NCBI C++ ToolKit
Public Types | Public Member Functions | Static Public Member Functions | Private Types | Private Member Functions | List of all members
CProt_ref Class Reference

Represents ASN.1 type Prot-ref defined in file seqfeat.asn

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#include <objects/seqfeat/Prot_ref.hpp>

+ Inheritance diagram for CProt_ref:
+ Collaboration diagram for CProt_ref:

Public Types

enum  EECNumberStatus {
  eEC_specific , eEC_ambiguous , eEC_replaced , eEC_deleted ,
  eEC_unknown
}
 Enzyme Commission number status. More...
 
enum  EECNumberFileStatus { eECFile_not_attempted , eECFile_not_found , eECFile_not_read , eECFile_read }
 Enzyme Commission file status. More...
 
- Public Types inherited from CProt_ref_Base
enum  EProcessed {
  eProcessed_not_set = 0 , eProcessed_preprotein = 1 , eProcessed_mature = 2 , eProcessed_signal_peptide = 3 ,
  eProcessed_transit_peptide = 4 , eProcessed_propeptide = 5
}
 processing status More...
 
enum class  E_memberIndex {
  e__allMandatory = 0 , e_name , e_desc , e_ec ,
  e_activity , e_db , e_processed
}
 
typedef list< stringTName
 
typedef string TDesc
 
typedef list< stringTEc
 
typedef list< stringTActivity
 
typedef vector< CRef< CDbtag > > TDb
 
typedef EProcessed TProcessed
 
typedef Tparent::CMemberIndex< E_memberIndex, 7 > 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< Uint8TCounter
 Counter type is CAtomiCounter. More...
 
typedef Uint8 TCount
 Alias for value type of counter. More...
 

Public Member Functions

 CProt_ref (void)
 
 ~CProt_ref (void)
 
void GetLabel (string *label) const
 
void AutoFixEC ()
 
void RemoveBadEC ()
 
- Public Member Functions inherited from CProt_ref_Base
 CProt_ref_Base (void)
 
virtual ~CProt_ref_Base (void)
 
 DECLARE_INTERNAL_TYPE_INFO ()
 
bool IsSetName (void) const
 protein name Check if a value has been assigned to Name data member. More...
 
bool CanGetName (void) const
 Check if it is safe to call GetName method. More...
 
void ResetName (void)
 Reset Name data member. More...
 
const TNameGetName (void) const
 Get the Name member data. More...
 
TNameSetName (void)
 Assign a value to Name data member. More...
 
bool IsSetDesc (void) const
 description (instead of name) 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 TDescGetDesc (void) const
 Get the Desc member data. More...
 
void SetDesc (const TDesc &value)
 Assign a value to Desc data member. More...
 
void SetDesc (TDesc &&value)
 
TDescSetDesc (void)
 Assign a value to Desc data member. More...
 
bool IsSetEc (void) const
 E.C. More...
 
bool CanGetEc (void) const
 Check if it is safe to call GetEc method. More...
 
void ResetEc (void)
 Reset Ec data member. More...
 
const TEcGetEc (void) const
 Get the Ec member data. More...
 
TEcSetEc (void)
 Assign a value to Ec data member. More...
 
bool IsSetActivity (void) const
 activities Check if a value has been assigned to Activity data member. More...
 
bool CanGetActivity (void) const
 Check if it is safe to call GetActivity method. More...
 
void ResetActivity (void)
 Reset Activity data member. More...
 
const TActivityGetActivity (void) const
 Get the Activity member data. More...
 
TActivitySetActivity (void)
 Assign a value to Activity data member. More...
 
bool IsSetDb (void) const
 ids in other dbases Check if a value has been assigned to Db data member. More...
 
bool CanGetDb (void) const
 Check if it is safe to call GetDb method. More...
 
void ResetDb (void)
 Reset Db data member. More...
 
const TDbGetDb (void) const
 Get the Db member data. More...
 
TDbSetDb (void)
 Assign a value to Db data member. More...
 
bool IsSetProcessed (void) const
 Check if a value has been assigned to Processed data member. More...
 
bool CanGetProcessed (void) const
 Check if it is safe to call GetProcessed method. More...
 
void ResetProcessed (void)
 Reset Processed data member. More...
 
void SetDefaultProcessed (void)
 Assign default value to Processed data member. More...
 
TProcessed GetProcessed (void) const
 Get the Processed member data. More...
 
void SetProcessed (TProcessed value)
 Assign a value to Processed data member. More...
 
