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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/Spliced__exon___8hpp_source.html below:

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

list< CRef< CSpliced_exon_chunk > >

;

list< CRef< CUser_object > >

;

e_acceptor_before_exon,

IsSetProduct_start(

)

;

CanGetProduct_start(

)

;

ResetProduct_start(

);

IsSetProduct_end(

)

;

CanGetProduct_end(

)

;

ResetProduct_end(

);

IsSetGenomic_start(

)

;

CanGetGenomic_start(

)

;

ResetGenomic_start(

);

IsSetGenomic_end(

)

;

CanGetGenomic_end(

)

;

ResetGenomic_end(

);

IsSetProduct_id(

)

;

CanGetProduct_id(

)

;

ResetProduct_id(

);

IsSetGenomic_id(

)

;

CanGetGenomic_id(

)

;

ResetGenomic_id(

);

IsSetProduct_strand(

)

;

CanGetProduct_strand(

)

;

ResetProduct_strand(

);

IsSetGenomic_strand(

)

;

CanGetGenomic_strand(

)

;

ResetGenomic_strand(

);

IsSetParts(

)

;

CanGetParts(

)

;

ResetParts(

);

& GetParts(

)

;

& SetParts(

);

IsSetScores(

)

;

CanGetScores(

)

;

ResetScores(

);

& GetScores(

)

;

IsSetAcceptor_before_exon(

)

;

CanGetAcceptor_before_exon(

)

;

ResetAcceptor_before_exon(

);

IsSetDonor_after_exon(

)

;

CanGetDonor_after_exon(

)

;

ResetDonor_after_exon(

);

IsSetPartial(

)

;

CanGetPartial(

)

;

ResetPartial(

);

IsSetExt(

)

;

CanGetExt(

)

;

ResetExt(

);

& GetExt(

)

;

& SetExt(

);

Reset(

);

list< CRef< CUser_object > >

;

void SetScores(objects::CSeq_align &seq_align, objects::CScope &scope, const string &matrix_name="BLOSUM62")

Base class for all serializable objects.

complete or partial exon two consecutive Spliced-exons may belong to one exon

unsigned int TSeqPos

Type for sequence locations and lengths.

static char UnassignedByte(void)

void ThrowUnassigned(TMemberIndex index) const

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

bool CanGetParts(void) const

Check if it is safe to call GetParts method.

bool IsSetProduct_strand(void) const

should be 'plus' or 'minus' Check if a value has been assigned to Product_strand data member.

bool CanGetGenomic_end(void) const

Check if it is safe to call GetGenomic_end method.

const TDonor_after_exon & GetDonor_after_exon(void) const

Get the Donor_after_exon member data.

CRef< TDonor_after_exon > m_Donor_after_exon

const TExt & GetExt(void) const

Get the Ext member data.

bool IsSetGenomic_end(void) const

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

void ResetGenomic_end(void)

Reset Genomic_end data member.

list< CRef< CUser_object > > m_Ext

bool CanGetPartial(void) const

Check if it is safe to call GetPartial method.

CRef< TProduct_id > m_Product_id

bool CanGetAcceptor_before_exon(void) const

Check if it is safe to call GetAcceptor_before_exon method.

ENa_strand TGenomic_strand

bool IsSetParts(void) const

basic seqments always are in biologic order Check if a value has been assigned to Parts data member.

TProduct_end & SetProduct_end(void)

Assign a value to Product_end data member.

void ResetGenomic_start(void)

Reset Genomic_start data member.

bool CanGetProduct_start(void) const

Check if it is safe to call GetProduct_start method.

CSpliced_exon_Base & operator=(const CSpliced_exon_Base &)

void ResetPartial(void)

Reset Partial data member.

DECLARE_INTERNAL_TYPE_INFO()

list< CRef< CSpliced_exon_chunk > > m_Parts

void ResetProduct_start(void)

Reset Product_start data member.

