Search Toolkit Book for CBlast_def_line
#include <objects/blastdb/Blast_def_line.hpp>
Inheritance diagram for CBlast_def_line:
Collaboration diagram for CBlast_def_line:
Public Types | |
| typedef set< TTaxId > | TTaxIds |
| Set of leaf-node taxonomy IDs associated with this entry in the. More... | |
| Public Types inherited from CBlast_def_line_Base | |
| enum class | E_memberIndex { e__allMandatory = 0 , e_title , e_seqid , e_taxid , e_memberships , e_links , e_other_info } |
| typedef string | TTitle |
| typedef list< CRef< CSeq_id > > | TSeqid |
| typedef NCBI_NS_NCBI::TTaxId | TTaxid |
| typedef list< int > | TMemberships |
| typedef list< int > | TLinks |
| typedef list< int > | TOther_info |
| typedef Tparent::CMemberIndex< E_memberIndex, 7 > | 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 | |
| CBlast_def_line (void) | |
| ~CBlast_def_line (void) | |
| TTaxIds | GetTaxIds () const |
| void | SetTaxIds (const TTaxIds &t) |
| TTaxIds | GetLeafTaxIds () const |
| void | SetLeafTaxIds (const TTaxIds &t) |
| Public Member Functions inherited from CBlast_def_line_Base | |
| CBlast_def_line_Base (void) | |
| virtual | ~CBlast_def_line_Base (void) |
| DECLARE_INTERNAL_TYPE_INFO () | |
| bool | IsSetTitle (void) const |
| simple title Check if a value has been assigned to Title data member. More... | |
| bool | CanGetTitle (void) const |
| Check if it is safe to call GetTitle method. More... | |
| void | ResetTitle (void) |
| Reset Title data member. More... | |
| const TTitle & | GetTitle (void) const |
| Get the Title member data. More... | |
| void | SetTitle (const TTitle &value) |
| Assign a value to Title data member. More... | |
| void | SetTitle (TTitle &&value) |
| TTitle & | SetTitle (void) |
| Assign a value to Title data member. More... | |
| bool | IsSetSeqid (void) const |
| Regular NCBI Seq-Id taxonomy id, should not be set if multiple taxids are available (see links below) Check if a value has been assigned to Seqid data member. More... | |
| bool | CanGetSeqid (void) const |
| Check if it is safe to call GetSeqid method. More... | |
| void | ResetSeqid (void) |
| Reset Seqid data member. More... | |
| const TSeqid & | GetSeqid (void) const |
| Get the Seqid member data. More... | |
| TSeqid & | SetSeqid (void) |
| Assign a value to Seqid data member. More... | |
| bool | IsSetTaxid (void) const |
| Check if a value has been assigned to Taxid data member. More... | |
| bool | CanGetTaxid (void) const |
| Check if it is safe to call GetTaxid method. More... | |
| void | ResetTaxid (void) |
| Reset Taxid data member. More... | |
| TTaxid | GetTaxid (void) const |
| Get the Taxid member data. More... | |
| void | SetTaxid (TTaxid value) |
| Assign a value to Taxid data member. More... | |
| TTaxid & | SetTaxid (void) |
| Assign a value to Taxid data member. More... | |
| bool | IsSetMemberships (void) const |
| bit arrays Repurposed to store the (multiple) taxIDs associated with WP proteins. More... | |
| bool | CanGetMemberships (void) const |
| Check if it is safe to call GetMemberships method. More... | |
| void | ResetMemberships (void) |
| Reset Memberships data member. More... | |
| const TMemberships & | GetMemberships (void) const |
| Get the Memberships member data. More... | |
| TMemberships & | SetMemberships (void) |
| Assign a value to Memberships data member. More... | |
| bool | IsSetLinks (void) const |
| Check if a value has been assigned to Links data member. More... | |
| bool | CanGetLinks (void) const |
| Check if it is safe to call GetLinks method. More... | |
| void | ResetLinks (void) |
| Reset Links data member. More... | |
| const TLinks & | GetLinks (void) const |
| Get the Links member data. More... | |
| TLinks & | SetLinks (void) |
| Assign a value to Links data member. More... | |
| bool | IsSetOther_info (void) const |
| In proteins this stores the PIG, in nucleotides this stores the "origin
GIs" (if one sequence is described in the ASN.1 as an identical copy of another) Check if a value has been assigned to Other_info data member. More... | |
| bool | CanGetOther_info (void) const |
| Check if it is safe to call GetOther_info method. More... | |
| void | ResetOther_info (void) |
| Reset Other_info data member. More... | |
| const TOther_info & | GetOther_info (void) const |
| Get the Other_info member data. More... | |
| TOther_info & | SetOther_info (void) |
| Assign a value to Other_info 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 CBlast_def_line_Base | Tparent |
Private Member Functions | |
| CBlast_def_line (const CBlast_def_line &value) | |
| CBlast_def_line & | operator= (const CBlast_def_line &value) |
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... | |
Detailed Description
Definition at line 54 of file Blast_def_line.hpp.
