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 &)

CDeflineGenerator &	operator= (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_feat >	x_GetLongestProtein (const CBioseq_Handle &bsh)

CConstRef< CGene_ref >	x_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< CSeqEntryIndex >	m_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< CBioSource >	m_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< CLowQualityTextFsm >	ms_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:

include/objmgr/util/create_defline.hpp
src/objmgr/util/create_defline.cpp

Classes

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Static Private Attributes

Detailed Description