Search Toolkit Book for CSeq_inst
#include <objects/seq/Seq_inst.hpp>
Inheritance diagram for CSeq_inst:
Collaboration diagram for CSeq_inst:
Public Member Functions | |
| CSeq_inst (void) | |
| ~CSeq_inst (void) | |
| bool | IsNa (void) const |
| bool | IsAa (void) const |
| bool | ConvertDeltaToRaw () |
| Public Member Functions inherited from CSeq_inst_Base | |
| CSeq_inst_Base (void) | |
| virtual | ~CSeq_inst_Base (void) |
| DECLARE_INTERNAL_TYPE_INFO () | |
| bool | IsSetRepr (void) const |
| Check if a value has been assigned to Repr data member. More... | |
| bool | CanGetRepr (void) const |
| Check if it is safe to call GetRepr method. More... | |
| void | ResetRepr (void) |
| Reset Repr data member. More... | |
| TRepr | GetRepr (void) const |
| Get the Repr member data. More... | |
| void | SetRepr (TRepr value) |
| Assign a value to Repr data member. More... | |
| TRepr & | SetRepr (void) |
| Assign a value to Repr data member. More... | |
| bool | IsSetMol (void) const |
| Check if a value has been assigned to Mol data member. More... | |
| bool | CanGetMol (void) const |
| Check if it is safe to call GetMol method. More... | |
| void | ResetMol (void) |
| Reset Mol data member. More... | |
| TMol | GetMol (void) const |
| Get the Mol member data. More... | |
| void | SetMol (TMol value) |
| Assign a value to Mol data member. More... | |
| TMol & | SetMol (void) |
| Assign a value to Mol data member. More... | |
| bool | IsSetLength (void) const |
| length of sequence in residues Check if a value has been assigned to Length data member. More... | |
| bool | CanGetLength (void) const |
| Check if it is safe to call GetLength method. More... | |
| void | ResetLength (void) |
| Reset Length data member. More... | |
| TLength | GetLength (void) const |
| Get the Length member data. More... | |
| void | SetLength (TLength value) |
| Assign a value to Length data member. More... | |
| TLength & | SetLength (void) |
| Assign a value to Length data member. More... | |
| bool | IsSetFuzz (void) const |
| length uncertainty Check if a value has been assigned to Fuzz data member. More... | |
| bool | CanGetFuzz (void) const |
| Check if it is safe to call GetFuzz method. More... | |
| void | ResetFuzz (void) |
| Reset Fuzz data member. More... | |
| const TFuzz & | GetFuzz (void) const |
| Get the Fuzz member data. More... | |
| void | SetFuzz (TFuzz &value) |
| Assign a value to Fuzz data member. More... | |
| TFuzz & | SetFuzz (void) |
| Assign a value to Fuzz data member. More... | |
| bool | IsSetTopology (void) const |
| Check if a value has been assigned to Topology data member. More... | |
| bool | CanGetTopology (void) const |
| Check if it is safe to call GetTopology method. More... | |
| void | ResetTopology (void) |
| Reset Topology data member. More... | |
| void | SetDefaultTopology (void) |
| Assign default value to Topology data member. More... | |
| TTopology | GetTopology (void) const |
| Get the Topology member data. More... | |
| void | SetTopology (TTopology value) |
| Assign a value to Topology data member. More... | |
| TTopology & | SetTopology (void) |
| Assign a value to Topology data member. More... | |
| bool | IsSetStrand (void) const |
| Check if a value has been assigned to Strand data member. More... | |
| bool | CanGetStrand (void) const |
| Check if it is safe to call GetStrand method. More... | |
| void | ResetStrand (void) |
| Reset Strand data member. More... | |
| TStrand | GetStrand (void) const |
| Get the Strand member data. More... | |
| void | SetStrand (TStrand value) |
| Assign a value to Strand data member. More... | |
| TStrand & | SetStrand (void) |
| Assign a value to Strand data member. More... | |
| bool | IsSetSeq_data (void) const |
| the sequence Check if a value has been assigned to Seq_data data member. More... | |
| bool | CanGetSeq_data (void) const |
| Check if it is safe to call GetSeq_data method. More... | |
| void | ResetSeq_data (void) |
| Reset Seq_data data member. More... | |
| const TSeq_data & | GetSeq_data (void) const |
| Get the Seq_data member data. More... | |
| void | SetSeq_data (TSeq_data &value) |
| Assign a value to Seq_data data member. More... | |
| TSeq_data & | SetSeq_data (void) |
| Assign a value to Seq_data data member. More... | |
| bool | IsSetExt (void) const |
| extensions for special types Check if a value has been assigned to Ext data member. More... | |
| bool | CanGetExt (void) const |
| Check if it is safe to call GetExt method. More... | |
| void | ResetExt (void) |
| Reset Ext data member. More... | |