Member Typedef Documentation
◆ Tparent
|
private |
Definition at line 56 of file Blast_def_line.hpp.
◆ TTaxIds
| typedef set<TTaxId> CBlast_def_line::TTaxIds |
Set of leaf-node taxonomy IDs associated with this entry in the.
Definition at line 65 of file Blast_def_line.hpp.
Constructor & Destructor Documentation
◆ CBlast_def_line() [1/2]
|
inline |
Definition at line 82 of file Blast_def_line.hpp.
◆ ~CBlast_def_line()
| CBlast_def_line::~CBlast_def_line | ( | void | ) |
Definition at line 50 of file Blast_def_line.cpp.
◆ CBlast_def_line() [2/2]
|
private |
Member Function Documentation
◆ GetLeafTaxIds()
| CBlast_def_line::TTaxIds CBlast_def_line::GetLeafTaxIds | ( | ) | const |
Definition at line 148 of file Blast_def_line.cpp.
References CBlast_def_line_Base::GetLinks(), set< Key, Compare >::insert(), CBlast_def_line_Base::IsSetLinks(), ITERATE, and TAX_ID_FROM.
Referenced by BOOST_AUTO_TEST_CASE().
◆ GetTaxIds()
| CBlast_def_line::TTaxIds CBlast_def_line::GetTaxIds | ( | ) | const |
Definition at line 98 of file Blast_def_line.cpp.
References CBlast_def_line_Base::CanGetTaxid(), set< Key, Compare >::erase(), CBlast_def_line_Base::GetLinks(), CBlast_def_line_Base::GetTaxid(), set< Key, Compare >::insert(), CBlast_def_line_Base::IsSetLinks(), ITERATE, set< Key, Compare >::size(), TAX_ID_FROM, and ZERO_TAX_ID.
Referenced by s_IncludeDefline_NegativeTaxid().
◆ operator=()
|
private |
◆ SetLeafTaxIds()
Definition at line 130 of file Blast_def_line.cpp.
References ITERATE, CBlast_def_line_Base::ResetLinks(), CBlast_def_line_Base::SetLinks(), t, and TAX_ID_TO.
Referenced by BOOST_AUTO_TEST_CASE().
◆ SetTaxIds()
Definition at line 56 of file Blast_def_line.cpp.
References CBlast_def_line_Base::GetTaxid(), CBlast_def_line_Base::IsSetTaxid(), ITERATE, CBlast_def_line_Base::ResetLinks(), CBlast_def_line_Base::ResetTaxid(), CBlast_def_line_Base::SetLinks(), CBlast_def_line_Base::SetTaxid(), t, TAX_ID_TO, and ZERO_TAX_ID.
The documentation for this class was generated from the following files:
- include/objects/blastdb/Blast_def_line.hpp
- src/objects/blastdb/Blast_def_line.cpp
