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CDeflineGenerator Class Reference

Search Toolkit Book for CDeflineGenerator

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

#include <objmgr/util/create_defline.hpp>

+ Collaboration diagram for CDeflineGenerator:

Classes

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").

PREFERRED USAGE:

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 modify_doxy.py rev. 669887