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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/Bioseq_8cpp_source.html below:

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

( loc.

() ) {

dseq->SetLoc().SetInt().Assign(**ii);

ext.

().push_back(dseq);

pnt_loc->

().SetPoint(*

);

pnt_loc->

().SetStrand(

dseq->SetLoc(*pnt_loc);

SerialAssign<CSeq_loc>(*cp_loc, loc);

( str_id.empty() ) {

->SetLocal().SetStr(str_id);

(desc.

()) {

taxid_from_source !=

? taxid_from_source : taxid_from_org;

=

().begin()->GetPointer();

& sid = **id_itr;

(sid.

()) {

->WriteAsFasta(os);

(!

->empty()) {

tv = CSeq_inst::GetTypeInfo_enum_ERepr();

tv = CSeq_inst::GetTypeInfo_enum_EMol();

*

().begin();

(

.

()) {

->BestRankScore();

(

.

()) {

}

( !id->

() ) {

((*it)->CheckNumRows() != 2) {

& id1 = (*it)->GetSeq_id(0);

& id2 = (*it)->GetSeq_id(1);

->BestRankScore();

(

.NotEmpty() && id->

()) {

(

.Which()) {

(ext.

().size() > 1) {

static int s_BestLocalRank(const CRef< CSeq_id > &id)

static int s_BestNonLocalRank(const CRef< CSeq_id > &id)

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.

const CSeq_id * GetNonLocalId() const

Find a non-local ID if present, consulting assembly details if all IDs for the overall sequence are l...

virtual bool UserOp_Equals(const CSerialUserOp &object) const

Will be called after comparing the datatool-generated members.

const CSeq_id * GetFirstId() const

static void x_SeqLoc_To_DeltaExt(const CSeq_loc &loc, CDelta_ext &ext)

TSeqPos GetLength(void) const

void GetLabel(string *label, ELabelType type, bool worst=false) const

bool IsSetLength(void) const

const CSeq_id * GetLocalId() const

Find a local ID if present.

TTaxId GetTaxId() const

Determine the tax-id for this bioseq.

virtual void UserOp_Assign(const CSerialUserOp &source)

Will be called after copying the datatool-generated members.

void PackAsDeltaSeq(bool gaps_ok=false)

Convert a raw nucleotide sequence with occasional ambiguities or gaps into a tighter (but somewhat mo...

static int sm_ConstructedId

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...

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

static bool IsAa(EMol mol)

static bool IsNa(EMol mol)

Base class for user-defined serializable classes to allow for objects assignment and comparison.

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

bool Empty(const CNcbiOstrstream &src)

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

SStrictId_Tax::TId TTaxId

Taxon id type.

#define ERR_POST_X(err_subcode, message)

Error posting with default error code and given error subcode.

void Warning(CExceptionArgs_Base &args)

const string & FindName(TEnumValueType value, bool allowBadValue) const

Find name of the enum by its numeric value.

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

Optimized implementation of CSerialObject::Assign, which is not so efficient.

bool Match(const CSeq_id &sid2) const

Match() - TRUE if SeqIds are equivalent.

static int WorstRank(const CRef< CSeq_id > &id)

const CTextseq_id * GetTextseq_Id(void) const

Return embedded CTextseq_id, if any.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

C::value_type FindBestChoice(const C &container, F score_func)

Find the best choice (lowest score) for values in a container.

static const char label[]

bool IsSetOrg(void) const

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

const TOrg & GetOrg(void) const

Get the Org member data.

TStr & SetStr(void)

Select the variant.

bool IsSetAccession(void) const

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

list< CRef< CSeq_interval > > Tdata

const Tdata & Get(void) const

Get the member data.

TStrand GetStrand(void) const

Get the Strand member data.

bool IsSetStrand(void) const

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

list< CRef< CSeq_loc > > Tdata

E_Choice Which(void) const

Which variant is currently selected.

const TId & GetId(void) const

Get the Id member data.

E_Choice Which(void) const

Which variant is currently selected.

const Tdata & Get(void) const

Get the member data.

const TPacked_pnt & GetPacked_pnt(void) const

Get the variant data.

vector< TSeqPos > TPoints

TLocal & SetLocal(void)

Select the variant.

void ResetName(void)

Reset Name data member.

bool IsLocal(void) const

Check if variant Local is selected.

const TPoints & GetPoints(void) const

Get the Points member data.

const TMix & GetMix(void) const

Get the variant data.

const TPacked_int & GetPacked_int(void) const

Get the variant data.

@ e_Other

for historical reasons, 'other' = 'refseq'

list< CRef< CSeqdesc > > Tdata

TId & SetId(void)

Assign a value to Id data member.

list< CRef< CSeq_align > > TAssembly

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.

TLoc & SetLoc(void)

Select the variant.

bool IsOrg(void) const

Check if variant Org is selected.

void SetExt(TExt &value)

Assign a value to Ext data member.

const TSource & GetSource(void) const

Get the variant data.

bool IsSource(void) const

Check if variant Source is selected.

const TId & GetId(void) const

Get the Id member data.

bool IsSetExt(void) const

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

Tdata & Set(void)

Assign a value to data member.

TLength GetLength(void) const

Get the Length member data.

const TOrg & GetOrg(void) const

Get the variant data.

const TAssembly & GetAssembly(void) const

Get the Assembly member data.

list< CRef< CSeq_id > > TId

static string SelectionName(E_Choice index)

Retrieve selection name (for diagnostic purposes).

TInst & SetInst(void)

Assign a value to Inst data member.

bool IsSetLength(void) const

length of sequence in residues Check if a value has been assigned to Length data member.

bool CanGetHist(void) const

Check if it is safe to call GetHist method.

const THist & GetHist(void) const

Get the Hist member data.

bool IsSetDescr(void) const

descriptors Check if a value has been assigned to Descr data member.

void SetRepr(TRepr value)

Assign a value to Repr data member.

const Tdata & Get(void) const

Get the member data.

void ResetExt(void)

Reset Ext data member.

const TSeq_data & GetSeq_data(void) const

Get the Seq_data member data.

const TDescr & GetDescr(void) const

Get the Descr member data.

void SetMol(TMol value)

Assign a value to Mol data member.

void ResetSeq_data(void)

Reset Seq_data data member.

bool CanGetAssembly(void) const

Check if it is safe to call GetAssembly method.

@ eRepr_const

constructed sequence

@ eRepr_delta

sequence made by changes (delta) to others

@ e_Ncbi2na

2 bit nucleic acid code

Definition of all error codes used in objects libraries.

const TYPE & Get(const CNamedParameterList *param)

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

Useful/utility classes and methods.

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