#include <algo/structure/cd_utils/cuCdCore.hpp>

Inheritance diagram for CCdCore:

Collaboration diagram for CCdCore:

Public Types
enum	AlignmentSrc { NORMAL_ALIGNMENT = 0 , PENDING_ALIGNMENT }

enum	AlignmentUsage { USE_NORMAL_ALIGNMENT =0 , USE_PENDING_ALIGNMENT , USE_ALL_ALIGNMENT }

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

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

Public Member Functions
	CCdCore (void)

virtual	~CCdCore (void)

string	GetAccession (int &Version) const

string	GetAccession () const

void	SetAccession (string Accession, int Version)

void	SetAccession (string Accession)

void	EraseUID ()

int	GetUID () const

bool	HasCddId (const CCdd_id &id) const

string	GetLongDescription ()

string	GetUpdateDate ()

int	GetNumRows () const

int	GetNumSequences () const

int	GetNumRowsWithSequences () const

int	GetAlignmentLength () const

int	GetPSSMLength () const

int	GetNumBlocks () const

bool	GetCDBlockLengths (vector< int > &lengths) const

bool	GetBlockStartsForRow (int rowIndex, vector< int > &starts) const

int	GetSeqIndexForRowIndex (int rowIndex) const

int	GetMasterSeqIndex () const

int	GetSeqIndex (const CRef< CSeq_id > &SeqID) const

int	GetNthMatchFor (CRef< CSeq_id > &ID, int N)

int	GetAllRowIndicesForSeqId (const CRef< CSeq_id > &SeqID, list< int > &rows) const

int	GetAllRowIndicesForSeqId (const CRef< CSeq_id > &SeqID, vector< int > &rows) const

bool	GetGI (int Row, TGi &GI, bool ignorePDBs=true)

bool	GetPDB (int Row, const CPDB_seq_id *&pPDB)

int	GetLowerBound (int Row) const

int	GetUpperBound (int Row) const

bool	Get_GI_or_PDB_String_FromAlignment (int RowIndex, std::string &Str, bool Pad, int Len) const

string	GetSpeciesForRow (int Row)

string	GetSequenceStringByRow (int rowId)

bool	GetSeqEntryForRow (int rowId, CRef< CSeq_entry > &seqEntry) const

bool	GetBioseqForRow (int rowId, CRef< CBioseq > &bioseq)

TGi	GetGIFromSequenceList (int SeqIndex) const

string	GetDefline (int SeqIndex) const

string	GetSequenceStringByIndex (int SeqIndex)

string	GetSpeciesForIndex (int SeqIndex)

bool	GetSeqEntryForIndex (int seqIndex, CRef< CSeq_entry > &seqEntry) const

bool	GetBioseqForIndex (int seqIndex, CRef< CBioseq > &bioseq)

bool	CopyBioseqForSeqId (const CRef< CSeq_id > &seqId, CRef< CBioseq > &bioseq) const

bool	GetBioseqWithSeqId (const CRef< CSeq_id > &seqid, const CBioseq *&bioseq) const

bool	HasSeqId (const CRef< CSeq_id > &ID) const

bool	HasSeqId (const CRef< CSeq_id > &ID, int &RowIndex) const

bool	GetSeqIDForRow (int Pair, int DenDiagRow, CRef< CSeq_id > &SeqID) const

bool	GetSeqIDFromAlignment (int RowIndex, CRef< CSeq_id > &SeqID) const

bool	GetSeqIDForIndex (int SeqIndex, CRef< CSeq_id > &SeqID) const

bool	GetSeqIDs (int SeqIndex, list< CRef< CSeq_id > > &SeqIDs)

const list< CRef< CSeq_id > > &	GetSeqIDs (int SeqIndex) const

bool	EraseOtherRows (const std::vector< int > &KeepRows)

bool	EraseTheseRows (const std::vector< int > &TossRows)

void	EraseSequence (int SeqIndex)

void	EraseSequences ()

void	ErasePendingRows (set< int > &rows)

void	ErasePendingRow (int row)

bool	Has3DMaster () const

int	Num3DAlignments () const

bool	GetRowsForMmdbId (int mmdbId, list< int > &rows) const

bool	GetRowsWithMmdbId (vector< int > &rows) const

bool	GetMmdbId (int SeqIndex, int &id) const

bool	SynchronizeMaster3D (bool checkRow1WhenConsensusMaster=true)

int	MapPositionToOtherRow (int thisRow, int thisPos, int otherRow) const

int	MapPositionToOtherRow (const CRef< CSeq_align > &seqAlign, int thisPos, CoordMapDir mapDir) const

bool	IsSeqAligns () const

bool	GetAlignment (CRef< CSeq_annot > &seqAnnot)

const CRef< CSeq_annot > &	GetAlignment () const

const list< CRef< CSeq_align > > &	GetSeqAligns () const

list< CRef< CSeq_align > > &	GetSeqAligns ()

bool	GetSeqAlign (int Row, CRef< CSeq_align > &seqAlign)

const CRef< CSeq_align > &	GetSeqAlign (int Row) const

bool	UsesConsensusSequenceAsMaster () const

bool	HasConsensusSequence () const

int	GetRowsWithConsensus (vector< int > &consensusRows) const

bool	FindConsensusInSequenceList (vector< int > *indices=NULL) const

int	GetNumPending () const

bool	AddSeqAlign (CRef< CSeq_align > seqAlign)

bool	AddPendingSeqAlign (CRef< CSeq_align > seqAlign)

bool	AddSequence (CRef< CSeq_entry > seqAntry)

void	Clear ()

void	SetComment (CCdd_descr::TComment oldComment, CCdd_descr::TComment newComment)

bool	AddComment (const string &comment)

bool	AddOthername (const string &othername)

bool	AddTitle (const string &title)

bool	AddPmidReference (TEntrezId pmid)

bool	AddSource (const string &source, bool removeExistingSources=true)

bool	AddCreateDate ()

string	GetTitle () const

unsigned int	GetTitles (vector< string > &titles) const

bool	RemoveCddDescrsOfType (int cddDescrChoice)

bool	AllResiduesInRangeAligned (int rowId, int from, int to) const

bool	AlignAnnotsValid (string *err=NULL) const

int	GetNumAlignmentAnnotations ()

string	GetAlignmentAnnotationDescription (int Index)

bool	HasParentType (EClassicalOrComponent parentType) const

bool	HasParentType (CDomain_parent::EParent_type parentType) const

bool	GetClassicalParentId (const CCdd_id *&parentId) const

string	GetClassicalParentAccession (int &Version) const

string	GetClassicalParentAccession () const

Public Member Functions inherited from CCdd
	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 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

Protected Member Functions
bool	AddCddDescr (CRef< CCdd_descr > &descr)

Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Private Member Functions
	CCdCore (const CCdCore &value)

CCdCore &	operator= (const CCdCore &value)

Static Private Member Functions
static bool	GetBioseqWithSeqid (const CRef< CSeq_id > &seqid, const list< CRef< CSeq_entry > > &bsset, const CBioseq *&bioseq)

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...

