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

int &	SetNum (void)

const EMSPeakListSort	GetSorted (void) const

EMSPeakListSort &	SetSorted (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...

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...

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 atomic< Uint8 >	TCounter
	Counter type is CAtomiCounter. More...

typedef Uint8	TCount
	Alias for value type of counter. More...

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 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::CMSPeakList ( void )

Definition at line 272 of file mspeak.cpp.

Member Function Documentation

◆ CreateLists()

void CMSPeakList::CreateLists ( int Size )

fill out the arrays and set defaults

Parameters

Size	size of the arrays

Definition at line 277 of file mspeak.cpp.

References eMSPeakListSortNone, SetMZI(), SetNum(), and SetSorted().

◆ GetMZI()

CMZI *const CMSPeakList::GetMZI ( void ) const

inline

Definition at line 607 of file mspeak.hpp.

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

Referenced by Rank(), and Sort().

◆ GetNum()

const int CMSPeakList::GetNum ( void ) const

inline

Definition at line 619 of file mspeak.hpp.

References Num.

Referenced by Rank(), and Sort().

◆ GetSorted()

const EMSPeakListSort CMSPeakList::GetSorted ( void ) const

inline

Definition at line 631 of file mspeak.hpp.

References Sorted.

Referenced by Sort().

◆ Rank()

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().

◆ SetMZI()

void CMSPeakList::SetMZI ( CMZI * In )

inline

Definition at line 613 of file mspeak.hpp.

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

Referenced by CreateLists().

◆ SetNum()

int & CMSPeakList::SetNum ( void )

inline

Definition at line 625 of file mspeak.hpp.

References Num.

Referenced by CreateLists().

◆ SetSorted()

EMSPeakListSort & CMSPeakList::SetSorted ( void )

inline

Definition at line 637 of file mspeak.hpp.

References Sorted.

Referenced by CreateLists(), and Sort().

◆ Sort()

void CMSPeakList::Sort ( EMSPeakListSort SortType )

sort the peak by sort type

Parameters

SortType which sort to perform

Definition at line 285 of file mspeak.cpp.

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

Member Data Documentation

◆ MZI

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().

◆ Num

int CMSPeakList::Num

private

number of CMZI

Definition at line 601 of file mspeak.hpp.

Referenced by GetNum(), and SetNum().

◆ Sorted

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:

src/algo/ms/omssa/mspeak.hpp
src/algo/ms/omssa/mspeak.cpp

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CMSPeakList()

Member Function Documentation

◆ CreateLists()

◆ GetMZI()

◆ GetNum()

◆ GetSorted()

◆ Rank()

◆ SetMZI()

◆ SetNum()

◆ SetSorted()

◆ Sort()

Member Data Documentation

◆ MZI

◆ Num

◆ Sorted