m_ChunkId(
info.GetChunkId())
94 info.x_UpdateComplete();
170ds.
x_Map(obj,
this);
231 if(
id.IsOther() ) {
258 if( zoom_level >= 0 ) {
263 if( !
type.IsStr() ||
type.GetStr() !=
"AnnotationTrack") {
291 if( !ret.empty() ) {
351obj->SetId() = src.
GetId();
354obj->SetDb(src.
GetDb());
360obj->SetDesc().Set() = src.
GetDesc().
Get();
377 if(
info.m_SNP_Info ) {
408 switch(
data.Which() ) {
498 for(
TAnnotIndexindex = 0; index < rows; ++index ) {
511 const C_Data& src_data =
info.x_GetObject().GetData();
514 switch( src_data.
Which() ) {
544 info.m_ObjectIndex.GetInfos() ) {
545 if( oit->IsRemoved() ) {
563 if( oit->IsRemoved() ) {
581 if( oit->IsRemoved() ) {
599 if( oit->IsRemoved() ) {
615 "CSeq_annot_Info::x_DoUpdate: unimplemented");
647 switch(
data.Which() ) {
676 if(
key.m_Range.Empty() ) {
679 if( !
info.IsRegular() ) {
680s <<
"unknown object";
682 else if(
info.IsFeat() ) {
685 else if(
info.IsGraph() ) {
688 else if(
info.IsAlign() ) {
692s <<
"unknown object";
697 boolnew_id = mapper.
Map(
key, index);
707 _ASSERT(keys_begin <= keys_end);
708 if( keys_begin + 1 == keys_end &&
715 info.SetKeys(keys_begin, keys_end);
729vector<CHandleRangeMap> hrmaps;
736 if(
info.IsRemoved() ) {
739 _ASSERT(
info.GetFeatType() ==
info.GetFeatFast()->GetData().Which());
744 if(
info.IsRemoved() ) {
747 _ASSERT(
info.GetFeatType() ==
info.GetFeatFast()->GetData().Which());
751 info.GetMaps(hrmaps, master);
755 ITERATE( vector<CHandleRangeMap>, hrmit, hrmaps ) {
756 boolmulti_id = hrmit->GetMap().size() > 1;
760 if(
key.m_Range.Empty() ) {
765 key.m_Handle = hrit->first;
770 if(
info.GetFeatFast()->IsSetPartial() ) {
804vector<CHandleRangeMap> hrmaps;
811 if(
info.IsRemoved() ) {
817 info.GetMaps(hrmaps, master);
820 ITERATE( vector<CHandleRangeMap>, hrmit, hrmaps ) {
824 if(
key.m_Range.Empty() ) {
829 key.m_Handle = hrit->first;
857list< vector<CHandleRangeMap> > all_hrmaps;
859 for(
auto& align_ref : sub_aligns ) {
860vector<CHandleRangeMap> hrmaps;
862 for(
auto& hrm : hrmaps ) {
864total_ranges_map[hrit->first] += hrit->second.GetOverlappingRange();
867all_hrmaps.push_back(hrmaps);
869 autohrmap_iter = all_hrmaps.
begin();
870 for(
auto& align_ref : sub_aligns ) {
875vector<CHandleRangeMap> hrmaps;
885vector<CHandleRangeMap>& hrmaps,
892 ITERATE( vector<CHandleRangeMap>, hrmit, hrmaps ) {
897 if(
key.m_Range.Empty() ) {
902 key.m_Handle = hrit->first;
903 if( total_ranges_map || hr.
HasGaps() ) {
930 if(
info.IsRemoved() ) {
949 if(
info.IsRemoved() ) {
956vector<CHandleRangeMap> hrmaps;
963 info.GetMaps(hrmaps, master);
966 ITERATE( vector<CHandleRangeMap>, hrmit, hrmaps ) {
970 if(
key.m_Range.Empty() ) {
975 key.m_Handle = hrit->first;
996seq_feat, seq_pnt, seq_int);
1007seq_loc, seq_pnt, seq_int);
1018seq_loc, seq_pnt, seq_int);
1041 if(
info.IsRemoved() ) {
1052 boolmulti_id = hrmap.
