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NCBI C++ ToolKit: src/objmgr/split/blob_splitter_parser.cpp Source File

&

(c);

( src.

() ) {

( src.

() ) {

);

( src.

() ) {

);

need_split_descr;

need_split_descr =

;

need_split_inst;

need_split_inst =

;

need_split_inst =

;

need_split_inst =

;

need_split_inst =

;

need_split_inst =

;

need_split_inst =

;

need_split_inst =

;

need_split_annot;

need_split_annot =

;

need_split_annot = !src.

().empty();

need_split = need_split_descr || need_split_inst || need_split_annot;

(2,

);

(

->m_PlaceId.IsBioseq() ) {

(3,

<<

->m_PlaceId = place_id;

->m_Bioseq.Reset(&dst);

need_split_descr = need_split_inst = need_split_annot =

;

( need_split_descr ) {

( need_split_inst ) {

( need_split_annot ) {

dst.

().SetId(

);

need_split_annot;

need_split_annot =

;

need_split_annot = !src.

().empty();

need_split_bioseq =

;

need_split_bioseq =

;

need_split =need_split_descr || need_split_annot || need_split_bioseq;

(4,

);

(

->m_PlaceId.IsBioseq_set() ) {

(5,

<<

->m_PlaceId = place_id;

->m_Bioseq_set.Reset(&dst);

need_split_descr = need_split_annot = need_split_bioseq = 0;

( need_split_descr ) {

( need_split_annot ) {

begin = seq_set.begin();

end = seq_set.end();

( need_split_bioseq ) {

old_size =

->m_Bioseqs.size();

( begin != end ) {

it =

(end);

reverse(

->m_Bioseqs.begin()+old_size,

->m_Bioseqs.end());

( begin != end ) {

(

->IsSeq() ) {

( *it !=

&& (*it)->IsSeq() ) {

.m_Seq_inst.Reset(&src);

range.

(0).SetLength(seq_length);

( src_seq.

() ) {

( src_data.

() ) {

range.

(pos).SetLength(length);

dst_delta.

().push_back(new_seq);

(

.m_Size.GetAsnSize() > 1024 ) {

seq.

().size() <= 4;

same_id =

;

(

->Equals(**j) ) {

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

static CSafeStatic< CSize > small_annot

static CSafeStatic< CAsnSizer > s_Sizer

NCBI_DEFINE_ERR_SUBCODE_X(12)

CRef< CMasterSeqSegments > m_Master

static size_t CountAnnotObjects(const CSeq_annot &annot)

bool CopyHist(CPlace_SplitInfo &place_info, const CSeq_hist &hist)

bool CopyAnnot(CPlace_SplitInfo &place_info, const CSeq_annot &annot)

TSeqPos GetLength(const CSeq_data &src) const

bool CopySequence(CPlace_SplitInfo &place_info, TSeqPos seq_length, CSeq_inst &dst, const CSeq_inst &src)

bool CopyDescr(CPlace_SplitInfo &place_info, TSeqPos seq_length, const CSeq_descr &descr)

CRef< CSeq_entry > m_Skeleton

bool CanSplitBioseq(const CBioseq &bioseq) const

bool SplitBioseq(CPlace_SplitInfo &place_info, const CBioseq &bioseq)

void CopySkeleton(CSeq_entry &dst, const CSeq_entry &src)

void AddSegments(const CSeqMap &seq)

void AddSegmentIds(int idx, const TIds &ids)

bool IsBioseq_set(void) const

bool IsBioseq(void) const

TBioseq_setId GetBioseq_setId(void) const

const TBioseqId & GetBioseqId(void) const

CRef< CSeq_inst_SplitInfo > m_Inst

CRef< CSeq_descr_SplitInfo > m_Descr

CRef< CSeq_hist_SplitInfo > m_Hist

CRef< CBioseq_set > m_Bioseq_set

static bool IsGoodFeatTable(const CSeq_table &table)

static size_t CountAnnotObjects(const CSeq_annot &annot)

TAnnotPriority m_Priority

@Seq_descr.hpp User-defined methods of the data storage class.

TSeqPos GetLength(void) const

TDataSize GetZipSize(void) const

Template class for iteration on objects of class C (non-medifiable version)

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

static DLIST_TYPE *DLIST_NAME() prev(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

#define REVERSE_ITERATE(Type, Var, Cont)

ITERATE macro to reverse sequence through container elements.

#define ERR_POST_X(err_subcode, message)

Error posting with default error code and given error subcode.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

const string & GetMsg(void) const

Get message string.

const TPrim & Get(void) const

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

string AsString(void) const

bool IsBetter(const CSeq_id_Handle &h) const

True if "this" is a better bioseq than "h".

