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NCBI C++ ToolKit: src/objtools/validator/validerror_annot.cpp Source File

m_GraphValidator(imp),

m_AlignValidator(imp),

& oid = iter->GetUser().GetType();

(oid.

() ==

) {

, annot);

}

(annot.

()) {

, annot);

}

(annot.

()) {

, annot);

}

(annot.

()) {

(appropriate_parent) {

= seq.

().front()->AsFastaString();

+

, *feat_it);

(

loc_it(feat_it->GetLocation()); loc_it; ++loc_it) {

&

= loc_it.GetSeq_id();

(

& id_it : seq.

()) {

loc_it.GetEmbeddingSeq_loc(),

(parent && parent.

()) {

(parent && parent.

()) {

answer =

;

* bioseq = b_ci->GetCompleteBioseq();

(

& id_it : bioseq->

()) {

(id_it->Which()) {

&

= loc_it.GetSeq_id();

, *feat_it);

}

(is_embl_or_ddbj_on_set) {

}

(!

.IsSetClass() ||

}

(feat_it->IsSetLocation() &&

found_one =

;

&

= loc_it.GetSeq_id();

(! loc_it.IsWhole() && loc_it.GetRange().GetFrom() > in_record.

() - 1) {

(! loc_it.IsWhole() && loc_it.GetRange().GetFrom() > seq_len - 1) {

(!

.IsSetLocation()) {

zero_gi = 0;

(lit.GetSeq_id().IsGi() && lit.GetSeq_id().GetGi() ==

) {

+

(zero_gi) +

+ (zero_gi > 1 ?

:

) +

+

,

User-defined methods of the data storage class.

User-defined methods of the data storage class.

@ eErr_SEQ_ANNOT_AnnotIDs

@ eErr_SEQ_FEAT_FeatureLocationIsGi0

@ eErr_SEQ_ALIGN_BlastAligns

@ eErr_SEQ_FEAT_UnindexedFeature

@ eErr_SEQ_ANNOT_AnnotLOCs

bool IsFtable(void) const

namespace ncbi::objects::

Seq-loc iterator class – iterates all intervals from a seq-loc in the correct order.

void ValidateSeqAlign(const CSeq_align &align, int order=-1)

~CValidError_annot() override

void ValidateSeqAnnot(const CSeq_annot_Handle &annot)

void ValidateSeqAnnotContext(const CSeq_annot &annot, const CBioseq &seq)

CValidError_align m_AlignValidator

bool IsLocationUnindexed(const CSeq_loc &loc)

void ReportLocationGI0(const CSeq_feat &f, const string &label)

CValidError_feat m_FeatValidator

CValidError_graph m_GraphValidator

static CSeq_entry_Handle GetAppropriateXrefParent(CSeq_entry_Handle seh)

void PostErr(EDiagSev sv, EErrType et, const string &msg, const CSerialObject &obj)

void SetScope(CScope &scope)

void SetTSE(CSeq_entry_Handle seh)

void ValidateSeqFeat(const CSeq_feat &feat)

void ValidateSeqGraph(const CSeq_graph &graph)

void ValidateSeqGraphContext(const CSeq_graph &graph, const CBioseq_set &set)

const CSeq_entry_Handle & GetTSEH()

void PostErr(EDiagSev sv, EErrType et, const string &msg, const CSerialObject &obj)

void IncrementMisplacedFeatureCount()

bool IsValidateAlignments() const

const CTSE_Handle & GetTSE_Handle()

bool IsSmallGenomeSet() const

void IncrementSmallGenomeSetMisplacedCount()

const CSeq_entry & GetTSE() const

bool ShouldSubdivide() const

CBioseq_Handle GetBioseqHandleFromLocation(CScope *scope, const CSeq_loc &loc, const CTSE_Handle &tse)

Include a standard set of the NCBI C++ Toolkit most basic headers.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

@ eDiag_Error

Error message.

@ eDiag_Critical

Critical error message.

virtual bool Equals(const CSerialObject &object, ESerialRecursionMode how=eRecursive) const

Check if both objects contain the same values.