GetMap().
size() > 1;
1056 if(
key.m_Range.Empty() ) {
1061 key.m_Handle = hrit->first;
1092SAnnotObjectsIndex::TObjectInfos::iterator it =
1094 for(
size_t row= 0;
row< object_count; ++
row, ++it ) {
1111 if(
info.IsRemoved() ) {
1128 if( loc.
IsSet() ) {
1133 boolmulti_id = hrmap.
GetMap().
size() > 1;
1137 if(
key.m_Range.Empty() ) {
1139 " Seq-table row "<<
row);
1142 key.m_Handle = hrit->first;
1181 if(
id.IsLocal() ) {
1191 if(
id.IsLocal() ) {
1229 if( !
info.IsRegular() ) {
1258 if( !
info.IsRegular() ) {
1301vector<CHandleRangeMap> hrmaps;
1307 info.GetMaps(hrmaps, master);
1310 ITERATE( vector<CHandleRangeMap>, hrmit, hrmaps ) {
1311 boolmulti_id = hrmit->GetMap().size() > 1;
1315 if(
key.m_Range.Empty() ) {
1323s <<
"unknown annotation";
1329 key.m_Handle = hrit->first;
1339 if(
x_Map(mapper,
key, index) ) {
1348 if(
x_Map(mapper,
key, index) ) {
1355 if(
info.IsFeat() ) {
1482 if(
info.HasSingleKey() ) {
1486 for(
size_t i=
info.GetKeysBegin();
i<
info.GetKeysEnd(); ++
i) {
1491 if(
info.IsFeat() ) {
1527 const char*
error)
1530 if(
data.Which() ==
data.e_not_set ) {
1554 returnobj1.
Equals(obj2);
1563 template<
classSet>
1564 boolsx_SameSets(
constSet& old_set,
constSet& new_set)
1566 typenameSet::const_iterator old_it = old_set.begin();
1567 ITERATE(
typenameSet, new_it, new_set ) {
1568 if( old_it == old_set.end() ) {
1571 if( !(*old_it)->Equals(**new_it) ) {
1576 returnold_it == old_set.end();
1592 if( !sx_SameLocation(old_obj, new_obj) ) {
1607 if( !sx_SameSets(old_obj.
GetIds(), new_obj.
GetIds()) ) {
1638 "CSeq_annot_Handle: cannot update index of SNP table");
1659 switch(
data.Which() ) {
1661 data.SetFtable().erase(
info.x_GetFeatIter());
1664 data.SetAlign().erase(
info.x_GetAlignIter());
1667 data.SetGraph().erase(
info.x_GetGraphIter());
1670 data.SetLocs().erase(
info.x_GetLocsIter());
1682pair<CSeq_annot_Info::TAnnotIndex, bool>
1686sx_CheckType(
data,
data.e_Ftable,
1687 "Cannot add Seq-feat: Seq-annot is not ftable");
1700pair<CSeq_annot_Info::TAnnotIndex, bool>
1704sx_CheckType(
data,
data.e_Align,
1705 "Cannot add Seq-align: Seq-annot is not align");
1718pair<CSeq_annot_Info::TAnnotIndex, bool>
1722sx_CheckType(
data,
data.e_Graph,
1723 "Cannot add Seq-graph: Seq-annot is not graph");
1739sx_CheckType(
data,
data.e_Ftable,
1740 "Cannot replace Seq-feat: Seq-annot is not ftable");
1742SAnnotObjectsIndex::TObjectInfos::iterator info_iter =
1745 if(
info.IsRemoved() ) {
1747TFtable::iterator cont_iter = cont.end();
1748SAnnotObjectsIndex::TObjectInfos::const_iterator it = info_iter;
1749SAnnotObjectsIndex::TObjectInfos::const_iterator it_end =
1751 for( ; it != it_end; ++it ) {
1752 if( !it->IsRemoved() ) {
1753cont_iter = it->x_GetFeatIter();
1758cont.insert(cont_iter,
Ref(
const_cast<CSeq_feat*
>(&new_obj)));
1763 else if( sx_SameFeatIndex(
info, new_obj) ) {
1765 info.x_SetObject(new_obj);
1771 info.x_SetObject(new_obj);
1780sx_CheckType(
data,
data.e_Align,
1781 "Cannot replace Seq-align: Seq-annot is not align");
1783SAnnotObjectsIndex::TObjectInfos::iterator info_iter =
1786 if(
info.IsRemoved() ) {
1788TAlign::iterator cont_iter = cont.end();
1789SAnnotObjectsIndex::TObjectInfos::const_iterator it = info_iter;
