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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/Seq__align___8hpp_source.html below:

NCBI C++ ToolKit: include/objects/seqalign/Seq_align_.hpp Source File

ResetSelection(

);

E_Choice Which(

)

;

CheckSelected(E_Choice index)

;

NCBI_NORETURN

ThrowInvalidSelection(E_Choice index)

;

SelectionName(E_Choice index);

list< CRef< CStd_seg > >

;

IsDendiag(

)

;

& GetDendiag(

)

;

IsDenseg(

)

;

& GetDenseg(

)

;

IsStd(

)

;

& GetStd(

)

;

& SetStd(

);

IsPacked(

)

;

& GetPacked(

)

;

IsDisc(

)

;

& GetDisc(

)

;

& SetDisc(

);

IsSpliced(

)

;

& GetSpliced(

)

;

IsSparse(

)

;

& GetSparse(

)

;

*

sm_SelectionNames[];

NCBI_NS_NCBI::CUnionBuffer<TStd>

;

vector< CRef< CScore > >

;

list< CRef< CObject_id > >

;

list< CRef< CUser_object > >

;

IsSetType(

)

;

CanGetType(

)

;

ResetType(

);

GetType(

)

;

& SetType(

);

IsSetDim(

)

;

CanGetDim(

)

;

ResetDim(

);

GetDim(

)

;

& SetDim(

);

IsSetScore(

)

;

CanGetScore(

)

;

ResetScore(

);

& GetScore(

)

;

& SetScore(

);

IsSetSegs(

)

;

CanGetSegs(

)

;

ResetSegs(

);

& GetSegs(

)

;

& SetSegs(

);

IsSetBounds(

)

;

CanGetBounds(

)

;

ResetBounds(

);

& GetBounds(

)

;

IsSetId(

)

;

CanGetId(

)

;

ResetId(

);

IsSetExt(

)

;

CanGetExt(

)

;

ResetExt(

);

& GetExt(

)

;

& SetExt(

);

Reset(

);

list< CRef< CObject_id > >

;

list< CRef< CUser_object > >

;

( m_choice != index )

ThrowInvalidSelection(index);

DoSelect(index, pool);

Select(index, reset, 0);

m_choice == e_Dendiag;

CheckSelected(e_Dendiag);

m_choice == e_Denseg;

m_choice == e_Std;

CheckSelected(e_Std);

m_choice == e_Packed;

m_choice == e_Disc;

m_choice == e_Spliced;

m_choice == e_Sparse;

.NotEmpty();

Base class for all serializable objects.

static char UnassignedByte(void)

void ThrowUnassigned(TMemberIndex index) const

#define ENUM_METHOD_NAME(EnumName)

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

uint32_t Uint4

4-byte (32-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define NCBI_SEQALIGN_EXPORT

const TId & GetId(void) const

Get the Id member data.

TId & SetId(void)

Assign a value to Id data member.

TScore & SetScore(void)

Assign a value to Score data member.

TSegs & SetSegs(void)

Assign a value to Segs data member.

void Select(E_Choice index, EResetVariant reset=eDoResetVariant)

Select the requested variant if needed.

CSeq_align_Base & operator=(const CSeq_align_Base &)

NCBI_NS_NCBI::CUnionBuffer< TStd > m_Std

bool IsSetBounds(void) const

regions of sequence over which align was computed Check if a value has been assigned to Bounds data m...

E_Choice Which(void) const

Which variant is currently selected.

E_ChoiceStopper

Maximum+1 value of the choice variant enumerator.

TStd & SetStd(void)

Select the variant.

TType & SetType(void)

Assign a value to Type data member.

vector< CRef< CScore > > TScore

list< CRef< CStd_seg > > TStd

bool CanGetBounds(void) const

Check if it is safe to call GetBounds method.

bool IsSetId(void) const

alignment id Check if a value has been assigned to Id data member.

bool CanGetType(void) const

Check if it is safe to call GetType method.

E_Choice

Choice variants.

bool IsSetExt(void) const

extra info Check if a value has been assigned to Ext data member.

void ResetSegs(void)

Reset Segs data member.

void ResetDim(void)

Reset Dim data member.

TDim GetDim(void) const

Get the Dim member data.

void CheckSelected(E_Choice index) const

Verify selection, throw exception if it differs from the expected.

list< CRef< CUser_object > > m_Ext

bool IsSetSegs(void) const

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

NCBI_NS_NCBI::CSerialObject * m_object

bool CanGetScore(void) const

Check if it is safe to call GetScore method.

vector< CRef< CScore > > m_Score

NCBI_NS_NCBI::CUnionBuffer< TDendiag > m_Dendiag

list< CRef< CObject_id > > TId

list< CRef< CUser_object > > TExt

bool IsPacked(void) const

Check if variant Packed is selected.

bool IsSparse(void) const

Check if variant Sparse is selected.

bool IsDendiag(void) const

Check if variant Dendiag is selected.

bool CanGetSegs(void) const

Check if it is safe to call GetSegs method.

list< CRef< CSeq_loc > > TBounds

bool IsSetType(void) const

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

TExt & SetExt(void)

Assign a value to Ext data member.

TDendiag & SetDendiag(void)

Select the variant.

const TStd & GetStd(void) const

Get the variant data.

Tparent::CMemberIndex< E_memberIndex, 8 > TmemberIndex

DECLARE_INTERNAL_TYPE_INFO()

bool CanGetExt(void) const

Check if it is safe to call GetExt method.

bool CanGetDim(void) const

Check if it is safe to call GetDim method.

const TDendiag & GetDendiag(void) const

Get the variant data.

bool IsStd(void) const

Check if variant Std is selected.

void Select(E_Choice index, EResetVariant reset, CObjectMemoryPool *pool)

Select the requested variant if needed, allocating CObject variants from memory pool.

CSeq_align_Base(const CSeq_align_Base &)

bool IsDisc(void) const

Check if variant Disc is selected.

TType GetType(void) const

Get the Type member data.

TDim & SetDim(void)

Assign a value to Dim data member.

bool IsSetDim(void) const

dimensionality Check if a value has been assigned to Dim data member.

const TExt & GetExt(void) const

Get the Ext member data.

C_Segs & operator=(const C_Segs &)

bool IsSetScore(void) const

for whole alignment Check if a value has been assigned to Score data member.

bool IsSpliced(void) const

Check if variant Spliced is selected.

DECLARE_INTERNAL_TYPE_INFO()

const TScore & GetScore(void) const

Get the Score member data.

TBounds & SetBounds(void)

Assign a value to Bounds data member.

list< CRef< CDense_diag > > TDendiag

const TSegs & GetSegs(void) const

Get the Segs member data.

list< CRef< CSeq_loc > > m_Bounds

bool IsDenseg(void) const

Check if variant Denseg is selected.

const TBounds & GetBounds(void) const

Get the Bounds member data.

bool CanGetId(void) const

Check if it is safe to call GetId method.

void ResetType(void)

Reset Type data member.

list< CRef< CObject_id > > m_Id

const GenericPointer< typename T::ValueType > T2 value

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