SSeqTableContent Struct Reference

Search Toolkit Book for SSeqTableContent

Collaboration diagram for SSeqTableContent:

Public Member Functions
	SSeqTableContent (void)
void	Add (const CSNPDbFeatIterator &it)
CRef< CSeq_annot >	GetAnnot (const string &annot_name, CSeq_id &seq_id)

Static Public Member Functions
static void	AddFixedString (CSeq_table &table, CSeqTable_column_info::EField_id id, const string &value)
static void	AddFixedSeq_id (CSeq_table &table, CSeqTable_column_info::EField_id id, CSeq_id &value)
static void	AddFixedSeq_loc (CSeq_table &table, const char *name, CSeq_loc &value)
static void	AddFixedInt (CSeq_table &table, const char *name, int value)

Public Attributes
int	m_TableSize
SIntColumn	col_from
SIntColumn	col_to
SSparseIndex	ind_to
SCommonStrings	col_alleles [kMaxTableAlleles]
SCommonStrings	col_subtype
SCommon8Bytes	col_bitfield
SInt8Column	col_dbxref

Detailed Description

Definition at line 1566 of file snpread.cpp.

Constructor & Destructor Documentation

SSeqTableContent()

SSeqTableContent::SSeqTableContent

(

void

)

Definition at line 1627 of file snpread.cpp.

References col_alleles, CSeqTable_column_info_Base::eField_id_qual, i, SColumn::Init(), and kMaxTableAlleles.

Member Function Documentation

Add()

void SSeqTableContent::Add ( const CSNPDbFeatIterator &  it )

inline

Definition at line 1644 of file snpread.cpp.

References _ASSERT, SCommonStrings::Add(), SSparseIndex::Add(), SIntColumn::Add(), SInt8Column::Add(), SCommon8Bytes::Add(), col_alleles, col_bitfield, col_dbxref, col_from, col_subtype, col_to, CSNPDbFeatIterator::GetAllele(), CSNPDbFeatIterator::GetBitfield(), CSNPDbFeatIterator::GetExtraRange(), CSNPDbFeatIterator::GetFeatId(), CSNPDbFeatIterator::GetFeatSubtypeString(), CSNPDbFeatIterator::GetSNPLength(), CSNPDbFeatIterator::GetSNPPosition(), i, ind_to, kMaxTableAlleles, len, m_TableSize, and compile_time_bits::range().

Referenced by SSeqTableConverter::AddToTable().

AddFixedInt()

static void SSeqTableContent::AddFixedInt ( CSeq_table &  table, const char *  name, int  value  )

inlinestatic

Definition at line 1616 of file snpread.cpp.

References CSeqTable_column_Base::SetDefault(), table, value, and x_MakeColumn().

Referenced by GetAnnot().

AddFixedSeq_id()

static void SSeqTableContent::AddFixedSeq_id ( CSeq_table &  table, CSeqTable_column_info::EField_id  id, CSeq_id &  value  )

inlinestatic

Definition at line 1598 of file snpread.cpp.

References CSeqTable_column_Base::SetDefault(), table, value, and x_MakeColumn().

Referenced by GetAnnot().

AddFixedSeq_loc()

static void SSeqTableContent::AddFixedSeq_loc ( CSeq_table &  table, const char *  name, CSeq_loc &  value  )

inlinestatic

Definition at line 1607 of file snpread.cpp.

References CSeqTable_column_Base::SetDefault(), table, value, and x_MakeColumn().

Referenced by GetAnnot().

AddFixedString()

static void SSeqTableContent::AddFixedString ( CSeq_table &  table, CSeqTable_column_info::EField_id  id, const string &  value  )

inlinestatic

Definition at line 1589 of file snpread.cpp.

References CSeqTable_column_Base::SetDefault(), table, value, and x_MakeColumn().

Referenced by GetAnnot().

GetAnnot()

CRef< CSeq_annot > SSeqTableContent::GetAnnot	(	const string &	annot_name,
		CSeq_id &	seq_id
	)

Definition at line 1670 of file snpread.cpp.

References _ASSERT, AddFixedInt(), AddFixedSeq_id(), AddFixedSeq_loc(), AddFixedString(), SColumn::Attach(), SCommonStrings::Attach(), SCommon8Bytes::Attach(), col_alleles, col_bitfield, col_dbxref, col_from, col_subtype, col_to, CSeqFeatData_Base::e_Imp, CSeqTable_column_info_Base::eField_id_data_imp_key, CSeqTable_column_info_Base::eField_id_ext_type, CSeqTable_column_info_Base::eField_id_location_id, CSeqFeatData::eSubtype_variation, i, ind_to, is_sorted(), kMaxSNPLength, kMaxTableAlleles, m_TableSize, SSparseIndex::Optimize(), CSeq_annot_Base::SetData(), CSeq_loc::SetInt(), table, SIntColumn::values, and x_NewAnnot().

Referenced by SSeqTableConverter::GetAnnots().

Member Data Documentation

col_alleles

SCommonStrings SSeqTableContent::col_alleles[kMaxTableAlleles]

Definition at line 1582 of file snpread.cpp.

Referenced by Add(), GetAnnot(), and SSeqTableContent().

col_bitfield

SCommon8Bytes SSeqTableContent::col_bitfield

Definition at line 1585 of file snpread.cpp.

Referenced by Add(), and GetAnnot().

col_dbxref

SInt8Column SSeqTableContent::col_dbxref

Definition at line 1587 of file snpread.cpp.

Referenced by Add(), and GetAnnot().

col_from

SIntColumn SSeqTableContent::col_from

Definition at line 1578 of file snpread.cpp.

Referenced by Add(), and GetAnnot().

col_subtype

SCommonStrings SSeqTableContent::col_subtype

Definition at line 1584 of file snpread.cpp.

Referenced by Add(), and GetAnnot().

col_to

SIntColumn SSeqTableContent::col_to

Definition at line 1579 of file snpread.cpp.

Referenced by Add(), and GetAnnot().

ind_to

SSparseIndex SSeqTableContent::ind_to

Definition at line 1580 of file snpread.cpp.

Referenced by Add(), and GetAnnot().

m_TableSize

int SSeqTableContent::m_TableSize

Definition at line 1575 of file snpread.cpp.

Referenced by Add(), and GetAnnot().

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The documentation for this struct was generated from the following file:

• src/sra/readers/sra/snpread.cpp