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NCBI C++ ToolKit: CTableAnnotDataSource Class Reference

Search Toolkit Book for CTableAnnotDataSource

CAnnotDataSource -. More...

#include <gui/widgets/loaders/table_annot_data_source.hpp>

CTableAnnotDataSource () ctor More...
void Clear () clears all columns rows and delimiters More...
void Init () size_t GetNumRows () const return total number of rows read More...
string GetField (size_t row, size_t col) const return a specific field from a specific row, based on current table type and delimiter More...
vector< STableLocation > FindLocations (string &msg, bool strand_required) Find colums that can be combined to form locations based on column info If no locations are found, missing info is given in msg. More...
bool AddSeqLoc (const STableLocation &fc, int loc_number, ICanceled *cancel=NULL) Add a location to the table based on the specified columns. More...
bool AddSnpSeqLoc (const STableLocation &fc, int loc_number, ICanceled *cancel=NULL) Add a location to the table using the rsid (snp/variation) ids location from the snp db. More...
bool CreateFeature (const STableLocation &fc, ICanceled *cancel=NULL) Create a feature using specified columns. More...
bool CreateSnpFeature (const STableLocation &fc, ICanceled *cancel=NULL) Create a region feature for each snp using specified snp (rsid) column. More...
bool CreateSnps (const STableLocation &fc, ICanceled *cancel=NULL) Create snips (features that show variations) for each row. More...
void RemoveSeqLocs () Remove any seqloc columns (can be used to undo the AddSeqLoc actions) More...
CRef< CSeq_annot > GetContainer () void WriteAsn (const string &fname) Write seqtable to file 'fname'. More...
CObject (void) Constructor. More...
CObject (const CObject &src) Copy constructor. More...
virtual ~CObject (void) Destructor. More...
CObject & operator= (const CObject &src) THROWS_NONE Assignment operator. More...
bool CanBeDeleted (void) const THROWS_NONE Check if object can be deleted. More...
bool IsAllocatedInPool (void) const THROWS_NONE Check if object is allocated in memory pool (not system heap) More...
bool Referenced (void) const THROWS_NONE Check if object is referenced. More...
bool ReferencedOnlyOnce (void) const THROWS_NONE Check if object is referenced only once. More...
void AddReference (void) const Add reference to object. More...
void RemoveReference (void) const Remove reference to object. More...
void ReleaseReference (void) const Remove reference without deleting object. More...
virtual void DoNotDeleteThisObject (void) Mark this object as not allocated in heap – do not delete this object. More...
virtual void DoDeleteThisObject (void) Mark this object as allocated in heap – object can be deleted. More...
void * operator new (size_t size) Define new operator for memory allocation. More...
void * operator new[] (size_t size) Define new[] operator for 'array' memory allocation. More...
void operator delete (void *ptr) Define delete operator for memory deallocation. More...
void operator delete[] (void *ptr) Define delete[] operator for memory deallocation. More...
void * operator new (size_t size, void *place) Define new operator. More...
void operator delete (void *ptr, void *place) Define delete operator. More...
void * operator new (size_t size, CObjectMemoryPool *place) Define new operator using memory pool. More...
void operator delete (void *ptr, CObjectMemoryPool *place) Define delete operator. More...
virtual void DebugDump (CDebugDumpContext ddc, unsigned int depth) const Define method for dumping debug information. More...
CDebugDumpable (void) virtual ~CDebugDumpable (void) void DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const void DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const void DumpToConsole (void) const

CAnnotDataSource -.

This class wraps a CSeq_annot that contains a CSeq_table. The class has features for finding fields in the table that respresent locations and then either adding those as location columns or converting the fields as needed to create region fetures.

Definition at line 58 of file table_annot_data_source.hpp.

◆ CTableAnnotDataSource() CTableAnnotDataSource::CTableAnnotDataSource ( ) ◆ AddSeqLoc()

Add a location to the table based on the specified columns.

Definition at line 367 of file table_annot_data_source.cpp.

