Search Toolkit Book for CSpliced_seg
#include <objects/seqalign/Spliced_seg.hpp>
Inheritance diagram for CSpliced_seg:
Collaboration diagram for CSpliced_seg:
Public Member Functions | |
| CSpliced_seg (void) | |
| ~CSpliced_seg (void) | |
| void | Validate (bool full_test=false) const |
| Validators. More... | |
| TDim | CheckNumRows (void) const |
| bool | IsConsistentBiologicalOrder (void) const |
| CRange< TSeqPos > | GetSeqRange (TDim row) const |
| GetSeqRange NB: In case the product-type is protein, these only return the amin part of Prot-pos. More... | |
| TSeqPos | GetSeqStart (TDim row) const |
| TSeqPos | GetSeqStop (TDim row) const |
| ENa_strand | GetSeqStrand (TDim row) const |
| Get strand (the first one if segments have different strands). More... | |
| CRef< CSeq_align > | AsDiscSeg () const |
| Convert this alignment to a discontinuous segment. More... | |
| Public Member Functions inherited from CSpliced_seg_Base | |
| CSpliced_seg_Base (void) | |
| virtual | ~CSpliced_seg_Base (void) |
| DECLARE_INTERNAL_TYPE_INFO () | |
| bool | IsSetProduct_id (void) const |
| product is either protein or transcript (cDNA) Check if a value has been assigned to Product_id data member. More... | |
| bool | CanGetProduct_id (void) const |
| Check if it is safe to call GetProduct_id method. More... | |
| void | ResetProduct_id (void) |
| Reset Product_id data member. More... | |
| const TProduct_id & | GetProduct_id (void) const |
| Get the Product_id member data. More... | |
| void | SetProduct_id (TProduct_id &value) |
| Assign a value to Product_id data member. More... | |
| TProduct_id & | SetProduct_id (void) |
| Assign a value to Product_id data member. More... | |
| bool | IsSetGenomic_id (void) const |
| Check if a value has been assigned to Genomic_id data member. More... | |
| bool | CanGetGenomic_id (void) const |
| Check if it is safe to call GetGenomic_id method. More... | |
| void | ResetGenomic_id (void) |
| Reset Genomic_id data member. More... | |
| const TGenomic_id & | GetGenomic_id (void) const |
| Get the Genomic_id member data. More... | |
| void | SetGenomic_id (TGenomic_id &value) |
| Assign a value to Genomic_id data member. More... | |
| TGenomic_id & | SetGenomic_id (void) |
| Assign a value to Genomic_id data member. More... | |
| bool | IsSetProduct_strand (void) const |
| should be 'plus' or 'minus' Check if a value has been assigned to Product_strand data member. More... | |
| bool | CanGetProduct_strand (void) const |
| Check if it is safe to call GetProduct_strand method. More... | |
| void | ResetProduct_strand (void) |
| Reset Product_strand data member. More... | |
| TProduct_strand | GetProduct_strand (void) const |
| Get the Product_strand member data. More... | |
| void | SetProduct_strand (TProduct_strand value) |
| Assign a value to Product_strand data member. More... | |
| TProduct_strand & | SetProduct_strand (void) |
| Assign a value to Product_strand data member. More... | |
| bool | IsSetGenomic_strand (void) const |
| Check if a value has been assigned to Genomic_strand data member. More... | |
| bool | CanGetGenomic_strand (void) const |
| Check if it is safe to call GetGenomic_strand method. More... | |
| void | ResetGenomic_strand (void) |
| Reset Genomic_strand data member. More... | |
| TGenomic_strand | GetGenomic_strand (void) const |
| Get the Genomic_strand member data. More... | |
| void | SetGenomic_strand (TGenomic_strand value) |
| Assign a value to Genomic_strand data member. More... | |
| TGenomic_strand & | SetGenomic_strand (void) |
| Assign a value to Genomic_strand data member. More... | |
| bool | IsSetProduct_type (void) const |
| Check if a value has been assigned to Product_type data member. More... | |
| bool | CanGetProduct_type (void) const |
| Check if it is safe to call GetProduct_type method. More... | |
