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CSeq_entry Class Reference

Represents ASN.1 type Seq-entry defined in file seqset.asn

Search Toolkit Book for CSeq_entry

#include <objects/seqset/Seq_entry.hpp>

+ Inheritance diagram for CSeq_entry:
+ Collaboration diagram for CSeq_entry:

Public Types

enum  ELabelType { eType , eContent , eBoth }
 
typedef list< CRef< CSeq_annot > > TAnnot
 
- Public Types inherited from CSeq_entry_Base
enum  E_Choice { e_not_set = 0 , e_Seq , e_Set }
 Choice variants. More...
 
enum  E_ChoiceStopper { e_MaxChoice = 3 }
 Maximum+1 value of the choice variant enumerator. More...
 
typedef CBioseq TSeq
 
typedef CBioseq_set TSet
 
- 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< Uint8TCounter
 Counter type is CAtomiCounter. More...
 
typedef Uint8 TCount
 Alias for value type of counter. More...
 

Public Member Functions

 CSeq_entry (void)
 
 ~CSeq_entry (void)
 
void Parentize (void)
 
void ParentizeOneLevel (void)
 
void ResetParentEntry (void)
 
void SetParentEntry (CSeq_entry *entry)
 
CSeq_entryGetParentEntry (void) const
 
bool IsSetDescr (void) const
 
const CSeq_descrGetDescr (void) const
 
void SetDescr (CSeq_descr &value)
 
CSeq_descrSetDescr (void)
 
bool IsSetAnnot (void) const
 
const TAnnotGetAnnot (void) const
 
TAnnotSetAnnot (void)
 
void GetLabel (string *label, ELabelType type) const
 
void ReassignConflictingIds (void)
 
- Public Member Functions inherited from CSeq_entry_Base
 CSeq_entry_Base (void)
 
virtual ~CSeq_entry_Base (void)
 
 DECLARE_INTERNAL_TYPE_INFO ()
 
virtual void Reset (void)
 Reset the whole object. More...
 
virtual void ResetSelection (void)
 Reset the selection (set it to e_not_set). More...
 
E_Choice Which (void) const
 Which variant is currently selected. More...
 
void CheckSelected (E_Choice index) const
 Verify selection, throw exception if it differs from the expected. More...
 
void ThrowInvalidSelection (E_Choice index) const
 Throw 'InvalidSelection' exception. More...
 
void Select (E_Choice index, EResetVariant reset=eDoResetVariant)
 Select the requested variant if needed. More...
 
void Select (E_Choice index, EResetVariant reset, CObjectMemoryPool *pool)
 Select the requested variant if needed, allocating CObject variants from memory pool. More...
 
bool IsSeq (void) const
 Check if variant Seq is selected. More...
 
const TSeqGetSeq (void) const
 Get the variant data. More...
 
TSeqSetSeq (void)
 Select the variant. More...
 
void SetSeq (TSeq &value)
 Select the variant and set its data. More...
 
bool IsSet (void) const
 Check if variant Set is selected. More...
 
const TSetGetSet (void) const
 Get the variant data. More...
 
TSetSetSet (void)
 Select the variant. More...
 
void SetSet (TSet &value)
 Select the variant and set its data. More...
 
- Public Member Functions inherited from CSerialObject
 CSerialObject (void)
 
virtual ~CSerialObject (void)
 
virtual const CTypeInfoGetThisTypeInfo (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 stringGetNamespaceName (void) const
 Get namespace name. More...
 
bool HasNamespacePrefix (void) const
 Check if data type has namespace prefix. More...
 
const stringGetNamespacePrefix (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...
 
CObjectoperator= (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
 
- Public Member Functions inherited from CSerialUserOp
virtual ~CSerialUserOp ()
 

Protected Member Functions

virtual void UserOp_Assign (const CSerialUserOp &source)
 Will be called after copying the datatool-generated members. More...
 
virtual bool UserOp_Equals (const CSerialUserOp &object) const
 Will be called after comparing the datatool-generated members. More...
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Private Types

typedef CSeq_entry_Base Tparent
 

Private Member Functions

 CSeq_entry (const CSeq_entry &value)
 
CSeq_entryoperator= (const CSeq_entry &value)
 

Private Attributes

CSeq_entrym_ParentEntry
 

Additional Inherited Members

- Static Public Member Functions inherited from CSeq_entry_Base
static string SelectionName (E_Choice index)
 Retrieve selection name (for diagnostic purposes). 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...
 