Detailed Description

Definition at line 55 of file cuCdCore.hpp.

Member Enumeration Documentation

◆ AlignmentSrc

enum CCdCore::AlignmentSrc

Enumerator
NORMAL_ALIGNMENT
PENDING_ALIGNMENT

Definition at line 58 of file cuCdCore.hpp.

◆ AlignmentUsage

enum CCdCore::AlignmentUsage

Enumerator
USE_NORMAL_ALIGNMENT
USE_PENDING_ALIGNMENT
USE_ALL_ALIGNMENT

Definition at line 62 of file cuCdCore.hpp.

Constructor & Destructor Documentation

◆ CCdCore() [1/2]

CCdCore::CCdCore ( void )

Definition at line 68 of file cuCdCore.cpp.

◆ ~CCdCore()

CCdCore::~CCdCore ( void )

virtual

Definition at line 64 of file cuCdCore.cpp.

◆ CCdCore() [2/2]

CCdCore::CCdCore ( const CCdCore & value )

private

Member Function Documentation

◆ AddCddDescr()

bool CCdCore::AddCddDescr ( CRef< CCdd_descr > & descr )

protected

Definition at line 2070 of file cuCdCore.cpp.

References CCdd_Base::IsSetDescription(), CRef< C, Locker >::NotEmpty(), CCdd_descr_set_Base::Set(), and CCdd_Base::SetDescription().

Referenced by AddComment(), AddOthername(), AddPmidReference(), AddSource(), AddTitle(), and CCdFromFasta::UpdateSourceId().

◆ AddComment()

bool CCdCore::AddComment ( const string & comment )

Definition at line 1926 of file cuCdCore.cpp.

References AddCddDescr(), CCdd_descr_set_Base::Get(), CCdd_Base::GetDescription(), CCdd_Base::IsSetDescription(), and result.

◆ AddCreateDate()

bool CCdCore::AddCreateDate ( )

Definition at line 2065 of file cuCdCore.cpp.

References SetCreationDate().

◆ AddOthername()

bool CCdCore::AddOthername ( const string & othername )

Definition at line 1947 of file cuCdCore.cpp.

References AddCddDescr(), CCdd_descr_set_Base::Get(), CCdd_Base::GetDescription(), CCdd_Base::IsSetDescription(), and result.

◆ AddPendingSeqAlign()

bool CCdCore::AddPendingSeqAlign ( CRef< CSeq_align > seqAlign )

Definition at line 1112 of file cuCdCore.cpp.

References CSerialObject::Assign(), CUpdate_align_Base::eType_other, and CCdd_Base::SetPending().

Referenced by ConsensusMaker::degapCdAlignmentToPending(), MultipleAlignment::transferOneRow(), and CDUpdater::update().

◆ AddPmidReference()

bool CCdCore::AddPmidReference ( TEntrezId pmid )

Definition at line 2028 of file cuCdCore.cpp.

References AddCddDescr(), Get(), CCdd_descr_set_Base::Get(), CCdd_Base::GetDescription(), CCdd_Base::IsSetDescription(), and CPub_Base::SetPmid().

◆ AddSeqAlign()

bool CCdCore::AddSeqAlign ( CRef< CSeq_align > seqAlign )

Definition at line 1104 of file cuCdCore.cpp.

References CSerialObject::Assign(), and CCdd_Base::SetSeqannot().

Referenced by SeqSwapper::promotePendingRows(), and MultipleAlignment::transferOneRow().

◆ AddSequence()

bool CCdCore::AddSequence ( CRef< CSeq_entry > seqAntry )

Definition at line 1153 of file cuCdCore.cpp.

References CSerialObject::Assign(), CBioseq_set_Base::SetSeq_set(), CCdd_Base::SetSequences(), and CSeq_entry_Base::SetSet().

Referenced by CDRefresher::refresh(), ConsensusMaker::remasterWithConsensus(), MultipleAlignment::transferOneRow(), MultipleAlignment::transferToCD(), and CDUpdater::update().

◆ AddSource()

bool CCdCore::AddSource	(	const string &	source,
		bool	removeExistingSources = `true`
	)

Definition at line 2050 of file cuCdCore.cpp.

References AddCddDescr(), CCdd_descr_Base::e_Source, RemoveCddDescrsOfType(), result, and rapidjson::source.

◆ AddTitle()

bool CCdCore::AddTitle ( const string & title )

Definition at line 1968 of file cuCdCore.cpp.

References AddCddDescr(), CCdd_descr_set_Base::Get(), CCdd_Base::GetDescription(), CCdd_Base::IsSetDescription(), and result.

◆ AlignAnnotsValid()

bool CCdCore::AlignAnnotsValid ( string * err = NULL ) const

Definition at line 1651 of file cuCdCore.cpp.

References AllResiduesInRangeAligned(), Get(), CAlign_annot_set_Base::Get(), CCdd_Base::GetAlignannot(), GetSeqAlign(), INVALID_POSITION, CCdd_Base::IsSetAlignannot(), MapPositionToOtherRow(), MASTER_TO_CHILD, n, CRef< C, Locker >::NotEmpty(), and result.

◆ AllResiduesInRangeAligned()

bool CCdCore::AllResiduesInRangeAligned	(	int	rowId,
		int	from,
		int	to
	)		const

Definition at line 1617 of file cuCdCore.cpp.

References GetBlockNumberForResidue(), GetSeqAlign(), i, and tmp.

Referenced by AlignAnnotsValid().

◆ Clear()

void CCdCore::Clear ( void )

Definition at line 1160 of file cuCdCore.cpp.

References CCdd_Base::SetPending(), CBioseq_set_Base::SetSeq_set(), CCdd_Base::SetSeqannot(), CCdd_Base::SetSequences(), and CSeq_entry_Base::SetSet().