| const TExt & | GetExt (void) const |
| Get the Ext member data. More... | |
| void | SetExt (TExt &value) |
| Assign a value to Ext data member. More... | |
| TExt & | SetExt (void) |
| Assign a value to Ext data member. More... | |
| bool | IsSetHist (void) const |
| sequence history Check if a value has been assigned to Hist data member. More... | |
| bool | CanGetHist (void) const |
| Check if it is safe to call GetHist method. More... | |
| void | ResetHist (void) |
| Reset Hist data member. More... | |
| const THist & | GetHist (void) const |
| Get the Hist member data. More... | |
| void | SetHist (THist &value) |
| Assign a value to Hist data member. More... | |
| THist & | SetHist (void) |
| Assign a value to Hist 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 |
Static Public Member Functions | |
| static bool | IsNa (EMol mol) |
| static bool | IsAa (EMol mol) |
| static string | GetMoleculeClass (EMol mol) |
| Static Public Member Functions inherited from CSeq_inst_Base | |
| static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME() | ERepr (void) |
| Access to ERepr's attributes (values, names) as defined in spec. More... | |
| static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME() | EMol (void) |
| Access to EMol's attributes (values, names) as defined in spec. More... | |
| static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME() | ETopology (void) |
| Access to ETopology's attributes (values, names) as defined in spec. More... | |
| static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME() | EStrand (void) |
| Access to EStrand's attributes (values, names) as defined in spec. 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) |
Private Types | |
| typedef CSeq_inst_Base | Tparent |
Private Member Functions | |
| CSeq_inst (const CSeq_inst &value) | |
| CSeq_inst & | operator= (const CSeq_inst &value) |
Additional Inherited Members | |
| Public Types inherited from CSeq_inst_Base | |
| enum | ERepr { eRepr_not_set = 0 , eRepr_virtual = 1 , eRepr_raw = 2 , eRepr_seg = 3 , eRepr_const = 4 , eRepr_ref = 5 , eRepr_consen = 6 , eRepr_map = 7 , eRepr_delta = 8 , eRepr_other = 255 } |
| representation class More... | |
| enum | EMol { eMol_not_set = 0 , eMol_dna = 1 , eMol_rna = 2 , eMol_aa = 3 , eMol_na = 4 , eMol_other = 255 } |
| molecule class in living organism More... | |
| enum | ETopology { eTopology_not_set = 0 , eTopology_linear = 1 , eTopology_circular = 2 , eTopology_tandem = 3 , eTopology_other = 255 } |
| topology of molecule More... | |
| enum | EStrand { eStrand_not_set = 0 , eStrand_ss = 1 , eStrand_ds = 2 , eStrand_mixed = 3 , eStrand_other = 255 } |
| strandedness in living organism More... | |
| enum class | E_memberIndex { e__allMandatory = 0 , e_repr , e_mol , e_length , e_fuzz , e_topology , e_strand , e_seq_data , e_ext , e_hist } |
| typedef ERepr | TRepr |
| typedef EMol | TMol |
| typedef TSeqPos | TLength |
| typedef CInt_fuzz | TFuzz |
| typedef ETopology | TTopology |
| typedef EStrand | TStrand |
| typedef CSeq_data | TSeq_data |
| typedef CSeq_ext | TExt |
| typedef CSeq_hist | THist |
| typedef Tparent::CMemberIndex< E_memberIndex, 10 > | 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 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 50 of file Seq_inst.hpp.
Member Typedef Documentation
◆ Tparent
|
private |
Definition at line 52 of file Seq_inst.hpp.
Constructor & Destructor Documentation
◆ CSeq_inst() [1/2]
|
inline |
Definition at line 84 of file Seq_inst.hpp.
◆ ~CSeq_inst()
| CSeq_inst::~CSeq_inst | ( | void | ) |
Definition at line 50 of file Seq_inst.cpp.
◆ CSeq_inst() [2/2]
Member Function Documentation
◆ ConvertDeltaToRaw()
| bool CSeq_inst::ConvertDeltaToRaw | ( | ) |
Definition at line 93 of file Seq_inst.cpp.
References CONVERT_AA_CODING_TO_STR, CONVERT_NA_CODING_TO_STR, CSeq_data_Base::e_Iupacna, NStr::Find(), Get(), CSeq_inst_Base::GetExt(), CSeq_data_Base::GetIupacaa(), CSeq_data_Base::GetIupacna(), CSeq_inst_Base::GetLength(), CSeq_literal_Base::GetLength(), CSeq_inst_Base::GetRepr(), CSeq_literal_Base::GetSeq_data(), IsAa(), CSeq_data_Base::IsGap(), CSeq_inst_Base::IsSetExt(), CSeq_inst_Base::IsSetMol(), CSeq_inst_Base::IsSetRepr(), CSeq_literal_Base::IsSetSeq_data(), ITERATE, NON_CONST_ITERATE, NPOS, CSeq_inst_Base::ResetExt(), CSeq_inst_Base::SetExt(), CSeq_data_Base::SetIupacaa(), CSeq_data_Base::SetIupacna(), CSeq_inst_Base::SetLength(), CSeq_data_Base::SetNcbieaa(), CSeq_inst_Base::SetRepr(), CSeq_inst_Base::SetSeq_data(), str(), string, and CSeq_data_Base::Which().
