NCBI C++ ToolKit
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Search Toolkit Book for CBlast4_mask_Base
Masking locations for a query's frame. More...
#include <objects/blast/Blast4_mask_.hpp>
Public Types | |
enum class | E_memberIndex { e__allMandatory = 0 , e_locations , e_frame } |
typedef list< CRef< CSeq_loc > > | TLocations |
typedef EBlast4_frame_type | TFrame |
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... | |
Public Member Functions | |
CBlast4_mask_Base (void) | |
virtual | ~CBlast4_mask_Base (void) |
DECLARE_INTERNAL_TYPE_INFO () | |
bool | IsSetLocations (void) const |
Check if a value has been assigned to Locations data member. More... | |
bool | CanGetLocations (void) const |
Check if it is safe to call GetLocations method. More... | |
void | ResetLocations (void) |
Reset Locations data member. More... | |
const TLocations & | GetLocations (void) const |
Get the Locations member data. More... | |
TLocations & | SetLocations (void) |
Assign a value to Locations data member. More... | |
bool | IsSetFrame (void) const |
Check if a value has been assigned to Frame data member. More... | |
bool | CanGetFrame (void) const |
Check if it is safe to call GetFrame method. More... | |
void | ResetFrame (void) |
Reset Frame data member. More... | |
TFrame | GetFrame (void) const |
Get the Frame member data. More... | |
void | SetFrame (TFrame value) |
Assign a value to Frame data member. More... | |
TFrame & | SetFrame (void) |
Assign a value to Frame 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 | |
CBlast4_mask_Base (const CBlast4_mask_Base &) | |
CBlast4_mask_Base & | operator= (const CBlast4_mask_Base &) |
Private Attributes | |
Uint4 | m_set_State [1] |
list< CRef< CSeq_loc > > | m_Locations |
EBlast4_frame_type | m_Frame |
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... | |
Masking locations for a query's frame.
The locations field is a single Seq-loc of type Packed-int, which contains all the masking locations for the translation frame specified by the frame field. Notes: On input (i.e.: when the client specifies masking locations as a Blast4-parameter), in the case of protein queries, the frame field must always be notset, in the case of nucleotide queries (regardless of whether the search will translate these or not), the frame must be plus1. Masking locations in the translated encoding are not permitted. On output (i.e.: when blast 4 server encodes these as part of the Blast4-get-search-results-reply), the same conventions as above apply for non-translated protein and nucleotide queries, but in the case of translated nucleotide queries, the frame field can be specified in any of the translation frames as appropriate.
Definition at line 91 of file Blast4_mask_.hpp.