Search Toolkit Book for CGC_AssemblyUnit
#include <objects/genomecoll/GC_AssemblyUnit.hpp>
Inheritance diagram for CGC_AssemblyUnit:
Collaboration diagram for CGC_AssemblyUnit:
Public Member Functions | |
| CGC_AssemblyUnit (void) | |
| ~CGC_AssemblyUnit (void) | |
| string | GetName () const |
| Retrieve this unit's name. More... | |
| string | GetAccession () const |
| Retrieve this unit's accession. More... | |
| string | GetDisplayName () const |
| Get full display name of assembly unit. More... | |
| string | GetFileSafeName () const |
| Retrieve the file-safe version of assembly name, if available; othwreise default to standard name. More... | |
| string | GetFileSafeDisplayName () const |
| Get file-safe version of full label for assmebly. More... | |
| int | GetReleaseId () const |
| Retrieve the release id for this assembly. More... | |
| CConstRef< CGC_Assembly > | GetFullAssembly () const |
| Access the most specific full assembly the assembly unit belongs to This is needed because assemblies are packaged as sets of assemblies; knowing the unit is not always enough. More... | |
| bool | IsPrimaryUnit () const |
| Is this the primary unit of its full assembly? More... | |
| bool | IsOrganelle () const |
| Is this a non-nuclear assembly unit? More... | |
| Public Member Functions inherited from CGC_AssemblyUnit_Base | |
| CGC_AssemblyUnit_Base (void) | |
| virtual | ~CGC_AssemblyUnit_Base (void) |
| DECLARE_INTERNAL_TYPE_INFO () | |
| bool | IsSetId (void) const |
| The identifier of this assembly Contains: GenColl internal id, GenColl accession.version, AGP id, UCSC name, Ensembl name Types of DbTags used: db "GenColl", tag id <assembly-release-id> db "GenColl", tag str <assembly-accession.version> db "AGP", tag id <agp-sumbission-id> db "GenColl_Chain", tag id <assembly-chain-id> "Ensembl_name" and "UCSC_name" will not appear in the Unit level since these organizations do not define assembly-units. More... | |
| bool | CanGetId (void) const |
| Check if it is safe to call GetId method. More... | |
| void | ResetId (void) |
| Reset Id data member. More... | |
| const TId & | GetId (void) const |
| Get the Id member data. More... | |
| TId & | SetId (void) |
| Assign a value to Id data member. More... | |
| bool | IsSetClass (void) const |
| Check if a value has been assigned to Class data member. More... | |
| bool | CanGetClass (void) const |
| Check if it is safe to call GetClass method. More... | |
| void | ResetClass (void) |
| Reset Class data member. More... | |
| TClass | GetClass (void) const |
| Get the Class member data. More... | |
| void | SetClass (TClass value) |
| Assign a value to Class data member. More... | |
| TClass & | SetClass (void) |
| Assign a value to Class data member. More... | |
| bool | IsSetDesc (void) const |
| descriptors live in a shared data block Check if a value has been assigned to Desc data member. More... | |
| bool | CanGetDesc (void) const |
| Check if it is safe to call GetDesc method. More... | |
| void | ResetDesc (void) |
| Reset Desc data member. More... | |
| const TDesc & | GetDesc (void) const |
| Get the Desc member data. More... | |
| void | SetDesc (TDesc &value) |
| Assign a value to Desc data member. More... | |
| TDesc & | SetDesc (void) |
| Assign a value to Desc data member. More... | |
| bool | IsSetMols (void) const |
| collections of molecules for this assembly Check if a value has been assigned to Mols data member. More... | |
| bool | CanGetMols (void) const |
| Check if it is safe to call GetMols method. More... | |
| void | ResetMols (void) |
| Reset Mols data member. More... | |
| const TMols & | GetMols (void) const |
| Get the Mols member data. More... | |
| TMols & | SetMols (void) |
| Assign a value to Mols data member. More... | |
| bool | IsSetOther_sequences (void) const |
| On primary assembly-unit: here will be the unplaced sequences On alt-loci: list of sequences aligned/unaligned to primary unit Check if a value has been assigned to Other_sequences data member. More... | |
| bool | CanGetOther_sequences (void) const |
| Check if it is safe to call GetOther_sequences method. More... | |
| void | ResetOther_sequences (void) |
| Reset Other_sequences data member. More... | |
| const TOther_sequences & | GetOther_sequences (void) const |
| Get the Other_sequences member data. More... | |
| TOther_sequences & | SetOther_sequences (void) |
| Assign a value to Other_sequences data member. More... | |
| bool | IsSetStats (void) const |
| statistics "stats" field holds stats for all chromosomes combined: ordered/unordered scaffolds "unplaced-stats" holds stats for ChrUn which is omitted from "stats" Check if a value has been assigned to Stats data member. More... | |