TProcessedSetProcessed (void)
 Assign a value to Processed 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 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
 

Static Public Member Functions

static EECNumberStatus GetECNumberStatus (const string &ecno)
 Determine an EC number's validity and specificity. More...
 
static const stringGetECNumberReplacement (const string &old_ecno)
 Return a replaced EC number's replacement. More...
 
static bool IsECNumberSplit (const string &old_ecno)
 
static bool IsValidECNumberFormat (const string &ecno)
 Verify correct form of EC number. More...
 
static EECNumberFileStatus GetECNumAmbiguousStatus ()
 
static EECNumberFileStatus GetECNumDeletedStatus ()
 
static EECNumberFileStatus GetECNumReplacedStatus ()
 
static EECNumberFileStatus GetECNumSpecificStatus ()
 
- Static Public Member Functions inherited from CProt_ref_Base
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME() EProcessed (void)
 Access to EProcessed'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)
 

Private Types

typedef CProt_ref_Base Tparent
 

Private Member Functions

 CProt_ref (const CProt_ref &value)
 
CProt_refoperator= (const CProt_ref &value)
 

Additional Inherited Members

- 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 50 of file Prot_ref.hpp.

Member Typedef Documentation

◆ Tparent

Definition at line 52 of file Prot_ref.hpp.

Member Enumeration Documentation

◆ EECNumberFileStatus

Enzyme Commission file status.

Enumerator
eECFile_not_attempted 

No attempt has been made to read the file.

eECFile_not_found 

File was not found in expected directory.

eECFile_not_read 

File was found but could not be read.

eECFile_read 

File was read successfully (and is being instead of the compiled fallback data.

Definition at line 72 of file Prot_ref.hpp.

◆ EECNumberStatus

Enzyme Commission number status.

Enumerator
eEC_specific 

Specifically identifies a valid classification.

eEC_ambiguous 

Valid wildcard for a broader family.

eEC_replaced 

Obsolete synonym for some other EC number.

eEC_deleted 

Withdrawn, with no (single?) replacement.

eEC_unknown 

Unrecognized; possibly malformed.

Definition at line 63 of file Prot_ref.hpp.

Constructor & Destructor Documentation

◆ CProt_ref() [1/2]

CProt_ref::CProt_ref ( void  )
inline

Definition at line 113 of file Prot_ref.hpp.

◆ ~CProt_ref()

CProt_ref::~CProt_ref ( void  )

Definition at line 57 of file Prot_ref.cpp.

◆ CProt_ref() [2/2]

CProt_ref::CProt_ref ( const CProt_ref value)
private

Member Function Documentation

◆ AutoFixEC()

void CProt_ref::AutoFixEC ( )

◆ GetECNumAmbiguousStatus()

CProt_ref::EECNumberFileStatus CProt_ref::GetECNumAmbiguousStatus ( )
static

Definition at line 85 of file Prot_ref.cpp.

References s_ECNumAmbiguousStatus.

Referenced by CSingleFeatValidator::x_ReportECNumFileStatus().

◆ GetECNumberReplacement()

const string & CProt_ref::GetECNumberReplacement ( const string old_ecno)
static

◆ GetECNumberStatus()

CProt_ref::EECNumberStatus CProt_ref::GetECNumberStatus ( const string ecno)
static

◆ GetECNumDeletedStatus()

CProt_ref::EECNumberFileStatus CProt_ref::GetECNumDeletedStatus ( )
static

Definition at line 86 of file Prot_ref.cpp.

References s_ECNumDeletedStatus.

Referenced by CSingleFeatValidator::x_ReportECNumFileStatus().

◆ GetECNumReplacedStatus()

CProt_ref::EECNumberFileStatus CProt_ref::GetECNumReplacedStatus ( )
static

Definition at line 87 of file Prot_ref.cpp.

References s_ECNumReplacedStatus.

Referenced by CSingleFeatValidator::x_ReportECNumFileStatus().

◆ GetECNumSpecificStatus()

CProt_ref::EECNumberFileStatus CProt_ref::GetECNumSpecificStatus ( )
static

Definition at line 88 of file Prot_ref.cpp.

References s_ECNumSpecificStatus.

Referenced by CSingleFeatValidator::x_ReportECNumFileStatus().

◆ GetLabel()

void CProt_ref::GetLabel ( string label) const

◆ IsECNumberSplit()

bool CProt_ref::IsECNumberSplit ( const string old_ecno)
static

◆ IsValidECNumberFormat()

bool CProt_ref::IsValidECNumberFormat ( const string ecno)
static

◆ operator=()

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

◆ RemoveBadEC()

void CProt_ref::RemoveBadEC ( )

The documentation for this class was generated from the following files:
Modified on Sun Apr 14 05:25:29 2024 by modify_doxy.py rev. 669887