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CGC_Assembly_Parser Class Reference

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CGC_Assembly_Parser –. More...

#include <objmgr/gc_assembly_parser.hpp>

+ Inheritance diagram for CGC_Assembly_Parser:
+ Collaboration diagram for CGC_Assembly_Parser:

Public Types

enum  FParserFlags {
  fIgnoreLocalIds = 1 << 0 , fIgnoreExternalIds = 1 << 1 , fIgnoreAnnots = 1 << 2 , fIgnoreDescr = 1 << 3 ,
  fSkipDuplicates = 1 << 4 , fDefault = fIgnoreLocalIds | fIgnoreAnnots | fIgnoreDescr | fSkipDuplicates
}
 Parser options. More...
 
typedef int TParserFlags
 
typedef set< CSeq_id_HandleTSeqIds
 
- 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

 CGC_Assembly_Parser (const CGC_Assembly &assembly, TParserFlags flags=fDefault)
 Parse the assembly, convert it to seq-entry, collect additional information (top-level sequences etc). More...
 
virtual ~CGC_Assembly_Parser (void)
 
CRef< CSeq_entryGetTSE (void) const
 Create seq-entry with all parsed sequences, annotations etc. More...
 
const TSeqIdsGetTopLevelSequences (void) const
 Get seq-ids for all top-level sequences in the assembly. 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...
 
virtual void DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. 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
 

Private Member Functions

void x_ParseGCAssembly (const CGC_Assembly &gc_assembly, CRef< CSeq_entry > parent_entry)
 
void x_ParseGCSequence (const CGC_Sequence &gc_seq, const CGC_Sequence *parent_seq, CRef< CSeq_entry > parent_entry, CRef< CSeq_id > override_id)
 
void x_AddBioseq (CRef< CSeq_entry > parent_entry, const TSeqIds &synonyms, const CGC_Sequence &gc_seq)
 
void x_InitSeq_entry (CRef< CSeq_entry > entry, CRef< CSeq_entry > parent)
 
void x_CopyData (const CGC_AssemblyDesc &assm_desc, CSeq_entry &entry)
 

Private Attributes

TParserFlags m_Flags
 
CRef< CSeq_entrym_TSE
 
TSeqIds m_TopSeqs
 
TSeqIds m_AllSeqs
 

Additional Inherited Members

- 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 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

CGC_Assembly_Parser –.

GC-Assembly parser used by CScope and CSeq_loc_Mapper to convert assemblies to seq-entries.

Definition at line 65 of file gc_assembly_parser.hpp.


The documentation for this class was generated from the following files:
Modified on Sat Jul 13 13:34:14 2024 by modify_doxy.py rev. 669887