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CCdd Class Reference

Represents ASN.1 type Cdd defined in file cdd.asn

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#include <objects/cdd/Cdd.hpp>

+ Inheritance diagram for CCdd:
+ Collaboration diagram for CCdd:

Public Member Functions

 CCdd (void)
 
 ~CCdd (void)
 
- Public Member Functions inherited from CCdd_Base
 CCdd_Base (void)
 
virtual ~CCdd_Base (void)
 
 DECLARE_INTERNAL_TYPE_INFO ()
 
bool IsSetName (void) const
 a short name (can be the accession..) 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...
 
void SetName (const TName &value)
 Assign a value to Name data member. More...
 
void SetName (TName &&value)
 
TNameSetName (void)
 Assign a value to Name data member. More...
 
bool IsSetId (void) const
 this CD's Ids Check if a value has been assigned to Id data member. More...
 
bool CanGetId (void) const
 Check if it is safe to call GetId method. More...
 
void ResetId (void)
 Reset Id data member. More...
 
const TIdGetId (void) const
 Get the Id member data. More...
 
void SetId (TId &value)
 Assign a value to Id data member. More...
 
TIdSetId (void)
 Assign a value to Id data member. More...
 
bool IsSetDescription (void) const
 status, references, etc. More...
 
bool CanGetDescription (void) const
 Check if it is safe to call GetDescription method. More...
 
void ResetDescription (void)
 Reset Description data member. More...
 
const TDescriptionGetDescription (void) const
 Get the Description member data. More...
 
void SetDescription (TDescription &value)
 Assign a value to Description data member. More...
 
TDescriptionSetDescription (void)
 Assign a value to Description data member. More...
 
bool IsSetSeqannot (void) const
 contains the CD alignment Check if a value has been assigned to Seqannot data member. More...
 
bool CanGetSeqannot (void) const
 Check if it is safe to call GetSeqannot method. More...
 
void ResetSeqannot (void)
 Reset Seqannot data member. More...
 
const TSeqannotGetSeqannot (void) const
 Get the Seqannot member data. More...
 
TSeqannotSetSeqannot (void)
 Assign a value to Seqannot data member. More...
 
bool IsSetFeatures (void) const
 contains structure alignment data or "core" definitions Check if a value has been assigned to Features data member. More...
 
bool CanGetFeatures (void) const
 Check if it is safe to call GetFeatures method. More...
 
void ResetFeatures (void)
 Reset Features data member. More...
 
const TFeaturesGetFeatures (void) const
 Get the Features member data. More...
 
void SetFeatures (TFeatures &value)
 Assign a value to Features data member. More...
 
TFeaturesSetFeatures (void)
 Assign a value to Features data member. More...
 
bool IsSetSequences (void) const
 store as bioseq-set inside seq-entry Check if a value has been assigned to Sequences data member. More...
 
bool CanGetSequences (void) const
 Check if it is safe to call GetSequences method. More...
 
void ResetSequences (void)
 Reset Sequences data member. More...
 
const TSequencesGetSequences (void) const
 Get the Sequences member data. More...
 
void SetSequences (TSequences &value)
 Assign a value to Sequences data member. More...
 
TSequencesSetSequences (void)
 Assign a value to Sequences data member. More...
 
bool IsSetProfile_range (void) const
 profile for this region only also stores the Seq-id of the master Check if a value has been assigned to Profile_range data member. More...
 
bool CanGetProfile_range (void) const
 Check if it is safe to call GetProfile_range method. More...
 
void ResetProfile_range (void)
 Reset Profile_range data member. More...
 
const TProfile_rangeGetProfile_range (void) const
 Get the Profile_range member data. More...
 
void SetProfile_range (TProfile_range &value)
 Assign a value to Profile_range data member. More...
 
