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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/create__defline_8hpp_source.html below:

NCBI C++ ToolKit: include/objmgr/util/create_defline.hpp Source File

1 #ifndef OBJMGR_UTIL___CREATE_DEFLINE__HPP 2 #define OBJMGR_UTIL___CREATE_DEFLINE__HPP 84

fIgnoreExisting = 1 << 0,

85

fAllProteinNames = 1 << 1,

86

fLocalAnnotsOnly = 1 << 2,

88 

fNoExpensiveOps = fLocalAnnotsOnly,

90

fOmitTaxonomicName = 1 << 4,

92

fShowModifiers = 1 << 6,

94

fFastaFormat = 1 << 8,

95

fDoNotUseAutoDef = 1 << 9,

96

fLeavePrefixSuffix = 1 << 10

101  string

GenerateDefline (

107  string

GenerateDefline (

114  string

GenerateDefline (

122  string

GenerateDefline (

124

feature::CFeatTree& ftree,

129  string

GenerateDefline (

136  string

GenerateDefline (

139

feature::CFeatTree& ftree,

156  void

x_Init (

void

);

169  void

x_SetBioSrcIdx (

177  bool

x_CDShasLowQualityException (

181  void

x_DescribeClones (

182

vector<CTempString>& desc,

192  void

x_SetTitleFromBioSrc (

void

);

193  void

x_SetTitleFromNC (

void

);

194  void

x_SetTitleFromNM (

197  void

x_SetTitleFromNR (

200  void

x_SetTitleFromPatent (

void

);

201  void

x_SetTitleFromPDB (

void

);

202  void

x_SetTitleFromGPipe (

void

);

203  void

x_SetTitleFromProtein (

206  void

x_SetTitleFromProteinIdx (

209  void

x_SetTitleFromSegSeq (

212  void

x_SetTitleFromWGS (

void

);

213  void

x_SetTitleFromMap (

void

);

225  void

x_AdjustProteinTitleSuffix (

228  void

x_AdjustProteinTitleSuffixIdx (

232  bool

x_IsComplete()

const

;

Class for computing sequences' titles ("definitions").

namespace ncbi::objects::

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

CRef< feature::CFeatTree > m_Feat_Tree

CTempString m_Chromosome

subsource fields

CTempString m_SpecimenVoucher

bool m_Reconstruct

ignore existing title is forced for certain types

int TUserFlags

Binary "OR" of EUserFlags.

CTempString m_PDBCompound

pdb block fields

bool m_HTGSCancelled

genbank or embl block keyword fields

CTempString m_UnreviewedPrefix

bool m_ConstructedFeatTree

string m_FirstSuperKingdom

CTempString m_LinkageGroup

bool m_UsePDBCompoundForDefline

bool m_IsNA

seq-inst fields

CSeq_inst::TLength m_Length

string m_rEnzyme

map fields

CTempString m_UnverifiedPrefix

bool m_InitializedFeatTree

CBioSource::TGenome m_Genome

CTempString m_Comment

comment fields

bool m_IsNC

seq-id fields

CConstRef< CBioSource > m_Source

biosource fields

CTempString m_TargetedLocus

bool UsePDBCompoundForDefline(void) const

static CSafeStatic< CLowQualityTextFsm > ms_p_Low_Quality_Fsa

bool m_IsUnverified

user object fields

CSeq_entry_Handle m_TopSEH

internal feature tree for parent mapping

CMolInfo::TCompleteness m_MICompleteness

string m_SecondSuperKingdom

CDeflineGenerator(const CDeflineGenerator &)

CTempString m_Breed

orgmod fields

CRef< CSeqEntryIndex > m_Idx

index with feature tree for each Bioseq

CTempString m_MetaGenomeSource

CSeq_inst::TTopology m_Topology

EUserFlags

User-settable flags for tuning behavior.

CMolInfo::TBiomol m_MIBiomol

molinfo fields

#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_XOBJUTIL_EXPORT

ETopology

topology of molecule

static const char * x_OrganelleName(TBIOSOURCE_GENOME genome, bool has_plasmid, bool virus_or_phage, bool wgs_suffix)

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