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EdwardsLippertIterator Class Reference

finds all Peptide Candidates with given masses and given fasta file More...

#include <OpenMS/CHEMISTRY/EdwardsLippertIterator.h>

Inheritance diagram for EdwardsLippertIterator:
PepIterator EdwardsLippertIteratorTryptic

List of all members.

Public Types

typedef std::pair< String, String > FASTAEntry

Public Member Functions

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

Static Public Member Functions

static const String getProductName ()
 needed by Factory
static PepIterator * create ()
 needed by Factory

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
virtual bool isInSpectrum_ (DoubleReal &mass)
 indicates if a mass is in spectrum

Protected Attributes

String f_file_
 fasta file location
std::string actual_pep_
 actual peptide
std::vector< DoubleReal > spec_
 given spectrum
DoubleReal tol_
 tolerance
DoubleReal masse_ [255]
 mass table
bool is_at_end_
 indicates if iterator is at end
PepIterator * f_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)
DoubleReal m_
DoubleReal massMax_
 mass and maximum masse

Detailed Description

finds all Peptide Candidates with given masses and given fasta file

The used algorithm was described by Edwards and Lippert. The algorithm uses two pointers to iterator over a sequence. One pointer represents the start the other the end.

Member Typedef Documentation

typedef std::pair<String, String> FASTAEntry

Reimplemented from PepIterator.

Constructor & Destructor Documentation

EdwardsLippertIterator (  ) 

Constructor.

EdwardsLippertIterator ( const EdwardsLippertIterator &   ) 

Copy Constructor.

virtual ~EdwardsLippertIterator (  )  [virtual]

Destructor.

Member Function Documentation

virtual bool begin (  )  [virtual]

initializing iterator

Returns:
true if everything was ok
Exceptions:
InvalidIterator is thrown if the begin iterator is invalid

Implements PepIterator.

static PepIterator* create (  )  [inline, static]

needed by Factory

Returns:
poiter to new object

Reimplemented in EdwardsLippertIteratorTryptic.

virtual String getFastaFile (  )  [virtual]

getter for FASTA file

Returns:
String with file location

Implements PepIterator.

static const String getProductName (  )  [inline, static]

needed by Factory

Returns:
const string name of class

Reimplemented in EdwardsLippertIteratorTryptic.

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

getter for spectrum

Returns:
the used spectrum

Implements PepIterator.

virtual DoubleReal getTolerance (  )  [virtual]

getter for tolerance

Returns:
tolerance

Implements PepIterator.

void goToNextAA_ (  )  [protected]

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

bool hasNext_ (  )  [protected]

indicates if there will be a next element

Returns:
true if iterator has more elements
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  ,
char   
) [virtual]

indicated if a digesting enzyme will cut at this position

Returns:
true if digenting enzym cuts the sequence

Reimplemented in EdwardsLippertIteratorTryptic.

virtual bool isInSpectrum_ ( DoubleReal &  mass  )  [protected, virtual]

indicates if a mass is in spectrum

Returns:
true if a given mass is in spectrum
virtual std::string next_ (  )  [protected, virtual]

getting the next candidate

Returns:
string with next sequence
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.

virtual PepIterator& operator++ (  )  [virtual]

opperator ++ for postincrement

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

Implements PepIterator.

virtual PepIterator* operator++ ( int  i  )  [virtual]

opperator ++ for preincrement

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

Implements PepIterator.

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.

virtual void setSpectrum ( const std::vector< DoubleReal > &  s  )  [virtual]

setter for spectrum

Parameters:
s spectrum as a vector of DoubleReals
Exceptions:
InvalidValue if spectrum is not sorted

Implements PepIterator.

virtual void setTolerance ( DoubleReal  t  )  [virtual]

setter for tolerance

Parameters:
t tolerance
Exceptions:
InvalidValue if tolerance is negative

Implements PepIterator.

Member Data Documentation

std::string actual_pep_ [protected]

actual peptide

unsigned int b_ [protected]
unsigned int e_ [protected]

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

FASTAEntry f_entry_ [protected]

actual fasta entry

String f_file_ [protected]

fasta file location

PepIterator* f_iterator_ [protected]

FastaIterator.

bool is_at_end_ [protected]

indicates if iterator is at end

DoubleReal m_ [protected]
DoubleReal masse_[255] [protected]

mass table

DoubleReal massMax_ [protected]

mass and maximum masse

std::vector<DoubleReal> spec_ [protected]

given spectrum

DoubleReal tol_ [protected]

tolerance

OpenMS / TOPP release 1.10.0 Documentation generated on Thu Mar 7 2013 09:42:50 using doxygen 1.7.1