CConstBeginInfo ConstBegin(const C &obj)

Get starting point of non-modifiable object hierarchy.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

const CSeqMap & GetSeqMap(void) const

Get sequence map.

CConstRef< C > ConstRef(const C *object)

Template function for conversion of const object pointer to CConstRef.

CRef< C > Ref(C *object)

Helper functions to get CRef<> and CConstRef<> objects.

void Reset(void)

Reset reference object.

#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.

void SetFrom(TFrom value)

Assign a value to From data member.

bool IsId(void) const

Check if variant Id is selected.

TId GetId(void) const

Get the variant data.

const TInt & GetInt(void) const

Get the variant data.

const TSeq & GetSeq(void) const

Get the variant data.

bool IsSetClass(void) const

Check if a value has been assigned to Class data member.

void SetRelease(const TRelease &value)

Assign a value to Release data member.

const TDescr & GetDescr(void) const

Get the Descr member data.

TSet & SetSet(void)

Select the variant.

bool IsSetColl(void) const

to identify a collection Check if a value has been assigned to Coll data member.

TClass GetClass(void) const

Get the Class member data.

bool IsSetDate(void) const

Check if a value has been assigned to Date data member.

bool IsSetRelease(void) const

Check if a value has been assigned to Release data member.

TAnnot & SetAnnot(void)

Assign a value to Annot data member.

const TSet & GetSet(void) const

Get the variant data.

bool IsSeq(void) const

Check if variant Seq is selected.

void SetId(TId &value)

Assign a value to Id data member.

bool IsSetId(void) const

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

void SetLevel(TLevel value)

Assign a value to Level data member.

const TRelease & GetRelease(void) const

Get the Release member data.

bool IsSetLevel(void) const

nesting level Check if a value has been assigned to Level data member.

bool IsSetDescr(void) const

Check if a value has been assigned to Descr data member.

E_Choice Which(void) const

Which variant is currently selected.

const TDate & GetDate(void) const

Get the Date member data.

list< CRef< CSeq_annot > > TAnnot

void SetDate(TDate &value)

Assign a value to Date data member.

const TSeq_set & GetSeq_set(void) const

Get the Seq_set member data.

void SetClass(TClass value)

Assign a value to Class data member.

const TAnnot & GetAnnot(void) const

Get the Annot member data.

void SetColl(TColl &value)

Assign a value to Coll data member.

void SetDescr(TDescr &value)

Assign a value to Descr data member.

const TColl & GetColl(void) const

Get the Coll member data.

virtual void Reset(void)

Reset the whole object.

list< CRef< CSeq_entry > > TSeq_set

TSeq & SetSeq(void)

Select the variant.

TSeq_set & SetSeq_set(void)

Assign a value to Seq_set data member.

const TId & GetId(void) const

Get the Id member data.

TLevel GetLevel(void) const

Get the Level member data.

@ eClass_segset

segmented sequence + parts

const TIupacaa & GetIupacaa(void) const

Get the variant data.

TRepr GetRepr(void) const

Get the Repr member data.

void SetLength(TLength value)

Assign a value to Length data member.

bool IsSetDeleted(void) const

Check if a value has been assigned to Deleted data member.

TId & SetId(void)

Assign a value to Id data member.

bool IsSetReplaced_by(void) const

these seqs make this one obsolete Check if a value has been assigned to Replaced_by data member.

bool IsSetSeq_data(void) const

the sequence Check if a value has been assigned to Seq_data data member.

TStrand GetStrand(void) const

Get the Strand member data.

const TInst & GetInst(void) const

Get the Inst member data.

void SetSeq_data(TSeq_data &value)

Assign a value to Seq_data data member.

bool IsSetAssembly(void) const

how was this assembled? Check if a value has been assigned to Assembly data member.

const TDeleted & GetDeleted(void) const

Get the Deleted member data.

TTopology GetTopology(void) const

Get the Topology member data.

const TIupacna & GetIupacna(void) const

Get the variant data.

void SetExt(TExt &value)

Assign a value to Ext data member.

void SetHist(THist &value)

Assign a value to Hist data member.

const TFuzz & GetFuzz(void) const

Get the Fuzz member data.

bool IsSetStrand(void) const

Check if a value has been assigned to Strand data member.

const TNcbi8aa & GetNcbi8aa(void) const

Get the variant data.

const TLiteral & GetLiteral(void) const

Get the variant data.