@ e_YES

SeqIds compared, but are different.

sequence::ECompare Compare(const CSeq_loc &loc1, const CSeq_loc &loc2, CScope *scope)

Returns the sequence::ECompare containment relationship between CSeq_locs.

CBioseq_Handle GetBioseqHandleFromTSE(const CSeq_id &id, const CTSE_Handle &tse)

Get bioseq handle for sequence withing one TSE.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

CSeq_entry_Handle AddTopLevelSeqEntry(CSeq_entry &top_entry, TPriority pri=kPriority_Default, EExist action=eExist_Default)

Add seq_entry, default priority is higher than for defaults or loaders Add object to the score with p...

TSeqPos GetSequenceLength(const CSeq_id &id, TGetFlags flags=0)

Get sequence length Return kInvalidSeqPos if sequence is not found.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

void AddDefaults(TPriority pri=kPriority_Default)

Add default data loaders from object manager.

CBioseq_set_Handle GetBioseq_setHandle(const CBioseq_set &seqset, EMissing action=eMissing_Default)

CSeq_annot_Handle GetSeq_annotHandle(const CSeq_annot &annot, EMissing action=eMissing_Default)

@ fDoNotRecalculate

avoid time-consuming recalculation of missing data

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

TClass GetClass(void) const

CBioseq_set_Handle GetParentBioseq_set(void) const

Return a handle for the parent Bioseq-set, or null handle.

CSeq_entry_Handle GetParentEntry(void) const

Get parent Seq-entry handle.

TSeqPos GetBioseqLength(void) const

CConstRef< CSeq_annot > GetCompleteSeq_annot(void) const

Complete and return const reference to the current seq-annot.

CConstRef< CBioseq_set > GetCompleteBioseq_set(void) const

Return the complete bioseq-set object.

CBioseq_set_Handle GetParentBioseq_set(void) const

Return a handle for the parent Bioseq-set, or null handle.

CSeq_entry_Handle GetParentEntry(void) const

Get parent Seq-entry handle.

CConstRef< CSeq_entry > GetCompleteSeq_entry(void) const

Complete and get const reference to the seq-entry.

CSeq_entry_Handle GetParentEntry(void) const

Get parent Seq-entry handle.

TObjectType * GetPointer(void) const THROWS_NONE

Get pointer,.

#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.

static string UIntToString(unsigned int value, TNumToStringFlags flags=0, int base=10)

Convert UInt to string.

static const char label[]

bool IsStr(void) const

Check if variant Str is selected.

const TStr & GetStr(void) const

Get the variant data.

@ e_Tpe

Third Party Annot/Seq EMBL.

@ e_Tpd

Third Party Annot/Seq DDBJ.

@ eClass_parts

parts for 2 or 3

@ eClass_nuc_prot

nuc acid and coded proteins

@ eClass_gen_prod_set

genomic products, chrom+mRNA+protein

@ eClass_segset

segmented sequence + parts

TRepr GetRepr(void) const

Get the Repr member data.

const Tdata & Get(void) const

Get the member data.

const TGraph & GetGraph(void) const

Get the variant data.

const TInst & GetInst(void) const

Get the Inst member data.

const TId & GetId(void) const

Get the Id member data.

const TDesc & GetDesc(void) const

Get the Desc member data.

bool IsSetDesc(void) const

used only for stand alone Seq-annots Check if a value has been assigned to Desc data member.

const TAlign & GetAlign(void) const

Get the variant data.

const TFtable & GetFtable(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

bool IsSetId(void) const

equivalent identifiers Check if a value has been assigned to Id data member.

@ eRepr_seg

segmented sequence

@ eRepr_raw

continuous sequence

bool s_IsBioseqInSet(CBioseq_Handle bsh, const CBioseq_set &set)

bool s_HasOneIntervalInSet(const CSeq_loc &loc, const CBioseq_set &set, CScope &scope, const CSeq_entry &tse)

static bool x_IsEmblOrDdbjOnSet(const CBioseq_set_Handle &set)

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