TProfile_rangeSetProfile_range (void)
 Assign a value to Profile_range data member. More...
 
bool IsSetTrunc_master (void) const
 holds the truncated master, which may be something like a consensus, uses the same sequence coordinate frame as the profile-range Check if a value has been assigned to Trunc_master data member. More...
 
bool CanGetTrunc_master (void) const
 Check if it is safe to call GetTrunc_master method. More...
 
void ResetTrunc_master (void)
 Reset Trunc_master data member. More...
 
const TTrunc_masterGetTrunc_master (void) const
 Get the Trunc_master member data. More...
 
void SetTrunc_master (TTrunc_master &value)
 Assign a value to Trunc_master data member. More...
 
TTrunc_masterSetTrunc_master (void)
 Assign a value to Trunc_master data member. More...
 
bool IsSetPosfreq (void) const
 relative residue frequencies Check if a value has been assigned to Posfreq data member. More...
 
bool CanGetPosfreq (void) const
 Check if it is safe to call GetPosfreq method. More...
 
void ResetPosfreq (void)
 Reset Posfreq data member. More...
 
const TPosfreqGetPosfreq (void) const
 Get the Posfreq member data. More...
 
void SetPosfreq (TPosfreq &value)
 Assign a value to Posfreq data member. More...
 
TPosfreqSetPosfreq (void)
 Assign a value to Posfreq data member. More...
 
bool IsSetScoremat (void) const
 Position dependent score matrix Check if a value has been assigned to Scoremat data member. More...
 
bool CanGetScoremat (void) const
 Check if it is safe to call GetScoremat method. More...
 
void ResetScoremat (void)
 Reset Scoremat data member. More...
 
const TScorematGetScoremat (void) const
 Get the Scoremat member data. More...
 
void SetScoremat (TScoremat &value)
 Assign a value to Scoremat data member. More...
 
TScorematSetScoremat (void)
 Assign a value to Scoremat data member. More...
 
bool IsSetDistance (void) const
 pairwise distances for all seqs. More...
 
bool CanGetDistance (void) const
 Check if it is safe to call GetDistance method. More...
 
void ResetDistance (void)
 Reset Distance data member. More...
 
const TDistanceGetDistance (void) const
 Get the Distance member data. More...
 
void SetDistance (TDistance &value)
 Assign a value to Distance data member. More...
 
TDistanceSetDistance (void)
 Assign a value to Distance data member. More...
 
bool IsSetParent (void) const
 this CD is the result of a split Check if a value has been assigned to Parent data member. More...
 
bool CanGetParent (void) const
 Check if it is safe to call GetParent method. More...
 
void ResetParent (void)
 Reset Parent data member. More...
 
const TParentGetParent (void) const
 Get the Parent member data. More...
 
void SetParent (TParent &value)
 Assign a value to Parent data member. More...
 
TParentSetParent (void)
 Assign a value to Parent data member. More...
 
bool IsSetChildren (void) const
 this CD has been split, not used Check if a value has been assigned to Children data member. More...
 
bool CanGetChildren (void) const
 Check if it is safe to call GetChildren method. More...
 
void ResetChildren (void)
 Reset Children data member. More...
 
const TChildrenGetChildren (void) const
 Get the Children member data. More...
 
void SetChildren (TChildren &value)
 Assign a value to Children data member. More...
 
TChildrenSetChildren (void)
 Assign a value to Children data member. More...
 
bool IsSetSiblings (void) const
 related CDs (common hits), clusters Check if a value has been assigned to Siblings data member. More...
 
bool CanGetSiblings (void) const
 Check if it is safe to call GetSiblings method. More...
 
void ResetSiblings (void)
 Reset Siblings data member. More...
 
const TSiblingsGetSiblings (void) const
 Get the Siblings member data. More...
 
void SetSiblings (TSiblings &value)
 Assign a value to Siblings data member. More...
 
TSiblingsSetSiblings (void)
 Assign a value to Siblings data member. More...
 
bool IsSetNeighbors (void) const
 co-occurring CDs, not used Check if a value has been assigned to Neighbors data member. More...
 
bool CanGetNeighbors (void) const
 Check if it is safe to call GetNeighbors method. More...
 
void ResetNeighbors (void)
 Reset Neighbors data member. More...
 
const TNeighborsGetNeighbors (void) const
 Get the Neighbors member data. More...
 
void SetNeighbors (TNeighbors &value)
 Assign a value to Neighbors data member. More...
 
