|
NCBI C++ ToolKit
|
This is the complete list of members for CNWAligner, including all inherited members.
| AddReference(void) const | CObject | inline |
| CanBeDeleted(void) const THROWS_NONE | CObject | inline |
| CDebugDumpable(void) | CDebugDumpable | inline |
| CheckReferenceOverflow(TCount count) const | CObject | private |
| CNWAligner(void) | CNWAligner | |
| CNWAligner(const char *seq1, size_t len1, const char *seq2, size_t len2, const SNCBIPackedScoreMatrix *scoremat=0) | CNWAligner | |
| CNWAligner(const string &seq1, const string &seq2, const SNCBIPackedScoreMatrix *scoremat=0) | CNWAligner | |
| CNWAlignerThread_Align class | CNWAligner | friend |
| CObject(void) | CObject | |
| CObject(const CObject &src) | CObject | |
| DebugDump(CDebugDumpContext ddc, unsigned int depth) const | CObject | virtual |
| DebugDumpFormat(CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const | CDebugDumpable | |
| DebugDumpText(ostream &out, const string &bundle, unsigned int depth) const | CDebugDumpable | |
| DeleteThis(void) | CObject | protectedvirtual |
| DoDeleteThisObject(void) | CObject | virtual |
| DoNotDeleteThisObject(void) | CObject | virtual |
| DumpToConsole(void) const | CDebugDumpable | |
| EAllocFillMode enum name | CObject | |
| eAllocFillNone enum value | CObject | |
| eAllocFillPattern enum value | CObject | |
| eAllocFillZero enum value | CObject | |
| eCounterBitsCanBeDeleted | CObject | static |
| eCounterBitsInPlainHeap | CObject | static |
| eCounterBitsPlaceMask | CObject | static |
| eCounterStateMask | CObject | static |
| eCounterStep | CObject | static |
| eCounterValid | CObject | static |
| eEarlier enum value | CNWAligner | |
| EGapPreference enum name | CNWAligner | |
| eLater enum value | CNWAligner | |
| EnableDebugDump(bool on) | CDebugDumpable | static |
| EnableMultipleThreads(bool enable=true) | CNWAligner | |
| ETranscriptSymbol enum name | CNWAligner | |
| eTS_Delete enum value | CNWAligner | |
| eTS_Insert enum value | CNWAligner | |
| eTS_Intron enum value | CNWAligner | |
| eTS_Match enum value | CNWAligner | |
| eTS_None enum value | CNWAligner | |
| eTS_Replace enum value | CNWAligner | |
| eTS_SlackDelete enum value | CNWAligner | |
| eTS_SlackInsert enum value | CNWAligner | |
| FProgressCallback typedef | CNWAligner | |
| GetAllocFillMode(void) | CObject | static |
| GetDefaultSpaceLimit(void) | CNWAligner | inlinestatic |
| GetDefaultWg(void) | CNWAligner | inlinestatic |
| GetDefaultWm(void) | CNWAligner | inlinestatic |
| GetDefaultWms(void) | CNWAligner | inlinestatic |
| GetDefaultWs(void) | CNWAligner | inlinestatic |
| GetDense_seg(TSeqPos query_start, objects::ENa_strand query_strand, TSeqPos subj_start, objects::ENa_strand subj_strand, bool trim_end_gaps=false) const | CNWAligner | |
| GetDense_seg(TSeqPos query_start, objects::ENa_strand query_strand, const objects::CSeq_id &query_id, TSeqPos subj_start, objects::ENa_strand subj_strand, const objects::CSeq_id &subj_id, bool trim_end_gaps=false) const | CNWAligner | |
| GetElemSize(void) const | CNWAligner | inlinevirtual |
| GetEndSpaceFree(bool *L1, bool *R1, bool *L2, bool *R2) const | CNWAligner | |
| GetGapPreference() const | CNWAligner | |
