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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/gene__model_8hpp_source.html below:

NCBI C++ ToolKit: include/algo/sequence/gene_model.hpp Source File

1 #ifndef ALGO_SEQUENCE___GENE_MODEL__HPP 2 #define ALGO_SEQUENCE___GENE_MODEL__HPP 62 switch

( GetErrCode() ) {

64 return "Unknown error"

;

66 return "MicroIntron generation failure"

;

88

fMaximizeTranslation = 0x2000,

99

fCreateCdregion = 0x004,

100

fPromoteAllFeatures = 0x008,

101

fPropagateOnly = 0x010,

102

fForceTranslateCds = 0x020,

103

fForceTranscribeMrna = 0x040,

104

fDensegAsExon = 0x080,

105

fGenerateLocalIds = 0x100,

106

fGenerateStableLocalIds = 0x200,

107

fPropagateNcrnaFeats = 0x400,

108

fTrustProteinSeq = 0x800,

111

fDeNovoProducts = 0x4000,

112

fAddTranslatedCDSAssembly = 0x8000,

113

fDropManeMarkup = 0x00010000,

114

fSkipLocationCheck = 0x00020000,

116

fDefaults = fCreateGene | fCreateMrna | fCreateCdregion |

117

fGenerateLocalIds | fPropagateNcrnaFeats

128 static const TSeqPos

kDefaultAllowedUnaligned = 10;

134 void

SetAllowedUnaligned(

TSeqPos

);

142

CleanAlignment(

const

objects::CSeq_align& align);

153

eTryToPreserveProductPositions

156

AdjustAlignment(

const

objects::CSeq_align& align,

TSeqRange

range, EProductPositionsMode

mode

= eForceProductFrom0);

164

objects::CSeq_annot& annot,

165

objects::CBioseq_set& seqs,

167 const

objects::CSeq_feat* cdregion_on_mrna =

NULL

);

170

objects::CSeq_annot &annot,

171

objects::CBioseq_set &seqs);

176 void

ConvertLocToAnnot(

177 const

objects::CSeq_loc &loc,

178

objects::CSeq_annot& annot,

179

objects::CBioseq_set& seqs,

180

objects::CCdregion::EFrame frame = objects::CCdregion::eFrame_one,

186 void

SetFeatureExceptions(objects::CSeq_feat& feat,

187 const

objects::CSeq_align* align =

NULL

);

196 void

RecomputePartialFlags(objects::CSeq_annot& annot);

214 size_t

unaligned_ends_partialness_thr = kDefaultAllowedUnaligned);

220 const

objects::CSeq_loc& product_cds_loc,

221 bool

convert_overlaps =

true

);

224 static void

CreateMicroIntrons(

225

objects::CScope& scope,

226

objects::CBioseq_Handle bsh,

227 const string

& annot_name =

""

229 bool

ignore_errors =

false

);

236 static void

x_SetAnnotName(objects::SAnnotSelector& sel,

const string

& annot_name);

250

fDefaults = fCreateGene | fCreateMrna | fCreateCdregion

257 static void

CreateGeneModelFromAlign(

const

objects::CSeq_align& align,

258

objects::CScope& scope,

259

objects::CSeq_annot& annot,

260

objects::CBioseq_set& seqs,

262 TSeqPos

allowed_unaligned = 10);

266

objects::CScope& scope,

267

objects::CSeq_annot& annot,

268

objects::CBioseq_set& seqs,

270 TSeqPos

allowed_unaligned = 10);

275 static void

SetFeatureExceptions(objects::CSeq_feat& feat,

276

objects::CScope& scope,

277 const

objects::CSeq_align* align =

NULL

);

280 static void

SetPartialFlags(objects::CScope& scope,

286 static void

RecomputePartialFlags(objects::CScope& scope,

287

objects::CSeq_annot& annot);

User-defined methods of the data storage class.

virtual const char * GetErrCodeString(void) const override

Get error code interpreted as text.

NCBI_EXCEPTION_DEFAULT(CAlgoFeatureGeneratorException, CException)

CRef< objects::CSeq_feat > ConvertAlignToAnnot(const objects::CSeq_align &align, objects::CSeq_annot &annot, objects::CBioseq_set &seqs, Int8 gene_id=0, const objects::CSeq_feat *cdregion_on_mrna=NULL)

Convert an alignment to an annotation.

unique_ptr< SImplementation > m_impl

CFeatureGenerator(objects::CScope &scope)

EProductPositionsMode

Adjust alignment to the specified range (cross-the-origin range on circular chromosome is indicated b...

EIntronStitchThresholdFlags

void ConvertAlignToAnnot(const list< CRef< objects::CSeq_align > > &aligns, objects::CSeq_annot &annot, objects::CBioseq_set &seqs)

CFeatureGenerator(CRef< objects::CScope > scope)

int TFeatureGeneratorFlags

int TGeneModelCreateFlags

namespace ncbi::objects::

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

unsigned int TSeqPos

Type for sequence locations and lengths.

virtual const char * GetErrCodeString(void) const

Get error code interpreted as text.

int64_t Int8

8-byte (64-bit) signed integer

#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_XALGOSEQ_EXPORT

Defines NCBI C++ exception handling.

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

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