◆ CopyBioseqForSeqId()

bool CCdCore::CopyBioseqForSeqId	(	const CRef< CSeq_id > &	seqId,
		CRef< CBioseq > &	bioseq
	)		const

Definition at line 1767 of file cuCdCore.cpp.

References CSerialObject::Assign(), CBioseq_set_Base::GetSeq_set(), CCdd_Base::GetSequences(), CSeq_entry_Base::GetSet(), CCdd_Base::IsSetSequences(), CSeq_id::Match(), and CRef< C, Locker >::Reset().

Referenced by CDUpdater::update().

◆ EraseOtherRows()

bool CCdCore::EraseOtherRows ( const std::vector< int > & KeepRows )

Definition at line 994 of file cuCdCore.cpp.

References EraseRow(), GetAlignment(), int, and CSeq_annot_Base::SetData().

◆ ErasePendingRow()

void CCdCore::ErasePendingRow ( int row )

Definition at line 1136 of file cuCdCore.cpp.

References CCdd_Base::SetPending().

Referenced by ErasePendingRows().

◆ ErasePendingRows()

void CCdCore::ErasePendingRows ( set< int > & rows )

Definition at line 1127 of file cuCdCore.cpp.

References ErasePendingRow(), and EraseSequences().

Referenced by CDUpdater::processPendingToNormal(), and SeqSwapper::promotePendingRows().

◆ EraseSequence()

void CCdCore::EraseSequence ( int SeqIndex )

Definition at line 1077 of file cuCdCore.cpp.

References CCdd_Base::GetSequences(), i, CCdd_Base::IsSetSequences(), CBioseq_set_Base::SetSeq_set(), CCdd_Base::SetSequences(), and CSeq_entry_Base::SetSet().

Referenced by EraseSequences(), and PurgeConsensusSequences().

◆ EraseSequences()

void CCdCore::EraseSequences ( )

Definition at line 1032 of file cuCdCore.cpp.

References EraseSequence(), GetNumSequences(), CBioseq_set_Base::GetSeq_set(), CCdd_Base::GetSequences(), CSeq_entry_Base::GetSet(), HasSeqId(), i, set< Key, Compare >::insert(), and set< Key, Compare >::size().

Referenced by ErasePendingRows(), and SeqSwapper::swapSequences().

◆ EraseTheseRows()

bool CCdCore::EraseTheseRows ( const std::vector< int > & TossRows )

Definition at line 958 of file cuCdCore.cpp.

References algSortQuickCallbackIndex(), EraseRow(), GetAlignment(), i, and intSortRowsFunction().

Referenced by PurgeConsensusSequences(), and SeqSwapper::swapSequences().

◆ EraseUID()

void CCdCore::EraseUID ( )

Definition at line 132 of file cuCdCore.cpp.

References i, CCdd_id_set_Base::Set(), and CCdd_Base::SetId().

Referenced by ResetFields().

◆ FindConsensusInSequenceList()

bool CCdCore::FindConsensusInSequenceList ( vector< int > * indices = NULL ) const

Definition at line 1536 of file cuCdCore.cpp.

References GetNumSequences(), GetSeqIDs(), i, IsConsensus(), NULL, and result.

Referenced by ConsensusMaker::addRows(), HasConsensusSequence(), PssmMaker::PssmMaker(), and PurgeConsensusSequences().

◆ Get_GI_or_PDB_String_FromAlignment()

bool CCdCore::Get_GI_or_PDB_String_FromAlignment	(	int	RowIndex,
		std::string &	Str,
		bool	Pad,
		int	Len
	)		const

Definition at line 510 of file cuCdCore.cpp.

References GetSeqIDForRow(), CSeq_id_Base::IsGi(), CSeq_id_Base::IsPdb(), Len, and Make_SeqID_String().

◆ GetAccession() [1/2]

string CCdCore::GetAccession ( ) const

Definition at line 76 of file cuCdCore.cpp.

◆ GetAccession() [2/2]

string CCdCore::GetAccession ( int & Version ) const

Definition at line 81 of file cuCdCore.cpp.

References Get(), CCdd_id_set_Base::Get(), CCdd_Base::GetId(), and i.

Referenced by SeqTreeAPI::annotateLeafNode(), MultipleAlignment::appendAlignment(), CDUpdater::checkBlastAndUpdate(), CDUpdater::checkDone(), RowSourceTable::convertFromCDRows(), SeqTreeAsnizer::fillAsnSeqTreeNode(), CDFamily::findCDByAccession(), CDFamily::findChildren(), SeqTree::fixRowName(), AlignmentCollection::GetAlignedResiduesForRow(), GetAlignmentColumnsForCD(), GetBioseqWithFootprintForNthRow(), CDUpdater::getHits(), GetMasterBioseqWithFootprintOld(), GetVerboseNameStr(), RowSourceTable::makeCDRowKey(), TaxNode::makeSubSeqLeaf(), SeqTreeAPI::makeTree(), PssmMaker::modifyQuery(), CDUpdater::processBlastHits(), SeqTreeAsnizer::refillAsnMembership(), SeqTreeAsnizer::resolveRowId(), CDUpdater::submitBlast(), CDUpdater::update(), and DistanceMatrix::writeMat().

◆ GetAlignment() [1/2]

const CRef< CSeq_annot > & CCdCore::GetAlignment ( ) const

Definition at line 1353 of file cuCdCore.cpp.

References EMPTY_CREF_SEQANNOT, CCdd_Base::GetSeqannot(), and CCdd_Base::IsSetSeqannot().

Referenced by EraseOtherRows(), EraseTheseRows(), and GetNumRows().

◆ GetAlignment() [2/2]

bool CCdCore::GetAlignment ( CRef< CSeq_annot > & seqAnnot )

Definition at line 1366 of file cuCdCore.cpp.

References CCdd_Base::IsSetSeqannot(), and CCdd_Base::SetSeqannot().

◆ GetAlignmentAnnotationDescription()

string CCdCore::GetAlignmentAnnotationDescription ( int Index )

Definition at line 1746 of file cuCdCore.cpp.

References i, CAlign_annot_set_Base::Set(), and CCdd_Base::SetAlignannot().

◆ GetAlignmentLength()

int CCdCore::GetAlignmentLength ( ) const

Definition at line 257 of file cuCdCore.cpp.

References GetNumAlignedResidues(), GetSeqAlign(), and CRef< C, Locker >::NotEmpty().