Detailed Description

Definition at line 55 of file Seq_entry.hpp.

Member Typedef Documentation

◆ TAnnot

typedef list< CRef< CSeq_annot > > CSeq_entry::TAnnot

Definition at line 86 of file Seq_entry.hpp.

◆ Tparent

Definition at line 57 of file Seq_entry.hpp.

Member Enumeration Documentation

◆ ELabelType

Enumerator
eType 
eContent 
eBoth 

Definition at line 91 of file Seq_entry.hpp.

Constructor & Destructor Documentation

◆ CSeq_entry() [1/2]

CSeq_entry::CSeq_entry ( void  )
inline

Definition at line 125 of file Seq_entry.hpp.

Referenced by CSraRun::GetSpotEntry().

◆ ~CSeq_entry()

CSeq_entry::~CSeq_entry ( void  )

Definition at line 57 of file Seq_entry.cpp.

◆ CSeq_entry() [2/2]

CSeq_entry::CSeq_entry ( const CSeq_entry value)
private

Member Function Documentation

◆ GetAnnot()

const CSeq_entry::TAnnot & CSeq_entry::GetAnnot ( void  ) const

◆ GetDescr()

const CSeq_descr & CSeq_entry::GetDescr ( void  ) const

◆ GetLabel()

void CSeq_entry::GetLabel ( string label,
ELabelType  type 
) const

◆ GetParentEntry()

CSeq_entry * CSeq_entry::GetParentEntry ( void  ) const
inline

◆ IsSetAnnot()

bool CSeq_entry::IsSetAnnot ( void  ) const

◆ IsSetDescr()

bool CSeq_entry::IsSetDescr ( void  ) const

◆ operator=()

CSeq_entry& CSeq_entry::operator= ( const CSeq_entry value)
private

◆ Parentize()

void CSeq_entry::Parentize ( void  )

◆ ParentizeOneLevel()

void CSeq_entry::ParentizeOneLevel ( void  )

◆ ReassignConflictingIds()

void CSeq_entry::ReassignConflictingIds ( void  )

◆ ResetParentEntry()

void CSeq_entry::ResetParentEntry ( void  )

Definition at line 61 of file Seq_entry.cpp.

References m_ParentEntry.

Referenced by CMultiReader::xApplyTemplate().

◆ SetAnnot()

CSeq_entry::TAnnot & CSeq_entry::SetAnnot ( void  )

◆ SetDescr() [1/2]

void CSeq_entry::SetDescr ( CSeq_descr value)

◆ SetDescr() [2/2]

CSeq_descr & CSeq_entry::SetDescr ( void  )

◆ SetParentEntry()

void CSeq_entry::SetParentEntry ( CSeq_entry entry)

Definition at line 66 of file Seq_entry.cpp.

References m_ParentEntry.

◆ UserOp_Assign()

void CSeq_entry::UserOp_Assign ( const CSerialUserOp source)
protectedvirtual

Will be called after copying the datatool-generated members.

Implements CSerialUserOp.

Definition at line 238 of file Seq_entry.cpp.

References m_ParentEntry, and ParentizeOneLevel().

◆ UserOp_Equals()

bool CSeq_entry::UserOp_Equals ( const CSerialUserOp object) const
protectedvirtual

Will be called after comparing the datatool-generated members.

Implements CSerialUserOp.

Definition at line 244 of file Seq_entry.cpp.

Member Data Documentation

◆ m_ParentEntry

CSeq_entry* CSeq_entry::m_ParentEntry
private

Definition at line 117 of file Seq_entry.hpp.

Referenced by GetParentEntry(), ResetParentEntry(), SetParentEntry(), and UserOp_Assign().


The documentation for this class was generated from the following files:
Modified on Thu Feb 29 12:24:06 2024 by modify_doxy.py rev. 669887