGenbankBlockCallback *pGenbankBlockCallback)

TGenbankBlocks m_fGenbankBlocks

CRef< CGenbankBlockCallback > GetGenbankBlockCallback(void) const

void SetView(const TView &view)

bool IsViewAll(void) const

const string & GetSingleAccession(void) const

bool IsViewProt(void) const

void SetPolicyExhaustive(void)

CRef< CGenbankBlockCallback > m_GenbankBlockCallback

void SetStyleContig(void)

CRef< IHTMLFormatter > m_html_formatter

void ThrowIfCanceled(void) const

This throws a CFlatException if flatfile generation cancellation has been requested via ICanceled.

unsigned int TGenbankBlocks

const TFlags & GetFlags(void) const

bool IsModeRelease(void) const

bool BasicCleanup(void) const

bool IsFormatEMBL(void) const

bool IsModeDump(void) const

bool IsModeEntrez(void) const

bool IsFormatLite(void) const

bool IsShownGenbankBlock(FGenbankBlocks fTGenbankBlocksMask) const

void SetPolicyAdaptive(void)

const TView & GetView(void) const

bool IsStyleNormal(void) const

bool IsStyleContig(void) const

bool IsFormatAGP(void) const

void SetModeRelease(void)

void SetStyleSegment(void)

void SetFormatFTable(void)

void SetFormatGBSeq(void)

~CHTMLEmptyFormatter() override

Interface for testing cancellation request in a long lasting operation.

virtual void FormatProteinId(string &str, const CSeq_id &seq_id, const string &prot_id) const =0

virtual void FormatModelEvidence(string &str, const SModelEvidance &me) const =0

virtual void FormatNucId(string &str, const CSeq_id &seq_id, TIntId gi, const string &acc_id) const =0

virtual void FormatGeneralId(ostream &os, const string &id) const =0

virtual void FormatTranscriptId(string &str, const CSeq_id &seq_id, const string &nuc_id) const =0

virtual void FormatLocation(string &str, const CSeq_loc &loc, TIntId gi, const string &visible_text) const =0

virtual void FormatUniProtId(string &str, const string &prot_id) const =0

virtual void FormatTranscript(string &str, const string &name) const =0

virtual void FormatNucSearch(ostream &os, const string &id) const =0

virtual void FormatGapLink(ostream &os, TSeqPos gap_size, const string &id, bool is_prot) const =0

virtual void FormatTaxid(string &str, const TTaxId taxid, const string &taxname) const =0

virtual ~IHTMLFormatter()

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

#define CUSTOM_ARG_IMP(x)

static const char * str(char *buf, int n)

unsigned int TSeqPos

Type for sequence locations and lengths.

SStrictId_Tax::TId TTaxId

Taxon id type.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

#define NCBI_FORMAT_EXPORT

The blob sat and sat key Both must be positive integers</td > n< td > Non empty string The interpretation of the blob id depends on a processor Cassandra n processor expects the following format

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

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