TNeighborsSetNeighbors (void)
 Assign a value to Neighbors data member. More...
 
bool IsSetPending (void) const
 contains alignments from update or "lower panel" Check if a value has been assigned to Pending data member. More...
 
bool CanGetPending (void) const
 Check if it is safe to call GetPending method. More...
 
void ResetPending (void)
 Reset Pending data member. More...
 
const TPendingGetPending (void) const
 Get the Pending member data. More...
 
TPendingSetPending (void)
 Assign a value to Pending data member. More...
 
bool IsSetRejects (void) const
 SeqIds of rejected CD- members, ignore in update Check if a value has been assigned to Rejects data member. More...
 
bool CanGetRejects (void) const
 Check if it is safe to call GetRejects method. More...
 
void ResetRejects (void)
 Reset Rejects data member. More...
 
const TRejectsGetRejects (void) const
 Get the Rejects member data. More...
 
TRejectsSetRejects (void)
 Assign a value to Rejects data member. More...
 
bool IsSetMaster3d (void) const
 record if CD has a 3D representative Check if a value has been assigned to Master3d data member. More...
 
bool CanGetMaster3d (void) const
 Check if it is safe to call GetMaster3d method. More...
 
void ResetMaster3d (void)
 Reset Master3d data member. More...
 
const TMaster3dGetMaster3d (void) const
 Get the Master3d member data. More...
 
TMaster3dSetMaster3d (void)
 Assign a value to Master3d data member. More...
 
bool IsSetAlignannot (void) const
 alignment annotation Check if a value has been assigned to Alignannot data member. More...
 
bool CanGetAlignannot (void) const
 Check if it is safe to call GetAlignannot method. More...
 
void ResetAlignannot (void)
 Reset Alignannot data member. More...
 
const TAlignannotGetAlignannot (void) const
 Get the Alignannot member data. More...
 
void SetAlignannot (TAlignannot &value)
 Assign a value to Alignannot data member. More...
 
TAlignannotSetAlignannot (void)
 Assign a value to Alignannot data member. More...
 
bool IsSetStyle_dictionary (void) const
 record rendering styles Check if a value has been assigned to Style_dictionary data member. More...
 
bool CanGetStyle_dictionary (void) const
 Check if it is safe to call GetStyle_dictionary method. More...
 
void ResetStyle_dictionary (void)
 Reset Style_dictionary data member. More...
 
const TStyle_dictionaryGetStyle_dictionary (void) const
 Get the Style_dictionary member data. More...
 
void SetStyle_dictionary (TStyle_dictionary &value)
 Assign a value to Style_dictionary data member. More...
 
TStyle_dictionarySetStyle_dictionary (void)
 Assign a value to Style_dictionary data member. More...
 
bool IsSetUser_annotations (void) const
 user annotations in Cn3D Check if a value has been assigned to User_annotations data member. More...
 
bool CanGetUser_annotations (void) const
 Check if it is safe to call GetUser_annotations method. More...
 
void ResetUser_annotations (void)
 Reset User_annotations data member. More...
 
const TUser_annotationsGetUser_annotations (void) const
 Get the User_annotations member data. More...
 
void SetUser_annotations (TUser_annotations &value)
 Assign a value to User_annotations data member. More...
 
TUser_annotationsSetUser_annotations (void)
 Assign a value to User_annotations data member. More...
 
bool IsSetAncestors (void) const
 list of parents Check if a value has been assigned to Ancestors data member. More...
 
bool CanGetAncestors (void) const
 Check if it is safe to call GetAncestors method. More...
 
void ResetAncestors (void)
 Reset Ancestors data member. More...
 
const TAncestorsGetAncestors (void) const
 Get the Ancestors member data. More...
 
