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

the Cdd is the basic ASN.1 object storing an annotated and curated set of alignments (formulated as a set of pairwise master-slave alignments). More...

#include <objects/cdd/Cdd_.hpp>

Inheritance diagram for CCdd_Base:

Collaboration diagram for CCdd_Base:

Public Types
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< Uint8 >	TCounter
	Counter type is CAtomiCounter. More...

typedef Uint8	TCount
	Alias for value type of counter. More...

Public Member Functions
	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 TName &	GetName (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)

TName &	SetName (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 TId &	GetId (void) const
	Get the Id member data. More...

void	SetId (TId &value)
	Assign a value to Id data member. More...

TId &	SetId (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 TDescription &	GetDescription (void) const
	Get the Description member data. More...

void	SetDescription (TDescription &value)
	Assign a value to Description data member. More...

TDescription &	SetDescription (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 TSeqannot &	GetSeqannot (void) const
	Get the Seqannot member data. More...

TSeqannot &	SetSeqannot (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 TFeatures &	GetFeatures (void) const
	Get the Features member data. More...

void	SetFeatures (TFeatures &value)
	Assign a value to Features data member. More...

TFeatures &	SetFeatures (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 TSequences &	GetSequences (void) const
	Get the Sequences member data. More...

void	SetSequences (TSequences &value)
	Assign a value to Sequences data member. More...

TSequences &	SetSequences (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_range &	GetProfile_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_range &	SetProfile_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_master &	GetTrunc_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_master &	SetTrunc_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 TPosfreq &	GetPosfreq (void) const
	Get the Posfreq member data. More...

void	SetPosfreq (TPosfreq &value)
	Assign a value to Posfreq data member. More...

TPosfreq &	SetPosfreq (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 TScoremat &	GetScoremat (void) const
	Get the Scoremat member data. More...

void	SetScoremat (TScoremat &value)
	Assign a value to Scoremat data member. More...

TScoremat &	SetScoremat (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 TDistance &	GetDistance (void) const
	Get the Distance member data. More...

void	SetDistance (TDistance &value)
	Assign a value to Distance data member. More...

TDistance &	SetDistance (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 TParent &	GetParent (void) const
	Get the Parent member data. More...

void	SetParent (TParent &value)
	Assign a value to Parent data member. More...

TParent &	SetParent (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 TChildren &	GetChildren (void) const
	Get the Children member data. More...

void	SetChildren (TChildren &value)
	Assign a value to Children data member. More...

TChildren &	SetChildren (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 TSiblings &	GetSiblings (void) const
	Get the Siblings member data. More...

void	SetSiblings (TSiblings &value)
	Assign a value to Siblings data member. More...

TSiblings &	SetSiblings (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 TNeighbors &	GetNeighbors (void) const
	Get the Neighbors member data. More...

void	SetNeighbors (TNeighbors &value)
	Assign a value to Neighbors data member. More...

TNeighbors &	SetNeighbors (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 TPending &	GetPending (void) const
	Get the Pending member data. More...

TPending &	SetPending (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 TRejects &	GetRejects (void) const
	Get the Rejects member data. More...

TRejects &	SetRejects (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 TMaster3d &	GetMaster3d (void) const
	Get the Master3d member data. More...

TMaster3d &	SetMaster3d (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 TAlignannot &	GetAlignannot (void) const
	Get the Alignannot member data. More...

void	SetAlignannot (TAlignannot &value)
	Assign a value to Alignannot data member. More...

TAlignannot &	SetAlignannot (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_dictionary &	GetStyle_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_dictionary &	SetStyle_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_annotations &	GetUser_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_annotations &	SetUser_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 TAncestors &	GetAncestors (void) const
	Get the Ancestors member data. More...

TAncestors &	SetAncestors (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 TScoreparams &	GetScoreparams (void) const
	Get the Scoreparams member data. More...

void	SetScoreparams (TScoreparams &value)
	Assign a value to Scoreparams data member. More...

TScoreparams &	SetScoreparams (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 TSeqtree &	GetSeqtree (void) const
	Get the Seqtree member data. More...

void	SetSeqtree (TSeqtree &value)
	Assign a value to Seqtree data member. More...

TSeqtree &	SetSeqtree (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 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

Private Types
typedef CSerialObject	Tparent

Private Member Functions
	CCdd_Base (const CCdd_Base &)

CCdd_Base &	operator= (const CCdd_Base &)

Private Attributes
Uint4	m_set_State [2]

string	m_Name

CRef< TId >	m_Id

CRef< TDescription >	m_Description

list< CRef< CSeq_annot > >	m_Seqannot

CRef< TFeatures >	m_Features

CRef< TSequences >	m_Sequences

CRef< TProfile_range >	m_Profile_range

CRef< TTrunc_master >	m_Trunc_master

CRef< TPosfreq >	m_Posfreq

CRef< TScoremat >	m_Scoremat

CRef< TDistance >	m_Distance

CRef< TParent >	m_Parent

CRef< TChildren >	m_Children

CRef< TSiblings >	m_Siblings

CRef< TNeighbors >	m_Neighbors

list< CRef< CUpdate_align > >	m_Pending

list< CRef< CReject_id > >	m_Rejects

list< CRef< CSeq_id > >	m_Master3d

CRef< TAlignannot >	m_Alignannot

CRef< TStyle_dictionary >	m_Style_dictionary

CRef< TUser_annotations >	m_User_annotations

list< CRef< CDomain_parent > >	m_Ancestors

CRef< TScoreparams >	m_Scoreparams

CRef< TSeqtree >	m_Seqtree

Additional Inherited Members
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

the Cdd is the basic ASN.1 object storing an annotated and curated set of alignments (formulated as a set of pairwise master-slave alignments).

The alignment data are contained in Seq-annots, and a special type of object, the Update-align, contains additional alignment data from unfinished editing sessions and update processes. The Biostruc-annot-set holds structure superposition information for multiple structure-derived rows in the alignment. Version numbers in Global-ids are meant to be updated every time the Cdd is changed in a way that does not require Global-ids to be changed (sequences added in update cycle, annotation changed, alignment errors fixed)

CCdd_Base –

Definition at line 105 of file Cdd_.hpp.

The documentation for this class was generated from the following files:

include/objects/cdd/Cdd_.hpp
src/objects/cdd/Cdd_.cpp

Public Types

Public Member Functions

Private Types

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description