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CDeflineGenerator Class Reference

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

#include <objmgr/util/create_defline.hpp>

+ Collaboration diagram for CDeflineGenerator:


class  CLowQualityTextFsm
 exception fields More...

Public Types

enum  EUserFlags {
  fIgnoreExisting = 1 << 0 , fAllProteinNames = 1 << 1 , fLocalAnnotsOnly = 1 << 2 , fNoExpensiveOps = fLocalAnnotsOnly ,
  fGpipeMode = 1 << 3 , fOmitTaxonomicName = 1 << 4 , fDevMode = 1 << 5 , fShowModifiers = 1 << 6 ,
  fUseAutoDef = 1 << 7 , fFastaFormat = 1 << 8 , fDoNotUseAutoDef = 1 << 9
 User-settable flags for tuning behavior. More...
typedef int TUserFlags
 Binary "OR" of EUserFlags. More...

Public Member Functions

 CDeflineGenerator (void)
 Constructor. More...
 CDeflineGenerator (const CSeq_entry_Handle &tseh)
 Constructor. More...
 ~CDeflineGenerator (void)
 Destructor. More...
string GenerateDefline (const CBioseq_Handle &bsh, TUserFlags flags=0)
 Main method. More...
string GenerateDefline (const CBioseq_Handle &bsh, CSeqEntryIndex &idx, TUserFlags flags=0)
 Main method. More...
string GenerateDefline (const CBioseq &bioseq, CScope &scope, CSeqEntryIndex &idx, TUserFlags flags=0)
 Main method. More...
string GenerateDefline (const CBioseq_Handle &bsh, feature::CFeatTree &ftree, TUserFlags flags=0)
 Main method. More...
string GenerateDefline (const CBioseq &bioseq, CScope &scope, TUserFlags flags=0)
 Main method. More...
string GenerateDefline (const CBioseq &bioseq, CScope &scope, feature::CFeatTree &ftree, TUserFlags flags=0)
 Main method. More...
string x_GetModifiers (const CBioseq_Handle &handle)
bool UsePDBCompoundForDefline (void) const

Private Member Functions

 CDeflineGenerator (const CDeflineGenerator &)
CDeflineGeneratoroperator= (const CDeflineGenerator &)
void x_Init (void)
 internal methods More...
void x_SetFlags (const CBioseq_Handle &bsh, TUserFlags flags)
void x_SetFlagsIdx (const CBioseq_Handle &bsh, TUserFlags flags)
void x_SetBioSrc (const CBioseq_Handle &bsh)
void x_SetBioSrcIdx (const CBioseq_Handle &bsh)
const char * x_OrganelleName (CBioSource::TGenome genome) const
bool x_CDShasLowQualityException (const CSeq_feat &sft)
void x_DescribeClones (vector< CTempString > &desc, string &buf)
CConstRef< CSeq_featx_GetLongestProtein (const CBioseq_Handle &bsh)
CConstRef< CGene_refx_GetGeneRefViaCDS (const CMappedFeat &mapped_cds)
void x_SetTitleFromBioSrc (void)
void x_SetTitleFromNC (void)
void x_SetTitleFromNM (const CBioseq_Handle &bsh)
void x_SetTitleFromNR (const CBioseq_Handle &bsh)
void x_SetTitleFromPatent (void)
void x_SetTitleFromPDB (void)
void x_SetTitleFromGPipe (void)
void x_SetTitleFromProtein (const CBioseq_Handle &bsh)
void x_SetTitleFromProteinIdx (const CBioseq_Handle &bsh)
void x_SetTitleFromSegSeq (const CBioseq_Handle &bsh)
void x_SetTitleFromWGS (void)
void x_SetTitleFromMap (void)
void x_SetPrefix (string &prefix, const CBioseq_Handle &bsh)
void x_SetSuffix (string &suffix, const CBioseq_Handle &bsh, bool appendComplete)
void x_AdjustProteinTitleSuffix (const CBioseq_Handle &bsh)
void x_AdjustProteinTitleSuffixIdx (const CBioseq_Handle &bsh)
bool x_IsComplete () const

