Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/classCSearch__Base.html below:
NCBI C++ ToolKit: CSearch_Base< LEGACY, NHITS, derived_t
Represents ASN.1 type Search defined in file blastxml2.asn
Search Toolkit Book for CSearch_Base
CSearch_Base –. More...
#include <objects/blastxml2/Search_.hpp>
enum class E_memberIndex {
e__allMandatory = 0 , e_query_id , e_query_title , e_query_len ,
e_query_masking , e_hits , e_stat , e_message
} typedef string TQuery_id typedef string TQuery_title typedef int TQuery_len typedef list< CRef< CRange > > TQuery_masking typedef list< CRef< CHit > > THits typedef CStatistics TStat typedef string TMessage typedef Tparent::CMemberIndex< E_memberIndex, 8 > TmemberIndex typedef CDbIndex_Impl< LEGACY > TIndex_Impl typedef TIndex_Impl::TSubjectMap TSubjectMap typedef CTrackedSeeds< NHITS > TTrackedSeeds typedef derived_t TDerived 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...
CSearch_Base (void) virtual ~CSearch_Base (void) DECLARE_INTERNAL_TYPE_INFO () bool IsSetQuery_id (void) const SeqId of query Check if a value has been assigned to Query_id data member. More...
bool CanGetQuery_id (void) const Check if it is safe to call GetQuery_id method. More...
void ResetQuery_id (void) Reset Query_id data member. More...
const TQuery_id & GetQuery_id (void) const Get the Query_id member data. More...
void SetQuery_id (const TQuery_id &value) Assign a value to Query_id data member. More...
void SetQuery_id (TQuery_id &&value) TQuery_id & SetQuery_id (void) Assign a value to Query_id data member. More...
bool IsSetQuery_title (void) const Definition line of query Check if a value has been assigned to Query_title data member. More...
bool CanGetQuery_title (void) const Check if it is safe to call GetQuery_title method. More...
void ResetQuery_title (void) Reset Query_title data member. More...
const TQuery_title & GetQuery_title (void) const Get the Query_title member data. More...
void SetQuery_title (const TQuery_title &value) Assign a value to Query_title data member. More...
void SetQuery_title (TQuery_title &&value) TQuery_title & SetQuery_title (void) Assign a value to Query_title data member. More...
bool IsSetQuery_len (void) const length of query sequence Check if a value has been assigned to Query_len data member. More...
bool CanGetQuery_len (void) const Check if it is safe to call GetQuery_len method. More...
void ResetQuery_len (void) Reset Query_len data member. More...
TQuery_len GetQuery_len (void) const Get the Query_len member data. More...
void SetQuery_len (TQuery_len value) Assign a value to Query_len data member. More...
TQuery_len & SetQuery_len (void) Assign a value to Query_len data member. More...
bool IsSetQuery_masking (void) const Masked offsets. More...
bool CanGetQuery_masking (void) const Check if it is safe to call GetQuery_masking method. More...
void ResetQuery_masking (void) Reset Query_masking data member. More...
const TQuery_masking & GetQuery_masking (void) const Get the Query_masking member data. More...
TQuery_masking & SetQuery_masking (void) Assign a value to Query_masking data member. More...
bool IsSetHits (void) const Hits one for every db sequence Check if a value has been assigned to Hits data member. More...
bool CanGetHits (void) const Check if it is safe to call GetHits method. More...
void ResetHits (void) Reset Hits data member. More...
const THits & GetHits (void) const Get the Hits member data. More...
THits & SetHits (void) Assign a value to Hits data member. More...
bool IsSetStat (void) const search statistics Check if a value has been assigned to Stat data member. More...
bool CanGetStat (void) const Check if it is safe to call GetStat method. More...
void ResetStat (void) Reset Stat data member. More...
const TStat & GetStat (void) const Get the Stat member data. More...
void SetStat (TStat &value) Assign a value to Stat data member. More...
TStat & SetStat (void) Assign a value to Stat data member. More...
bool IsSetMessage (void) const Some (error?) information Check if a value has been assigned to Message data member. More...
bool CanGetMessage (void) const Check if it is safe to call GetMessage method. More...
void ResetMessage (void) Reset Message data member. More...
const TMessage & GetMessage (void) const Get the Message member data. More...
void SetMessage (const TMessage &value) Assign a value to Message data member. More...
void SetMessage (TMessage &&value) TMessage & SetMessage (void) Assign a value to Message data member. More...
virtual void Reset (void) Reset the whole object. More...
CSearch_Base (const TIndex_Impl &index_impl, const BLAST_SequenceBlk *query, const BlastSeqLoc *locs, const TSearchOptions &options) Object constructor. More...
CConstRef< CDbIndex::CSearchResults > operator() () Performs the search. 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 template<bool LEGACY, unsigned long NHITS, typename derived_t>
class CSearch_Base< LEGACY, NHITS, derived_t >
CSearch_Base –.
This is the object representing the state of a search over the index.
Use of a separate class for searches allows for multiple simultaneous searches against the same index.
Definition at line 85 of file Search_.hpp.