1790SAnnotObjectsIndex::TObjectInfos::const_iterator it_end =
1792 for( ; it != it_end; ++it ) {
1793 if( !it->IsRemoved() ) {
1794cont_iter = it->x_GetAlignIter();
1799cont.insert(cont_iter,
Ref(
const_cast<CSeq_align*
>(&new_obj)));
1804 else if( sx_SameLocation(
info.GetAlign(), new_obj) ) {
1806 info.x_SetObject(new_obj);
1812 info.x_SetObject(new_obj);
1821sx_CheckType(
data,
data.e_Graph,
1822 "Cannot replace Seq-graph: Seq-annot is not graph");
1824SAnnotObjectsIndex::TObjectInfos::iterator info_iter =
1827 if(
info.IsRemoved() ) {
1829TGraph::iterator cont_iter = cont.end();
1830SAnnotObjectsIndex::TObjectInfos::const_iterator it = info_iter;
1831SAnnotObjectsIndex::TObjectInfos::const_iterator it_end =
1833 for( ; it != it_end; ++it ) {
1834 if( !it->IsRemoved() ) {
1835cont_iter = it->x_GetGraphIter();
1840cont.insert(cont_iter,
Ref(
const_cast<CSeq_graph*
>(&new_obj)));
1845 else if( sx_SameLocation(
info.GetGraph(), new_obj) ) {
1847 info.x_SetObject(new_obj);
1853 info.x_SetObject(new_obj);
1862 if( !
data.IsFtable() ) {
1864 "ReorderFtable: Seq-annot annot is not ftable");
1867 ITERATE( vector<CSeq_feat_Handle>, it, feats ) {
1868 if( &it->x_GetSeq_annot_Info() !=
this) {
1872 if( !
info.IsRegular() ) {
1894feat_xref->SetId(*feat_id);
1895feat->
SetXref().push_back(feat_xref);
1897 else if( !feat->
IsSetId() ) {
1898feat->
SetId(*feat_id);
1901feat->
SetIds().push_back(feat_id);
1915 boolremoved_id =
false;
1920 if( !feat_xref.
IsSetId() ) {
1926 if( feat->
SetXref().empty() ) {
1945feat->
SetIds().erase(it);
1946 if( feat->
SetIds().empty() ) {
1955 if( !removed_id ) {
1957 "CSeq_feat_EditHandle::RemoveFeatId: Feat-id not found");
1975 if( !feat_xref.
IsSetId() ) {
2045 size_t a= 0,
b= num_rows;
2046 while(
b-
a> 1 ) {
2047 size_tm =
a+ (
b-
a)/2;
2049 if( pos < min_pos ) {
2082 while( *
this&& !
x_Valid() ) {
User-defined methods of the data storage class.
User-defined methods of the data storage class.
User-defined methods of the data storage class.
#define NCBI_ANNOT_TRACK_ZOOM_LEVEL_SUFFIX
Named annotations zoom level can be encoded in the accession string with @ suffix,...
User-defined methods of the data storage class.
Annotation iterators exceptions.
void SetNamed(const string &name)
const string & GetName(void) const
static void x_ProcessAlign(vector< CHandleRangeMap > &hrmaps, const CSeq_align &align, const CMasterSeqSegments *master)
const CSeq_entry_Info & GetParentSeq_entry_Info(void) const
void Guard(CDataSource &ds)
void x_Unmap(const CObject *obj, const CTSE_Info_Object *info)
void x_Map(const CObject *obj, const CTSE_Info_Object *info)
void AddLocation(const CSeq_loc &loc, ETransSplicing trans_splcing=eNoTransSplicing)
void SetMasterSeq(const CMasterSeqSegments *master_seq)
const TLocMap & GetMap(void) const
TTotalRangeFlags GetStrandsFlag(void) const
bool IsCircular(void) const
TRange GetCircularRangeStart(bool include_origin=true) const
TRange GetCircularRangeEnd(bool include_origin=true) const
TRange GetOverlappingRange(TTotalRangeFlags flags=eStrandAny) const
CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:
Base class for all object manager exceptions.