Referenced by GetAlignmentColumnsForCD(), and SetAlignedResiduesForCD().

◆ GetAllRowIndicesForSeqId() [1/2]

int CCdCore::GetAllRowIndicesForSeqId	(	const CRef< CSeq_id > &	SeqID,
		list< int > &	rows
	)		const

Definition at line 406 of file cuCdCore.cpp.

References GetNumRows(), GetSeqIDFromAlignment(), i, and CSeq_id::Match().

Referenced by GetAllRowIndicesForSeqId(), and GetMappedRowIds().

◆ GetAllRowIndicesForSeqId() [2/2]

int CCdCore::GetAllRowIndicesForSeqId	(	const CRef< CSeq_id > &	SeqID,
		vector< int > &	rows
	)		const

Definition at line 389 of file cuCdCore.cpp.

References GetAllRowIndicesForSeqId().

◆ GetBioseqForIndex()

bool CCdCore::GetBioseqForIndex	(	int	seqIndex,
		CRef< CBioseq > &	bioseq
	)

Definition at line 702 of file cuCdCore.cpp.

References GetNumSequences(), i, CCdd_Base::IsSetSequences(), CRef< C, Locker >::Reset(), CBioseq_set_Base::SetSeq_set(), CCdd_Base::SetSequences(), and CSeq_entry_Base::SetSet().

Referenced by AlignmentCollection::GetBioseqForRow(), GetBioseqForRow(), GetSequenceStringByIndex(), and GetSpeciesForIndex().

◆ GetBioseqForRow()

bool CCdCore::GetBioseqForRow	(	int	rowId,
		CRef< CBioseq > &	bioseq
	)

Definition at line 561 of file cuCdCore.cpp.

References GetBioseqForIndex(), and GetSeqIndexForRowIndex().

Referenced by findHighestScoringRowByPssm(), CDUpdater::findRowsWithOldSeq(), GetBioseqWithFootprintForNthRow(), GetCommonTax(), GetMasterBioseqWithFootprintOld(), and GetSpeciesForRow().

◆ GetBioseqWithSeqId()

bool CCdCore::GetBioseqWithSeqId	(	const CRef< CSeq_id > &	seqid,
		const CBioseq *&	bioseq
	)		const

Definition at line 1793 of file cuCdCore.cpp.

References GetBioseqWithSeqid(), CBioseq_set_Base::GetSeq_set(), CCdd_Base::GetSequences(), CSeq_entry_Base::GetSet(), and CCdd_Base::IsSetSequences().

◆ GetBioseqWithSeqid()

bool CCdCore::GetBioseqWithSeqid	(	const CRef< CSeq_id > &	seqid,
		const list< CRef< CSeq_entry > > &	bsset,
		const CBioseq *&	bioseq
	)

staticprivate

Definition at line 1804 of file cuCdCore.cpp.

References CSeq_id::Match(), and result.

Referenced by GetBioseqWithSeqId().

◆ GetBlockStartsForRow()

bool CCdCore::GetBlockStartsForRow	(	int	rowIndex,
		vector< int > &	starts
	)		const

Definition at line 301 of file cuCdCore.cpp.

References GetBlockStarts(), GetSeqAlign(), IsSeqAligns(), CRef< C, Locker >::NotEmpty(), result, and ct::sort().

◆ GetCDBlockLengths()

bool CCdCore::GetCDBlockLengths ( vector< int > & lengths ) const

Definition at line 291 of file cuCdCore.cpp.

References GetBlockLengths(), GetSeqAlign(), IsSeqAligns(), and CRef< C, Locker >::NotEmpty().

◆ GetClassicalParentAccession() [1/2]

string CCdCore::GetClassicalParentAccession ( ) const

Definition at line 1899 of file cuCdCore.cpp.

◆ GetClassicalParentAccession() [2/2]

string CCdCore::GetClassicalParentAccession ( int & Version ) const

Definition at line 1904 of file cuCdCore.cpp.

References CGlobal_id_Base::GetAccession(), GetClassicalParentId(), CCdd_id_Base::GetGid(), CGlobal_id_Base::GetVersion(), CCdd_id_Base::IsGid(), and CGlobal_id_Base::IsSetVersion().

Referenced by CDFamily::findParent().

◆ GetClassicalParentId()

bool CCdCore::GetClassicalParentId ( const CCdd_id *& parentId ) const

Definition at line 1887 of file cuCdCore.cpp.

References eClassicalParent, CCdd_Base::GetAncestors(), CCdd_Base::GetParent(), HasParentType(), CCdd_Base::IsSetAncestors(), and result.

Referenced by GetClassicalParentAccession().

◆ GetDefline()

string CCdCore::GetDefline ( int SeqIndex ) const

Definition at line 625 of file cuCdCore.cpp.

References CBioseq_set_Base::GetSeq_set(), CCdd_Base::GetSequences(), CSeq_entry_Base::GetSet(), i, CCdd_Base::IsSetSequences(), and kEmptyStr.

◆ GetGI()

bool CCdCore::GetGI	(	int	Row,
		TGi &	GI,
		bool	ignorePDBs = `true`
	)

Definition at line 433 of file cuCdCore.cpp.

References CSeq_id_Base::GetGi(), GetGIFromSequenceList(), GetSeqIDForRow(), GetSeqIndex(), CSeq_id_Base::IsGi(), and CSeq_id_Base::IsPdb().

Referenced by GetCommonTax().

◆ GetGIFromSequenceList()

TGi CCdCore::GetGIFromSequenceList ( int SeqIndex ) const

Definition at line 588 of file cuCdCore.cpp.

References CBioseq_set_Base::GetSeq_set(), CCdd_Base::GetSequences(), CSeq_entry_Base::GetSet(), i, INVALID_GI, and CCdd_Base::IsSetSequences().

Referenced by CSeqAnnotFromFasta::CacheSequences(), GetGI(), and AlignmentCollection::GetGI().

◆ GetLongDescription()

string CCdCore::GetLongDescription ( )

Definition at line 179 of file cuCdCore.cpp.

References Get(), CCdd_descr_set_Base::Get(), CCdd_Base::GetDescription(), i, and CCdd_Base::IsSetDescription().

◆ GetLowerBound()

int CCdCore::GetLowerBound ( int Row ) const

Definition at line 471 of file cuCdCore.cpp.

References GetFirstOrLastDenDiag(), GetSeqAlign(), i, INVALID_POSITION, and CRef< C, Locker >::NotEmpty().

