Search Toolkit Book for CPacked_seg_Base
for (multiway) global or partial alignments More...
#include <objects/seqalign/Packed_seg_.hpp>
Inheritance diagram for CPacked_seg_Base:
Collaboration diagram for CPacked_seg_Base:
Public Types | |
| enum class | E_memberIndex { e__allMandatory = 0 , e_dim , e_numseg , e_ids , e_starts , e_present , e_lens , e_strands , e_scores } |
| typedef int | TDim |
| typedef int | TNumseg |
| typedef vector< CRef< CSeq_id > > | TIds |
| typedef vector< TSeqPos > | TStarts |
| typedef vector< char > | TPresent |
| typedef vector< TSeqPos > | TLens |
| typedef vector< ENa_strand > | TStrands |
| typedef vector< CRef< CScore > > | TScores |
| typedef Tparent::CMemberIndex< E_memberIndex, 9 > | 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 | |
| CPacked_seg_Base (void) | |
| virtual | ~CPacked_seg_Base (void) |
| DECLARE_INTERNAL_TYPE_INFO () | |
| bool | IsSetDim (void) const |
| dimensionality Check if a value has been assigned to Dim data member. More... | |
| bool | CanGetDim (void) const |
| Check if it is safe to call GetDim method. More... | |
| void | ResetDim (void) |
| Reset Dim data member. More... | |
| void | SetDefaultDim (void) |
| Assign default value to Dim data member. More... | |
| TDim | GetDim (void) const |
| Get the Dim member data. More... | |
| void | SetDim (TDim value) |
| Assign a value to Dim data member. More... | |
| TDim & | SetDim (void) |
| Assign a value to Dim data member. More... | |
| bool | IsSetNumseg (void) const |
| number of segments here Check if a value has been assigned to Numseg data member. More... | |
| bool | CanGetNumseg (void) const |
| Check if it is safe to call GetNumseg method. More... | |
| void | ResetNumseg (void) |
| Reset Numseg data member. More... | |
| TNumseg | GetNumseg (void) const |
| Get the Numseg member data. More... | |
| void | SetNumseg (TNumseg value) |
| Assign a value to Numseg data member. More... | |
| TNumseg & | SetNumseg (void) |
| Assign a value to Numseg data member. More... | |
| bool | IsSetIds (void) const |
| sequences in order Check if a value has been assigned to Ids data member. More... | |
| bool | CanGetIds (void) const |
| Check if it is safe to call GetIds method. More... | |
| void | ResetIds (void) |
| Reset Ids data member. More... | |
| const TIds & | GetIds (void) const |
| Get the Ids member data. More... | |
| TIds & | SetIds (void) |
| Assign a value to Ids data member. More... | |
| bool | IsSetStarts (void) const |
| start OFFSETS in ids order for whole alignment Check if a value has been assigned to Starts data member. More... | |
| bool | CanGetStarts (void) const |
| Check if it is safe to call GetStarts method. More... | |
| void | ResetStarts (void) |
| Reset Starts data member. More... | |
| const TStarts & | GetStarts (void) const |
| Get the Starts member data. More... | |
| TStarts & | SetStarts (void) |
| Assign a value to Starts data member. More... | |
| bool | IsSetPresent (void) const |
| Boolean if each sequence present or absent in each segment Check if a value has been assigned to Present data member. More... | |
| bool | CanGetPresent (void) const |
| Check if it is safe to call GetPresent method. More... | |
| void | ResetPresent (void) |
| Reset Present data member. More... | |
| const TPresent & | GetPresent (void) const |
| Get the Present member data. More... | |
| TPresent & | SetPresent (void) |
| Assign a value to Present data member. More... | |
| bool | IsSetLens (void) const |
| length of each segment Check if a value has been assigned to Lens data member. More... | |
| bool | CanGetLens (void) const |
| Check if it is safe to call GetLens method. More... | |
| void | ResetLens (void) |
| Reset Lens data member. More... | |
| const TLens & | GetLens (void) const |
| Get the Lens member data. More... | |
| TLens & | SetLens (void) |
| Assign a value to Lens data member. More... | |
| bool | IsSetStrands (void) const |
| Check if a value has been assigned to Strands data member. More... | |
| bool | CanGetStrands (void) const |
| Check if it is safe to call GetStrands method. More... | |
| void | ResetStrands (void) |
| Reset Strands data member. More... | |
| const TStrands & | GetStrands (void) const |
| Get the Strands member data. More... | |
| TStrands & | SetStrands (void) |
| Assign a value to Strands data member. More... | |
| bool | IsSetScores (void) const |
| score for each segment Check if a value has been assigned to Scores data member. More... | |
| bool | CanGetScores (void) const |
| Check if it is safe to call GetScores method. More... | |
| void | ResetScores (void) |
| Reset Scores data member. More... | |
| const TScores & | GetScores (void) const |
| Get the Scores member data. More... | |
| TScores & | SetScores (void) |
| Assign a value to Scores 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 CSerialObject | Tparent |
Private Member Functions | |
| CPacked_seg_Base (const CPacked_seg_Base &) | |
| CPacked_seg_Base & | operator= (const CPacked_seg_Base &) |
Private Attributes | |
| Uint4 | m_set_State [1] |
| int | m_Dim |
| int | m_Numseg |
| vector< CRef< CSeq_id > > | m_Ids |
| vector< TSeqPos > | m_Starts |
| vector< char > | m_Present |
| vector< TSeqPos > | m_Lens |
| vector< ENa_strand > | m_Strands |
| vector< CRef< CScore > > | m_Scores |
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
for (multiway) global or partial alignments
Definition at line 79 of file Packed_seg_.hpp.
The documentation for this class was generated from the following files:
- include/objects/seqalign/Packed_seg_.hpp
- src/objects/seqalign/Packed_seg_.cpp