Private Attributes

CRef< CSeqEntryIndexm_Idx
 index with feature tree for each Bioseq More...
CSeq_entry_Handle m_TopSEH
 internal feature tree for parent mapping More...
CRef< feature::CFeatTree > m_Feat_Tree
bool m_ConstructedFeatTree
bool m_InitializedFeatTree
bool m_Reconstruct
 ignore existing title is forced for certain types More...
bool m_AllProtNames
bool m_LocalAnnotsOnly
bool m_GpipeMode
bool m_OmitTaxonomicName
bool m_DevMode
bool m_IsNA
 seq-inst fields More...
bool m_IsAA
CSeq_inst::TTopology m_Topology
CSeq_inst::TLength m_Length
bool m_IsSeg
bool m_IsDelta
bool m_IsVirtual
bool m_IsMap
bool m_IsNC
 seq-id fields More...
bool m_IsNM
bool m_IsNR
bool m_IsNZ
bool m_IsPatent
bool m_IsPDB
bool m_IsWP
bool m_ThirdParty
bool m_WGSMaster
bool m_TSAMaster
bool m_TLSMaster
string m_MainTitle
string m_GeneralStr
int m_GeneralId
string m_PatentCountry
string m_PatentNumber
int m_PatentSequence
int m_PDBChain
string m_PDBChainID
CMolInfo::TBiomol m_MIBiomol
 molinfo fields More...
CMolInfo::TTech m_MITech
CMolInfo::TCompleteness m_MICompleteness
bool m_HTGTech
bool m_HTGSUnfinished
bool m_IsTLS
bool m_IsTSA
bool m_IsWGS
bool m_IsEST_STS_GSS
bool m_UseBiosrc
bool m_HTGSCancelled
 genbank or embl block keyword fields More...
bool m_HTGSDraft
bool m_HTGSPooled
bool m_TPAExp
bool m_TPAInf
bool m_TPAReasm
bool m_Unordered
CTempString m_PDBCompound
 pdb block fields More...
CConstRef< CBioSourcem_Source
 biosource fields More...
CTempString m_Taxname
CTempString m_Genus
CTempString m_Species
bool m_Multispecies
CBioSource::TGenome m_Genome
bool m_IsPlasmid
bool m_IsChromosome
CTempString m_Organelle
string m_FirstSuperKingdom
string m_SecondSuperKingdom
bool m_IsCrossKingdom
CTempString m_Chromosome
 subsource fields More...
CTempString m_LinkageGroup
CTempString m_Clone
bool m_has_clone
CTempString m_Map
CTempString m_Plasmid
CTempString m_Segment
CTempString m_Breed
 orgmod fields More...
CTempString m_Cultivar
CTempString m_SpecimenVoucher
CTempString m_Isolate
CTempString m_Strain
CTempString m_Substrain
CTempString m_MetaGenomeSource
bool m_IsUnverified
 user object fields More...
CTempString m_UnverifiedPrefix
bool m_IsUnreviewed
CTempString m_UnreviewedPrefix
CTempString m_TargetedLocus
CTempString m_Comment
 comment fields More...
bool m_IsPseudogene
string m_rEnzyme
 map fields More...
bool m_UsePDBCompoundForDefline
bool m_FastaFormat

Static Private Attributes

static CSafeStatic< CLowQualityTextFsmms_p_Low_Quality_Fsa

Detailed Description

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


CDeflineGenerator gen(tseh);

const string& title = gen.GenerateDefline(bsh, flags);

Same CDeflineGenerator should be used for all titles within nuc-prot set blob, since it tracks presence or absence of biosource features to speed up protein title generation

Definition at line 70 of file create_defline.hpp.

The documentation for this class was generated from the following files:
Modified on Sun Apr 14 05:24:36 2024 by rev. 669887