NCBI C++ ToolKit
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CMSPeakList Class Reference

Search Toolkit Book for CMSPeakList

class for holding a set of peaks More...

#include "mspeak.hpp"
(Private to src/algo/ms/omssa.)

+ Inheritance diagram for CMSPeakList:
+ Collaboration diagram for CMSPeakList:

Public Member Functions

 CMSPeakList (void)
 
CMZI *const GetMZI (void) const
 
void SetMZI (CMZI *In)
 
const int GetNum (void) const
 
intSetNum (void)
 
const EMSPeakListSort GetSorted (void) const
 
EMSPeakListSortSetSorted (void)
 
void CreateLists (int Size)
 fill out the arrays and set defaults More...
 
void Sort (EMSPeakListSort SortType)
 sort the peak by sort type More...
 
void Rank (void)
 Rank the given spectrum by intensity. More...
 
- Public Member Functions inherited from CObject
 CObject (void)
 Constructor. More...
 
 CObject (const CObject &src)
 Copy constructor. More...
 
virtual ~CObject (void)
 Destructor. More...
 
CObjectoperator= (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...
 
virtual void DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. 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 Attributes

AutoPtr< CMZI, ArrayDeleter< CMZI > > MZI
 m/z values and intensities More...
 
int Num
 number of CMZI More...
 
EMSPeakListSort Sorted
 have the CMZI been sorted? More...
 

Additional Inherited Members

- 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 CAtomicCounter TCounter
 Counter type is CAtomiCounter. More...
 
typedef TCounter::TValue TCount
 Alias for value type of counter. More...
 
- Static Public Member Functions inherited from CObject
static NCBI_NORETURN void ThrowNullPointerException (void)
 Define method to throw null pointer exception. More...
 
static NCBI_NORETURN 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 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

class for holding a set of peaks

Definition at line 563 of file mspeak.hpp.

Constructor & Destructor Documentation

CMSPeakList::CMSPeakList ( void  )

Definition at line 272 of file mspeak.cpp.

Member Function Documentation

void CMSPeakList::CreateLists ( int  Size)

fill out the arrays and set defaults

Parameters
Sizesize of the arrays

Definition at line 277 of file mspeak.cpp.

References eMSPeakListSortNone, SetMZI(), SetNum(), SetSorted(), and DDRPC::DataType::Size.

CMZI *const CMSPeakList::GetMZI ( void  ) const
inline
const int CMSPeakList::GetNum ( void  ) const
inline

Definition at line 619 of file mspeak.hpp.

References Num.

Referenced by CMSPeak::CompareSortedRank(), CMSPeak::CompareTop(), CMSPeak::ContainsFast(), Rank(), and Sort().

const EMSPeakListSort CMSPeakList::GetSorted ( void  ) const
inline

Definition at line 631 of file mspeak.hpp.

References Sorted.

Referenced by Sort().

void CMSPeakList::Rank ( void  )

Rank the given spectrum by intensity.

assumes the spectrum is sorted by intensity. highest intensity is given rank 1.

Definition at line 300 of file mspeak.cpp.

References GetMZI(), GetNum(), i, and CMZI::SetRank().

void CMSPeakList::SetMZI ( CMZI In)
inline

Definition at line 613 of file mspeak.hpp.

References MZI, and AutoPtr< X, Del >::reset().

Referenced by CreateLists().

int & CMSPeakList::SetNum ( void  )
inline

Definition at line 625 of file mspeak.hpp.

References Num.

Referenced by CreateLists().

EMSPeakListSort & CMSPeakList::SetSorted ( void  )
inline

Definition at line 637 of file mspeak.hpp.

References Sorted.

Referenced by CreateLists(), and Sort().

void CMSPeakList::Sort ( EMSPeakListSort  SortType)

sort the peak by sort type

Parameters
SortTypewhich sort to perform

Definition at line 285 of file mspeak.cpp.

References eMSPeakListSortIntensity, eMSPeakListSortMZ, GetMZI(), GetNum(), GetSorted(), and SetSorted().

Member Data Documentation

AutoPtr<CMZI, ArrayDeleter<CMZI> > CMSPeakList::MZI
private

m/z values and intensities

Definition at line 598 of file mspeak.hpp.

Referenced by GetMZI(), and SetMZI().

int CMSPeakList::Num
private

number of CMZI

Definition at line 601 of file mspeak.hpp.

Referenced by GetNum(), and SetNum().

EMSPeakListSort CMSPeakList::Sorted
private

have the CMZI been sorted?

Definition at line 603 of file mspeak.hpp.

Referenced by GetSorted(), and SetSorted().


The documentation for this class was generated from the following files:
Modified on Mon Apr 23 11:43:05 2018 by modify_doxy.py rev. 546573