TGenomic_start GetGenomic_start(void) const

Get the Genomic_start member data.

const TProduct_id & GetProduct_id(void) const

Get the Product_id member data.

bool IsSetPartial(void) const

flag: is this exon complete or partial? Check if a value has been assigned to Partial data member.

const TAcceptor_before_exon & GetAcceptor_before_exon(void) const

Get the Acceptor_before_exon member data.

bool CanGetGenomic_id(void) const

Check if it is safe to call GetGenomic_id method.

bool IsSetProduct_end(void) const

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

CSplice_site TDonor_after_exon

bool IsSetAcceptor_before_exon(void) const

splice sites Check if a value has been assigned to Acceptor_before_exon data member.

void ResetProduct_end(void)

Reset Product_end data member.

CRef< TGenomic_id > m_Genomic_id

TGenomic_strand & SetGenomic_strand(void)

Assign a value to Genomic_strand data member.

TExt & SetExt(void)

Assign a value to Ext data member.

void ResetGenomic_strand(void)

Reset Genomic_strand data member.

bool IsSetGenomic_strand(void) const

genomic-strand represents the strand of translation Check if a value has been assigned to Genomic_str...

CProduct_pos TProduct_start

CProduct_pos TProduct_end

bool IsSetProduct_id(void) const

product is either protein or transcript (cDNA) Check if a value has been assigned to Product_id data ...

const TParts & GetParts(void) const

Get the Parts member data.

const TProduct_start & GetProduct_start(void) const

Get the Product_start member data.

const TProduct_end & GetProduct_end(void) const

Get the Product_end member data.

CRef< TAcceptor_before_exon > m_Acceptor_before_exon

bool IsSetGenomic_start(void) const

genomic-end >= genomic-start Check if a value has been assigned to Genomic_start data member.

bool IsSetProduct_start(void) const

product-end >= product-start Check if a value has been assigned to Product_start data member.

bool CanGetGenomic_strand(void) const

Check if it is safe to call GetGenomic_strand method.

bool IsSetExt(void) const

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

const TScores & GetScores(void) const

Get the Scores member data.

TGenomic_start & SetGenomic_start(void)

Assign a value to Genomic_start data member.

ENa_strand TProduct_strand

TProduct_strand & SetProduct_strand(void)

Assign a value to Product_strand data member.

TPartial GetPartial(void) const

Get the Partial member data.

TGenomic_strand GetGenomic_strand(void) const

Get the Genomic_strand member data.

bool CanGetExt(void) const

Check if it is safe to call GetExt method.

CSpliced_exon_Base(const CSpliced_exon_Base &)

TProduct_strand GetProduct_strand(void) const

Get the Product_strand member data.

TParts & SetParts(void)

Assign a value to Parts data member.

TPartial & SetPartial(void)

Assign a value to Partial data member.

TProduct_start & SetProduct_start(void)

Assign a value to Product_start data member.

bool CanGetProduct_id(void) const

Check if it is safe to call GetProduct_id method.

ENa_strand m_Genomic_strand

bool CanGetScores(void) const

Check if it is safe to call GetScores method.

list< CRef< CUser_object > > TExt

list< CRef< CSpliced_exon_chunk > > TParts

bool CanGetProduct_strand(void) const

Check if it is safe to call GetProduct_strand method.

bool CanGetDonor_after_exon(void) const

Check if it is safe to call GetDonor_after_exon method.

TGenomic_end GetGenomic_end(void) const

Get the Genomic_end member data.

TGenomic_end & SetGenomic_end(void)

Assign a value to Genomic_end data member.

bool IsSetGenomic_id(void) const

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

CSplice_site TAcceptor_before_exon

ENa_strand m_Product_strand

CRef< TProduct_end > m_Product_end

Tparent::CMemberIndex< E_memberIndex, 15 > TmemberIndex

bool CanGetGenomic_start(void) const

Check if it is safe to call GetGenomic_start method.

void ResetProduct_strand(void)

Reset Product_strand data member.

CRef< TProduct_start > m_Product_start

const TGenomic_id & GetGenomic_id(void) const

Get the Genomic_id member data.

bool IsSetDonor_after_exon(void) const

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

bool CanGetProduct_end(void) const

Check if it is safe to call GetProduct_end method.

bool IsSetScores(void) const

scores for this exon Check if a value has been assigned to Scores data member.

ENa_strand

strand of nucleic acid

const GenericPointer< typename T::ValueType > T2 value

void SetPartial(CSeq_loc &loc, CRef< CSeq_feat > feat, CSeq_loc::TStrand strand, bool partial_start, bool partial_stop)

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