Referenced by CDUpdater::blast(), GetBioseqWithFootprintForNthRow(), GetMappedRowIds(), GetMasterBioseqWithFootprintOld(), GetPSSMLength(), and CDUpdater::overlapWithCDRow().

◆ GetMasterSeqIndex()

int CCdCore::GetMasterSeqIndex ( ) const

Definition at line 333 of file cuCdCore.cpp.

References GetSeqIndexForRowIndex().

◆ GetMmdbId()

bool CCdCore::GetMmdbId	(	int	SeqIndex,
		int &	id
	)		const

Definition at line 1314 of file cuCdCore.cpp.

References GetMMDBId(), CBioseq_set_Base::GetSeq_set(), CCdd_Base::GetSequences(), CSeq_entry_Base::GetSet(), i, and CCdd_Base::IsSetSequences().

Referenced by GetRowsForMmdbId(), and GetRowsWithMmdbId().

◆ GetNthMatchFor()

int CCdCore::GetNthMatchFor	(	CRef< CSeq_id > &	ID,
		int	N
	)

Definition at line 365 of file cuCdCore.cpp.

References GetNumRows(), GetSeqIDFromAlignment(), N, and SeqIdsMatch().

◆ GetNumAlignmentAnnotations()

int CCdCore::GetNumAlignmentAnnotations ( )

Definition at line 1735 of file cuCdCore.cpp.

References CCdd_Base::IsSetAlignannot(), CCdd_Base::SetAlignannot(), and ncbi::grid::netcache::search::fields::size.

◆ GetNumBlocks()

int CCdCore::GetNumBlocks ( ) const

Definition at line 281 of file cuCdCore.cpp.

References GetBlockCount(), GetSeqAlign(), IsSeqAligns(), and CRef< C, Locker >::NotEmpty().

◆ GetNumPending()

int CCdCore::GetNumPending ( ) const

inline

Definition at line 201 of file cuCdCore.hpp.

References CCdd_Base::GetPending(), and ncbi::grid::netcache::search::fields::size.

◆ GetNumRows()

int CCdCore::GetNumRows ( ) const

Definition at line 215 of file cuCdCore.cpp.

References CSeq_annot_Base::C_Data::GetAlign(), GetAlignment(), CSeq_annot_Base::GetData(), CSeq_annot_Base::C_Data::IsAlign(), and CRef< C, Locker >::NotEmpty().

Referenced by ConsensusMaker::degapAlignment(), findHighestScoringRowByPssm(), CDUpdater::findRowsWithOldSeq(), GetAlignmentColumnsForCD(), GetAllRowIndicesForSeqId(), GetBioseqWithFootprintForNRows(), GetBioseqWithFootprintForNthRow(), GetCommonTax(), GetNthMatchFor(), GetNumRowsWithSequences(), GetOverlappedRows(), GetRowsForMmdbId(), GetRowsWithConsensus(), GetRowsWithMmdbId(), GetSeqIndexForRowIndex(), HasConsensusSequence(), HasSeqId(), IntersectByMaster(), CDUpdater::mergePending(), CDUpdater::overlapWithCDRow(), SeqSwapper::promotePendingRows(), remasterAlignannot(), ReorderStructureAlignments(), SetAlignedResiduesForCD(), SeqSwapper::swapSequences(), MultipleAlignment::transferOneRow(), and MultipleAlignment::transferToCD().

◆ GetNumRowsWithSequences()

int CCdCore::GetNumRowsWithSequences ( ) const

Definition at line 231 of file cuCdCore.cpp.

References GetNumRows(), GetSeqIndexForRowIndex(), and i.

◆ GetNumSequences()

int CCdCore::GetNumSequences ( ) const

Definition at line 244 of file cuCdCore.cpp.

References CCdd_Base::GetSequences(), CCdd_Base::IsSetSequences(), and ncbi::grid::netcache::search::fields::size.

Referenced by CSeqAnnotFromFasta::CacheSequences(), CSeqAnnotFromFasta::DetermineMasterIndex(), EraseSequences(), FindConsensusInSequenceList(), GetBioseqForIndex(), GetSeqEntryForIndex(), GetSeqIndex(), CSeqAnnotFromFasta::MakeAsIsSeqAnnot(), CSeqAnnotFromFasta::MakeIBMSeqAnnot(), CSeqAnnotFromFasta::MakeSeqAnnotFromFasta(), and SetConvertedSequencesForCD().

◆ GetPDB()

bool CCdCore::GetPDB	(	int	Row,
		const CPDB_seq_id *&	pPDB
	)

Definition at line 454 of file cuCdCore.cpp.

References CSeq_id_Base::GetPdb(), GetSeqIDForRow(), and CSeq_id_Base::IsPdb().

Referenced by CSeqAnnotFromFasta::DetermineMasterIndex(), and ReorderStructureAlignments().

◆ GetPSSMLength()

int CCdCore::GetPSSMLength ( ) const

Definition at line 271 of file cuCdCore.cpp.

References GetLowerBound(), and GetUpperBound().

◆ GetRowsForMmdbId()

bool CCdCore::GetRowsForMmdbId	(	int	mmdbId,
		list< int > &	rows
	)		const

Definition at line 1268 of file cuCdCore.cpp.

References GetMmdbId(), GetNumRows(), and GetSeqIndexForRowIndex().

◆ GetRowsWithConsensus()

int CCdCore::GetRowsWithConsensus ( vector< int > & consensusRows ) const

Definition at line 1572 of file cuCdCore.cpp.

References GetNumRows(), GetSeqIDFromAlignment(), i, and IsConsensus().

Referenced by PurgeConsensusSequences().

◆ GetRowsWithMmdbId()

bool CCdCore::GetRowsWithMmdbId ( vector< int > & rows ) const

Definition at line 1293 of file cuCdCore.cpp.

References GetMmdbId(), GetNumRows(), and GetSeqIndexForRowIndex().

◆ GetSeqAlign() [1/2]

const CRef< CSeq_align > & CCdCore::GetSeqAlign ( int Row ) const

Definition at line 1444 of file cuCdCore.cpp.

References EMPTY_CREF_SEQALIGN, ctll::front(), GetSeqAligns(), and IsSeqAligns().

◆ GetSeqAlign() [2/2]

bool CCdCore::GetSeqAlign	(	int	Row,
		CRef< CSeq_align > &	seqAlign
	)

Definition at line 1419 of file cuCdCore.cpp.

