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NCBI C++ ToolKit: src/objects/genomecoll/GC_Sequence.cpp Source File

, m_AssemblyUnit(

)

, m_ParentSequence(

)

, m_SeqLengthRetrieved(

)

( ; top && top->GetParent(); top = top->GetParent()) {

( (*it_syn)->Which() == syn_type )

typed_seq_id = *it_syn;

( typed_seq_id.

() )

( alias_type )

( seq_id_alias->IsSetPublic() )

( seq_id_alias->IsSetGpipe() )

( seq_id_alias->IsSetGi() )

( (*it_syn)->IsExternal() &&

ret = &((*it_syn)->GetExternal().GetId());

(*roleiter == Role)

(level == 0 || level == 1) {

is_in_subset =

;

is_in_subset =

;

);

children.push_back(child);

child->x_GetChildren(children, subset, 0,

(level-1,0));

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.

CGC_Replicon * m_Replicon

CGC_Sequence * m_ParentSequence

list< CConstRef< CGC_Sequence > > TSequenceList

CConstRef< CGC_Replicon > GetReplicon() const

Access the replicon the sequence belongs to.

string GetChrName() const

Get name of chromosome that this sequence belongs to, if any.

CGC_AssemblyUnit * m_AssemblyUnit

CConstRef< CSeq_id > GetSubmitterName() const

bool CanGetLength() const

Is the length statistic available?

CConstRef< CGC_AssemblyUnit > GetAssemblyUnit() const

Access the assembly unit the sequence belongs to.

CConstRef< CSeq_id > GetSynonymSeq_id(CGC_TypedSeqId::E_Choice type, CGC_SeqIdAlias::E_AliasTypes) const

void GetChildren(TSequenceList &children, EChildrenSubset subset=eAll, CGC_TaggedSequences::TState state=0, int level=0) const

Get sub-sequences.

TSeqPos GetLength() const

return the length of this sequence.

bool m_SeqLengthRetrieved

CConstRef< CGC_Assembly > GetFullAssembly() const

Access the most specific full assembly the sequence belongs to This is needed because assemblies are ...

void x_GetChildren(TSequenceList &children, EChildrenSubset subset, CGC_TaggedSequences::TState state, int level) const

TSeqPos x_GetLength() const

bool HasRole(int Role) const

string GetUnitDisplayName() const

Get full display name of assmebly unit.

bool IsOrganelle() const

Is this aN organelle sequence?

CConstRef< CGC_Sequence > GetTopLevelParent() const

Access the top-most parent sequence of this sequence.

CGC_TaggedSequences::TState GetParentRelation() const

Access the relationship to the parent.

CConstRef< CGC_Sequence > GetParent() const

Access the parent sequence of this sequence.

CGC_Assembly * m_Assembly

CGC_TaggedSequences::TState m_ParentRel

Thrown on an attempt to write unassigned data member.

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NCBI_THROW(exception_class, err_code, message)

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

bool IsNull(void) const THROWS_NONE

Check if pointer is null – same effect as Empty().

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another string.

E_Choice

Choice variants.

const TStats & GetStats(void) const

Get the Stats member data.

const TRoles & GetRoles(void) const

Get the Roles member data.

bool CanGetStats(void) const

Check if it is safe to call GetStats method.

list< CRef< CGC_TypedSeqId > > TSeq_id_synonyms

const TSeq_id_synonyms & GetSeq_id_synonyms(void) const

Get the Seq_id_synonyms member data.

bool CanGetRoles(void) const

Check if it is safe to call GetRoles method.

const TSequences & GetSequences(void) const

Get the Sequences member data.

bool CanGetAll_scaf(void) const

Check if it is safe to call GetAll_scaf method.

bool IsSetSeq_id_synonyms(void) const

Other known identifiers: Local / gpipe-satellite / genbank / refseq Check if a value has been assigne...

@ eGC_SequenceRole_component

@ eGC_SequenceRole_scaffold

@ eGC_SequenceRole_chromosome

@ eStats_category_total_length

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