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PepIterator Class Reference

#include <OpenMS/CHEMISTRY/PepIterator.h>

Inheritance diagram for PepIterator:

FactoryProduct EdwardsLippertIterator FastaIterator FastaIteratorIntern TrypticIterator EdwardsLippertIteratorTryptic

List of all members.


Detailed Description

Abstract base class for different peptide iterators.

Note:
every derived class has to implement the static functions "PepIterator * create()" and "const String getName()" (see FactoryProduct for details)

Public Types

typedef std::pair< String, StringFASTAEntry

Public Member Functions

 PepIterator ()
 constructor
virtual ~PepIterator ()
 destructor
 PepIterator (const PepIterator &source)
 copy constructor
virtual FASTAEntry operator * ()=0 throw (Exception::InvalidIterator)
 * operator for accessing the value of the iterator
virtual PepIteratoroperator++ ()=0 throw (Exception::InvalidIterator)
 opperator ++ for postincrement
virtual PepIteratoroperator++ (int)=0 throw (Exception::InvalidIterator)
 opperator ++ for preincrement
virtual void setFastaFile (const String &f)=0 throw (Exception::FileNotFound, Exception::ParseError)
 setter for FASTA file
virtual String getFastaFile ()=0
 getter for FASTA file
virtual void setSpectrum (const std::vector< float > &s)=0 throw (Exception::InvalidValue, Exception::NotImplemented)
 setter for spectrum
virtual const std::vector
< float > & 
getSpectrum ()=0
 getter for spectrum
virtual void setTolerance (float t)=0 throw (Exception::InvalidValue, Exception::NotImplemented)
 setter for tolerance
virtual float getTolerance ()=0
 getter for tolerance
virtual bool begin ()=0
 initializing iterator
virtual bool isAtEnd ()=0
 idicator where iterator is at end

Static Public Member Functions

static void registerChildren ()
 all children has to be registered here

Member Typedef Documentation

typedef std::pair<String, String> FASTAEntry

Reimplemented in EdwardsLippertIterator, TrypticIterator, FastaIterator, and FastaIteratorIntern.


Constructor & Destructor Documentation

PepIterator (  ) 

constructor

virtual ~PepIterator (  )  [virtual]

destructor

PepIterator ( const PepIterator source  ) 

copy constructor


Member Function Documentation

virtual FASTAEntry operator * (  )  throw (Exception::InvalidIterator) [pure virtual]

* operator for accessing the value of the iterator

Returns:
FASTAEntry representing a peptide
Exceptions:
Exception::InvalidIterator if iterator has not been initialized

Implemented in EdwardsLippertIterator, TrypticIterator, FastaIterator, and FastaIteratorIntern.

virtual PepIterator& operator++ (  )  throw (Exception::InvalidIterator) [pure virtual]

opperator ++ for postincrement

Returns:
Reference to PepIterator
Exceptions:
Exception::InvalidIterator if iterator has not been initialized

Implemented in EdwardsLippertIterator, TrypticIterator, FastaIterator, and FastaIteratorIntern.

virtual PepIterator* operator++ ( int   )  throw (Exception::InvalidIterator) [pure virtual]

opperator ++ for preincrement

Returns:
pointer to PepIterator
Exceptions:
Exception::InvalidIterator if iterator has not been initialized

Implemented in EdwardsLippertIterator, TrypticIterator, FastaIterator, and FastaIteratorIntern.

virtual void setFastaFile ( const String f  )  throw (Exception::FileNotFound, Exception::ParseError) [pure virtual]

setter for FASTA file

Parameters:
f const String reference representing file location
Exceptions:
Exception::FileNotFound 
Exception::ParseError 

Implemented in EdwardsLippertIterator, TrypticIterator, FastaIterator, and FastaIteratorIntern.

virtual String getFastaFile (  )  [pure virtual]

getter for FASTA file

Returns:
String with file location

Implemented in EdwardsLippertIterator, TrypticIterator, FastaIterator, and FastaIteratorIntern.

virtual void setSpectrum ( const std::vector< float > &  s  )  throw (Exception::InvalidValue, Exception::NotImplemented) [pure virtual]

setter for spectrum

Parameters:
s ms spectrum given as vector of floats
Exceptions:
Exception::InvalidValue if spectrum is not sorted acendingly

Implemented in EdwardsLippertIterator, TrypticIterator, FastaIterator, and FastaIteratorIntern.

virtual const std::vector<float>& getSpectrum (  )  [pure virtual]

getter for spectrum

Returns:
the used spectrum

Implemented in EdwardsLippertIterator, TrypticIterator, FastaIterator, and FastaIteratorIntern.

virtual void setTolerance ( float  t  )  throw (Exception::InvalidValue, Exception::NotImplemented) [pure virtual]

setter for tolerance

Parameters:
t tolerance value
Exceptions:
Exception::InvalidValue if tolerance is negative

Implemented in EdwardsLippertIterator, TrypticIterator, FastaIterator, and FastaIteratorIntern.

virtual float getTolerance (  )  [pure virtual]

getter for tolerance

Returns:
tolerance

Implemented in EdwardsLippertIterator, TrypticIterator, FastaIterator, and FastaIteratorIntern.

virtual bool begin (  )  [pure virtual]

initializing iterator

Implemented in EdwardsLippertIterator, TrypticIterator, FastaIterator, and FastaIteratorIntern.

virtual bool isAtEnd (  )  [pure virtual]

idicator where iterator is at end

Implemented in EdwardsLippertIterator, TrypticIterator, FastaIterator, and FastaIteratorIntern.

static void registerChildren (  )  [static]

all children has to be registered here

See also:
FactoryProduct


The documentation for this class was generated from the following file:
Generated Tue Apr 1 15:36:43 2008 -- using doxygen 1.5.4 OpenMS / TOPP 1.1