| void | ResetProduct_type (void) |
| Reset Product_type data member. More... | |
| TProduct_type | GetProduct_type (void) const |
| Get the Product_type member data. More... | |
| void | SetProduct_type (TProduct_type value) |
| Assign a value to Product_type data member. More... | |
| TProduct_type & | SetProduct_type (void) |
| Assign a value to Product_type data member. More... | |
| bool | IsSetExons (void) const |
| set of segments involved each segment corresponds to one exon exons are always in biological order Check if a value has been assigned to Exons data member. More... | |
| bool | CanGetExons (void) const |
| Check if it is safe to call GetExons method. More... | |
| void | ResetExons (void) |
| Reset Exons data member. More... | |
| const TExons & | GetExons (void) const |
| Get the Exons member data. More... | |
| TExons & | SetExons (void) |
| Assign a value to Exons data member. More... | |
| bool | IsSetPoly_a (void) const |
| start of poly(A) tail on the transcript For sense transcripts: aligned product positions < poly-a <= product-length poly-a == product-length indicates inferred poly(A) tail at transcript's end For antisense transcripts: -1 <= poly-a < aligned product positions poly-a == -1 indicates inferred poly(A) tail at transcript's start Check if a value has been assigned to Poly_a data member. More... | |
| bool | CanGetPoly_a (void) const |
| Check if it is safe to call GetPoly_a method. More... | |
| void | ResetPoly_a (void) |
| Reset Poly_a data member. More... | |
| TPoly_a | GetPoly_a (void) const |
| Get the Poly_a member data. More... | |
| void | SetPoly_a (TPoly_a value) |
| Assign a value to Poly_a data member. More... | |
| TPoly_a & | SetPoly_a (void) |
| Assign a value to Poly_a data member. More... | |
| bool | IsSetProduct_length (void) const |
| length of the product, in bases/residues from this (or from poly-a if present), a 3' unaligned length can be extracted Check if a value has been assigned to Product_length data member. More... | |
| bool | CanGetProduct_length (void) const |
| Check if it is safe to call GetProduct_length method. More... | |
| void | ResetProduct_length (void) |
| Reset Product_length data member. More... | |
| TProduct_length | GetProduct_length (void) const |
| Get the Product_length member data. More... | |
| void | SetProduct_length (TProduct_length value) |
| Assign a value to Product_length data member. More... | |
| TProduct_length & | SetProduct_length (void) |
| Assign a value to Product_length data member. More... | |
| bool | IsSetModifiers (void) const |
| alignment descriptors / modifiers this provides us a set for extension Check if a value has been assigned to Modifiers data member. More... | |
| bool | CanGetModifiers (void) const |
| Check if it is safe to call GetModifiers method. More... | |
| void | ResetModifiers (void) |
| Reset Modifiers data member. More... | |
| const TModifiers & | GetModifiers (void) const |
| Get the Modifiers member data. More... | |
| TModifiers & | SetModifiers (void) |
| Assign a value to Modifiers 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 CSpliced_seg_Base | Tparent |
Private Member Functions | |
| CSpliced_seg (const CSpliced_seg &value) | |
| CSpliced_seg & | operator= (const CSpliced_seg &value) |
Additional Inherited Members | |
| Static Public Member Functions inherited from CSpliced_seg_Base | |
| static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME() | EProduct_type (void) |
| Access to EProduct_type'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) |
| 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 56 of file Spliced_seg.hpp.
Member Typedef Documentation
◆ TDim
| typedef int CSpliced_seg::TDim |
types
Definition at line 66 of file Spliced_seg.hpp.
◆ Tparent
|
private |
Definition at line 58 of file Spliced_seg.hpp.