References CScope::AddDefaults(), CUser_object::AddField(), column, data, CSeq_id_Base::e_Gi, CSeqTable_multi_data_Base::e_Loc, CSeqTable_multi_data_Base::e_String, CTableImportColumn::eChromosome, CSeqTable_column_info_Base::eField_id_comment, CSeqTable_column_info_Base::eField_id_location, CIdMapperGCAssembly::eGenBankAcc, eNa_strand_minus, eNa_strand_plus, eNa_strand_unknown, CIdMapperGCAssembly::eRefSeqAcc, CTableImportColumn::eUnspecifiedText, CUser_field_Base::GetData(), CUser_object_Base::GetData(), CTableImportColumn::GetDataTypeFromString(), CSeqTable_column_Base::GetHeader(), CGencollSvc::GetInstance(), CObjectManager::GetInstance(), CException::GetMsg(), CRef< C, Locker >::GetObject(), CConstRef< C, Locker >::GetObject(), CUser_field_Base::C_Data::GetStr(), CTableImportColumn::GetStringFromDataType(), CSeqTable_column_info_Base::GetTitle(), NStr::IntToString(), ICanceled::IsCanceled(), CRef< C, Locker >::IsNull(), CGC_Assembly::IsRefSeq(), CSeq_annot_Base::C_Data::IsSeq_table(), CUser_field_Base::IsSetData(), CSeq_annot_Base::IsSetData(), CUser_field_Base::C_Data::IsStr(), label, len, location, LOG_POST, m_AnnotContainer, CTableAnnotDataSource::STableLocation::m_IdCol, CTableAnnotDataSource::STableLocation::m_LengthCol, CTableAnnotDataSource::STableLocation::m_StartPosCol, CTableAnnotDataSource::STableLocation::m_StopPosCol, CTableAnnotDataSource::STableLocation::m_StrandCol, CSeqUtils::MapStringId(), NULL, NStr::NumericToString(), CRef< C, Locker >::Reset(), CConstRef< C, Locker >::Reset(), row, CSeq_annot_Base::SetData(), CSeqTable_column_Base::SetData(), CSeqTable_column_info_Base::SetField_id(), CSeqTable_column_Base::SetHeader(), CSeq_annot_Base::C_Data::SetSeq_table(), CSeqTable_column_info_Base::SetTitle(), string, swap(), table, x_GetColumnMetaInfo(), x_GetMetaInfoTag(), and x_GetStrand().

Referenced by CTestApplication::LoadTable(), and CTableXformPanel::x_AddLocations().

◆ AddSnpSeqLoc()

Add a location to the table using the rsid (snp/variation) ids location from the snp db.

Definition at line 802 of file table_annot_data_source.cpp.

References CScope::AddDefaults(), CUser_object::AddField(), column, data, CSeqTable_multi_data_Base::e_Loc, CSeqTable_multi_data_Base::e_String, CSeqTable_column_info_Base::eField_id_comment, CSeqTable_column_info_Base::eField_id_location, CTableImportColumn::eRsid, CTableImportColumn::eUnspecifiedText, CUser_field_Base::GetData(), CUser_object_Base::GetData(), CTableImportColumn::GetDataTypeFromString(), CSeqTable_column_Base::GetHeader(), CObjectManager::GetInstance(), CException::GetMsg(), CUser_field_Base::C_Data::GetStr(), CTableImportColumn::GetStringFromDataType(), CSeqTable_column_info_Base::GetTitle(), ICanceled::IsCanceled(), CSeq_annot_Base::C_Data::IsSeq_table(), CUser_field_Base::IsSetData(), CSeq_annot_Base::IsSetData(), CUser_field_Base::C_Data::IsStr(), label, location, LOG_POST, m_AnnotContainer, CTableAnnotDataSource::STableLocation::m_IdCol, NULL, NStr::NumericToString(), om, CRef< C, Locker >::Reset(), row, NSNPWebServices::Search(), CSeq_annot_Base::SetData(), CSeqTable_column_Base::SetData(), CSeqTable_column_info_Base::SetField_id(), CSeqTable_column_Base::SetHeader(), CSeq_annot_Base::C_Data::SetSeq_table(), CSeqTable_column_info_Base::SetTitle(), string, table, x_GetColumnMetaInfo(), x_GetMetaInfoTag(), and x_LogErr().

Referenced by CTestApplication::LoadTable(), and CTableXformPanel::x_AddLocations().