ESubtype GetSubtype(void) const
static bool IsGoodFeatTable(const CSeq_table &table)
string GetLabel(size_t row) const
bool IsPartial(size_t row) const
size_t GetNumRows(void) const
bool HasLabel(size_t row) const
bool IsFeatTable(void) const
const CSeqTableLocColumns & GetLocation(void) const
bool MatchBitFilter(const SAnnotSelector &sel, size_t row) const
const CSeqTableLocColumns & GetProduct(void) const
void UpdateSeq_feat(size_t row, CRef< CSeq_feat > &seq_feat, CRef< CSeq_point > &seq_pnt, CRef< CSeq_interval > &seq_int) const
SAnnotTypeSelector GetType(void) const
bool IsSorted(void) const
CRange< TSeqPos > GetLocationRange(size_t row) const
TSeqPos GetLocationFrom(size_t row) const
TSeqPos GetSortedMaxLength(void) const
CConstRef< CSeq_loc > GetTableLocation(void) const
bool RowIsDisabled(size_t row) const
void SetTableKeyAndIndex(size_t row, SAnnotObject_Key &key, SAnnotObject_Index &index) const
bool IsRealLoc(void) const
void UpdateSeq_loc(size_t row, CRef< CSeq_loc > &seq_loc, CRef< CSeq_point > &seq_pnt, CRef< CSeq_interval > &seq_int) const
CConstRef< CSeq_loc > GetLoc(size_t row) const
void x_InitFeatList(TFtable &objs)
virtual void x_DSAttachContents(CDataSource &ds)
void x_MapFeatById(const CFeat_id &id, CAnnotObject_Info &info, EFeatIdType id_type)
void x_UnmapFeatIds(CAnnotObject_Info &info)
const TAnnotObjectInfos & GetAnnotObjectInfos(void) const
CRef< CSeq_annot_SNP_Info > m_SNP_Info
virtual void x_TSEDetachContents(CTSE_Info &tse)
void Remove(TAnnotIndex index)
virtual string GetDescription(void) const
void AddFeatId(TAnnotIndex index, const CObject_id &id, EFeatIdType id_type)
const CAnnotObject_Info & GetInfo(TAnnotIndex index) const
void x_MapFeatIds(CAnnotObject_Info &info)
void x_InitAlignList(TAlign &objs)
void x_ParentDetach(CBioseq_Base_Info &parent)
void UpdateTableFeatLocation(CRef< CSeq_loc > &seq_loc, CRef< CSeq_point > &seq_point, CRef< CSeq_interval > &seq_interval, const CAnnotObject_Info &feat_info) const
void x_DSUnmapObject(CConstRef< TObject > obj, CDataSource &ds)
void x_InitLocsKeys(CTSE_Info &tse)
void x_InitAnnotKeys(CTSE_Info &tse)
void x_InitAlignKeys(CTSE_Info &tse)
TAnnotIndex x_GetSNPFeatCount(void) const
void x_AddAlignIndex(CAnnotObject_Info &info, const CSeq_align &align, CTSEAnnotObjectMapper &mapper, vector< CHandleRangeMap > &hrmaps, const TTotalRangesMap *total_ranges_map=0)
virtual void x_TSEAttachContents(CTSE_Info &tse)
void x_SetObject(TObject &obj)
void x_InitFeatKeys(CTSE_Info &tse)
void x_SetSNP_annot_Info(CSeq_annot_SNP_Info &snp_info)
void x_InitFeatTableKeys(CTSE_Info &tse)
bool TableFeat_HasLabel(TAnnotIndex index) const
void x_InitFeatTable(TSeq_table &table)
string TableFeat_GetLabel(TAnnotIndex index) const
bool x_MapAnnotObject(CAnnotObject_Info &info)
CConstRef< TObject > GetCompleteSeq_annot(void) const
bool MatchBitFilter(const SAnnotSelector &sel, const CSeq_annot_SortedIter &iter) const
bool IsSortedTable(void) const