| bool | CanGetStats (void) const |
| Check if it is safe to call GetStats method. More... | |
| void | ResetStats (void) |
| Reset Stats data member. More... | |
| const TStats & | GetStats (void) const |
| Get the Stats member data. More... | |
| void | SetStats (TStats &value) |
| Assign a value to Stats data member. More... | |
| TStats & | SetStats (void) |
| Assign a value to Stats data member. More... | |
| bool | IsSetUnplaced_stats (void) const |
| Check if a value has been assigned to Unplaced_stats data member. More... | |
| bool | CanGetUnplaced_stats (void) const |
| Check if it is safe to call GetUnplaced_stats method. More... | |
| void | ResetUnplaced_stats (void) |
| Reset Unplaced_stats data member. More... | |
| const TUnplaced_stats & | GetUnplaced_stats (void) const |
| Get the Unplaced_stats member data. More... | |
| TUnplaced_stats & | SetUnplaced_stats (void) |
| Assign a value to Unplaced_stats data member. More... | |
| bool | IsSetUnplaced_unlocalized_stats (void) const |
| Check if a value has been assigned to Unplaced_unlocalized_stats data member. More... | |
| bool | CanGetUnplaced_unlocalized_stats (void) const |
| Check if it is safe to call GetUnplaced_unlocalized_stats method. More... | |
| void | ResetUnplaced_unlocalized_stats (void) |
| Reset Unplaced_unlocalized_stats data member. More... | |
| const TUnplaced_unlocalized_stats & | GetUnplaced_unlocalized_stats (void) const |
| Get the Unplaced_unlocalized_stats member data. More... | |
| TUnplaced_unlocalized_stats & | SetUnplaced_unlocalized_stats (void) |
| Assign a value to Unplaced_unlocalized_stats data member. More... | |
| virtual void | Reset (void) |
| Reset the whole object. More... | |
| Public Member Functions inherited from CSerialObject | |
| CSerialObject (void) | |
| virtual | ~CSerialObject (void) |
| virtual const CTypeInfo * | GetThisTypeInfo (void) const =0 |
| virtual void | Assign (const CSerialObject &source, ESerialRecursionMode how=eRecursive) |
| Set object to copy of another one. More... | |
| virtual bool | Equals (const CSerialObject &object, ESerialRecursionMode how=eRecursive) const |
| Check if both objects contain the same values. More... | |
| virtual void | DebugDump (CDebugDumpContext ddc, unsigned int depth) const |
| Define method for dumping debug information. More... | |
| void | ThrowUnassigned (TMemberIndex index) const |
| void | ThrowUnassigned (TMemberIndex index, const char *file_name, int file_line) const |
| bool | HasNamespaceName (void) const |
| Check if object data type has namespace name. More... | |
| const string & | GetNamespaceName (void) const |
| Get namespace name. More... | |
| bool | HasNamespacePrefix (void) const |
| Check if data type has namespace prefix. More... | |
| const string & | GetNamespacePrefix (void) const |
| Get namespace prefix. More... | |
| Public Member Functions inherited from CObject | |
| CObject (void) | |
| Constructor. More... | |
| CObject (const CObject &src) | |
| Copy constructor. More... | |
| virtual | ~CObject (void) |
| Destructor. More... | |
| CObject & | operator= (const CObject &src) THROWS_NONE |
| Assignment operator. More... | |
| bool | CanBeDeleted (void) const THROWS_NONE |
| Check if object can be deleted. More... | |
| bool | IsAllocatedInPool (void) const THROWS_NONE |
| Check if object is allocated in memory pool (not system heap) More... | |
| bool | Referenced (void) const THROWS_NONE |
| Check if object is referenced. More... | |
| bool | ReferencedOnlyOnce (void) const THROWS_NONE |
| Check if object is referenced only once. More... | |
| void | AddReference (void) const |
| Add reference to object. More... | |
| void | RemoveReference (void) const |
| Remove reference to object. More... | |
| void | ReleaseReference (void) const |
| Remove reference without deleting object. More... | |
| virtual void | DoNotDeleteThisObject (void) |
| Mark this object as not allocated in heap – do not delete this object. More... | |
| virtual void | DoDeleteThisObject (void) |
| Mark this object as allocated in heap – object can be deleted. More... | |
| void * | operator new (size_t size) |
| Define new operator for memory allocation. More... | |
| void * | operator new[] (size_t size) |
| Define new[] operator for 'array' memory allocation. More... | |
| void | operator delete (void *ptr) |
| Define delete operator for memory deallocation. More... | |
| void | operator delete[] (void *ptr) |
| Define delete[] operator for memory deallocation. More... | |