| GetLeftSeg(size_t *q0, size_t *q1, size_t *s0, size_t *s1, size_t min_size) const | CNWAligner | |
| GetLongestSeg(size_t *q0, size_t *q1, size_t *s0, size_t *s1) const | CNWAligner | |
| GetPositivesAsMatches(void) const | CNWAligner | inline |
| GetRightSeg(size_t *q0, size_t *q1, size_t *s0, size_t *s1, size_t min_size) const | CNWAligner | |
| GetScore(void) const | CNWAligner | |
| GetScoreMatrix(void) const | CNWAligner | inline |
| GetSeq1(void) const | CNWAligner | inline |
| GetSeq2(void) const | CNWAligner | inline |
| GetSeqLen1(void) const | CNWAligner | inline |
| GetSeqLen2(void) const | CNWAligner | inline |
| GetSpaceLimit(void) const | CNWAligner | inline |
| GetTranscript(bool reversed=true) const | CNWAligner | |
| GetTranscriptString(void) const | CNWAligner | |
| GetWg(void) const | CNWAligner | inline |
| GetWm(void) const | CNWAligner | inline |
| GetWms(void) const | CNWAligner | inline |
| GetWs(void) const | CNWAligner | inline |
| InitCounter(void) | CObject | inlineprivate |
| InvalidObject(void) const | CObject | private |
| IsAllocatedInPool(void) const THROWS_NONE | CObject | inline |
| IsSmithWaterman() const | CNWAligner | |
| m_abc | CNWAligner | protected |
| m_Counter | CObject | mutableprivate |
| m_esf_L1 | CNWAligner | protected |
| m_esf_L2 | CNWAligner | protected |
| m_esf_R1 | CNWAligner | protected |
| m_esf_R2 | CNWAligner | protected |
| m_GapPreference | CNWAligner | protected |
| m_guides | CNWAligner | protected |
| m_MaxMem | CNWAligner | protected |
| m_maxthreads | CNWAligner | protected |
| m_mt | CNWAligner | protected |
| m_PositivesAsMatches | CNWAligner | protected |
| m_prg_callback | CNWAligner | protected |
| m_prg_info | CNWAligner | mutableprotected |
| m_score | CNWAligner | protected |
| m_ScoreMatrix | CNWAligner | protected |
| m_ScoreMatrixInvalid | CNWAligner | protected |
| m_Seq1 | CNWAligner | protected |
| m_Seq1Vec | CNWAligner | protected |
| m_Seq2 | CNWAligner | protected |
| m_Seq2Vec | CNWAligner | protected |
| m_SeqLen1 | CNWAligner | protected |
| m_SeqLen2 | CNWAligner | protected |
| m_SmithWaterman | CNWAligner | protected |
| m_terminate | CNWAligner | mutableprotected |
| m_Transcript | CNWAligner | protected |
| m_Wg | CNWAligner | protected |
| m_Wm | CNWAligner | protected |
| m_Wms | CNWAligner | protected |
| m_Ws | CNWAligner | protected |
| MakePattern(const size_t hit_size=100, const size_t core_size=28) | CNWAligner | |
| ObjectStateCanBeDeleted(TCount count) | CObject | inlineprivatestatic |
| ObjectStateIsAllocatedInPool(TCount count) | CObject | inlineprivatestatic |
| ObjectStateReferenced(TCount count) | CObject | inlineprivatestatic |
| ObjectStateReferencedOnlyOnce(TCount count) | CObject | inlineprivatestatic |
| ObjectStateUnreferenced(TCount count) | CObject | inlineprivatestatic |
| ObjectStateValid(TCount count) | CObject | inlineprivatestatic |
| operator delete(void *ptr) | CObject | |
| operator delete(void *ptr, void *place) | CObject | |
| operator delete(void *ptr, CObjectMemoryPool *place) | CObject | |
| operator delete[](void *ptr) | CObject | |
| operator new(size_t size) | CObject | |
| operator new(size_t size, void *place) | CObject | |
| operator new(size_t size, CObjectMemoryPool *place) | CObject | |