TAnnot & SetAnnot(void)

Assign a value to Annot data member.

const TAnnot & GetAnnot(void) const

Get the Annot member data.

const TId & GetId(void) const

Get the Id member data.

bool IsSetHist(void) const

sequence history Check if a value has been assigned to Hist data member.

bool IsSetExt(void) const

extensions for special types Check if a value has been assigned to Ext data member.

const Tdata & Get(void) const

Get the member data.

bool IsSetReplaces(void) const

seq makes these seqs obsolete Check if a value has been assigned to Replaces data member.

Tdata & Set(void)

Assign a value to data member.

TLength GetLength(void) const

Get the Length member data.

TLength GetLength(void) const

Get the Length member data.

list< CRef< CSeq_id > > TId

const TFuzz & GetFuzz(void) const

Get the Fuzz member data.

TMol GetMol(void) const

Get the Mol member data.

const TNcbieaa & GetNcbieaa(void) const

Get the variant data.

bool IsSetFuzz(void) const

could be unsure Check if a value has been assigned to Fuzz data member.

void SetFuzz(TFuzz &value)

Assign a value to Fuzz data member.

void SetInst(TInst &value)

Assign a value to Inst data member.

bool IsSetLength(void) const

length of sequence in residues Check if a value has been assigned to Length data member.

const THist & GetHist(void) const

Get the Hist member data.

virtual void Reset(void)

Reset the whole object.

const TExt & GetExt(void) const

Get the Ext member data.

E_Choice Which(void) const

Which variant is currently selected.

bool IsSetDescr(void) const

descriptors Check if a value has been assigned to Descr data member.

void SetTopology(TTopology value)

Assign a value to Topology data member.

const TSeq_table & GetSeq_table(void) const

Get the variant data.

void SetDescr(TDescr &value)

Assign a value to Descr data member.

E_Choice Which(void) const

Which variant is currently selected.

const TDelta & GetDelta(void) const

Get the variant data.

const TNcbi4na & GetNcbi4na(void) const

Get the variant data.

const TLoc & GetLoc(void) const

Get the variant data.

void SetRepr(TRepr value)

Assign a value to Repr data member.

const TNcbi2na & GetNcbi2na(void) const

Get the variant data.

const Tdata & Get(void) const

Get the member data.

const TData & GetData(void) const

Get the Data member data.

void SetFuzz(TFuzz &value)

Assign a value to Fuzz data member.

list< CRef< CSeq_annot > > TAnnot

bool IsSetSeq_data(void) const

may have the data Check if a value has been assigned to Seq_data data member.

void SetLength(TLength value)

Assign a value to Length data member.

list< CRef< CDelta_seq > > Tdata

const TReplaces & GetReplaces(void) const

Get the Replaces member data.

void SetStrand(TStrand value)

Assign a value to Strand data member.

bool IsGap(void) const

Check if variant Gap is selected.

const TSeq_data & GetSeq_data(void) const

Get the Seq_data member data.

const TReplaced_by & GetReplaced_by(void) const

Get the Replaced_by member data.

const TNcbi8na & GetNcbi8na(void) const

Get the variant data.

const TDescr & GetDescr(void) const

Get the Descr member data.

const TSeq_data & GetSeq_data(void) const

Get the Seq_data member data.

E_Choice Which(void) const

Which variant is currently selected.

void SetMol(TMol value)

Assign a value to Mol data member.

bool IsSetTopology(void) const

Check if a value has been assigned to Topology data member.

bool IsSetFuzz(void) const

length uncertainty Check if a value has been assigned to Fuzz data member.

E_Choice Which(void) const

Which variant is currently selected.

@ e_Ncbieaa

extended ASCII 1 letter aa codes

@ e_Ncbi2na

2 bit nucleic acid code

@ e_Iupacna

IUPAC 1 letter nuc acid code.

@ e_Ncbi8na

8 bit extended nucleic acid code

@ e_Ncbi4na

4 bit nucleic acid code

@ e_Iupacaa

IUPAC 1 letter amino acid code.

@ e_Ncbi8aa

8 bit extended amino acid codes

@ e_Literal

a piece of sequence

@ e_Loc

point to a sequence

Definition of all error codes used in objmgr libraries (xobjmgr.lib, xobjutil.lib and others).

const struct ncbi::grid::netcache::search::fields::SIZE size

@ eAnnotPriority_skeleton

bool m_DisableSplitDescriptions

bool m_DisableSplitAssembly

bool m_DisableSplitSequence

bool m_DisableSplitAnnotations

bool m_SplitNonFeatureSeqTables

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