pair< TAnnotIndex, bool > Add(const CSeq_feat &new_obj)
void ClearFeatIds(TAnnotIndex index, EFeatIdType id_type)
const CAnnotName & GetName(void) const
void Update(TAnnotIndex index)
CSeq_annot_Info(CSeq_annot &annot, int chunk_id=0)
void x_ParentAttach(CBioseq_Base_Info &parent)
void x_DoUpdate(TNeedUpdateFlags flags)
void UpdateTableFeatProduct(CRef< CSeq_loc > &seq_loc, CRef< CSeq_point > &seq_point, CRef< CSeq_interval > &seq_interval, const CAnnotObject_Info &feat_info) const
void UpdateTableFeat(CRef< CSeq_feat > &seq_feat, CRef< CSeq_point > &seq_point, CRef< CSeq_interval > &seq_interval, const CAnnotObject_Info &feat_info) const
void x_AddAlignKeys(CAnnotObject_Info &info, const CSeq_align &align, const CMasterSeqSegments *master, CTSEAnnotObjectMapper &mapper)
CConstRef< TObject > GetSeq_annotCore(void) const
void x_DropAnnotObjects(CTSE_Info &tse)
bool IsTableFeatPartial(const CAnnotObject_Info &feat_info) const
void x_UpdateAnnotIndexContents(CTSE_Info &tse)
void UpdateAnnotIndex(void) const
const CBioseq_Base_Info & GetParentBioseq_Base_Info(void) const
const CSeq_entry_Info & GetXrefTSE(void) const
void x_UpdateObjectKeys(CAnnotObject_Info &info, size_t keys_begin)
void RemoveFeatId(TAnnotIndex index, const CObject_id &id, EFeatIdType id_type)
void x_MapFeatByGene(const CGene_ref &gene, CAnnotObject_Info &info)
TAnnotIndex x_GetAnnotCount(void) const
CRef< CSeqTableInfo > m_Table_Info
void ReorderFtable(const vector< CSeq_feat_Handle > &feats)
bool x_Map(const CTSEAnnotObjectMapper &mapper, const SAnnotObject_Key &key, const SAnnotObject_Index &index)
void x_InitGraphKeys(CTSE_Info &tse)
void x_DSMapObject(CConstRef< TObject > obj, CDataSource &ds)
bool x_RemapAnnotObject(CAnnotObject_Info &info)
void x_UnmapFeatByGene(const CGene_ref &gene, CAnnotObject_Info &info)
void x_UnmapFeatById(const CFeat_id &id, CAnnotObject_Info &info, EFeatIdType id_type)
void x_InitAnnotList(void)
void x_InitGraphList(TGraph &objs)
const CSeq_entry_Info & GetParentSeq_entry_Info(void) const
static const TAnnotIndex kWholeAnnotIndex
bool Replace(TAnnotIndex index, const CSeq_feat &new_obj)
CSeq_annot_SortedIter StartSortedIterator(CRange< TSeqPos > range) const
void x_UnmapAnnotObject(CAnnotObject_Info &info)
void x_UnmapAnnotObjects(CTSE_Info &tse)
virtual void x_DSDetachContents(CDataSource &ds)
SAnnotObjectsIndex m_ObjectIndex
const CSeq_annot_SNP_Info & x_GetSNP_annot_Info(void) const
void x_InitLocsList(TLocs &annot)
bool HasLabel(size_t index) const
void x_DropAnnotObjects(CTSE_Info &tse)
const CSeq_annot_Info & GetParentSeq_annot_Info(void) const
void x_ParentAttach(CSeq_annot_Info &parent)
string GetLabel(size_t index) const
CSeq_annot & GetRemainingSeq_annot(void)
void x_UnmapAnnotObjects(CTSE_Info &tse)
CRange< TSeqPos > m_RequestRange
CRange< TSeqPos > m_ObjectRange
CRef< CSeqTableInfo > m_Table_Info
size_t GetRow(void) const
const CSeq_entry_Info & GetXrefTSE() const
namespace ncbi::objects::
Base class for all serializable objects.
