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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/annot__object_8cpp_source.html below:

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

: m_Seq_annot_Info(&annot),

TFtable::iterator iter)

: m_Seq_annot_Info(&annot),

m_ObjectIndex(index),

.m_Feat.Construct();

TAlign::iterator iter)

: m_Seq_annot_Info(&annot),

m_ObjectIndex(index),

.m_Align.Construct();

TGraph::iterator iter)

: m_Seq_annot_Info(&annot),

m_ObjectIndex(index),

.m_Graph.Construct();

TLocs::iterator iter)

: m_Seq_annot_Info(&annot),

m_ObjectIndex(index),

.m_Locs.Construct();

: m_Seq_annot_Info(&annot),

m_ObjectIndex(index),

.m_Feat.Construct();

*

.m_Feat = cont.insert(cont.end(),

: m_Seq_annot_Info(&annot),

m_ObjectIndex(index),

.m_Align.Construct();

*

.m_Align = cont.insert(cont.end(),

: m_Seq_annot_Info(&annot),

m_ObjectIndex(index),

.m_Graph.Construct();

*

.m_Graph = cont.insert(cont.end(),

: m_Seq_annot_Info(&annot),

m_ObjectIndex(index),

.m_Locs.Construct();

*

.m_Locs = cont.insert(cont.end(),

: m_Seq_annot_Info(0),

m_ObjectIndex(eChunkStub),

.m_Chunk = &chunk_info;

: m_Seq_annot_Info(

.m_Seq_annot_Info),

m_ObjectIndex(

.m_ObjectIndex),

m_Type(

.m_Type)

(

.IsRegular() ) {

(

.IsFeat() ) {

.m_Feat.Construct();

(

.IsAlign() ) {

.m_Align.Construct();

(

.IsGraph() ) {

.m_Graph.Construct();

(

.IsLocs() ) {

.m_Locs.Construct();

(

!= &

) {

(

.IsRegular() ) {

(

.IsFeat() ) {

.m_Feat.Construct();

(

.IsAlign() ) {

.m_Align.Construct();

(

.IsGraph() ) {

.m_Graph.Construct();

(

.IsLocs() ) {

.m_Locs.Construct();

.m_Feat.Destruct();

.m_Align.Destruct();

.m_Graph.Destruct();

.m_Locs.Destruct();

(

() ) {

(

() ) {

( (*desc_it)->IsRegion() ) {

region.

(&(*desc_it)->GetRegion());

hrmaps[0].SetMasterSeq(master);

hrmaps[0].AddLocation(*region);

hrmaps[0].SetMasterSeq(master);

hrmaps[1].SetMasterSeq(master);

hrmaps[0].SetMasterSeq(master);

hrmaps[0].AddLocation(graph.

());

( !(*desc_it)->IsUser() ) {

(

==

) {

(

==

) {

(

==

) {

( obj.

().size() == 0 ) {

dim = diag.

();

(dim != (

)diag.

().size()) {

dim =

(dim, (

)diag.

().size());

(dim != (

)diag.

().size()) {

&& dim != (

)diag.

().size()) {

((

)hrmaps.size() < dim) {

( (*it)->IsSetStrands() ) {

strand = (*it)->GetStrands()[

];

hrmaps[

].SetMasterSeq(master);

hrmaps[

].AddRange(

, from, to, strand);

dim = size_t(denseg.GetDim());

numseg = size_t(denseg.GetNumseg());

(numseg != denseg.GetLens().size()) {

numseg =

(numseg, denseg.GetLens().size());

(dim != denseg.GetIds().size()) {

dim =

(dim, denseg.GetIds().size());

(dim*numseg != denseg.GetStarts().size()) {

dim =

(dim*numseg, denseg.GetStarts().size()) / numseg;

(denseg.IsSetStrands()

&& dim*numseg != denseg.GetStrands().size()) {

dim =

(dim*numseg, denseg.GetStrands().size()) / numseg;

(hrmaps.size() < dim) {

(

seg = 0; seg < numseg; seg++) {

(

= 0;

< dim;

++) {

(denseg.GetStarts()[seg*dim +

] < 0 ) {

from = denseg.GetStarts()[seg*dim +

];

to = from + denseg.GetLens()[seg] - 1;

( denseg.IsSetStrands() ) {

strand = denseg.GetStrands()[seg*dim +

];

hrmaps[

].SetMasterSeq(master);

hrmaps[

].AddRange(

, from, to, strand);

dim = size_t((*it)->GetDim());

(hrmaps.size() < dim) {

hrmaps.resize((*it)->GetDim());

(

= 0; row_it; ++row_it, ++

) {

(

>= hrmaps.size()) {

hrmaps.resize(

+ 1);

hrmaps[

].SetMasterSeq(master);

hrmaps[

].AddRange(

, from, to, strand);

dim = size_t(packed.GetDim());

numseg = size_t(packed.GetNumseg());