References GetSeqAligns(), and IsSeqAligns().

Referenced by AlignAnnotsValid(), AllResiduesInRangeAligned(), ConsensusMaker::degapAlignment(), findHighestScoringRowByPssm(), GetAlignmentColumnsForCD(), GetAlignmentLength(), GetBlockStartsForRow(), GetCDBlockLengths(), GetLowerBound(), GetNumBlocks(), GetSeqIDForRow(), GetUpperBound(), MapPositionToOtherRow(), remasterAlignannot(), ReMasterCdWithoutUnifiedBlocks(), and SetAlignedResiduesForCD().

◆ GetSeqAligns() [1/2]

list< CRef< CSeq_align > > & CCdCore::GetSeqAligns ( )

Definition at line 1410 of file cuCdCore.cpp.

References CCdd_Base::SetSeqannot().

◆ GetSeqAligns() [2/2]

const list< CRef< CSeq_align > > & CCdCore::GetSeqAligns ( ) const

Definition at line 1398 of file cuCdCore.cpp.

References CCdd_Base::GetSeqannot(), and i.

Referenced by AlignmentCollection::addNormalAlignment(), GetSeqAlign(), IntersectByMaster(), CDUpdater::processPendingToNormal(), CDRefresher::refresh(), ReMasterCdWithoutUnifiedBlocks(), and Reorder().

◆ GetSeqEntryForIndex()

bool CCdCore::GetSeqEntryForIndex	(	int	seqIndex,
		CRef< CSeq_entry > &	seqEntry
	)		const

Definition at line 679 of file cuCdCore.cpp.

References GetNumSequences(), CBioseq_set_Base::GetSeq_set(), CCdd_Base::GetSequences(), CSeq_entry_Base::GetSet(), i, CCdd_Base::IsSetSequences(), and CRef< C, Locker >::Reset().

Referenced by PssmMaker::PssmMaker().

◆ GetSeqEntryForRow()

bool CCdCore::GetSeqEntryForRow	(	int	rowId,
		CRef< CSeq_entry > &	seqEntry
	)		const

Definition at line 529 of file cuCdCore.cpp.

References CBioseq_set_Base::GetSeq_set(), GetSeqIDFromAlignment(), CCdd_Base::GetSequences(), CSeq_entry_Base::GetSet(), CCdd_Base::IsSetSequences(), CSeq_id::Match(), and result.

Referenced by CDUpdater::blast(), CDUpdater::mergePending(), PssmMaker::PssmMaker(), and CDUpdater::update().

◆ GetSeqIDForIndex()

bool CCdCore::GetSeqIDForIndex	(	int	SeqIndex,
		CRef< CSeq_id > &	SeqID
	)		const

Definition at line 829 of file cuCdCore.cpp.

References CBioseq_set_Base::GetSeq_set(), CCdd_Base::GetSequences(), CSeq_entry_Base::GetSet(), i, CCdd_Base::IsSetSequences(), and CRef< C, Locker >::NotEmpty().

Referenced by CSeqAnnotFromFasta::MakeAsIsSeqAnnot(), and CSeqAnnotFromFasta::MakeIBMSeqAnnot().

◆ GetSeqIDForRow()

bool CCdCore::GetSeqIDForRow	(	int	Pair,
		int	DenDiagRow,
		CRef< CSeq_id > &	SeqID
	)		const

Definition at line 787 of file cuCdCore.cpp.

References GetFirstOrLastDenDiag(), GetSeqAlign(), i, and CRef< C, Locker >::NotEmpty().

Referenced by Get_GI_or_PDB_String_FromAlignment(), GetGI(), GetPDB(), GetSeqIDFromAlignment(), HasSeqId(), CDUpdater::mergePending(), ReMasterCdWithoutUnifiedBlocks(), RemasterWithStructure(), and SynchronizeMaster3D().

◆ GetSeqIDFromAlignment()

bool CCdCore::GetSeqIDFromAlignment	(	int	RowIndex,
		CRef< CSeq_id > &	SeqID
	)		const

Definition at line 815 of file cuCdCore.cpp.

References GetSeqIDForRow().

Referenced by GetAllRowIndicesForSeqId(), GetMappedRowIds(), GetNthMatchFor(), GetRowsWithConsensus(), GetSeqEntryForRow(), GetSeqIndexForRowIndex(), HasConsensusSequence(), CDUpdater::overlapWithCDRow(), PssmMaker::PssmMaker(), and UsesConsensusSequenceAsMaster().

◆ GetSeqIDs() [1/2]

const list< CRef< CSeq_id > > & CCdCore::GetSeqIDs ( int SeqIndex ) const

Definition at line 929 of file cuCdCore.cpp.

References CBioseq_set_Base::GetSeq_set(), CCdd_Base::GetSequences(), CSeq_entry_Base::GetSet(), and i.

◆ GetSeqIDs() [2/2]

bool CCdCore::GetSeqIDs	(	int	SeqIndex,
		list< CRef< CSeq_id > > &	SeqIDs
	)

Definition at line 900 of file cuCdCore.cpp.

References CBioseq_set_Base::GetSeq_set(), CCdd_Base::GetSequences(), CSeq_entry_Base::GetSet(), i, and CCdd_Base::IsSetSequences().

Referenced by FindConsensusInSequenceList().

◆ GetSeqIndex()

int CCdCore::GetSeqIndex ( const CRef< CSeq_id > & SeqID ) const

Definition at line 337 of file cuCdCore.cpp.

References GetNumSequences(), CBioseq_set_Base::GetSeq_set(), CCdd_Base::GetSequences(), CSeq_entry_Base::GetSet(), i, CCdd_Base::IsSetSequences(), CRef< C, Locker >::NotEmpty(), SeqIdHasMatchInBioseq(), and ncbi::grid::netcache::search::fields::size.

Referenced by ConsensusMaker::addRows(), AlignmentCollection::GetBioseqForRow(), GetGI(), AlignmentCollection::GetGI(), GetSeqIndexForRowIndex(), AlignmentCollection::GetSpeciesForRow(), and MultipleAlignment::transferOneRow().

◆ GetSeqIndexForRowIndex()

int CCdCore::GetSeqIndexForRowIndex ( int rowIndex ) const

Definition at line 319 of file cuCdCore.cpp.

References GetNumRows(), GetSeqIDFromAlignment(), and GetSeqIndex().

