finds all tryptic Peptides with every missed cleavage More...

#include <OpenMS/CHEMISTRY/TrypticIterator.h>

Inheritance diagram for TrypticIterator:

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

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

Public Member Functions
	TrypticIterator ()
	Constructor. More...

	TrypticIterator (const TrypticIterator &)
	Copy Constructor. More...

virtual	~TrypticIterator ()
	Destructor. More...

virtual FASTAEntry	operator* ()
	* operator for getting the value of the iterator More...

virtual PepIterator &	operator++ ()
	operator ++ for post-increment More...

virtual PepIterator *	operator++ (int i)
	operator ++ for pre-increment More...

virtual void	setFastaFile (const String &f)
	setter for fasta file More...

virtual String	getFastaFile ()
	getter for FASTA file More...

virtual void	setTolerance (double)
	setter for tolerance More...

virtual double	getTolerance ()
	getter for tolerance More...

virtual void	setSpectrum (const std::vector< double > &)
	setter for spectrum More...

virtual const std::vector< double > &	getSpectrum ()
	getter for spectrum More...

virtual bool	begin ()
	initializing iterator More...

virtual bool	isAtEnd ()
	indicates whether iterator is at end More...

virtual bool	isDigestingEnd (char aa1, char aa2)
	indicated if a digesting enzyme will cut at this position 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 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 Member Functions
virtual std::string	next_ ()
	getting the next candidate More...

bool	hasNext_ ()
	indicates if there will be a next element More...

void	goToNextAA_ ()
	finds the next starting position where a digesting enzyme will cut the sequence More...

Protected Attributes
String	f_file_
	fasta file location More...

std::string	actual_pep_
	actual peptide More...

bool	is_at_end_
	indicates if iterator is at end More...

PepIterator *	f_iterator_
	FastaIterator. More...

FASTAEntry	f_entry_
	actual fasta entry More...

unsigned int	b_

unsigned int	e_
	to ints representing a position within the actual string (b = begin, e = end) More...

Detailed Description

finds all tryptic Peptides with every missed cleavage

Member Typedef Documentation

◆ FASTAEntry

typedef std::pair<String, String> FASTAEntry

Constructor & Destructor Documentation

◆ TrypticIterator() [1/2]

TrypticIterator ( )

Constructor.

◆ TrypticIterator() [2/2]

TrypticIterator ( const TrypticIterator & )

Copy Constructor.

◆ ~TrypticIterator()

virtual ~TrypticIterator ( )

virtual

Destructor.

Member Function Documentation

◆ begin()

virtual bool begin ( )

virtual

initializing iterator

Returns: true if everything was ok

Exceptions

throws InvalidIterator if begin iterator is not valid

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 String getProductName ( )

inlinestatic

needed by Factory

Returns: const string name of class

◆ getSpectrum()

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

inlinevirtual

getter for spectrum

Returns: the used spectrum

Exceptions

NotImplemented because its not available for tryptic iterator

Implements PepIterator.

◆ getTolerance()

virtual double getTolerance ( )

inlinevirtual

getter for tolerance

Returns: tolerance

Exceptions

NotImplemented because its not available for tryptic iterator

Implements PepIterator.

◆ goToNextAA_()

void goToNextAA_ ( )

protected

finds the next starting position where a digesting enzyme will cut the sequence

◆ hasNext_()

bool hasNext_ ( )

protected

indicates if there will be a next element

Returns: true if iterator has more elements

◆ isAtEnd()

virtual bool isAtEnd ( )

virtual

indicates whether iterator is at end

Returns: true if iterator is at end

See also: hasNext

Implements PepIterator.

◆ isDigestingEnd()

virtual bool isDigestingEnd	(	char	aa1,
		char	aa2
	)

virtual

indicated if a digesting enzyme will cut at this position

Returns: true if digesting enzyme cuts the sequence

◆ next_()

virtual std::string next_ ( )

protectedvirtual

getting the next candidate

Returns: string with next sequence

◆ operator*()

virtual FASTAEntry operator* ( )

virtual

* operator for getting the value of the iterator

Returns: FASTAEntry with specific candidate

Exceptions

InvalidIterator if iterator has not been initialized

Implements PepIterator.

◆ operator++() [1/2]

virtual PepIterator& operator++ ( )

virtual

operator ++ for post-increment

Returns: Reference to PepIterator

Exceptions

InvalidIterator if iterator has not been initialized

Implements PepIterator.

◆ operator++() [2/2]

virtual PepIterator* operator++ ( int i )

virtual

operator ++ for pre-increment

Returns: pointer to PepIterator

Exceptions

InvalidIterator if iterator has not been initialized

Implements PepIterator.

◆ setFastaFile()

virtual void setFastaFile ( const String & f )

virtual

setter for fasta file

Parameters

f	String with fasta file location

Exceptions

FileNotFound if file could not be found

Implements PepIterator.

◆ setSpectrum()

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

inlinevirtual

setter for spectrum

Exceptions

NotImplemented because its not available for tryptic iterator

Implements PepIterator.

◆ setTolerance()

virtual void setTolerance ( double )

inlinevirtual

setter for tolerance

Exceptions

NotImplemented because its not available for tryptic iterator

Implements PepIterator.

Member Data Documentation

◆ actual_pep_

std::string actual_pep_

protected

actual peptide

◆ b_

unsigned int b_

protected

◆ e_

unsigned int e_

protected

to ints representing a position within the actual string (b = begin, e = end)

◆ f_entry_

FASTAEntry f_entry_

protected

actual fasta entry

◆ f_file_

String f_file_

protected

fasta file location

◆ f_iterator_

PepIterator* f_iterator_

protected

FastaIterator.

◆ is_at_end_

bool is_at_end_

protected

indicates if iterator is at end

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Member Typedef Documentation

◆ FASTAEntry

Constructor & Destructor Documentation

◆ TrypticIterator() [1/2]

◆ TrypticIterator() [2/2]

◆ ~TrypticIterator()

Member Function Documentation

◆ begin()

◆ create()

◆ getFastaFile()

◆ getProductName()

◆ getSpectrum()

◆ getTolerance()

◆ goToNextAA_()

◆ hasNext_()

◆ isAtEnd()

◆ isDigestingEnd()

◆ next_()

◆ operator*()

◆ operator++() [1/2]

◆ operator++() [2/2]

◆ setFastaFile()

◆ setSpectrum()

◆ setTolerance()

Member Data Documentation

◆ actual_pep_

◆ b_

◆ e_

◆ f_entry_

◆ f_file_

◆ f_iterator_

◆ is_at_end_