Search Toolkit Book for CBlast4_simple_alignment
CBlast4_simple_alignment –. More...
#include <objects/blast/Blast4_simple_alignment.hpp>
Inheritance diagram for CBlast4_simple_alignment:
Collaboration diagram for CBlast4_simple_alignment:
Public Member Functions | |
| CBlast4_simple_alignment (void) | |
| ~CBlast4_simple_alignment (void) | |
| Public Member Functions inherited from CBlast4_simple_alignment_Base | |
| CBlast4_simple_alignment_Base (void) | |
| virtual | ~CBlast4_simple_alignment_Base (void) |
| DECLARE_INTERNAL_TYPE_INFO () | |
| bool | IsSetSubject_id (void) const |
| Subject sequence identifier (normally a GI from the SeqAlign) Check if a value has been assigned to Subject_id data member. More... | |
| bool | CanGetSubject_id (void) const |
| Check if it is safe to call GetSubject_id method. More... | |
| void | ResetSubject_id (void) |
| Reset Subject_id data member. More... | |
| const TSubject_id & | GetSubject_id (void) const |
| Get the Subject_id member data. More... | |
| void | SetSubject_id (const TSubject_id &value) |
| Assign a value to Subject_id data member. More... | |
| void | SetSubject_id (TSubject_id &&value) |
| TSubject_id & | SetSubject_id (void) |
| Assign a value to Subject_id data member. More... | |
| bool | IsSetE_value (void) const |
| E-Value Check if a value has been assigned to E_value data member. More... | |
| bool | CanGetE_value (void) const |
| Check if it is safe to call GetE_value method. More... | |
| void | ResetE_value (void) |
| Reset E_value data member. More... | |
| TE_value | GetE_value (void) const |
| Get the E_value member data. More... | |
| void | SetE_value (TE_value value) |
| Assign a value to E_value data member. More... | |
| TE_value & | SetE_value (void) |
| Assign a value to E_value data member. More... | |
| bool | IsSetBit_score (void) const |
| Bit score Check if a value has been assigned to Bit_score data member. More... | |
| bool | CanGetBit_score (void) const |
| Check if it is safe to call GetBit_score method. More... | |
| void | ResetBit_score (void) |
| Reset Bit_score data member. More... | |
| TBit_score | GetBit_score (void) const |
| Get the Bit_score member data. More... | |
| void | SetBit_score (TBit_score value) |
| Assign a value to Bit_score data member. More... | |
| TBit_score & | SetBit_score (void) |
| Assign a value to Bit_score data member. More... | |
| bool | IsSetNum_identities (void) const |
| Number of identities Check if a value has been assigned to Num_identities data member. More... | |
| bool | CanGetNum_identities (void) const |
| Check if it is safe to call GetNum_identities method. More... | |
| void | ResetNum_identities (void) |
| Reset Num_identities data member. More... | |
| TNum_identities | GetNum_identities (void) const |
| Get the Num_identities member data. More... | |
| void | SetNum_identities (TNum_identities value) |
| Assign a value to Num_identities data member. More... | |
| TNum_identities & | SetNum_identities (void) |
| Assign a value to Num_identities data member. More... | |
| bool | IsSetNum_indels (void) const |
| Number of insertions/deletions Check if a value has been assigned to Num_indels data member. More... | |
| bool | CanGetNum_indels (void) const |
| Check if it is safe to call GetNum_indels method. More... | |
| void | ResetNum_indels (void) |
| Reset Num_indels data member. More... | |
| TNum_indels | GetNum_indels (void) const |
| Get the Num_indels member data. More... | |
| void | SetNum_indels (TNum_indels value) |
| Assign a value to Num_indels data member. More... | |
| TNum_indels & | SetNum_indels (void) |
| Assign a value to Num_indels data member. More... | |
| bool | IsSetFull_query_range (void) const |
| Full query range covered by this HSP Check if a value has been assigned to Full_query_range data member. More... | |
| bool | CanGetFull_query_range (void) const |
| Check if it is safe to call GetFull_query_range method. More... | |
| void | ResetFull_query_range (void) |
| Reset Full_query_range data member. More... | |
| const TFull_query_range & | GetFull_query_range (void) const |
| Get the Full_query_range member data. More... | |
| void | SetFull_query_range (TFull_query_range &value) |
| Assign a value to Full_query_range data member. More... | |
| TFull_query_range & | SetFull_query_range (void) |
| Assign a value to Full_query_range data member. More... | |
| bool | IsSetFull_subject_range (void) const |
| Full subject range covered by this HSP Check if a value has been assigned to Full_subject_range data member. More... | |
| bool | CanGetFull_subject_range (void) const |
| Check if it is safe to call GetFull_subject_range method. More... | |
| void | ResetFull_subject_range (void) |
| Reset Full_subject_range data member. More... | |
| const TFull_subject_range & | GetFull_subject_range (void) const |
| Get the Full_subject_range member data. More... | |
| void | SetFull_subject_range (TFull_subject_range &value) |
| Assign a value to Full_subject_range data member. More... | |
| TFull_subject_range & | SetFull_subject_range (void) |
| Assign a value to Full_subject_range 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 CBlast4_simple_alignment_Base | Tparent |
Private Member Functions | |
| CBlast4_simple_alignment (const CBlast4_simple_alignment &value) | |
| CBlast4_simple_alignment & | operator= (const CBlast4_simple_alignment &value) |
Additional Inherited Members | |
| Public Types inherited from CBlast4_simple_alignment_Base | |
| enum class | E_memberIndex { e__allMandatory = 0 , e_subject_id , e_e_value , e_bit_score , e_num_identities , e_num_indels , e_full_query_range , e_full_subject_range } |
| typedef string | TSubject_id |
| typedef double | TE_value |
| typedef double | TBit_score |
| typedef int | TNum_identities |
| typedef int | TNum_indels |
| typedef CBlast4_range | TFull_query_range |
| typedef CBlast4_range | TFull_subject_range |
| typedef Tparent::CMemberIndex< E_memberIndex, 8 > | 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 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
Definition at line 65 of file Blast4_simple_alignment.hpp.
The documentation for this class was generated from the following files:
- include/objects/blast/Blast4_simple_alignment.hpp
- src/objects/blast/Blast4_simple_alignment.cpp