void Unmap(const SAnnotObject_Key &key, const CAnnotObject_Info &info) const
bool Map(const SAnnotObject_Key &key, const SAnnotObject_Index &index) const
void x_SetDirtyAnnotIndex(void)
void x_UpdateCore(void) const
virtual void SetBioObjectId(const CBioObjectId &id)
virtual void x_DSDetachContents(CDataSource &ds)
CDataSource & GetDataSource(void) const
void x_BaseParentAttach(CTSE_Info_Object &parent)
bool HasDataSource(void) const
void x_UpdateAnnotIndex(CTSE_Info &tse)
void x_BaseParentDetach(CTSE_Info_Object &parent)
virtual void x_TSEAttachContents(CTSE_Info &tse)
void x_DSAttach(CDataSource &ds)
virtual void x_DSAttachContents(CDataSource &ds)
void x_TSEAttach(CTSE_Info &tse)
virtual void x_TSEDetachContents(CTSE_Info &tse)
const CTSE_Info & GetTSE_Info(void) const
bool x_DirtyAnnotIndex(void) const
void x_UpdateComplete(void) const
const CTSE_Info_Object & GetBaseParent_Info(void) const
bool HasParent_Info(void) const
void x_TSEDetach(CTSE_Info &tse)
void x_AttachObject(CTSE_Info_Object &object)
void x_DSDetach(CDataSource &ds)
virtual void x_UpdateAnnotIndexContents(CTSE_Info &tse)
bool HasTSE_Info(void) const
CRef< CSeq_annot_SNP_Info > x_GetSNP_Info(const CConstRef< CSeq_annot > &annot)
void x_MapFeatByLocus(const string &locus, bool tag, CAnnotObject_Info &info)
void UpdateAnnotIndex(const CSeq_id_Handle &id) const
void x_MapFeatById(TFeatIdInt id, CAnnotObject_Info &info, EFeatIdType type)
CConstRef< CMasterSeqSegments > GetMasterSeqSegments(void) const
void x_UnmapFeatByLocus(const string &locus, bool tag, CAnnotObject_Info &info)
virtual string GetDescription(void) const
void x_UnmapFeatById(TFeatIdInt id, CAnnotObject_Info &info, EFeatIdType type)
CBioObjectId x_RegisterBioObject(CTSE_Info_Object &info)
void x_UnmapAnnotObjects(const SAnnotObjectsIndex &infos)
TAnnotLock & GetAnnotLock(void) const
const CAnnotName & GetName(void) const
void x_UnregisterBioObject(CTSE_Info_Object &info)
CConstRef< CUser_field > GetFieldRef(const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const
const_iterator begin() const
const_iterator find(const key_type &key) const
unsigned int TSeqPos
Type for sequence locations and lengths.
#define ITERATE(Type, Var, Cont)
ITERATE macro to sequence through container elements.
#define ERASE_ITERATE(Type, Var, Cont)
Non-constant version with ability to erase current element, if container permits.
#define VECTOR_ERASE(Var, Cont)
Use this macro inside body of ERASE_ITERATE cycle to erase from vector-like container.
#define NON_CONST_ITERATE(Type, Var, Cont)
Non constant version of ITERATE macro.
#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.
virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)
Set object to copy of another one.
#define MSerial_AsnText
I/O stream manipulators â.
virtual bool Equals(const CSerialObject &object, ESerialRecursionMode how=eRecursive) const
Check if both objects contain the same values.
static CSeq_id_Handle GetHandle(const CSeq_id &id)
Normal way of getting a handle, works for any seq-id.
TRange GetTotalRange(void) const
CRef< C > Ref(C *object)
Helper functions to get CRef<> and CConstRef<> objects.
T & GetData(void)
Get data as a reference.
void Reset(void)
Reset reference object.
position_type GetToOpen(void) const
#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 IntToString(int value, TNumToStringFlags flags=0, int base=10)
Convert int to string.
TFrom GetFrom(void) const
Get the From member data.
const TDesc & GetDesc(void) const
Get the Desc member data.
bool IsSetLocus_tag(void) const
systematic gene name (e.g., MI0001, ORF0069) Check if a value has been assigned to Locus_tag data mem...
bool IsSetLocus(void) const
Official gene symbol Check if a value has been assigned to Locus data member.
bool IsSetDesc(void) const
descriptive name Check if a value has been assigned to Desc data member.
const TLocus_tag & GetLocus_tag(void) const
Get the Locus_tag member data.
const TLocus & GetLocus(void) const
Get the Locus member data.
const TData & GetData(void) const
Get the Data member data.
bool IsInt(void) const
Check if variant Int is selected.
TInt GetInt(void) const
Get the variant data.
const TType & GetType(void) const
Get the Type member data.
bool IsDisc(void) const
Check if variant Disc is selected.
list< CRef< CSeq_align > > Tdata
const TDisc & GetDisc(void) const
Get the variant data.
const Tdata & Get(void) const
Get the member data.
const TSegs & GetSegs(void) const
Get the Segs member data.