Referenced by CCleanup::ConvertDeltaSeqToRaw(), and CMacroFunction_DeltaSeqToRaw::s_ConvertDeltaToRaw().
◆ GetMoleculeClass()
|
static |
Definition at line 72 of file Seq_inst.cpp.
References kEmptyStr.
Referenced by CValidError_bioseq::x_ReportLineageConflictWithMol().
◆ IsAa() [1/2]
Definition at line 99 of file Seq_inst.hpp.
References CSeq_inst_Base::eMol_aa.
Referenced by CCleanup::AddPartialToProteinTitle(), CMolInfoEditDlg::ApplyToInst(), CMolInfoEditDlg::ApplyToMolInfo(), CFastaReader::AssembleSeq(), CGapsEditor::ConvertNs2Gaps(), GetNucleotideParent(), CReadBlastApp::is_prot_entry(), CBioseq::IsAa(), CBioseq::PackAsDeltaSeq(), CReadBlastApp::skip_toprot(), CValidError_bioseq::ValidateRawConst(), CValidError_bioseq::ValidateSeqIds(), CSequenceDataTester::x_Init(), CFastaReader::x_NucOrProt(), CSequenceDataTester::x_TestSingleNucleotide_Remote(), CSequenceDataTester::x_TestSingleProtein_Remote(), and CSequenceDataTester::x_TestSingleSequence_Remote().
◆ IsAa() [2/2]
|
inline |
Definition at line 113 of file Seq_inst.hpp.
References CSeq_inst_Base::GetMol().
Referenced by AddBioseqToBioseq(), CValidError_bioseq::CdError(), ConvertDeltaToRaw(), sequpd::FindMatches(), GetModelEvidance(), SDubiousShortSequence::IsProtein(), CBioseq_Handle::IsProtein(), CSeqVector::IsProtein(), IAlnSeqId::IsProtein(), RetrieveGi555WithTimeOut(), RetrieveLargeNuclSequence(), RetrieveLargeProteinWithTimeOut(), RetrievePartsOfLargeChromosome(), s_AddBioseqToNucProtSet(), s_AddProtToNuc(), CAlnSeqId::SetBioseqHandle(), CValidError_bioseq::ValidateSeqFeatContext(), CBioseqContext::x_Init(), CCleanupHugeAsnReader::x_LooksLikeNucProtSet(), CNewCleanup_imp::x_SeqIntervalBC(), and CNewCleanup_imp::x_SeqPointBC().
◆ IsNa() [1/2]
Definition at line 90 of file Seq_inst.hpp.
References CSeq_inst_Base::eMol_dna, CSeq_inst_Base::eMol_na, and CSeq_inst_Base::eMol_rna.
Referenced by CMolInfoEditDlg::ApplyToInst(), CMolInfoEditDlg::ApplyToMolInfo(), EmblAscii(), GenBankAsciiOrig(), CBioseq::IsNa(), RawBioseqPack(), CValidError_bioseqset::ValidatePartsSet(), CValidError_bioseq::ValidateRawConst(), CValidError_bioseqset::ValidateSegSet(), and XMLAscii().
◆ IsNa() [2/2]
|
inline |
Definition at line 106 of file Seq_inst.hpp.
References CSeq_inst_Base::GetMol().
Referenced by AddBioseqToBioseq(), BOOST_AUTO_TEST_CASE(), CValidError_bioseq::CheckSourceDescriptor(), sequpd::FindMatches(), CScoreBuilder::GetBlastScoreDenseg(), CScoreBuilder::GetBlastScoreStd(), CBioseq_Handle::IsNucleotide(), CSeqVector::IsNucleotide(), IAlnSeqId::IsNucleotide(), s_AddBioseqToNucProtSet(), s_AddProtToNuc(), s_FixBioseqDeltas(), CBlastTabularInfo::SetFields(), CValidError_bioseqset::ValidatePartsSet(), CValidError_bioseqset::ValidateSegSet(), CCleanupHugeAsnReader::x_CreateSmallGenomeSets(), CFlatFileGenerator::x_DeduceTarget(), CAsn2FlatApp::x_DeduceTarget(), and CCleanupHugeAsnReader::x_LooksLikeNucProtSet().
◆ operator=()
The documentation for this class was generated from the following files:
- include/objects/seq/Seq_inst.hpp
- src/objects/seq/Seq_inst.cpp