(dim * numseg > packed.GetStarts().size()) {

dim = packed.GetStarts().size() / numseg;

(dim * numseg > packed.GetPresent().size()) {

dim = packed.GetPresent().size() / numseg;

(dim > packed.GetLens().size()) {

dim = packed.GetLens().size();

(hrmaps.size() < dim) {

(

seg = 0; seg < numseg; seg++) {

(

= 0;

< dim;

++) {

( packed.GetPresent()[seg*dim +

] ) {

hrmaps[

].SetMasterSeq(master);

from = packed.GetStarts()[seg*dim +

];

to = from + packed.GetLens()[seg] - 1;

( packed.IsSetStrands() ) {

strand = packed.GetStrands()[seg*dim +

];

hrmaps[

].AddRange(

, from, to, strand);

* gen_id = spliced.IsSetGenomic_id() ?

&spliced.GetGenomic_id() : 0;

* prod_id = spliced.IsSetProduct_id() ?

&spliced.GetProduct_id() : 0;

&

= *ex_gen_id;

( spliced.IsSetGenomic_strand() ) {

strand = spliced.GetGenomic_strand();

hrmaps[1].SetMasterSeq(master);

hrmaps[1].AddRange(

, from, to, strand);

&

= *ex_prod_id;

( spliced.IsSetProduct_strand() ) {

strand = spliced.GetProduct_strand();

hrmaps[0].SetMasterSeq(master);

hrmaps[0].AddRange(

, from, to, strand);

dim = sparse.

().size() + 1;

(hrmaps.size() < dim) {

hrmaps[0].SetMasterSeq(master);

);

);

(numseg != aln_row.

().size()) {

);

numseg =

(numseg, aln_row.

().size());

);

hrmaps[

+1].SetMasterSeq(master);

(

seg = 0; seg < numseg; ++seg) {

hrmaps[0].AddRange(

, from, to);

hrmaps[

+1].AddRange(

, from, to, strand);

TFtable::iterator old_iter = *

.m_Feat;

*

.m_Feat = cont.insert(cont.end(), *old_iter);

cont.erase(old_iter);

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

const CTempString kAnnotTypePrefix

NCBI_DEFINE_ERR_SUBCODE_X(12)

const TFtable::iterator & x_GetFeatIter(void) const

TAnnotType Which(void) const

const CSeq_loc & GetLocs(void) const

const CSeq_entry_Info & GetSeq_entry_Info(void) const

void GetLocsTypes(TTypeIndexSet &idx_set) const

CConstRef< CObject > GetObject(void) const

const CSeq_annot_Info & GetSeq_annot_Info(void) const

const CObject * GetObjectPointer(void) const

static void x_ProcessFeat(vector< CHandleRangeMap > &hrmaps, const CSeq_feat &feat, const CMasterSeqSegments *master)

void x_Locs_AddFeatSubtype(int ftype, int subtype, TTypeIndexSet &idx_set) const

void x_MoveToBack(TFtable &cont)

void x_SetObject(const CSeq_feat &new_obj)

const TGraph::iterator & x_GetGraphIter(void) const

bool IsRegular(void) const

union CAnnotObject_Info::@740 m_Iter

vector< TIndexRange > TTypeIndexSet

static void x_ProcessAlign(vector< CHandleRangeMap > &hrmaps, const CSeq_align &align, const CMasterSeqSegments *master)

void GetMaps(vector< CHandleRangeMap > &hrmaps, const CMasterSeqSegments *master=0) const

const CSeq_feat * GetFeatFast(void) const

CSeq_annot_Info * m_Seq_annot_Info

CDataSource & GetDataSource(void) const

static void x_ProcessGraph(vector< CHandleRangeMap > &hrmaps, const CSeq_graph &graph, const CMasterSeqSegments *master)

SAnnotTypeSelector m_Type

const TAlign::iterator & x_GetAlignIter(void) const

bool IsChunkStub(void) const

pair< size_t, size_t > TIndexRange

const CSeq_align & GetAlign(void) const

const CTSE_Info & GetTSE_Info(void) const

bool IsRemoved(void) const

const CSeq_graph * GetGraphFast(void) const

static TIndexRange GetFeatTypeRange(CSeqFeatData::E_Choice type)

static size_t GetSubtypeIndex(CSeqFeatData::ESubtype subtype)

static TIndexRange GetAnnotTypeRange(CSeq_annot::C_Data::E_Choice type)

ESubtype GetSubtype(void) const

CConstRef< TObject > GetCompleteSeq_annot(void) const

const CSeq_entry_Info & GetParentSeq_entry_Info(void) const

namespace ncbi::objects::

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

CDataSource & GetDataSource(void) const

const CTSE_Info & GetTSE_Info(void) const

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

int GetSubtype(CFieldNamePanel *field_name_panel, string &ncRNA_class)

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define ERR_POST_X(err_subcode, message)

Error posting with default error code and given error subcode.

void Warning(CExceptionArgs_Base &args)

TRange GetRange(void) const

Get the range.

