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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/Delta__ext_8cpp_source.html below:

NCBI C++ ToolKit: src/objects/seq/Delta_ext.cpp Source File

71 if

( !

Get

().

empty

() &&

Get

().back()->IsLiteral()

72

&& !

Get

().back()->GetLiteral().IsSetSeq_data()

73

&& !

Get

().back()->GetLiteral().IsSetFuzz()) {

75 Set

().back()->SetLiteral().SetLength() +=

len

;

76 return

Set

().back();

80

seg->SetLiteral().SetLength(

len

);

82 Set

().push_back(seg);

97

seg->SetLiteral().SetSeq_data().SetIupacaa().Set().assign(iupac_seq.

data

(), iupac_seq.

length

());

103

seg->SetLiteral().SetSeq_data().SetIupacna().Set().assign(iupac_seq.

data

(), iupac_seq.

length

());

110 "CDelta_ext::AddLiteral(): unhandled mol type"

);

114 Set

().push_back(seg);

153 #define CODING_CASE_EX(key, type, setter, len) \ 154 case CSeqUtil::key: \ 156 type& dest = lit.SetSeq_data().setter(); \ 157 dest.Set().resize(len); \ 158 return &dest.Set()[0]; \ 160 #define CODING_CASE(name, type) \ 161 CODING_CASE_EX(e_##name, type, Set##name, length) 174 #undef CODING_CASE_EX 178 "CDelta_ext_PackTarget: unexpected coding"

);

185 bool

gaps_ok,

bool

allow_packing)

214 Set

().push_back(ds);

224

seg->SetLoc().SetInt().SetFrom(from);

225

seg->SetLoc().SetInt().SetTo (to);

226

seg->SetLoc().SetId(

id

);

227

seg->SetLoc().SetStrand(strand);

229 Set

().push_back(seg);

#define CODING_CASE(name, type)

#define CODING_CASE_EX(key, type, setter, len)

User-defined methods of the data storage class.

CDelta_ext_PackTarget(CDelta_ext &obj, bool gaps_ok)

virtual bool GapsOK(TCodingType) const

char * NewSegment(TCoding coding, TSeqPos length)

SIZE_TYPE GetOverhead(TCoding coding) const

void AddAndSplit(const CTempString &src, CSeq_data::E_Choice format, TSeqPos length, bool gaps_ok=false, bool allow_packing=true)

add a chunk of sequence, splitting it as necessary for the sake of compactness (isolating ambiguous p...

CDelta_seq & AddSeqRange(const CSeq_id &id, TSeqPos from, TSeqPos to, ENa_strand strand=eNa_strand_plus)

add a segment that refers to another segment

CDelta_seq & AddLiteral(TSeqPos len)

add a literal segment at the end this variant adds a gap literal

CSeqUtil::ECoding TCoding

static SIZE_TYPE Pack(const string &src, TCoding src_coding, vector< char > &dst, TCoding &dst_coding, TSeqPos length=ncbi::numeric_limits< TSeqPos >::max())

static TSeqPos Pack(CSeq_data *in_seq, TSeqPos uLength=ncbi::numeric_limits< TSeqPos >::max())

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

unsigned int TSeqPos

Type for sequence locations and lengths.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

NCBI_NS_STD::string::size_type SIZE_TYPE

const char * data(void) const

Return a pointer to the array represented.

size_type length(void) const

Return the length of the represented array.

size_type size(void) const

Return the length of the represented array.

ENa_strand

strand of nucleic acid

void SetLength(TLength value)

Assign a value to Length data member.

void SetSeq_data(TSeq_data &value)

Assign a value to Seq_data data member.

E_Choice

Choice variants.

Tdata & Set(void)

Assign a value to data member.

EMol

molecule class in living organism

const Tdata & Get(void) const

Get the member data.

@ e_Ncbieaa

extended ASCII 1 letter aa codes

@ e_Ncbistdaa

consecutive codes for std aas

@ e_Iupacna

IUPAC 1 letter nuc acid code.

@ e_Ncbi8na

8 bit extended nucleic acid code

@ e_Ncbi4na

4 bit nucleic acid code

@ e_Iupacaa

IUPAC 1 letter amino acid code.

@ e_Ncbi8aa

8 bit extended amino acid codes

@ eMol_na

just a nucleic acid

constexpr bool empty(list< Ts... >) noexcept

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