NCBI C++ ToolKit
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Search Toolkit Book for CDeflineGenerator
Class for computing sequences' titles ("definitions"). More...
#include <objmgr/util/create_defline.hpp>
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 |
Static Private Attributes | |
static CSafeStatic< CLowQualityTextFsm > | ms_p_Low_Quality_Fsa |
Class for computing sequences' titles ("definitions").
PREFERRED USAGE:
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.