Search Toolkit Book for CGC_Scaf_stats

#include <objects/genomecoll/GC_Scaf_stats.hpp>

Inheritance diagram for CGC_Scaf_stats:

Collaboration diagram for CGC_Scaf_stats:

Public Member Functions
	CGC_Scaf_stats (void)

	~CGC_Scaf_stats (void)

Public Member Functions inherited from CGC_Scaf_stats_Base
	CGC_Scaf_stats_Base (void)

virtual	~CGC_Scaf_stats_Base (void)

	DECLARE_INTERNAL_TYPE_INFO ()

bool	IsSetStats_category (void) const
	Check if a value has been assigned to Stats_category data member. More...

bool	CanGetStats_category (void) const
	Check if it is safe to call GetStats_category method. More...

void	ResetStats_category (void)
	Reset Stats_category data member. More...

TStats_category	GetStats_category (void) const
	Get the Stats_category member data. More...

void	SetStats_category (TStats_category value)
	Assign a value to Stats_category data member. More...

TStats_category &	SetStats_category (void)
	Assign a value to Stats_category data member. More...

bool	IsSetValue (void) const
	Check if a value has been assigned to Value data member. More...

bool	CanGetValue (void) const
	Check if it is safe to call GetValue method. More...

void	ResetValue (void)
	Reset Value data member. More...

TValue	GetValue (void) const
	Get the Value member data. More...

void	SetValue (TValue value)
	Assign a value to Value data member. More...

TValue &	SetValue (void)
	Assign a value to Value 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 CGC_Scaf_stats_Base	Tparent

Private Member Functions
	CGC_Scaf_stats (const CGC_Scaf_stats &value)

CGC_Scaf_stats &	operator= (const CGC_Scaf_stats &value)

Additional Inherited Members
Public Types inherited from CGC_Scaf_stats_Base
enum	EStats_category { eStats_category_replicon_count = 70 , eStats_category_scaffold_count = 22 , eStats_category_component_count = 23 , eStats_category_component_span_count = 24 , eStats_category_total_length = 1 , eStats_category_ungapped_length = 2 , eStats_category_min_gapped_scaf_length = 25 , eStats_category_max_gapped_scaf_length = 26 , eStats_category_min_ungapped_scaf_length = 27 , eStats_category_max_ungapped_scaf_length = 28 , eStats_category_active_finishing_bases = 3 , eStats_category_draft_bases = 5 , eStats_category_finished_bases = 7 , eStats_category_whole_genome_finishing_bases = 9 , eStats_category_other_sequences = 11 , eStats_category_pre_draft = 13 , eStats_category_wgs_bases = 15 , eStats_category_bases_in_spanned_gaps = 17 , eStats_category_n50 = 19 , eStats_category_spanned_gaps = 20 , eStats_category_unspanned_gaps = 21 , eStats_category_bases_in_unspanned_gaps = 29 , eStats_category_count_contig = 30 , eStats_category_contig_n50 = 31 , eStats_category_contig_L50 = 32 , eStats_category_contig_n75 = 33 , eStats_category_contig_n90 = 34 , eStats_category_scaf_L50 = 35 , eStats_category_scaf_n75 = 36 , eStats_category_scaf_n90 = 37 , eStats_category_gc_count = 38 , eStats_category_atgc_count = 39 , eStats_category_gc_perc = 40 , eStats_category_is_there_unplaced_scaf = 72 , eStats_category_count_singleton_unordered_scaffold = 73 , eStats_category_count_chr_made_of_singleton_ordered_scaffold = 74 , eStats_category_count_chr_with_single_component = 75 , eStats_category_count_singleton_in_minus_orientation = 76 , eStats_category_count_unknown_gaps = 80 , eStats_category_count_implicit_scaf_src_name = 82 , eStats_category_count_explicit_scaf_src_name = 83 , eStats_category_all_chr_has_single_component = 84 , eStats_category_count_scaf_with_terminal_gaps = 85 , eStats_category_count_chr_with_terminal_gaps = 86 , eStats_category_count_uniq_components = 87 , eStats_category_count_uniq_component_diff_from_last_release = 88 , eStats_category_count_chromosome_types = 89 , eStats_category_count_chromosome_terminal_gap_types = 90 , eStats_category_count_dropped_components = 91 , eStats_category_count_non_chromosome_replicon = 92 , eStats_category_count_assembly_units = 93 , eStats_category_count_alt_loci_units = 94 , eStats_category_count_fixed_patches = 95 , eStats_category_count_novel_patches = 96 , eStats_category_count_regions = 97 , eStats_category_count_patches = 98 , eStats_category_count_par_regions = 99 , eStats_category_count_genomic_regions = 100 , eStats_category_count_chromosome_replicons = 101 , eStats_category_assembly_status = 102 , eStats_category_net_count_scaffold = 103 , eStats_category_net_count_component = 104 , eStats_category_count_regions_contain_alt_loci = 105 , eStats_category_count_regions_contain_fix_patch = 106 , eStats_category_count_regions_contain_novel_patch = 107 , eStats_category_count_fix_patch_with_alignment = 108 , eStats_category_count_novel_patch_with_alignment = 109 , eStats_category_count_alt_scaf_with_alignment = 110 , eStats_category_count_alt_loci_scaf = 111 , eStats_category_count_real_scaffolds = 112 , eStats_category_top_level_count = 113 , eStats_category_total_gap_length = 114 , eStats_category_count_replicons_without_ordered_scaf = 115 , eStats_category_other = 255 }
	NOTE: These values equal to the stats_cd values in CodeStatistics table in GenomeColl. More...

enum class	E_memberIndex { e__allMandatory = 0 , e_stats_category , e_value }

typedef int	TStats_category

typedef Uint8	TValue

typedef Tparent::CMemberIndex< E_memberIndex, 3 >	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...

Static Public Member Functions inherited from CGC_Scaf_stats_Base
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME()	EStats_category (void)
	Access to EStats_category's attributes (values, names) as defined in spec. More...

Static Public Member Functions inherited from CSerialObject
static void	SetVerifyDataThread (ESerialVerifyData verify)

static void	SetVerifyDataGlobal (ESerialVerifyData verify)

static string	UnassignedString (void)

static CStringUTF8	UnassignedStringUTF8 (void)

static char	UnassignedByte (void)

Static Public Member Functions inherited from CObject
static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (void)
	Define method to throw null pointer exception. More...

static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (const type_info &type)

static EAllocFillMode	GetAllocFillMode (void)

static void	SetAllocFillMode (EAllocFillMode mode)

static void	SetAllocFillMode (const string &value)
	Set mode from configuration parameter value. More...

Static Public Member Functions inherited from CDebugDumpable
static void	EnableDebugDump (bool on)

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

CGC_Scaf_stats –.

Definition at line 65 of file GC_Scaf_stats.hpp.

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

include/objects/genomecoll/GC_Scaf_stats.hpp
src/objects/genomecoll/GC_Scaf_stats.cpp

Public Member Functions

Private Types

Private Member Functions

Additional Inherited Members

Detailed Description