| void * | operator new (size_t size, void *place) |
| Define new operator. More... | |
| void | operator delete (void *ptr, void *place) |
| Define delete operator. More... | |
| void * | operator new (size_t size, CObjectMemoryPool *place) |
| Define new operator using memory pool. More... | |
| void | operator delete (void *ptr, CObjectMemoryPool *place) |
| Define delete operator. More... | |
| Public Member Functions inherited from CDebugDumpable | |
| CDebugDumpable (void) | |
| virtual | ~CDebugDumpable (void) |
| void | DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const |
| void | DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const |
| void | DumpToConsole (void) const |
Protected Attributes | |
| CGC_Assembly * | m_Assembly |
Private Types | |
| typedef CGC_AssemblyUnit_Base | Tparent |
Private Member Functions | |
| CGC_AssemblyUnit (const CGC_AssemblyUnit &value) | |
| CGC_AssemblyUnit & | operator= (const CGC_AssemblyUnit &value) |
Friends | |
| class | CGC_Assembly |
Additional Inherited Members | |
| Public Types inherited from CGC_AssemblyUnit_Base | |
| enum | EClass { eClass_haploid_unit = 1 , eClass_alt_loci = 2 , eClass_assembly_patch = 3 , eClass_other = 255 } |
| 'class' defines the semantics of how to interpret this item More... | |
| enum class | E_memberIndex { e__allMandatory = 0 , e_id , e_class , e_desc , e_mols , e_other_sequences , e_stats , e_unplaced_stats , e_unplaced_unlocalized_stats } |
| typedef list< CRef< CDbtag > > | TId |
| typedef int | TClass |
| typedef CGC_AssemblyDesc | TDesc |
| typedef list< CRef< CGC_Replicon > > | TMols |
| typedef list< CRef< CGC_TaggedSequences > > | TOther_sequences |
| typedef CGC_SequenceStats | TStats |
| typedef list< CRef< CGC_Scaf_stats > > | TUnplaced_stats |
| typedef list< CRef< CGC_Scaf_stats > > | TUnplaced_unlocalized_stats |
| typedef Tparent::CMemberIndex< E_memberIndex, 9 > | TmemberIndex |
| Public Types inherited from CObject | |
| enum | EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern } |
| Control filling of newly allocated memory. More... | |
| typedef CObjectCounterLocker | TLockerType |
| Default locker type for CRef. More... | |
| typedef atomic< Uint8 > | TCounter |
| Counter type is CAtomiCounter. More... | |
| typedef Uint8 | TCount |
| Alias for value type of counter. More... | |
| Static Public Member Functions inherited from CGC_AssemblyUnit_Base | |
| static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME() | EClass (void) |
| Access to EClass's attributes (values, names) as defined in spec. More... | |
| Static Public Member Functions inherited from CSerialObject | |
| static void | SetVerifyDataThread (ESerialVerifyData verify) |
| static void | SetVerifyDataGlobal (ESerialVerifyData verify) |
| static string | UnassignedString (void) |
| static CStringUTF8 | UnassignedStringUTF8 (void) |
| static char | UnassignedByte (void) |
| Static Public Member Functions inherited from CObject | |
| static NCBI_XNCBI_EXPORT void | ThrowNullPointerException (void) |
| Define method to throw null pointer exception. More... | |
| static NCBI_XNCBI_EXPORT void | ThrowNullPointerException (const type_info &type) |
| static EAllocFillMode | GetAllocFillMode (void) |
| static void | SetAllocFillMode (EAllocFillMode mode) |
| static void | SetAllocFillMode (const string &value) |
| Set mode from configuration parameter value. More... | |
| Static Public Member Functions inherited from CDebugDumpable | |
| static void | EnableDebugDump (bool on) |
| Static Public Attributes inherited from CSerialObject | |
| static const char * | ms_UnassignedStr = "<*unassigned*>" |
| static const char | ms_UnassignedByte = char(0xcd) |
| Static Public Attributes inherited from CObject | |
| static const TCount | eCounterBitsCanBeDeleted = 1 << 0 |
| Define possible object states. More... | |
| static const TCount | eCounterBitsInPlainHeap = 1 << 1 |
| Heap signature was found. More... | |
| static const TCount | eCounterBitsPlaceMask |
| Mask for 'in heap' state flags. More... | |
| static const int | eCounterStep = 1 << 2 |
| Skip over the "in heap" bits. More... | |
| static const TCount | eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2) |
| Minimal value for valid objects (reference counter is zero) Must be a single bit value. More... | |
| static const TCount | eCounterStateMask |
| Valid object, and object in heap. More... | |
| Protected Member Functions inherited from CObject | |
| virtual void | DeleteThis (void) |
| Virtual method "deleting" this object. More... | |
Detailed Description
Definition at line 55 of file GC_AssemblyUnit.hpp.