◆ TDerived
template<bool LEGACY, unsigned long NHITS, typename derived_t >
Definition at line 870 of file dbindex_search.cpp.
◆ TIndex_Impl
template<bool LEGACY, unsigned long NHITS, typename derived_t >
Definition at line 867 of file dbindex_search.cpp.
◆ TSearchOptions
template<bool LEGACY, unsigned long NHITS, typename derived_t >
◆ TSubjectMap
template<bool LEGACY, unsigned long NHITS, typename derived_t >
Definition at line 868 of file dbindex_search.cpp.
◆ TTrackedSeed
template<bool LEGACY, unsigned long NHITS, typename derived_t >
◆ TTrackedSeeds
template<bool LEGACY, unsigned long NHITS, typename derived_t >
Definition at line 869 of file dbindex_search.cpp.
◆ TTrackedSeedsSet
template<bool LEGACY, unsigned long NHITS, typename derived_t >
Representation of the set of currently tracked seeds for all subject sequences.
Definition at line 898 of file dbindex_search.cpp.
◆ CSearch_Base()
template<bool LEGACY, unsigned long NHITS, typename derived_t >
◆ ComputeSeeds()
template<bool LEGACY, unsigned long NHITS, typename derived_t >
◆ ExtendLeft()
template<bool LEGACY, unsigned long NHITS, typename derived_t >
Extend a seed candidate to the left.
No more than word_length - hkey_width positions are inspected.
-
Parameters
-
seed [I] the seed candidate nmax [I] if non-zero - additional restriction for the number of positions to consider
Definition at line 998 of file dbindex_search.cpp.
References ambig(), CDbIndex::CR, CR, i, and seed.
◆ ExtendRight()
template<bool LEGACY, unsigned long NHITS, typename derived_t >
Extend a seed candidate to the right.
Extends as far right as possible, unless nmax parameter is non-zeroA
-
Parameters
-
seed [I] the seed candidate nmax [I] if non-zero - search no more than this many positions
Definition at line 1070 of file dbindex_search.cpp.
References ambig(), CDbIndex::CR, CR, i, and seed.
◆ operator()()
template<bool LEGACY, unsigned long NHITS, typename derived_t >
◆ ProcessBoundaryOffset()
template<bool LEGACY, unsigned long NHITS, typename derived_t >
Process a seed candidate that is close to the masked out or ambigous region of the subject.
The second parameter is encoded as follows: bits 3-5 (0-2) ' is the distance to the left (right) boundary of the valid subject region plus 1. Value 0 in either field indicates that the corresponding distance is greater than 5.
-
Parameters
-
offset [I] uncompressed offset value bounds [I] distance to the left and/or right boundary of the valid subject region.
Definition at line 1142 of file dbindex_search.cpp.
References bounds, offset, and seed.
◆ ProcessOffset()
template<bool LEGACY, unsigned long NHITS, typename derived_t >
Process a regular seed candidate.
-
Parameters
-
offset [I] uncompressed offset value
Definition at line 1177 of file dbindex_search.cpp.
References offset, and seed.
◆ ProcessRoot()
template<bool LEGACY, unsigned long NHITS, typename derived_t >
◆ SearchInt()
template<bool LEGACY, unsigned long NHITS, typename derived_t >
◆ code_bits_
template<bool LEGACY, unsigned long NHITS, typename derived_t >
unsigned long CSearch_Base< LEGACY, NHITS, derived_t >::code_bits_ protected ◆ index_impl_
template<bool LEGACY, unsigned long NHITS, typename derived_t >
◆ locs_
template<bool LEGACY, unsigned long NHITS, typename derived_t >
◆ min_offset_
template<bool LEGACY, unsigned long NHITS, typename derived_t >
unsigned long CSearch_Base< LEGACY, NHITS, derived_t >::min_offset_ protected ◆ options_
template<bool LEGACY, unsigned long NHITS, typename derived_t >
◆ qoff_
template<bool LEGACY, unsigned long NHITS, typename derived_t >
◆ qstart_
template<bool LEGACY, unsigned long NHITS, typename derived_t >
◆ qstop_
template<bool LEGACY, unsigned long NHITS, typename derived_t >
◆ query_
template<bool LEGACY, unsigned long NHITS, typename derived_t >
◆ roots_
template<bool LEGACY, unsigned long NHITS, typename derived_t >
◆ seeds_
template<bool LEGACY, unsigned long NHITS, typename derived_t >
◆ soff_
template<bool LEGACY, unsigned long NHITS, typename derived_t >
◆ subj_end_
template<bool LEGACY, unsigned long NHITS, typename derived_t >
◆ subj_end_off_
template<bool LEGACY, unsigned long NHITS, typename derived_t >
◆ subj_start_
template<bool LEGACY, unsigned long NHITS, typename derived_t >
◆ subj_start_off_
template<bool LEGACY, unsigned long NHITS, typename derived_t >
◆ subject_
template<bool LEGACY, unsigned long NHITS, typename derived_t >
The documentation for this class was generated from the following files:
RetroSearch is an open source project built by @garambo
| Open a GitHub Issue
Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo
HTML:
3.2
| Encoding:
UTF-8
| Version:
0.7.4