TXref & SetXref(void)
Assign a value to Xref data member.
const TIds & GetIds(void) const
Get the Ids member data.
TIds & SetIds(void)
Assign a value to Ids data member.
const TId & GetId(void) const
Get the Id member data.
const TLocal & GetLocal(void) const
Get the variant data.
bool IsSetXref(void) const
cite other relevant features Check if a value has been assigned to Xref data member.
const TLocation & GetLocation(void) const
Get the Location member data.
bool IsLocal(void) const
Check if variant Local is selected.
const TId & GetId(void) const
Get the Id member data.
void ResetIds(void)
Reset Ids data member.
TLocal & SetLocal(void)
Select the variant.
void ResetId(void)
Reset Id data member.
const TData & GetData(void) const
Get the Data member data.
void SetId(TId &value)
Assign a value to Id data member.
list< CRef< CFeat_id > > TIds
bool IsSetIds(void) const
set of Ids; will replace 'id' field Check if a value has been assigned to Ids data member.
bool IsSetId(void) const
Check if a value has been assigned to Id data member.
const TProduct & GetProduct(void) const
Get the Product member data.
const TGene & GetGene(void) const
Get the variant data.
bool IsSetId(void) const
the feature copied Check if a value has been assigned to Id data member.
const TXref & GetXref(void) const
Get the Xref member data.
vector< CRef< CSeqFeatXref > > TXref
void ResetXref(void)
Reset Xref data member.
bool IsSetProduct(void) const
product of process Check if a value has been assigned to Product data member.
const TId & GetId(void) const
Get the Id member data.
bool IsInt(void) const
Check if variant Int is selected.
const TInt & GetInt(void) const
Get the variant data.
const TLoc & GetLoc(void) const
Get the Loc member data.
const Tdata & Get(void) const
Get the member data.
TVersion GetVersion(void) const
Get the Version member data.
const TName & GetName(void) const
Get the Name member data.
list< CRef< CAnnot_id > > TId
const TAccession & GetAccession(void) const
Get the Accession member data.
bool IsSetName(void) const
source if "other" above Check if a value has been assigned to Name data member.
bool IsSetVersion(void) const
Check if a value has been assigned to Version data member.
const TUser & GetUser(void) const
Get the variant data.
const TIds & GetIds(void) const
Get the variant data.
E_Choice Which(void) const
Which variant is currently selected.
E_Choice
Choice variants.
bool IsSetDb(void) const
Check if a value has been assigned to Db data member.
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.
bool IsSetAccession(void) const
Check if a value has been assigned to Accession data member.
bool IsSetId(void) const
Check if a value has been assigned to Id data member.
TDb GetDb(void) const
Get the Db member data.
const TId & GetId(void) const
Get the Id member data.
list< CRef< CSeq_feat > > TFtable
const TName & GetName(void) const
Get the variant data.
E_Choice Which(void) const
Which variant is currently selected.
list< CRef< CAnnotdesc > > Tdata
@ e_Ids
used for communication between tools
@ e_not_set
No variant selected.
@ e_Locs
used for communication between tools
@ e_Name
a short name for this collection
@ e_User
user defined object
Definition of all error codes used in objmgr libraries (xobjmgr.lib, xobjutil.lib and others).
<!DOCTYPE HTML >< html > n< header > n< title > PubSeq Gateway Help Page</title > n< style > n table
const struct ncbi::grid::netcache::search::fields::SIZE size
const struct ncbi::grid::netcache::search::fields::KEY key
NCBI_DEFINE_ERR_SUBCODE_X(9)
#define row(bind, expected)
CRef< CObjectFor< CHandleRange > > m_HandleRange
CAnnotObject_Info * m_AnnotObject_Info
void SetMultiIdFlag(void)
void SetPartial(bool partial)
Uint2 m_AnnotLocationIndex
bool IsSingle(void) const
bool IsIndexed(void) const
void SetName(const CAnnotName &name)
void AddInfo(const CAnnotObject_Info &info)
void ReserveMapSize(size_t size)
TObjectInfos & GetInfos(void)
const SAnnotObject_Key & GetKey(size_t i) const
deque< CAnnotObject_Info > TObjectInfos
void AddMap(const SAnnotObject_Key &key, const SAnnotObject_Index &index)
const TObjectKeys & GetKeys(void) const
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