|
| CGC_Scaf_stats (void) |
|
| ~CGC_Scaf_stats (void) |
|
| 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...
|
|
| 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...
|
|
| 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...
|
|
| 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 |
|
|
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 |
|
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 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 void | SetVerifyDataThread (ESerialVerifyData verify) |
|
static void | SetVerifyDataGlobal (ESerialVerifyData verify) |
|
static string | UnassignedString (void) |
|
static CStringUTF8 | UnassignedStringUTF8 (void) |
|
static char | UnassignedByte (void) |
|
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 void | EnableDebugDump (bool on) |
|
static const char * | ms_UnassignedStr = "<*unassigned*>" |
|
static const char | ms_UnassignedByte = char(0xcd) |
|
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...
|
|
virtual void | DeleteThis (void) |
| Virtual method "deleting" this object. More...
|
|
CGC_Scaf_stats –.
Definition at line 65 of file GC_Scaf_stats.hpp.