Constructor & Destructor Documentation
◆ CSpliced_seg() [1/2]
|
inline |
Definition at line 99 of file Spliced_seg.hpp.
◆ ~CSpliced_seg()
| CSpliced_seg::~CSpliced_seg | ( | void | ) |
Definition at line 50 of file Spliced_seg.cpp.
◆ CSpliced_seg() [2/2]
|
private |
Member Function Documentation
◆ AsDiscSeg()
| CRef< CSeq_align > CSpliced_seg::AsDiscSeg | ( | ) | const |
Convert this alignment to a discontinuous segment.
Definition at line 492 of file Spliced_seg.cpp.
References eNa_strand_plus, CSpliced_seg_Base::eProduct_type_protein, CSpliced_seg_Base::eProduct_type_transcript, CSeq_align_Base::eType_disc, CSeq_align_Base::eType_partial, eUnknown, CSpliced_seg_Base::GetExons(), CSpliced_seg_Base::GetGenomic_id(), CSpliced_seg_Base::GetGenomic_strand(), CSpliced_seg_Base::GetProduct_id(), CSpliced_seg_Base::GetProduct_strand(), CSpliced_seg_Base::GetProduct_type(), CSpliced_seg_Base::IsSetGenomic_strand(), CSpliced_seg_Base::IsSetProduct_strand(), ITERATE, NCBI_THROW, s_ExonToDenseg(), CSeq_align_Base::SetSegs(), CSeq_align_Base::SetType(), and CDense_seg::SetWidths().
Referenced by CFeaturePropagator::CFeaturePropagator(), s_GetIndels(), and CCIGAR_Formatter::x_FormatAlignmentRows().
◆ CheckNumRows()
|
inline |
Definition at line 70 of file Spliced_seg.hpp.
Referenced by CAlnSpanVertModel::x_Init().
◆ GetSeqRange()
GetSeqRange NB: In case the product-type is protein, these only return the amin part of Prot-pos.
The frame is ignored.
Definition at line 299 of file Spliced_seg.cpp.
References ctll::empty(), CSpliced_seg_Base::eProduct_type_protein, CSpliced_seg_Base::eProduct_type_transcript, CSpliced_seg_Base::GetExons(), CSpliced_seg_Base::GetProduct_type(), ITERATE, NCBI_THROW, result, and row.
Referenced by CSeq_align::GetSeqRange().
◆ GetSeqStart()
Definition at line 348 of file Spliced_seg.cpp.
References eNa_strand_minus, CSpliced_seg_Base::GetExons(), CRange_Base::GetFrom(), CSpliced_exon::GetRowSeq_range(), GetSeqStrand(), and row.
Referenced by CSeq_align::GetSeqStart(), CReportEntry::SetAlignment(), CAlnSpanVertModel::x_PopulateRowsSpliced(), and CPslRecord::xInitializeSequenceInfo().
◆ GetSeqStop()
Definition at line 357 of file Spliced_seg.cpp.
References eNa_strand_minus, CSpliced_seg_Base::GetExons(), CSpliced_exon::GetRowSeq_range(), GetSeqStrand(), CRange_Base::GetTo(), and row.
Referenced by CSeq_align::GetSeqStop(), CReportEntry::SetAlignment(), CAlnSpanVertModel::x_PopulateRowsSpliced(), and CPslRecord::xInitializeSequenceInfo().
◆ GetSeqStrand()
| ENa_strand CSpliced_seg::GetSeqStrand | ( | TDim | row | ) | const |
Get strand (the first one if segments have different strands).
Definition at line 56 of file Spliced_seg.cpp.
References CSpliced_seg_Base::CanGetGenomic_strand(), CSpliced_seg_Base::CanGetProduct_strand(), eNa_strand_unknown, CSpliced_seg_Base::GetExons(), CSpliced_seg_Base::GetGenomic_strand(), CSpliced_seg_Base::GetProduct_strand(), NCBI_THROW, and row.
