41 #ifndef OBJECTS_GENOMECOLL_GC_ASSEMBLYUNIT_BASE_HPP
42 #define OBJECTS_GENOMECOLL_GC_ASSEMBLYUNIT_BASE_HPP
52 #ifndef BEGIN_objects_SCOPE
53 # define BEGIN_objects_SCOPE BEGIN_SCOPE(objects)
54 # define END_objects_SCOPE END_SCOPE(objects)
95 eClass_haploid_unit = 1,
97 eClass_assembly_patch = 3,
105 typedef list< CRef< CDbtag > >
TId;
108 typedef list< CRef< CGC_Replicon > >
TMols;
124 e_unplaced_unlocalized_stats
148 bool IsSetId(
void)
const;
155 bool CanGetId(
void)
const;
179 bool IsSetClass(
void)
const;
186 bool CanGetClass(
void)
const;
189 void ResetClass(
void);
195 TClass GetClass(
void)
const;
217 bool IsSetDesc(
void)
const;
224 bool CanGetDesc(
void)
const;
227 void ResetDesc(
void);
233 const TDesc& GetDesc(
void)
const;
245 TDesc& SetDesc(
void);
255 bool IsSetMols(
void)
const;
262 bool CanGetMols(
void)
const;
265 void ResetMols(
void);
271 const TMols& GetMols(
void)
const;
277 TMols& SetMols(
void);
288 bool IsSetOther_sequences(
void)
const;
295 bool CanGetOther_sequences(
void)
const;
298 void ResetOther_sequences(
void);
323 bool IsSetStats(
void)
const;
330 bool CanGetStats(
void)
const;
333 void ResetStats(
void);
339 const TStats& GetStats(
void)
const;
360 bool IsSetUnplaced_stats(
void)
const;
367 bool CanGetUnplaced_stats(
void)
const;
370 void ResetUnplaced_stats(
void);
391 bool IsSetUnplaced_unlocalized_stats(
void)
const;
398 bool CanGetUnplaced_unlocalized_stats(
void)
const;
401 void ResetUnplaced_unlocalized_stats(
void);
416 virtual void Reset(
void);
Base class for all serializable objects.
static char UnassignedByte(void)
void ThrowUnassigned(TMemberIndex index) const
#define ENUM_METHOD_NAME(EnumName)
const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)
If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...
uint32_t Uint4
4-byte (32-bit) unsigned integer
#define END_NCBI_SCOPE
End previously defined NCBI scope.
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
#define NCBI_GENOME_COLLECTION_EXPORT
bool CanGetDesc(void) const
Check if it is safe to call GetDesc method.
bool IsSetId(void) const
The identifier of this assembly Contains: GenColl internal id, GenColl accession.version,...
bool CanGetId(void) const
Check if it is safe to call GetId method.
TMols & SetMols(void)
Assign a value to Mols data member.
const TUnplaced_stats & GetUnplaced_stats(void) const
Get the Unplaced_stats member data.
const TUnplaced_unlocalized_stats & GetUnplaced_unlocalized_stats(void) const
Get the Unplaced_unlocalized_stats member data.
const TDesc & GetDesc(void) const
Get the Desc member data.
CGC_AssemblyUnit_Base(const CGC_AssemblyUnit_Base &)
void ResetClass(void)
Reset Class data member.
TClass GetClass(void) const
Get the Class member data.
bool CanGetClass(void) const
Check if it is safe to call GetClass method.
list< CRef< CDbtag > > TId
bool IsSetMols(void) const
collections of molecules for this assembly Check if a value has been assigned to Mols data member.
CGC_AssemblyUnit_Base & operator=(const CGC_AssemblyUnit_Base &)
list< CRef< CGC_Scaf_stats > > TUnplaced_stats
list< CRef< CGC_Replicon > > m_Mols
bool IsSetUnplaced_stats(void) const
Check if a value has been assigned to Unplaced_stats data member.
list< CRef< CGC_Scaf_stats > > m_Unplaced_unlocalized_stats
bool IsSetOther_sequences(void) const
On primary assembly-unit: here will be the unplaced sequences On alt-loci: list of sequences aligned/...
const TOther_sequences & GetOther_sequences(void) const
Get the Other_sequences member data.
void ResetDesc(void)
Reset Desc data member.
list< CRef< CDbtag > > m_Id
TDesc & SetDesc(void)
Assign a value to Desc data member.
TId & SetId(void)
Assign a value to Id data member.
bool IsSetDesc(void) const
descriptors live in a shared data block Check if a value has been assigned to Desc data member.
DECLARE_INTERNAL_TYPE_INFO()
const TMols & GetMols(void) const
Get the Mols member data.
list< CRef< CGC_Replicon > > TMols
bool CanGetMols(void) const
Check if it is safe to call GetMols method.
TUnplaced_unlocalized_stats & SetUnplaced_unlocalized_stats(void)
Assign a value to Unplaced_unlocalized_stats data member.
bool IsSetUnplaced_unlocalized_stats(void) const
Check if a value has been assigned to Unplaced_unlocalized_stats data member.
const TStats & GetStats(void) const
Get the Stats member data.
TUnplaced_stats & SetUnplaced_stats(void)
Assign a value to Unplaced_stats data member.
bool CanGetOther_sequences(void) const
Check if it is safe to call GetOther_sequences method.
list< CRef< CGC_Scaf_stats > > m_Unplaced_stats
EClass
'class' defines the semantics of how to interpret this item
TClass & SetClass(void)
Assign a value to Class data member.
bool IsSetClass(void) const
Check if a value has been assigned to Class data member.
bool CanGetUnplaced_unlocalized_stats(void) const
Check if it is safe to call GetUnplaced_unlocalized_stats method.
TOther_sequences & SetOther_sequences(void)
Assign a value to Other_sequences data member.
Tparent::CMemberIndex< E_memberIndex, 9 > TmemberIndex
bool CanGetStats(void) const
Check if it is safe to call GetStats method.
list< CRef< CGC_Scaf_stats > > TUnplaced_unlocalized_stats
bool CanGetUnplaced_stats(void) const
Check if it is safe to call GetUnplaced_stats method.
list< CRef< CGC_TaggedSequences > > m_Other_sequences
list< CRef< CGC_TaggedSequences > > TOther_sequences
bool IsSetStats(void) const
statistics "stats" field holds stats for all chromosomes combined: ordered/unordered scaffolds "unpla...
const TId & GetId(void) const
Get the Id member data.
const GenericPointer< typename T::ValueType > T2 value