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NCBI C++ ToolKit: src/objtools/edit/gaps_edit.cpp Source File

(

.Which()) {

(!Make_Iupacna(

, decoded,

))

(

.GetLiteral().IsSetSeq_data())

(

.IsLiteral() &&

.GetLiteral().IsSetSeq_data())

MakeGap(

.GetLiteral().GetSeq_data(),

, ext, gap_start,

);

CloneLiteral(

, ext, gap_start);

(

->IsLiteral())

(!

->GetLiteral().IsSetLength())

(gap_start < lit_len)

it = ext.

().erase(it);

ext.

().insert(it, new_ext.

().begin(), new_ext.

().end());

(lit_len > gap_start)

gap_start -= lit_len;

(ext.

().size() > 1) {

m_gap_type(gap_type),

m_DefaultEvidence(evidences),

m_gap_Unknown_length(gap_Unknown_length)

m_gap_type(gap_type),

m_DefaultEvidence(defaultEvidence),

m_GapsizeToEvidenceMap(countToEvidenceMap),

m_gap_Unknown_length(gap_Unknown_length)

(!Make_Iupacna(

, decoded,

))

(current.

() > 0)

(ext.

().size() > 1) {

dst_data.

().clear();

(!(**it).IsLiteral())

dst_data.

().push_back(*it);

dst_data.

().push_back(*it);

(length_unknown) {

& evidenceSet =

(evidenceSet.empty()) {

(

& evidence : evidenceSet) {

pEvidence->SetType(evidence);

gap.

().SetGap().SetLinkage_evidence().emplace_back(std::move(pEvidence));

(entry.

())

delta_seq->SetLiteral().SetSeq_data(bioseq.

().SetSeq_data());

delta_seq->SetLiteral().SetLength(

);

delta_ext.

().push_back(delta_seq);

bioseq.

().ResetSeq_data();

bioseq.

().SetExt().SetDelta().Set().push_back(delta_seq);

& delta_set = parent.

().SetExt().SetDelta().Set();

(!delta_set.empty() && delta_set.back()->GetLiteral().IsSetSeq_data())

delta_set.splice(delta_set.end(), bioseq.

().SetExt().SetDelta().Set());

delta_seq->SetLiteral().SetSeq_data(bioseq.

().SetSeq_data());

delta_set.push_back(delta_seq);

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.

TSeqPos GetLength(void) 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 & AddLiteral(TSeqPos len)

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

CRef< CDelta_seq > CreateGap(CBioseq &bioseq, TSeqPos gap_start, TSeqPos gap_length)

void AppendGap(CBioseq &bioseq)

void ConvertBioseqToDelta(CBioseq &bioseq)

TSeqPos m_gap_Unknown_length

void AddBioseqAsLiteral(CBioseq &parent, CBioseq &seqset)

TEvidenceSet m_DefaultEvidence

void ConvertNs2Gaps(CSeq_entry &entry)

void x_SetGapParameters(CDelta_seq &gap)

CGapsEditor(CSeq_gap::EType gap_type, const TEvidenceSet &evidences, TSeqPos gapNmin, TSeqPos gap_Unknown_length)

TCountToEvidenceMap m_GapsizeToEvidenceMap

CSeq_gap::EType m_gap_type

static bool IsAa(EMol mol)

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

const_iterator end() const

const_iterator find(const key_type &key) const

unsigned int TSeqPos

Type for sequence locations and lengths.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

CRef< C > Ref(C *object)

Helper functions to get CRef<> and CConstRef<> objects.

bool NotEmpty(void) const THROWS_NONE

Check if CRef is not empty – pointing to an object and has a non-null value.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

CTempString & assign(const char *src_str, size_type len)

Assign new values to the content of the a string.

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 find_first_not_of(const CTempString match, size_type pos=0) const

Find the first occurrence of any character not in the matching string within the current string,...

size_type find_first_of(const CTempString match, size_type pos=0) const

Find the first occurrence of any character in the matching string within the current string,...

static const size_type npos

TSet & SetSet(void)

Select the variant.

E_Choice Which(void) const

Which variant is currently selected.

list< CRef< CSeq_entry > > TSeq_set

TSeq & SetSeq(void)

Select the variant.

TSeq_set & SetSeq_set(void)

Assign a value to Seq_set data member.

TLiteral & SetLiteral(void)

Select the variant.

void SetLength(TLength value)

Assign a value to Length data member.

bool IsSetSeq_data(void) const

the sequence Check if a value has been assigned to Seq_data data member.

const TInst & GetInst(void) const

Get the Inst member data.

void SetSeq_data(TSeq_data &value)

Assign a value to Seq_data data member.

const TGap & GetGap(void) const

Get the variant data.

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.

bool IsSetInst(void) const

the sequence data Check if a value has been assigned to Inst data member.

Tdata & Set(void)

Assign a value to data member.

TLength GetLength(void) const

Get the Length member data.

TLength GetLength(void) const

Get the Length member data.

const TLinkage_evidence & GetLinkage_evidence(void) const

Get the Linkage_evidence member data.

bool IsDelta(void) const

Check if variant Delta is selected.

void SetFuzz(TFuzz &value)

Assign a value to Fuzz data member.

void SetInst(TInst &value)

Assign a value to Inst data member.

const TExt & GetExt(void) const

Get the Ext member data.

bool IsSetLength(void) const

must give a length in residues Check if a value has been assigned to Length data member.

const TDelta & GetDelta(void) const

Get the variant data.

void SetRepr(TRepr value)

Assign a value to Repr data member.

const Tdata & Get(void) const

Get the member data.

bool IsSetSeq_data(void) const

may have the data Check if a value has been assigned to Seq_data data member.

list< CRef< CDelta_seq > > Tdata

bool IsGap(void) const

Check if variant Gap is selected.

void ResetExt(void)

Reset Ext data member.

const TSeq_data & GetSeq_data(void) const

Get the Seq_data member data.

const TSeq_data & GetSeq_data(void) const

Get the Seq_data member data.

void ResetSeq_data(void)

Reset Seq_data data member.

@ eRepr_delta

sequence made by changes (delta) to others

@ e_Iupacna

IUPAC 1 letter nuc acid code.

bm::gap_word_t gap_length(const bm::gap_word_t *buf) noexcept

Returs GAP block length.

if(yy_accept[yy_current_state])

Useful/utility classes and methods.

Int4 delta(size_t dimension_, const Int4 *score_)

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