NCBI C++ ToolKit
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Search Toolkit Book for CDistanceMatrix
#include <objects/biotree/DistanceMatrix.hpp>
Public Types | |
enum | EFormat { eSquare , eUpper , eLower , eGuess } |
Public Types inherited from CDistanceMatrix_Base | |
enum class | E_memberIndex { e__allMandatory = 0 , e_labels , e_distances } |
typedef vector< string > | TLabels |
typedef vector< double > | TDistances |
typedef Tparent::CMemberIndex< E_memberIndex, 3 > | 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 | |
CDistanceMatrix (void) | |
~CDistanceMatrix (void) | |
void | AsMatrix (CNcbiMatrix< double > &mat) const |
void | FromMatrix (const CNcbiMatrix< double > &mat) |
void | Read (istream &istr, EFormat format=eGuess) |
Public Member Functions inherited from CDistanceMatrix_Base | |
CDistanceMatrix_Base (void) | |
virtual | ~CDistanceMatrix_Base (void) |
DECLARE_INTERNAL_TYPE_INFO () | |
bool | IsSetLabels (void) const |
n labels Check if a value has been assigned to Labels data member. More... | |
bool | CanGetLabels (void) const |
Check if it is safe to call GetLabels method. More... | |
void | ResetLabels (void) |
Reset Labels data member. More... | |
const TLabels & | GetLabels (void) const |
Get the Labels member data. More... | |
TLabels & | SetLabels (void) |
Assign a value to Labels data member. More... | |
bool | IsSetDistances (void) const |
n(n-1)/2 pairwise distances (0, 1)...(0, n), (1, 2)...(1, n)... More... | |
bool | CanGetDistances (void) const |
Check if it is safe to call GetDistances method. More... | |
void | ResetDistances (void) |
Reset Distances data member. More... | |
const TDistances & | GetDistances (void) const |
Get the Distances member data. More... | |
TDistances & | SetDistances (void) |
Assign a value to Distances 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 CDistanceMatrix_Base | Tparent |
Private Member Functions | |
CDistanceMatrix (const CDistanceMatrix &value) | |
CDistanceMatrix & | operator= (const CDistanceMatrix &value) |
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... | |
Definition at line 55 of file DistanceMatrix.hpp.
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private |
Definition at line 57 of file DistanceMatrix.hpp.
Enumerator | |
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eSquare | |
eUpper | |
eLower | |
eGuess |
Definition at line 60 of file DistanceMatrix.hpp.
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inline |
Definition at line 90 of file DistanceMatrix.hpp.
CDistanceMatrix::~CDistanceMatrix | ( | void | ) |
Definition at line 50 of file DistanceMatrix.cpp.
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private |
void CDistanceMatrix::AsMatrix | ( | CNcbiMatrix< double > & | mat | ) | const |
Definition at line 55 of file DistanceMatrix.cpp.
References CDistanceMatrix_Base::GetDistances(), CDistanceMatrix_Base::GetLabels(), i, CNcbiMatrix< T >::Resize(), CNcbiMatrix< T >::Set(), and ncbi::grid::netcache::search::fields::size.
void CDistanceMatrix::FromMatrix | ( | const CNcbiMatrix< double > & | mat | ) |
Definition at line 74 of file DistanceMatrix.cpp.
References CNcbiMatrix< T >::GetCols(), CNcbiMatrix< T >::GetRows(), i, CDistanceMatrix_Base::ResetDistances(), and CDistanceMatrix_Base::SetDistances().
Referenced by Read().
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private |
Definition at line 103 of file DistanceMatrix.cpp.
References CT_POS_TYPE, eGuess, eLower, eSquare, eUpper, format, FromMatrix(), NStr::fSplit_Tokenize, i, ITERATE, names, NcbiGetlineEOL(), CDistanceMatrix_Base::ResetLabels(), CDistanceMatrix_Base::SetLabels(), ncbi::grid::netcache::search::fields::size, NStr::Split(), NStr::StringToDouble(), NStr::StringToUInt(), and NStr::TruncateSpaces().