Search Toolkit Book for CTableAnnotDataSource

CAnnotDataSource -. More...

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

Inheritance diagram for CTableAnnotDataSource:

Collaboration diagram for CTableAnnotDataSource:

Classes
struct	STableLocation

Public Member Functions
	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...

Public Member Functions inherited from CObject
	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...

Public Member Functions inherited from CDebugDumpable
	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

Protected Member Functions
CAnnotdesc::TUser *	x_GetColumnMetaInfo ()
	Get meta information stored in User_Data in m_AnnotContainer. More...

ENa_strand	x_GetStrand (string strand)
	Return enumerated strand type based on string. More...

void	x_LogErr (const string &logstr, string &errstr, int &err_count, int row)
	Log an error (but stop logging if error count gets high. More...

string	x_GetMetaInfoTag (const string &meta_string, const string &tag_name)
	Search string 'meta_string' for the value assigned to 'tag_name', e.g. More...

bool	x_UpdateMetaInfoTag (string &meta_string, const string &tag_name, const string &new_value)
	Change the value for 'tag_name' in 'meta_string' to 'new_value'. More...

Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Protected Attributes
CRef< CSeq_annot >	m_AnnotContainer

Additional Inherited Members
Public Types inherited from CObject
enum	EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern }
	Control filling of newly allocated memory. More...

typedef CObjectCounterLocker	TLockerType
	Default locker type for CRef. More...

typedef atomic< Uint8 >	TCounter
	Counter type is CAtomiCounter. More...

typedef Uint8	TCount
	Alias for value type of counter. More...

Static Public Member Functions inherited from CObject
static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (void)
	Define method to throw null pointer exception. More...

static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (const type_info &type)

static EAllocFillMode	GetAllocFillMode (void)

static void	SetAllocFillMode (EAllocFillMode mode)

static void	SetAllocFillMode (const string &value)
	Set mode from configuration parameter value. More...

Static Public Member Functions inherited from CDebugDumpable
static void	EnableDebugDump (bool on)

Static Public Attributes inherited from CObject
static const TCount	eCounterBitsCanBeDeleted = 1 << 0
	Define possible object states. More...

static const TCount	eCounterBitsInPlainHeap = 1 << 1
	Heap signature was found. More...

static const TCount	eCounterBitsPlaceMask
	Mask for 'in heap' state flags. More...

static const int	eCounterStep = 1 << 2
	Skip over the "in heap" bits. More...

static const TCount	eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2)
	Minimal value for valid objects (reference counter is zero) Must be a single bit value. More...

static const TCount	eCounterStateMask
	Valid object, and object in heap. More...

Detailed Description

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.

Constructor & Destructor Documentation

◆ CTableAnnotDataSource()

CTableAnnotDataSource::CTableAnnotDataSource ( )

ctor

Definition at line 111 of file table_annot_data_source.cpp.

References m_AnnotContainer, and CRef< C, Locker >::Reset().

Member Function Documentation

◆ AddSeqLoc()

bool CTableAnnotDataSource::AddSeqLoc	(	const STableLocation &	fc,
		int	loc_number,
		ICanceled *	cancel = `NULL`
	)

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, 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, fc, CUser_field_Base::GetData(), CUser_object_Base::GetData(), CTableImportColumn::GetDataTypeFromString(), CSeqTable_column_Base::GetHeader(), CGencollSvc::GetInstance(), CObjectManager::GetInstance(), CException::GetMsg(), CRef< C, Locker >::GetNCObject(), 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, CSeqUtils::MapStringId(), NULL, NStr::NumericToString(), CRef< C, Locker >::Reset(), CConstRef< C, Locker >::Reset(), CSeqTable_multi_data_Base::Select(), CSeq_annot_Base::SetData(), CSeqTable_column_Base::SetData(), CSeqTable_column_info_Base::SetField_id(), CSeqTable_column_Base::SetHeader(), CSeqTable_multi_data_Base::SetLoc(), 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()

bool CTableAnnotDataSource::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.

Definition at line 802 of file table_annot_data_source.cpp.

References CScope::AddDefaults(), CUser_object::AddField(), column, 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, fc, CUser_field_Base::GetData(), CUser_object_Base::GetData(), CTableImportColumn::GetDataTypeFromString(), CSeqTable_column_Base::GetHeader(), CObjectManager::GetInstance(), CException::GetMsg(), CRef< C, Locker >::GetNCObject(), 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, NULL, NStr::NumericToString(), om, CRef< C, Locker >::Reset(), NSNPWebServices::Search(), CSeqTable_multi_data_Base::Select(), CSeq_annot_Base::SetData(), CSeqTable_column_Base::SetData(), CSeqTable_column_info_Base::SetField_id(), CSeqTable_column_Base::SetHeader(), CSeqTable_multi_data_Base::SetLoc(), 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 )

clears all columns rows and delimiters

Definition at line 116 of file table_annot_data_source.cpp.

◆ CreateFeature()

bool CTableAnnotDataSource::CreateFeature	(	const STableLocation &	fc,
		ICanceled *	cancel = `NULL`
	)

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()

bool CTableAnnotDataSource::CreateSnpFeature	(	const STableLocation &	fc,
		ICanceled *	cancel = `NULL`
	)

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()

bool CTableAnnotDataSource::CreateSnps	(	const STableLocation &	fc,
		ICanceled *	cancel = `NULL`
	)

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()

vector< CTableAnnotDataSource::STableLocation > CTableAnnotDataSource::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.

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()

CRef<CSeq_annot> CTableAnnotDataSource::GetContainer ( )

inline

Definition at line 139 of file table_annot_data_source.hpp.

References m_AnnotContainer.

Referenced by CTableObjectLoader::CTableObjectLoader(), CTestApplication::LoadTable(), CAttribTableColumnIdPanel::OnApplyNoCloseClick(), CTableXformPanel::Show(), CQualTableLoadManager::x_ConvertToSeqAnnot(), and CTableImportWizard::x_ConvertToSeqAnnot().

◆ GetField()

string CTableAnnotDataSource::GetField	(	size_t	row,
		size_t	col
	)		const

return a specific field from a specific row, based on current table type and delimiter

Definition at line 121 of file table_annot_data_source.cpp.

◆ GetNumRows()

size_t CTableAnnotDataSource::GetNumRows ( void ) const

inline

return total number of rows read

Definition at line 111 of file table_annot_data_source.hpp.

◆ Init()

void CTableAnnotDataSource::Init ( void )

inline

Definition at line 106 of file table_annot_data_source.hpp.

◆ 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 )

Write seqtable to file 'fname'.

If write_extended_form is not true a seq-table will be written, otherwise a seq-annot with meta- information will be written with an embedded seq-table.

Definition at line 2578 of file table_annot_data_source.cpp.

References Error(), CException::GetMsg(), CRef< C, Locker >::IsNull(), LOG_POST, m_AnnotContainer, and MSerial_AsnText.

Referenced by CTestApplication::LoadTable().