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NCBI C++ ToolKit: src/gui/objutils/fingp_seqalign.cpp Source File

= (*it)->GetIndex();

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

Checksum and hash calculation classes.

CChecksum – Checksum calculator.

void Fingerprint(CChecksum &checksum, const CObject &obj, objects::CScope *scope) const

static void Register(TTypeInfo type_info, TFingerPFunc func)

static void s_Fingerprint_Sparse_seg(CChecksum &checksum, const CObject &object, CScope *scope, const CObjFingerprint &fingerP)

static void s_Fingerprint_Seq_align(CChecksum &checksum, const CObject &object, CScope *scope, const CObjFingerprint &fingerP)

static void s_Fingerprint_Packed_seg(CChecksum &checksum, const CObject &object, CScope *scope, const CObjFingerprint &fingerP)

static void s_Fingerprint_Spliced_exon(CChecksum &checksum, const CObject &object, CScope *scope, const CObjFingerprint &fingerP)

static void s_Fingerprint_Product_pos(CChecksum &checksum, const CObject &object, CScope *scope, const CObjFingerprint &fingerP)

static void s_Fingerprint_Spliced_seg(CChecksum &checksum, const CObject &object, CScope *scope, const CObjFingerprint &fingerP)

static void s_Fingerprint_Spliced_exon_chunk(CChecksum &checksum, const CObject &object, CScope *, const CObjFingerprint &)

static void s_Fingerprint_Dense_diag(CChecksum &checksum, const CObject &object, CScope *scope, const CObjFingerprint &fingerP)

static void s_Fingerprint_Std_seg(CChecksum &checksum, const CObject &object, CScope *scope, const CObjFingerprint &fingerP)

static void s_Fingerprint_Prot_pos(CChecksum &checksum, const CObject &object, CScope *, const CObjFingerprint &)

static void s_Fingerprint_Sparse_align(CChecksum &checksum, const CObject &object, CScope *scope, const CObjFingerprint &fingerP)

static void s_Fingerprint_Seq_align_set(CChecksum &checksum, const CObject &object, CScope *scope, const CObjFingerprint &fingerP)

static void s_Fingerprint_Dense_seg(CChecksum &checksum, const CObject &object, CScope *scope, const CObjFingerprint &fingerP)

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

vector< CRef< CSeq_id > > TIds

const TProtpos & GetProtpos(void) const

Get the variant data.

vector< TSeqPos > TStarts

const TDenseg & GetDenseg(void) const

Get the variant data.

const TExt & GetExt(void) const

Get the Ext member data.

vector< CRef< CSeq_loc > > TLoc

vector< ENa_strand > TStrands

vector< CRef< CSparse_align > > TRows

E_Choice

Choice variants.

E_Choice Which(void) const

Which variant is currently selected.

const TGenomic_id & GetGenomic_id(void) const

Get the Genomic_id member data.

E_Choice Which(void) const

Which variant is currently selected.

bool IsSetParts(void) const

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

const TLoc & GetLoc(void) const

Get the Loc member data.

list< CRef< CStd_seg > > TStd

bool IsSetStrands(void) const

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

E_Choice

Choice variants.

const TStarts & GetStarts(void) const

Get the Starts member data.

const TStarts & GetStarts(void) const

Get the Starts member data.

const TProduct_id & GetProduct_id(void) const

Get the Product_id member data.

const TProduct_id & GetProduct_id(void) const

Get the Product_id member data.

vector< ENa_strand > TStrands

const TLens & GetLens(void) const

Get the Lens member data.

const TIds & GetIds(void) const

Get the Ids member data.

const TFirst_id & GetFirst_id(void) const

Get the First_id member data.

TLen GetLen(void) const

Get the Len member data.

vector< TSignedSeqPos > TStarts

const TMaster_id & GetMaster_id(void) const

Get the Master_id member data.

vector< TSeqPos > TStarts

bool IsSetStrands(void) const

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

bool IsSetProduct_id(void) const

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

vector< CRef< CSeq_id > > TIds

const TParts & GetParts(void) const

Get the Parts member data.

E_Choice

Choice variants.

const TProduct_start & GetProduct_start(void) const

Get the Product_start member data.

vector< CRef< CSeq_id > > TIds

const TIds & GetIds(void) const

Get the Ids member data.

const TProduct_end & GetProduct_end(void) const

Get the Product_end member data.

bool IsSetProduct_id(void) const

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

const TSpliced & GetSpliced(void) const

Get the variant data.

vector< CRef< CSeq_id > > TIds

const TLens & GetLens(void) const

Get the Lens member data.

const TSecond_starts & GetSecond_starts(void) const

Get the Second_starts member data.

const TPacked & GetPacked(void) const

Get the variant data.

const TStd & GetStd(void) const

Get the variant data.

const TLens & GetLens(void) const

Get the Lens member data.

const TIds & GetIds(void) const

Get the Ids member data.

list< CRef< CSpliced_exon > > TExons

const TExons & GetExons(void) const

Get the Exons member data.

bool IsSetSecond_strands(void) const

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

vector< int > TSecond_starts

const TFirst_starts & GetFirst_starts(void) const

Get the First_starts member data.

const TDendiag & GetDendiag(void) const

Get the variant data.

bool IsSetStrands(void) const

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

const TPresent & GetPresent(void) const

Get the Present member data.

vector< ENa_strand > TStrands

const TStrands & GetStrands(void) const

Get the Strands member data.

const TIds & GetIds(void) const

Get the Ids member data.

const TStrands & GetStrands(void) const

Get the Strands member data.

const TSecond_strands & GetSecond_strands(void) const

Get the Second_strands member data.

vector< CRef< CSparse_seg_ext > > TExt

list< CRef< CSpliced_exon_chunk > > TParts

const TSecond_id & GetSecond_id(void) const

Get the Second_id member data.

vector< int > TFirst_starts

const TStarts & GetStarts(void) const

Get the Starts member data.

bool IsSetExt(void) const

index of extra items Check if a value has been assigned to Ext data member.

list< CRef< CSeq_align > > Tdata

const TSparse & GetSparse(void) const

Get the variant data.

bool IsSetGenomic_id(void) const

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

const TRows & GetRows(void) const

Get the Rows member data.

vector< ENa_strand > TSecond_strands

const TDisc & GetDisc(void) const

Get the variant data.

list< CRef< CDense_diag > > TDendiag

const TStrands & GetStrands(void) const

Get the Strands member data.

const Tdata & Get(void) const

Get the member data.

const TSegs & GetSegs(void) const

Get the Segs member data.

const TGenomic_id & GetGenomic_id(void) const

Get the Genomic_id member data.

bool IsSetGenomic_id(void) const

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

E_Choice Which(void) const

Which variant is currently selected.

@ e_Product_ins

insertion in product sequence (i.e. gap in the genomic sequence)

@ e_Diag

both sequences are represented, there is sufficient similarity between product and genomic sequences....

@ e_Genomic_ins

insertion in genomic sequence (i.e. gap in the product sequence)

@ e_Match

both sequences represented, product and genomic sequences match

@ e_Mismatch

both sequences represented, product and genomic sequences do not match

@ e_not_set

No variant selected.

ENa_strand

strand of nucleic acid

const GenericPointer< typename T::ValueType > T2 value

#define CKSUM_INTEGER_FIELD2(cksum, Type, field)

#define CKSUM_INTEGER_FIELD(cksum, Type, field)

#define CKSUM_ADD_INTEGER(cksum, value)

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