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TrypticIterator Class Reference

#include <OpenMS/CHEMISTRY/TrypticIterator.h>

Inheritance diagram for TrypticIterator:

PepIterator FactoryProduct

List of all members.


Detailed Description

finds all tryptic Peptides with every missed cleavage

Public Types

typedef std::pair< String, StringFASTAEntry

Public Member Functions

 TrypticIterator ()
 Constructor.
 TrypticIterator (const TrypticIterator &)
 Copy Constructor.
virtual ~TrypticIterator ()
 Destructor.
virtual FASTAEntry operator * () throw (Exception::InvalidIterator)
 * operator for getting the value of the iterator
virtual PepIteratoroperator++ () throw (Exception::InvalidIterator)
 opperator ++ for postincrement
virtual PepIteratoroperator++ (int i) throw (Exception::InvalidIterator)
 opperator ++ for preincrement
virtual void setFastaFile (const String &f) throw (Exception::FileNotFound)
 setter for fasta file
virtual String getFastaFile ()
 getter for FASTA file
virtual void setTolerance (float) throw (Exception::InvalidValue, Exception::NotImplemented)
 setter for tolerance
virtual float getTolerance () throw (Exception::InvalidValue, Exception::NotImplemented)
 getter for tolerance
virtual void setSpectrum (const std::vector< float > &) throw (Exception::InvalidValue, Exception::NotImplemented)
 setter for spectrum
virtual const std::vector
< float > & 
getSpectrum () throw (Exception::InvalidValue, Exception::NotImplemented)
 getter for spectrum
virtual bool begin () throw (Exception::InvalidIterator)
 initializing iterator
virtual bool isAtEnd ()
 indicates whether iterator is at end
virtual bool isDigestingEnd (char aa1, char aa2)
 indicated if a digesting enzyme will cut at this position

Static Public Member Functions

static const std::string getName ()
 needed by FactoryProduct
static PepIteratorcreate ()
 needed by FactoryProduct

Protected Member Functions

virtual std::string next_ ()
 getting the next candidate
bool hasNext_ ()
 indicates if there will be a next element
void goToNextAA_ ()
 finds the next starting position where a digesting enzyme will cut the sequence

Protected Attributes

String f_file_
 fasta file location
std::string actual_pep_
 actual peptide
bool is_at_end_
 indicates if iterator is at end
PepIteratorf_iterator_
 FastaIterator.
FASTAEntry f_entry_
 actual fasta entry
unsigned int b_
unsigned int e_
 to ints representing a position within the actual string (b = begin, e = end)

Member Typedef Documentation

typedef std::pair<String,String> FASTAEntry

Reimplemented from PepIterator.


Constructor & Destructor Documentation

TrypticIterator (  ) 

Constructor.

TrypticIterator ( const TrypticIterator  ) 

Copy Constructor.

virtual ~TrypticIterator (  )  [virtual]

Destructor.


Member Function Documentation

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

* operator for getting the value of the iterator

Returns:
FASTAEntry with specific candidate
Exceptions:
Exception::InvalidIterator if iterator has not been initialized

Implements PepIterator.

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

opperator ++ for postincrement

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

Implements PepIterator.

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

opperator ++ for preincrement

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

Implements PepIterator.

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

setter for fasta file

Parameters:
f String with fasta file location
Exceptions:
Exception::FileNotFound if file could not be found

Implements PepIterator.

virtual String getFastaFile (  )  [virtual]

getter for FASTA file

Returns:
String with file location

Implements PepIterator.

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

setter for tolerance

Exceptions:
Exception::NotImplemented because its not available for tryptic iterator

Implements PepIterator.

virtual float getTolerance (  )  throw (Exception::InvalidValue, Exception::NotImplemented) [inline, virtual]

getter for tolerance

Returns:
tolerance
Exceptions:
Exception::NotImplemented because its not available for tryptic iterator

Implements PepIterator.

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

setter for spectrum

Exceptions:
Exception::NotImplemented because its not available for tryptic iterator

Implements PepIterator.

virtual const std::vector<float>& getSpectrum (  )  throw (Exception::InvalidValue, Exception::NotImplemented) [inline, virtual]

getter for spectrum

Returns:
the used spectrum
Exceptions:
Exception::NotImplemented because its not available for tryptic iterator

Implements PepIterator.

virtual bool begin (  )  throw (Exception::InvalidIterator) [virtual]

initializing iterator

Returns:
true if everything was ok

Implements PepIterator.

virtual bool isAtEnd (  )  [virtual]

indicates whether iterator is at end

Returns:
true if iterator is at end
See also:
hasNext

Implements PepIterator.

virtual bool isDigestingEnd ( char  aa1,
char  aa2 
) [virtual]

indicated if a digesting enzyme will cut at this position

Returns:
true if digenting enzym cuts the sequence

static const std::string getName (  )  [inline, static]

needed by FactoryProduct

Returns:
const string name of class

static PepIterator* create (  )  [inline, static]

needed by FactoryProduct

Returns:
poiter to new object

virtual std::string next_ (  )  [protected, virtual]

getting the next candidate

Returns:
string with next sequence

bool hasNext_ (  )  [protected]

indicates if there will be a next element

Returns:
true if iterator has more elements

void goToNextAA_ (  )  [protected]

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


Member Data Documentation

String f_file_ [protected]

fasta file location

std::string actual_pep_ [protected]

actual peptide

bool is_at_end_ [protected]

indicates if iterator is at end

PepIterator* f_iterator_ [protected]

FastaIterator.

FASTAEntry f_entry_ [protected]

actual fasta entry

unsigned int b_ [protected]

unsigned int e_ [protected]

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


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