Referenced by GetBioseqForRow(), GetMasterSeqIndex(), GetNumRowsWithSequences(), GetRowsForMmdbId(), GetRowsWithMmdbId(), and GetSequenceStringByRow().

◆ GetSequenceStringByIndex()

string CCdCore::GetSequenceStringByIndex ( int SeqIndex )

Definition at line 724 of file cuCdCore.cpp.

References GetBioseqForIndex(), GetNcbieaaString(), and kEmptyStr.

Referenced by ConsensusMaker::addRows(), CSeqAnnotFromFasta::CacheSequences(), CSeqAnnotFromFasta::DetermineMasterIndex(), GetSequenceStringByRow(), and SetConvertedSequencesForCD().

◆ GetSequenceStringByRow()

string CCdCore::GetSequenceStringByRow ( int rowId )

Definition at line 578 of file cuCdCore.cpp.

References GetSeqIndexForRowIndex(), and GetSequenceStringByIndex().

Referenced by CDUpdater::blast(), IntersectByMaster(), CDUpdater::processPendingToNormal(), and SetAlignedResiduesForCD().

◆ GetSpeciesForIndex()

string CCdCore::GetSpeciesForIndex ( int SeqIndex )

Definition at line 670 of file cuCdCore.cpp.

References GetBioseqForIndex(), GetSpeciesFromBioseq(), CRef< C, Locker >::IsNull(), and kEmptyStr.

Referenced by AlignmentCollection::GetSpeciesForRow().

◆ GetSpeciesForRow()

string CCdCore::GetSpeciesForRow ( int Row )

Definition at line 568 of file cuCdCore.cpp.

References GetBioseqForRow(), GetSpeciesFromBioseq(), CRef< C, Locker >::IsNull(), and kEmptyStr.

◆ GetTitle()

string CCdCore::GetTitle ( void ) const

Definition at line 1989 of file cuCdCore.cpp.

References CCdd_descr_set_Base::Get(), CCdd_Base::GetDescription(), CCdd_Base::IsSetDescription(), kEmptyStr, and result.

Referenced by PssmMaker::modifyQuery().

◆ GetTitles()

unsigned int CCdCore::GetTitles ( vector< string > & titles ) const

Definition at line 2008 of file cuCdCore.cpp.

References CCdd_descr_set_Base::Get(), CCdd_Base::GetDescription(), CCdd_Base::IsSetDescription(), kEmptyStr, and result.

◆ GetUID()

int CCdCore::GetUID ( ) const

Definition at line 146 of file cuCdCore.cpp.

References CCdd_id_set_Base::Get(), and CCdd_Base::GetId().

◆ GetUpdateDate()

string CCdCore::GetUpdateDate ( )

Definition at line 196 of file cuCdCore.cpp.

References Get(), CCdd_descr_set_Base::Get(), CCdd_Base::GetDescription(), i, and CCdd_Base::IsSetDescription().

◆ GetUpperBound()

int CCdCore::GetUpperBound ( int Row ) const

Definition at line 490 of file cuCdCore.cpp.

References GetFirstOrLastDenDiag(), GetSeqAlign(), i, INVALID_POSITION, and CRef< C, Locker >::NotEmpty().

Referenced by CDUpdater::blast(), GetBioseqWithFootprintForNthRow(), GetMappedRowIds(), GetMasterBioseqWithFootprintOld(), GetPSSMLength(), and CDUpdater::overlapWithCDRow().

◆ Has3DMaster()

bool CCdCore::Has3DMaster ( ) const

Definition at line 1197 of file cuCdCore.cpp.

References CSeq_align_Base::C_Segs::GetDendiag(), CSeq_align_Base::GetSegs(), CCdd_Base::GetSeqannot(), CSeq_align_Base::C_Segs::IsDendiag(), CCdd_Base::IsSetSeqannot(), and result.

Referenced by Num3DAlignments(), ReorderStructureAlignments(), and SynchronizeMaster3D().

◆ HasCddId()

bool CCdCore::HasCddId ( const CCdd_id & id ) const

Definition at line 161 of file cuCdCore.cpp.

References CCdd_id_set_Base::Get(), and CCdd_Base::GetId().

◆ HasConsensusSequence()

bool CCdCore::HasConsensusSequence ( ) const

Definition at line 1509 of file cuCdCore.cpp.

References FindConsensusInSequenceList(), GetNumRows(), GetSeqIDFromAlignment(), i, IsConsensus(), and result.

◆ HasParentType() [1/2]

bool CCdCore::HasParentType ( CDomain_parent::EParent_type parentType ) const

Definition at line 1862 of file cuCdCore.cpp.

References CDomain_parent_Base::eParent_type_classical, CCdd_Base::GetAncestors(), CCdd_Base::IsSetAncestors(), CCdd_Base::IsSetParent(), obeysParentTypeConstraints(), and result.

◆ HasParentType() [2/2]

bool CCdCore::HasParentType ( EClassicalOrComponent parentType ) const

Definition at line 1838 of file cuCdCore.cpp.

References eClassicalParent, eComponentParent, CDomain_parent_Base::eParent_type_classical, CDomain_parent_Base::eParent_type_other, CCdd_Base::GetAncestors(), CCdd_Base::IsSetAncestors(), obeysParentTypeConstraints(), and result.

Referenced by GetClassicalParentId().

◆ HasSeqId() [1/2]

bool CCdCore::HasSeqId ( const CRef< CSeq_id > & ID ) const

Definition at line 738 of file cuCdCore.cpp.

Referenced by EraseSequences().

◆ HasSeqId() [2/2]

bool CCdCore::HasSeqId	(	const CRef< CSeq_id > &	ID,
		int &	RowIndex
	)		const

Definition at line 747 of file cuCdCore.cpp.

References CSeq_align_Base::C_Segs::GetDendiag(), CDense_diag_Base::GetIds(), GetNumRows(), CCdd_Base::GetPending(), CSeq_align_Base::GetSegs(), GetSeqIDForRow(), and SeqIdsMatch().

◆ IsSeqAligns()

bool CCdCore::IsSeqAligns ( ) const

Definition at line 1383 of file cuCdCore.cpp.

References CCdd_Base::GetSeqannot(), i, and CCdd_Base::IsSetSeqannot().

Referenced by AlignmentCollection::addNormalAlignment(), GetBlockStartsForRow(), GetCDBlockLengths(), GetNumBlocks(), GetSeqAlign(), Reorder(), and ReorderStructureAlignments().

