eClean_NoReporting = 0x1,
74eClean_GpipeMode = 0x2,
75eClean_NoNcbiUserObjects = 0x4,
76eClean_SyncGenCodes = 0x8,
77eClean_NoProteinTitles = 0x10,
78eClean_KeepTopSet = 0x20,
79eClean_KeepSingleSeqSet = 0x40,
80eClean_InHugeSeqSet = 0x80,
81eClean_FlatfileGenerator = 0x100,
82eClean_FlatfileHTMLMode = 0x200,
91 CCleanup(
CScope* scope =
nullptr, EScopeOptions scope_handling = eScope_Copy);
97 voidSetScope(
CScope* scope);
140 static boolShouldStripPubSerial(
const CBioseq& bs);
177 static boolRemoveNonsuppressingGeneXrefs(
CSeq_feat&
f);
259 static boolExtendStopPosition(
CSeq_feat&
f,
const CSeq_feat* cdregion,
size_textension = 0);
285 static boolSetCDSPartialsByFrameAndTranslation(
CSeq_feat& cds,
CScope& scope);
289 static boolClearInternalPartials(
CSeq_loc& loc,
boolis_first =
true,
boolis_last =
true);
290 static boolClearInternalPartials(
CSeq_loc_mix& mix,
boolis_first =
true,
boolis_last =
true);
291 static boolClearInternalPartials(
CPacked_seqint& pint,
boolis_first =
true,
boolis_last =
true);
295 static boolSetFeaturePartial(
CSeq_feat&
f);
316 static boolSetGenePartialByLongestContainedFeature(
CSeq_feat& gene,
CScope& scope);
319 static voidSetProteinName(
CSeq_feat& cds,
const string& protein_name,
bool append,
CScope& scope);
320 static voidSetMrnaName(
CSeq_feat& mrna,
const string& protein_name);
340 static boolAddMissingMolInfo(
CBioseq& seq,
boolis_product);
349 static boolRemoveNcbiCleanupObject(
CSeq_descr& descr);
354 static boolRemoveNcbiCleanupObject(
CSeq_entry&seq_entry);
357 static voidAddNcbiCleanupObject(
intncbi_cleanup_version,
CSeq_descr& descr);
392 static boolWGSCleanup(
CSeq_entry_Handleentry,
boolinstantiate_missing_proteins =
true,
Uint4options = 0,
393 boolrun_extended_cleanup =
true,
boolalso_fix_location =
true);
405 static boolNormalizeDescriptorOrder(
CSeq_descr& descr);
434vector<TEntrezId>& pmids, vector<TEntrezId>& muids, vector<int>& serials,
435vector<string>& published_labels, vector<string>& unpublished_labels);
442 staticvector<CConstRef<CPub> > GetCitationList(
CBioseq_Handlebsh);
445 static boolRemoveDuplicatePubs(
CSeq_descr& descr);
448 static boolOkToPromoteNpPub(
const CPubdesc& pd);
451 static boolOkToPromoteNpPub(
const CBioseq&
b);
466 static boolIsMinPub(
const CPubdesc& pd,
boolis_refseq_prot);
472 static boolRemoveDupBioSource(
CSeq_descr& descr);
478 static boolMergeDupBioSources(
CSeq_descr& descr);
524 static boolParseCodeBreak(
const CSeq_feat& feat,
572 static boolFixRNAEditingCodingRegion(
CSeq_feat& cds);
597 staticvector<TFeatGenePair> GetNormalizableGeneQualPairs(
CBioseq_Handlebsh);
604 static boolCleanupAuthor(
CAuthor& author,
boolfix_initials =
true);
605 static boolCleanupAuthList(
CAuth_list& al,
boolfix_initials =
true);
607 static boolCleanupAffil(
CAffil& af);
616 static charValidAminoAcid(string_view abbrev);
621 static boolx_CleanupUserField(
CUser_field& field);
626 static boolx_HasShortIntron(
const CSeq_loc& loc,
size_tmin_len = 11);
627 static boolx_AddLowQualityException(
CSeq_feat& feat);
630 static bools_IsProductOnFeat(
const CSeq_feat& cds);
631 static voids_SetProductOnFeat(
CSeq_feat& feat,
const string& protein_name,
bool append);
634 static bools_CleanupStructuredComment(
CUser_object& obj);
636 static bools_CleanupGenomeAssembly(
CUser_object& obj);
638 static bools_AddNumToUserField(
CUser_field&field);
640 static bools_CleanupNameStdBC(
CName_std& name,
boolfix_initials);
641 static voids_ExtractSuffixFromInitials(
CName_std& name);
642 static voids_FixEtAl(
CName_std& name);
User-defined methods of the data storage class.
static CRef< CSeq_loc > ExtendToStopCodon(CRef< CSeq_feat > feat, CScope *scope)
@Affil.hpp User-defined methods of the data storage class.
@Auth_list.hpp User-defined methods of the data storage class.
CBioseq_set_EditHandle â.
CCleanup(const CCleanup &)=delete
static bool s_Flatten(CPub_equiv &pub_equiv)
pair< CSeq_feat_Handle, CSeq_feat_Handle > TFeatGenePair
CCleanup & operator=(const CCleanup &)=delete
@Name_std.hpp User-defined methods of the data storage class.
@Pubdesc.hpp User-defined methods of the data storage class.
@Seq_descr.hpp User-defined methods of the data storage class.
namespace ncbi::objects::
CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...
static const struct name_t names[]
static void DLIST_NAME() append(DLIST_LIST_TYPE *list, DLIST_TYPE *item)
static const char * str(char *buf, int n)
string GetProteinName(const CBioseq_Handle &seq)
Return protein name from corresponding Prot-ref feature.
uint32_t Uint4
4-byte (32-bit) unsigned integer
#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_CLEANUP_EXPORT
EMol
molecule class in living organism
@ eMol_not_set
> cdna = rna
where boath are integers</td > n< td ></td > n</tr > n< tr > n< td > tse</td > n< td > optional</td > n< td > String</td > n< td class=\"description\"> TSE option controls what blob is orig
CRef< CSeq_loc > SeqLocExtend(const CSeq_loc &loc, size_t pos, CScope *scope)
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