PepIterator Class Reference

Abstract base class for different peptide iterators. More...

#include <OpenMS/CHEMISTRY/PepIterator.h>

Inheritance diagram for PepIterator:

Public Types
typedef std::pair< String, String >	FASTAEntry

Public Member Functions
	PepIterator ()
	constructor More...
virtual	~PepIterator ()
	destructor More...
	PepIterator (const PepIterator &source)
	copy constructor More...
virtual FASTAEntry	operator* ()=0
	* operator for accessing the value of the iterator More...
virtual PepIterator &	operator++ ()=0
	operator ++ for pre-increment More...
virtual PepIterator *	operator++ (int)=0
	operator ++ for post-increment More...
virtual void	setFastaFile (const String &f)=0
	setter for FASTA file More...
virtual String	getFastaFile ()=0
	getter for FASTA file More...
virtual void	setSpectrum (const std::vector< double > &s)=0
	setter for spectrum More...
virtual const std::vector< double > &	getSpectrum ()=0
	getter for spectrum More...
virtual void	setTolerance (double t)=0
	setter for tolerance More...
virtual double	getTolerance ()=0
	getter for tolerance More...
virtual bool	begin ()=0
	initializing iterator More...
virtual bool	isAtEnd ()=0
	indicator where iterator is at end More...

Static Public Member Functions
static void	registerChildren ()
	all children has to be registered here More...

Detailed Description

Abstract base class for different peptide iterators.

Note

every derived class has to implement the static functions "PepIterator * create()" and "const String getProductName()" (see Factory for details)

Member Typedef Documentation

FASTAEntry

typedef std::pair<String, String> FASTAEntry

Constructor & Destructor Documentation

PepIterator() [1/2]

PepIterator

(

)

constructor

~PepIterator()

virtual ~PepIterator ( )

virtual

destructor

PepIterator() [2/2]

PepIterator

(

const PepIterator &

source

)

copy constructor

Member Function Documentation

begin()

virtual bool begin ( )

pure virtual

initializing iterator

Implemented in FastaIteratorIntern, FastaIterator, and TrypticIterator.

getFastaFile()

virtual String getFastaFile ( )

pure virtual

getter for FASTA file

Returns

String with file location

Implemented in FastaIteratorIntern, FastaIterator, and TrypticIterator.

getSpectrum()

virtual const std::vector<double>& getSpectrum ( )

pure virtual

getter for spectrum

Returns

the used spectrum

Implemented in TrypticIterator, FastaIteratorIntern, and FastaIterator.

getTolerance()

virtual double getTolerance ( )

pure virtual

getter for tolerance

Returns

tolerance

Implemented in FastaIteratorIntern, FastaIterator, and TrypticIterator.

isAtEnd()

virtual bool isAtEnd ( )

pure virtual

indicator where iterator is at end

Implemented in FastaIteratorIntern, FastaIterator, and TrypticIterator.

operator*()

virtual FASTAEntry operator* ( )

pure virtual

* operator for accessing the value of the iterator

Returns

FASTAEntry representing a peptide

Exceptions

InvalidIterator

if iterator has not been initialized

Implemented in FastaIteratorIntern, FastaIterator, and TrypticIterator.

operator++() [1/2]

virtual PepIterator& operator++ ( )

pure virtual

operator ++ for pre-increment

Returns

Reference to PepIterator

Exceptions

InvalidIterator

if iterator has not been initialized

Implemented in FastaIteratorIntern, FastaIterator, and TrypticIterator.

operator++() [2/2]

virtual PepIterator* operator++ ( int  )

pure virtual

operator ++ for post-increment

Returns

pointer to PepIterator

Exceptions

Exception::InvalidIterator

if iterator has not been initialized

Implemented in FastaIteratorIntern, FastaIterator, and TrypticIterator.

registerChildren()

static void registerChildren ( )

static

all children has to be registered here

See also

Factory

setFastaFile()

virtual void setFastaFile ( const String &  f )

pure virtual

setter for FASTA file

Parameters

f	const String reference representing file location

Exceptions

Exception::FileNotFound
Exception::ParseError

Implemented in FastaIteratorIntern, FastaIterator, and TrypticIterator.

setSpectrum()

virtual void setSpectrum ( const std::vector< double > &  s )

pure virtual

setter for spectrum

Parameters

s	ms spectrum given as vector of doubles

Exceptions

Exception::InvalidValue

if spectrum is not sorted ascendingly

Implemented in TrypticIterator, FastaIteratorIntern, and FastaIterator.

setTolerance()

virtual void setTolerance ( double  t )

pure virtual

setter for tolerance

Parameters

t	tolerance value

Exceptions

Exception::InvalidValue

if tolerance is negative

Implemented in FastaIteratorIntern, FastaIterator, and TrypticIterator.