◆ MapPositionToOtherRow() [1/2]

int CCdCore::MapPositionToOtherRow	(	const CRef< CSeq_align > &	seqAlign,
		int	thisPos,
		CoordMapDir	mapDir
	)		const

Definition at line 1499 of file cuCdCore.cpp.

References CHILD_TO_MASTER, INVALID_POSITION, MapPositionToChild(), and MapPositionToMaster().

◆ MapPositionToOtherRow() [2/2]

int CCdCore::MapPositionToOtherRow	(	int	thisRow,
		int	thisPos,
		int	otherRow
	)		const

Definition at line 1467 of file cuCdCore.cpp.

References GetSeqAlign(), INVALID_POSITION, MapPositionToChild(), MapPositionToMaster(), and CRef< C, Locker >::NotEmpty().

Referenced by AlignAnnotsValid().

◆ Num3DAlignments()

int CCdCore::Num3DAlignments ( ) const

Definition at line 1227 of file cuCdCore.cpp.

References CCdd_Base::GetSeqannot(), Has3DMaster(), CCdd_Base::IsSetSeqannot(), and UsesConsensusSequenceAsMaster().

Referenced by CSeqAnnotFromFasta::DetermineMasterIndex(), and ReorderStructureAlignments().

◆ operator=()

CCdCore& CCdCore::operator= ( const CCdCore & value )

private

◆ RemoveCddDescrsOfType()

bool CCdCore::RemoveCddDescrsOfType ( int cddDescrChoice )

Definition at line 2087 of file cuCdCore.cpp.

References CCdd_descr_Base::e_MaxChoice, i, CCdd_Base::IsSetDescription(), CCdd_descr_set_Base::Set(), and CCdd_Base::SetDescription().

Referenced by AddSource().

◆ SetAccession() [1/2]

void CCdCore::SetAccession ( string Accession )

Definition at line 102 of file cuCdCore.cpp.

References SetAccession().

◆ SetAccession() [2/2]

void CCdCore::SetAccession	(	string	Accession,
		int	Version
	)

Definition at line 106 of file cuCdCore.cpp.

References i, CCdd_id_set_Base::Set(), CCdd_id_Base::SetGid(), and CCdd_Base::SetId().

Referenced by CCdFromFasta::InitializeParameters(), CSeqAnnotFromFasta::MakeSeqAnnotFromFasta(), and SetAccession().

◆ SetComment()

void CCdCore::SetComment	(	CCdd_descr::TComment	oldComment,
		CCdd_descr::TComment	newComment
	)

Definition at line 1592 of file cuCdCore.cpp.

References i, CCdd_Base::IsSetDescription(), CCdd_descr_set_Base::Set(), and CCdd_Base::SetDescription().

◆ SynchronizeMaster3D()

bool CCdCore::SynchronizeMaster3D ( bool checkRow1WhenConsensusMaster = true )

Definition at line 1170 of file cuCdCore.cpp.

References GetSeqIDForRow(), Has3DMaster(), CSeq_id_Base::IsPdb(), CCdd_Base::ResetMaster3d(), result, CCdd_Base::SetMaster3d(), and UsesConsensusSequenceAsMaster().

◆ UsesConsensusSequenceAsMaster()

bool CCdCore::UsesConsensusSequenceAsMaster ( ) const

Definition at line 1558 of file cuCdCore.cpp.

References GetSeqIDFromAlignment(), and IsConsensus().

Referenced by Num3DAlignments(), PurgeConsensusSequences(), ConsensusMaker::remasterWithConsensus(), and SynchronizeMaster3D().

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

include/algo/structure/cd_utils/cuCdCore.hpp
src/algo/structure/cd_utils/cuCdCore.cpp

Public Types

Public Member Functions

Protected Member Functions

Private Member Functions

Static Private Member Functions

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ AlignmentSrc

◆ AlignmentUsage

Constructor & Destructor Documentation

◆ CCdCore() [1/2]

◆ ~CCdCore()

◆ CCdCore() [2/2]

Member Function Documentation

◆ AddCddDescr()

◆ AddComment()

◆ AddCreateDate()

◆ AddOthername()

◆ AddPendingSeqAlign()

◆ AddPmidReference()

◆ AddSeqAlign()

◆ AddSequence()

◆ AddSource()

◆ AddTitle()

◆ AlignAnnotsValid()

◆ AllResiduesInRangeAligned()

◆ Clear()

◆ CopyBioseqForSeqId()

◆ EraseOtherRows()

◆ ErasePendingRow()

◆ ErasePendingRows()

◆ EraseSequence()

◆ EraseSequences()

◆ EraseTheseRows()

◆ EraseUID()

◆ FindConsensusInSequenceList()

◆ Get_GI_or_PDB_String_FromAlignment()

◆ GetAccession() [1/2]

◆ GetAccession() [2/2]

◆ GetAlignment() [1/2]

◆ GetAlignment() [2/2]

◆ GetAlignmentAnnotationDescription()

◆ GetAlignmentLength()

◆ GetAllRowIndicesForSeqId() [1/2]

◆ GetAllRowIndicesForSeqId() [2/2]

◆ GetBioseqForIndex()

◆ GetBioseqForRow()

◆ GetBioseqWithSeqId()

◆ GetBioseqWithSeqid()

◆ GetBlockStartsForRow()

◆ GetCDBlockLengths()

◆ GetClassicalParentAccession() [1/2]

◆ GetClassicalParentAccession() [2/2]

◆ GetClassicalParentId()

◆ GetDefline()

◆ GetGI()

◆ GetGIFromSequenceList()

◆ GetLongDescription()

◆ GetLowerBound()

◆ GetMasterSeqIndex()

◆ GetMmdbId()

◆ GetNthMatchFor()

◆ GetNumAlignmentAnnotations()

◆ GetNumBlocks()

◆ GetNumPending()

◆ GetNumRows()

◆ GetNumRowsWithSequences()

◆ GetNumSequences()

◆ GetPDB()

◆ GetPSSMLength()

◆ GetRowsForMmdbId()

◆ GetRowsWithConsensus()

◆ GetRowsWithMmdbId()

◆ GetSeqAlign() [1/2]

◆ GetSeqAlign() [2/2]

◆ GetSeqAligns() [1/2]

◆ GetSeqAligns() [2/2]

◆ GetSeqEntryForIndex()

◆ GetSeqEntryForRow()