Member Typedef Documentation
◆ Tparent
|
private |
Definition at line 57 of file GC_AssemblyUnit.hpp.
Constructor & Destructor Documentation
◆ CGC_AssemblyUnit() [1/2]
| CGC_AssemblyUnit::CGC_AssemblyUnit | ( | void | ) |
Definition at line 53 of file GC_AssemblyUnit.cpp.
◆ ~CGC_AssemblyUnit()
| CGC_AssemblyUnit::~CGC_AssemblyUnit | ( | void | ) |
Definition at line 60 of file GC_AssemblyUnit.cpp.
◆ CGC_AssemblyUnit() [2/2]
|
private |
Member Function Documentation
◆ GetAccession()
| string CGC_AssemblyUnit::GetAccession | ( | void | ) | const |
Retrieve this unit's accession.
Definition at line 70 of file GC_AssemblyUnit.cpp.
References CGC_AssemblyUnit_Base::GetId(), and ITERATE.
◆ GetDisplayName()
| string CGC_AssemblyUnit::GetDisplayName | ( | ) | const |
Get full display name of assembly unit.
Definition at line 85 of file GC_AssemblyUnit.cpp.
References GetFullAssembly(), CGC_Assembly::GetName(), and GetName().
Referenced by CGC_Assembly::GetDisplayName().
◆ GetFileSafeDisplayName()
| string CGC_AssemblyUnit::GetFileSafeDisplayName | ( | ) | const |
Get file-safe version of full label for assmebly.
Definition at line 99 of file GC_AssemblyUnit.cpp.
References CGC_Assembly::GetFileSafeName(), GetFileSafeName(), and GetFullAssembly().
Referenced by CGC_Assembly::GetFileSafeDisplayName().
◆ GetFileSafeName()
| string CGC_AssemblyUnit::GetFileSafeName | ( | ) | const |
Retrieve the file-safe version of assembly name, if available; othwreise default to standard name.
Definition at line 91 of file GC_AssemblyUnit.cpp.
References CGC_AssemblyUnit_Base::GetDesc(), CGC_AssemblyDesc_Base::GetFilesafe_name(), GetName(), CGC_AssemblyDesc_Base::IsSetFilesafe_name(), and NStr::Replace().
Referenced by GetFileSafeDisplayName().
◆ GetFullAssembly()
| CConstRef< CGC_Assembly > CGC_AssemblyUnit::GetFullAssembly | ( | ) | const |
Access the most specific full assembly the assembly unit belongs to This is needed because assemblies are packaged as sets of assemblies; knowing the unit is not always enough.
Access the assembly the sequence belongs to.
Definition at line 126 of file GC_AssemblyUnit.cpp.
References m_Assembly.
Referenced by GetDisplayName(), GetFileSafeDisplayName(), and CGC_Assembly::IsTargetSetReference().
◆ GetName()
| string CGC_AssemblyUnit::GetName | ( | void | ) | const |
Retrieve this unit's name.
Definition at line 64 of file GC_AssemblyUnit.cpp.
References CGC_AssemblyUnit_Base::GetDesc(), and CGC_AssemblyDesc_Base::GetName().
Referenced by GetDisplayName(), GetFileSafeName(), and IsOrganelle().
◆ GetReleaseId()
| int CGC_AssemblyUnit::GetReleaseId | ( | ) | const |
Retrieve the release id for this assembly.
Definition at line 105 of file GC_AssemblyUnit.cpp.
References CGC_AssemblyUnit_Base::GetId(), and ITERATE.
◆ IsOrganelle()
| bool CGC_AssemblyUnit::IsOrganelle | ( | ) | const |
Is this a non-nuclear assembly unit?
Definition at line 119 of file GC_AssemblyUnit.cpp.
References GetName().
◆ IsPrimaryUnit()
| bool CGC_AssemblyUnit::IsPrimaryUnit | ( | ) | const |
Is this the primary unit of its full assembly?
Definition at line 131 of file GC_AssemblyUnit.cpp.
References CGC_Assembly_Base::GetAssembly_set(), CGC_AssemblySet_Base::GetPrimary_assembly(), CGC_Assembly_Base::GetUnit(), CGC_Assembly_Base::IsUnit(), and m_Assembly.
◆ operator=()
|
private |
Friends And Related Function Documentation
◆ CGC_Assembly
|
friend |
Definition at line 58 of file GC_AssemblyUnit.hpp.
Member Data Documentation
◆ m_Assembly
|
protected |
Definition at line 97 of file GC_AssemblyUnit.hpp.
Referenced by GetFullAssembly(), IsPrimaryUnit(), and CGC_Assembly::x_Index().
The documentation for this class was generated from the following files:
- include/objects/genomecoll/GC_AssemblyUnit.hpp
- src/objects/genomecoll/GC_AssemblyUnit.cpp