ENa_strand GetStrand(void) const

const CSeq_id & GetSeq_id(void) const

Get seq_id of the current location.

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.

size_type size(void) const

Return the length of the represented array.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

bool IsStr(void) const

Check if variant Str is selected.

bool IsId(void) const

Check if variant Id is selected.

const TData & GetData(void) const

Get the Data member data.

const TStr & GetStr(void) const

Get the variant data.

TInt GetInt(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

const TLabel & GetLabel(void) const

Get the Label member data.

const TType & GetType(void) const

Get the Type member data.

vector< CRef< CUser_field > > TData

TId GetId(void) const

Get the variant data.

E_Choice Which(void) const

Which variant is currently selected.

const TInts & GetInts(void) const

Get the variant data.

bool IsSetProduct_strand(void) const

should be 'plus' or 'minus' Check if a value has been assigned to Product_strand data member.

const TProtpos & GetProtpos(void) const

Get the variant data.

const TDenseg & GetDenseg(void) const

Get the variant data.

vector< CRef< CSeq_loc > > TLoc

vector< CRef< CSparse_align > > TRows

E_Choice Which(void) const

Which variant is currently selected.

list< CRef< CStd_seg > > TStd

TGenomic_start GetGenomic_start(void) const

Get the Genomic_start member data.

const TProduct_id & GetProduct_id(void) const

Get the Product_id member data.

const TFirst_id & GetFirst_id(void) const

Get the First_id member data.

bool IsSetGenomic_strand(void) const

genomic-strand represents the strand of translation Check if a value has been assigned to Genomic_str...

TAmin GetAmin(void) const

Get the Amin member data.

bool IsSetProduct_id(void) const

product is either protein or transcript (cDNA) Check if a value has been assigned to Product_id data ...

const TProduct_start & GetProduct_start(void) const

Get the Product_start member data.

TDim GetDim(void) const

Get the Dim member data.

const TIds & GetIds(void) const

Get the Ids member data.

const TProduct_end & GetProduct_end(void) const

Get the Product_end member data.

const TSpliced & GetSpliced(void) const

Get the variant data.

const TSecond_starts & GetSecond_starts(void) const

Get the Second_starts member data.

const TPacked & GetPacked(void) const

Get the variant data.

const TStd & GetStd(void) const

Get the variant data.

const TLens & GetLens(void) const

Get the Lens member data.

list< CRef< CSpliced_exon > > TExons

bool IsSetSecond_strands(void) const

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

const TFirst_starts & GetFirst_starts(void) const

Get the First_starts member data.

const TDendiag & GetDendiag(void) const

Get the variant data.

TGenomic_strand GetGenomic_strand(void) const

Get the Genomic_strand member data.

bool IsSetStrands(void) const

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

TNumseg GetNumseg(void) const

Get the Numseg member data.

TProduct_strand GetProduct_strand(void) const

Get the Product_strand member data.

const TStrands & GetStrands(void) const

Get the Strands member data.

const TSecond_strands & GetSecond_strands(void) const

Get the Second_strands member data.

const TSecond_id & GetSecond_id(void) const

Get the Second_id member data.

TGenomic_end GetGenomic_end(void) const

Get the Genomic_end member data.

const TStarts & GetStarts(void) const

Get the Starts member data.

list< CRef< CSeq_align > > Tdata

const TSparse & GetSparse(void) const

Get the variant data.

bool IsSetGenomic_id(void) const

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

bool IsNucpos(void) const

Check if variant Nucpos is selected.

const TRows & GetRows(void) const

Get the Rows member data.

const TDisc & GetDisc(void) const

Get the variant data.

list< CRef< CDense_diag > > TDendiag

TNucpos GetNucpos(void) const

Get the variant data.

const TSegs & GetSegs(void) const

Get the Segs member data.

const TGenomic_id & GetGenomic_id(void) const

Get the Genomic_id member data.

@ e_not_set

No variant selected.

const TLocation & GetLocation(void) const

Get the Location member data.

E_Choice

Choice variants.

const TData & GetData(void) const

Get the Data member data.

const TExcept_text & GetExcept_text(void) const

Get the Except_text member data.

bool IsSetExcept_text(void) const

explain if except=TRUE Check if a value has been assigned to Except_text data member.

const TProduct & GetProduct(void) const

Get the Product member data.

bool IsSetProduct(void) const

product of process Check if a value has been assigned to Product data member.

ENa_strand

strand of nucleic acid

const TLoc & GetLoc(void) const

Get the Loc member data.

const Tdata & Get(void) const

Get the 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.

list< CRef< CAnnotdesc > > Tdata

@ e_not_set

No variant selected.

@ e_Locs

used for communication between tools

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

#define row(bind, expected)

void SetAnnotType(TAnnotType type)

void SetFeatSubtype(TFeatSubtype subtype)

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