| operator new[](size_t size) | CObject | |
| operator=(const CObject &src) THROWS_NONE | CObject | inline |
| Referenced(void) const THROWS_NONE | CObject | inline |
| ReferencedOnlyOnce(void) const THROWS_NONE | CObject | inline |
| ReleaseReference(void) const | CObject | |
| RemoveLastReference(TCount count) const | CObject | private |
| RemoveReference(void) const | CObject | inline |
| Run(void) | CNWAligner | virtual |
| Run(objects::CScope &scope, const objects::CSeq_loc &loc1, const objects::CSeq_loc &loc2, bool trim_end_gaps=true) | CNWAligner | |
| Run(objects::CScope &scope, const objects::CSeq_id &id1, const objects::CSeq_id &id2, bool trim_end_gaps=true) | CNWAligner | |
| ScoreFromTranscript(const TTranscript &transcript, size_t start1=kMax_UInt, size_t start2=kMax_UInt) const | CNWAligner | virtual |
| SetAllocFillMode(EAllocFillMode mode) | CObject | static |
| SetAllocFillMode(const string &value) | CObject | static |
| SetEndSpaceFree(bool Left1, bool Right1, bool Left2, bool Right2) | CNWAligner | |
| SetGapPreference(EGapPreference p) | CNWAligner | |
| SetPattern(const vector< size_t > &pattern) | CNWAligner | |
| SetPositivesAsMatches(bool positives_as_matches=true) | CNWAligner | inline |
| SetProgressCallback(FProgressCallback prg_callback, void *data) | CNWAligner | |
| SetScoreMatrix(const SNCBIPackedScoreMatrix *scoremat) | CNWAligner | |
| SetSequences(const char *seq1, size_t len1, const char *seq2, size_t len2, bool verify=true) | CNWAligner | virtual |
| SetSequences(const string &seq1, const string &seq2, bool verify=true) | CNWAligner | |
| SetSmithWaterman(bool SW) | CNWAligner | |
| SetSpaceLimit(const size_t &maxmem) | CNWAligner | inline |
| SetTranscript(const TTranscript &transcript) | CNWAligner | |
| SetWg(TScore value) | CNWAligner | inline |
| SetWm(TScore value) | CNWAligner | |
| SetWms(TScore value) | CNWAligner | |
| SetWs(TScore value) | CNWAligner | inline |
| sm_DumpEnabled | CDebugDumpable | privatestatic |
| TCount typedef | CObject | |
| TCounter typedef | CObject | |
| ThrowNullPointerException(void) | CObject | static |
| ThrowNullPointerException(const type_info &type) | CObject | static |
| TLockerType typedef | CObject | |
| TScore typedef | CNWAligner | |
| TTranscript typedef | CNWAligner | |
| x_Align(SAlignInOut *data) | CNWAligner | protectedvirtual |
| x_CalcFingerPrint64(const char *beg, const char *end, size_t &err_index) | CNWAligner | protected |
| x_CheckMemoryLimit(void) | CNWAligner | protectedvirtual |
| x_CheckSequence(const char *seq, size_t len) const | CNWAligner | protected |
| x_DoBackTrace(const CBacktraceMatrix4 &backtrace, SAlignInOut *data) | CNWAligner | protected |
| x_FindFingerPrint64(const char *beg, const char *end, unsigned char fingerprint, size_t size, size_t &err_index) | CNWAligner | protected |
| x_GetDiagTS(size_t i1, size_t i2) const | CNWAligner | protectedvirtual |
| x_Run(void) | CNWAligner | protectedvirtual |
| x_SWDoBackTrace(const CBacktraceMatrix4 &backtrace, SAlignInOut *data) | CNWAligner | private |
| ~CDebugDumpable(void) | CDebugDumpable | virtual |
| ~CNWAligner(void) | CNWAligner | inlinevirtual |
| ~CObject(void) | CObject | virtual |
1.9.0
Modified on Sat May 04 13:14:59 2024 by modify_doxy.py rev. 669887