◆ Clear() void CTableAnnotDataSource::Clear ( void ) ◆ CreateFeature()

Create a feature using specified columns.

Definition at line 1027 of file table_annot_data_source.cpp.

Referenced by CTestApplication::LoadTable(), and CTableXformPanel::x_CreateFeatures().

◆ CreateSnpFeature()

Create a region feature for each snp using specified snp (rsid) column.

Definition at line 1597 of file table_annot_data_source.cpp.

Referenced by CTestApplication::LoadTable(), and CTableXformPanel::x_CreateFeatures().

◆ CreateSnps()

Create snips (features that show variations) for each row.

Definition at line 2061 of file table_annot_data_source.cpp.

Referenced by CTableXformPanel::x_CreateFeatures().

◆ FindLocations()

Find colums that can be combined to form locations based on column info If no locations are found, missing info is given in msg.

Definition at line 127 of file table_annot_data_source.cpp.

Referenced by CTestApplication::LoadTable(), CTableXformPanel::OnConvertToFeaturesSelected(), CTableXformPanel::OnConvertToSnpSelected(), CTableXformPanel::OnCreateLocationsSelected(), CTableXformPanel::x_AddLocations(), and CTableXformPanel::x_CreateFeatures().

◆ GetContainer() ◆ GetField() string CTableAnnotDataSource::GetField ( size_t row, size_t col ) const ◆ GetNumRows() size_t CTableAnnotDataSource::GetNumRows ( void ) const inline ◆ Init() ◆ RemoveSeqLocs() void CTableAnnotDataSource::RemoveSeqLocs ( )

Remove any seqloc columns (can be used to undo the AddSeqLoc actions)

Definition at line 2545 of file table_annot_data_source.cpp.

References CSeqTable_column_info_Base::eField_id_location, Error(), CSeqTable_column_info_Base::GetField_id(), NASNCacheFileName::GetHeader(), CSeq_annot_Base::C_Data::IsSeq_table(), CSeq_annot_Base::IsSetData(), LOG_POST, m_AnnotContainer, NULL, CSeq_annot_Base::SetData(), CUser_object_Base::SetData(), CSeq_annot_Base::C_Data::SetSeq_table(), table, and x_GetColumnMetaInfo().

◆ WriteAsn() void CTableAnnotDataSource::WriteAsn ( const string & fname ) ◆ x_GetColumnMetaInfo()

Get meta information stored in User_Data in m_AnnotContainer.

Definition at line 2665 of file table_annot_data_source.cpp.

References CAnnot_descr_Base::CanGet(), CSeq_annot_Base::CanGetDesc(), LOG_POST, m_AnnotContainer, NULL, CAnnot_descr_Base::Set(), and CSeq_annot_Base::SetDesc().

Referenced by AddSeqLoc(), AddSnpSeqLoc(), CreateFeature(), CreateSnpFeature(), CreateSnps(), FindLocations(), and RemoveSeqLocs().

◆ x_GetMetaInfoTag()

Search string 'meta_string' for the value assigned to 'tag_name', e.g.

GetMetaInfoTag("&genome_assembly=GRCh37.p5 &one_based=true", "genome_assembly") == "GRCh37.p5"

Definition at line 2604 of file table_annot_data_source.cpp.

References string, tag, NStr::TruncateSpaces(), and rapidjson::value.

Referenced by AddSeqLoc(), AddSnpSeqLoc(), CreateFeature(), CreateSnpFeature(), CreateSnps(), and FindLocations().

◆ x_GetStrand() ◆ x_LogErr() ◆ x_UpdateMetaInfoTag() ◆ m_AnnotContainer

Definition at line 168 of file table_annot_data_source.hpp.

Referenced by AddSeqLoc(), AddSnpSeqLoc(), CreateFeature(), CreateSnpFeature(), CreateSnps(), CTableAnnotDataSource(), FindLocations(), GetContainer(), RemoveSeqLocs(), WriteAsn(), and x_GetColumnMetaInfo().

The documentation for this class was generated from the following files:

include/gui/widgets/loaders/table_annot_data_source.hpp
src/gui/widgets/loaders/table_annot_data_source.cpp

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