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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/expand__gaps_8cpp_source.html below:

NCBI C++ ToolKit: src/gui/packages/pkg_sequence_edit/expand_gaps.cpp Source File

(

.IsSet() && !

.Get().empty() &&

.Get().back()->IsLiteral() &&

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

&&

.Get().back()->GetLiteral().GetSeq_data().IsIupacna())

seq =

.Get().back()->GetLiteral().GetSeq_data().GetIupacna().Get();

.Set().back()->SetLiteral().SetSeq_data().SetIupacna().Set().assign(seq.data(), seq.length());

has_loc(

);

( (*iter)->IsLoc() )

modified(

);

(delta_i->Empty())

cur_finish = pos + delta_len;

((

)cur_finish <

&& sv[cur_finish] ==

&& !sv.

(cur_finish))

length = cur_finish - prev_finish + 1;

modified |= (length != delta_len);

new_seg->Assign(seg);

new_seg->SetLiteral().SetLength(length);

new_inst->

().SetDelta().Set().push_back(new_seg);

prev_finish = cur_finish + 1;

(pos > (

)prev_finish)

new_seg->Assign(seg);

new_inst->

().SetDelta().Set().push_back(new_seg);

prev_finish = pos + delta_len;

cur_finish = pos + delta_len - 1;

(cur_finish >= prev_finish && sv[cur_finish] ==

&& !sv.

(cur_finish))

(cur_finish > prev_finish)

sv.

(prev_finish, cur_finish, iupac);

prev_finish = cur_finish;

(std::exception )

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

void AddCommand(IEditCommand &command)

static CRef< CCmdComposite > apply(objects::CSeq_entry_Handle tse)

static void AppendLiteral(objects::CDelta_ext &delta, const string &iupac)

static bool IsSkipGap(const objects::CDelta_seq &seg)

USING_SCOPE(ncbi::objects)

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Set object to copy of another one.

TSeqPos GetBioseqLength(void) const

bool IsSetInst(void) const

CSeqVector GetSeqVector(EVectorCoding coding, ENa_strand strand=eNa_strand_plus) const

Get sequence: Iupacna or Iupacaa if use_iupac_coding is true.

const TInst & GetInst(void) const

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

bool IsInGap(TSeqPos pos) const

true if sequence at 0-based position 'pos' has gap Note: this method is not MT-safe,...

void GetSeqData(TSeqPos start, TSeqPos stop, string &buffer) const

Fill the buffer string with the sequence data for the interval [start, stop).

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

void SetExt(TExt &value)

Assign a value to Ext data member.

const TLiteral & GetLiteral(void) const

Get the variant data.

bool IsSetExt(void) const

extensions for special types Check if a value has been assigned to Ext data member.

TLength GetLength(void) const

Get the Length member data.

bool IsSetFuzz(void) const

could be unsure Check if a value has been assigned to Fuzz data member.

bool IsDelta(void) const

Check if variant Delta is selected.

const TExt & GetExt(void) const

Get the Ext member data.

const TDelta & GetDelta(void) const

Get the variant data.

const Tdata & Get(void) const

Get the member data.

bool IsLiteral(void) const

Check if variant Literal is selected.

list< CRef< CDelta_seq > > Tdata

void ResetExt(void)

Reset Ext data member.

@ eMol_na

just a nucleic acid

Int4 delta(size_t dimension_, const Int4 *score_)

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