TAncestorsSetAncestors (void)
 Assign a value to Ancestors data member. More...
 
bool IsSetScoreparams (void) const
 Check if a value has been assigned to Scoreparams data member. More...
 
bool CanGetScoreparams (void) const
 Check if it is safe to call GetScoreparams method. More...
 
void ResetScoreparams (void)
 Reset Scoreparams data member. More...
 
const TScoreparamsGetScoreparams (void) const
 Get the Scoreparams member data. More...
 
void SetScoreparams (TScoreparams &value)
 Assign a value to Scoreparams data member. More...
 
TScoreparamsSetScoreparams (void)
 Assign a value to Scoreparams data member. More...
 
bool IsSetSeqtree (void) const
 Check if a value has been assigned to Seqtree data member. More...
 
bool CanGetSeqtree (void) const
 Check if it is safe to call GetSeqtree method. More...
 
void ResetSeqtree (void)
 Reset Seqtree data member. More...
 
const TSeqtreeGetSeqtree (void) const
 Get the Seqtree member data. More...
 
void SetSeqtree (TSeqtree &value)
 Assign a value to Seqtree data member. More...
 
TSeqtreeSetSeqtree (void)
 Assign a value to Seqtree 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
 

Private Types

typedef CCdd_Base Tparent
 

Private Member Functions

 CCdd (const CCdd &value)
 
CCddoperator= (const CCdd &value)
 

Additional Inherited Members

- Public Types inherited from CCdd_Base
enum class  E_memberIndex {
  e__allMandatory = 0 , e_name , e_id , e_description ,
  e_seqannot , e_features , e_sequences , e_profile_range ,
  e_trunc_master , e_posfreq , e_scoremat , e_distance ,
  e_parent , e_children , e_siblings , e_neighbors ,
  e_pending , e_rejects , e_master3d , e_alignannot ,
  e_style_dictionary , e_user_annotations , e_ancestors , e_scoreparams ,
  e_seqtree
}
 
typedef string TName
 
typedef CCdd_id_set TId
 
typedef CCdd_descr_set TDescription
 
typedef list< CRef< CSeq_annot > > TSeqannot
 
typedef CBiostruc_annot_set TFeatures
 
typedef CSeq_entry TSequences
 
typedef CSeq_interval TProfile_range
 
typedef CBioseq TTrunc_master
 
typedef CMatrix TPosfreq
 
typedef CMatrix TScoremat
 
typedef CTriangle TDistance
 
typedef CCdd_id TParent
 
typedef CCdd_id_set TChildren
 
typedef CCdd_id_set TSiblings
 
typedef CCdd_id_set TNeighbors
 
typedef list< CRef< CUpdate_align > > TPending
 
typedef list< CRef< CReject_id > > TRejects
 
typedef list< CRef< CSeq_id > > TMaster3d
 
typedef CAlign_annot_set TAlignannot
 
typedef CCn3d_style_dictionary TStyle_dictionary
 
typedef CCn3d_user_annotations TUser_annotations
 
typedef list< CRef< CDomain_parent > > TAncestors
 
typedef CPssmWithParameters TScoreparams
 
typedef CSequence_tree TSeqtree
 
typedef Tparent::CMemberIndex< E_memberIndex, 25 > 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...
 
- 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 50 of file Cdd.hpp.

Member Typedef Documentation

◆ Tparent

typedef CCdd_Base CCdd::Tparent
private

Definition at line 52 of file Cdd.hpp.

Constructor & Destructor Documentation

◆ CCdd() [1/2]

CCdd::CCdd ( void  )
inline

Definition at line 70 of file Cdd.hpp.

◆ ~CCdd()

CCdd::~CCdd ( void  )

Definition at line 50 of file Cdd.cpp.

◆ CCdd() [2/2]

CCdd::CCdd ( const CCdd value)
private

Member Function Documentation

◆ operator=()

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

The documentation for this class was generated from the following files:
Modified on Thu Mar 28 17:11:52 2024 by modify_doxy.py rev. 669887