Referenced by GetSeqStart(), GetSeqStop(), CSeq_align::GetSeqStrand(), CAlignGlyph::x_DrawNonConsensusSpliceSites(), and CAlnSpanVertModel::x_PopulateRowsSpliced().
◆ IsConsistentBiologicalOrder()
| bool CSpliced_seg::IsConsistentBiologicalOrder | ( | void | ) | const |
Definition at line 88 of file Spliced_seg.cpp.
References CSpliced_exon_Base::CanGetGenomic_strand(), CSpliced_seg_Base::CanGetGenomic_strand(), CSpliced_exon_Base::CanGetProduct_strand(), CSpliced_seg_Base::CanGetProduct_strand(), CSpliced_seg_Base::GetExons(), CSpliced_exon_Base::GetGenomic_end(), CSpliced_exon_Base::GetGenomic_start(), CSpliced_exon_Base::GetGenomic_strand(), CSpliced_seg_Base::GetGenomic_strand(), CSpliced_exon_Base::GetProduct_end(), CSpliced_exon_Base::GetProduct_start(), CSpliced_exon_Base::GetProduct_strand(), CSpliced_seg_Base::GetProduct_strand(), CProduct_pos_Base::IsNucpos(), IsReverse(), ITERATE, and kInvalidSeqPos.
◆ operator=()
|
private |
◆ Validate()
Validators.
Definition at line 159 of file Spliced_seg.cpp.
References CProduct_pos::AsSeqPos(), CSpliced_exon_Base::CanGetProduct_strand(), CSpliced_seg_Base::CanGetProduct_strand(), CSpliced_exon_chunk_Base::e_Diag, CSpliced_exon_chunk_Base::e_Genomic_ins, CSpliced_exon_chunk_Base::e_Match, CSpliced_exon_chunk_Base::e_Mismatch, CSpliced_exon_chunk_Base::e_Product_ins, ctll::empty(), eNa_strand_minus, CSpliced_seg_Base::eProduct_type_protein, CSpliced_exon_chunk_Base::GetDiag(), CSpliced_seg_Base::GetExons(), CRange_Base::GetFrom(), CSpliced_exon_Base::GetGenomic_end(), CSpliced_exon_chunk_Base::GetGenomic_ins(), CSpliced_exon_Base::GetGenomic_start(), CSpliced_exon_chunk_Base::GetMatch(), CSpliced_exon_chunk_Base::GetMismatch(), CSpliced_exon_Base::GetParts(), CSpliced_seg_Base::GetPoly_a(), CSpliced_exon_Base::GetProduct_end(), CSpliced_exon_chunk_Base::GetProduct_ins(), CSpliced_seg_Base::GetProduct_length(), CSpliced_exon_Base::GetProduct_start(), CSpliced_exon_Base::GetProduct_strand(), CSpliced_seg_Base::GetProduct_strand(), CSpliced_seg_Base::GetProduct_type(), CRange_Base::GetTo(), COpenRange< TSeqPos >::GetWhole(), CSpliced_exon_Base::IsSetGenomic_id(), CSpliced_seg_Base::IsSetGenomic_id(), CSpliced_exon_Base::IsSetParts(), CSpliced_seg_Base::IsSetPoly_a(), CSpliced_exon_Base::IsSetProduct_id(), CSpliced_seg_Base::IsSetProduct_id(), CSpliced_seg_Base::IsSetProduct_length(), CSpliced_exon_Base::IsSetProduct_strand(), CSpliced_seg_Base::IsSetProduct_strand(), ITERATE, NCBI_THROW, prot, CRange_Base::SetFrom(), CRange_Base::SetTo(), and CSpliced_exon_chunk_Base::Which().
Referenced by InitSplicedsegFromPairwiseAln(), MakeSplicedSeg(), and CSeq_align::Validate().
The documentation for this class was generated from the following files:
- include/objects/seqalign/Spliced_seg.hpp
- src/objects/seqalign/Spliced_seg.cpp
