FastaIteratorIntern Class Reference

Iterator for a FASTA file. More...

#include <OpenMS/FORMAT/FastaIteratorIntern.h>

Inheritance diagram for FastaIteratorIntern:

Public Types
typedef std::pair< String, String >	FASTAEntry
Public Types inherited from PepIterator
typedef std::pair< String, String >	FASTAEntry

Public Member Functions
	FastaIteratorIntern ()
	constructor More...
	FastaIteratorIntern (const FastaIteratorIntern &)
	copy constructor More...
virtual	~FastaIteratorIntern ()
	constructor More...
virtual FASTAEntry	operator* ()
	* Operator for dereferencing of iterator More...
virtual PepIterator &	operator++ ()
	++ Operator for the iterator More...
virtual PepIterator *	operator++ (int i)
	++ Operator for the iterator More...
virtual void	setFastaFile (const String &f)
	setter for FASTA file More...
virtual String	getFastaFile ()
	getter for FASTA file More...
virtual void	setSpectrum (const std::vector< double > &)
	setter for spectrum More...
virtual const std::vector< double > &	getSpectrum ()
	getter for spectrum More...
virtual void	setTolerance (double)
	setter for tolerance More...
virtual double	getTolerance ()
	getter for tolerance More...
virtual bool	begin ()
	initializing of iterator More...
virtual bool	isAtEnd ()
	indicates whether iterator is at end More...
Public Member Functions inherited from PepIterator
	PepIterator ()
	constructor More...
virtual	~PepIterator ()
	destructor More...
	PepIterator (const PepIterator &source)
	copy constructor More...

Static Public Member Functions
static const std::string	getProductName ()
	needed by Factory More...
static PepIterator *	create ()
	needed by Factory More...
Static Public Member Functions inherited from PepIterator
static void	registerChildren ()
	all children has to be registered here More...

Protected Attributes
String	fasta_file_
	location of the fasta file More...
std::vector< FASTAEntry >	entrys_
	content of fasta file More...
std::vector< FASTAEntry >::iterator	it_
	iterator over fasta file content More...

Detailed Description

Iterator for a FASTA file.

In comparison to FastaIterator the FASTA file will be loaded first and stored to RAM, while the FastaIterator just iterates over the FASTA file without loading it completely to memory.

See also

FastaIterator

Member Typedef Documentation

FASTAEntry

typedef std::pair<String, String> FASTAEntry

Constructor & Destructor Documentation

FastaIteratorIntern() [1/2]

FastaIteratorIntern

(

)

constructor

FastaIteratorIntern() [2/2]

FastaIteratorIntern

(

const FastaIteratorIntern &

)

copy constructor

~FastaIteratorIntern()

virtual ~FastaIteratorIntern ( )

virtual

constructor

Member Function Documentation

begin()

virtual bool begin ( )

virtual

initializing of iterator

Returns

true if everything went right

Exceptions

Exception::InvalidIterator

if fastaFile was not set

Implements PepIterator.

create()

static PepIterator* create ( )

inlinestatic

needed by Factory

Returns

pointer to new object

getFastaFile()

virtual String getFastaFile ( )

virtual

getter for FASTA file

Returns

String with file location

Implements PepIterator.

getProductName()

static const std::string getProductName ( )

inlinestatic

needed by Factory

Returns

const string name of class

getSpectrum()

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

inlinevirtual

getter for spectrum

Note

note available for FastaIterator

Exceptions

Exception::NotImplemented

Implements PepIterator.

getTolerance()

virtual double getTolerance ( )

inlinevirtual

getter for tolerance

Note

note available for FastaIterator

Returns

tolerance

Exceptions

Exception::NotImplemented

Implements PepIterator.

isAtEnd()

virtual bool isAtEnd ( )

virtual

indicates whether iterator is at end

Returns

bool true if iterator is at end

Implements PepIterator.

operator*()

virtual FASTAEntry operator* ( )

virtual

* Operator for dereferencing of iterator

Returns

FASTEEntry iterator at actual position

Exceptions

Exception::InvalidIterator

if iterator has not been initialized

Implements PepIterator.

operator++() [1/2]

virtual PepIterator& operator++ ( )

virtual

++ Operator for the iterator

Returns

reference to PepIterator

Exceptions

Exception::InvalidIterator

if iterator has not been initialized

Implements PepIterator.

operator++() [2/2]

virtual PepIterator* operator++ ( int  i )

virtual

++ Operator for the iterator

Returns

pointer to PepIterator

Exceptions

Exception::InvalidIterator

if iterator has not been initialized

Implements PepIterator.

setFastaFile()

virtual void setFastaFile ( const String &  f )

virtual

setter for FASTA file

Parameters

f	const String reference representing file location

Exceptions

Exception::FileNotFound
Exception::ParseError

Implements PepIterator.

setSpectrum()

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

inlinevirtual

setter for spectrum

Note

note available for FastaIterator

Exceptions

Exception::NotImplemented

Implements PepIterator.

setTolerance()

virtual void setTolerance ( double  )

inlinevirtual

setter for tolerance

Note

note available for FastaIterator

Exceptions

Exception::NotImplemented

Implements PepIterator.

Member Data Documentation

entrys_

std::vector<FASTAEntry> entrys_

protected

content of fasta file

fasta_file_

String fasta_file_

protected

location of the fasta file

it_

std::vector<FASTAEntry>::iterator it_

protected

iterator over fasta file content