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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

Public Types

typedef std::pair< String, StringFASTAEntry
 
- Public Types inherited from PepIterator
typedef std::pair< String, StringFASTAEntry
 

Public Member Functions

 EdwardsLippertIterator ()
 Constructor. More...
 
 EdwardsLippertIterator (const EdwardsLippertIterator &)
 Copy Constructor. More...
 
virtual ~EdwardsLippertIterator ()
 Destructor. More...
 
virtual FASTAEntry operator* ()
 * operator for getting the value of the iterator More...
 
virtual PepIteratoroperator++ ()
 operator ++ for postincrement More...
 
virtual PepIteratoroperator++ (int i)
 operator ++ for preincrement More...
 
virtual void setFastaFile (const String &f)
 setter for fasta file More...
 
virtual String getFastaFile ()
 getter for FASTA file More...
 
virtual void setTolerance (double t)
 setter for tolerance More...
 
virtual double getTolerance ()
 getter for tolerance More...
 
virtual void setSpectrum (const std::vector< double > &s)
 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, char)
 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 PepIteratorcreate ()
 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...
 
virtual bool isInSpectrum_ (double &mass)
 indicates if a mass is in spectrum More...
 

Protected Attributes

String f_file_
 fasta file location More...
 
std::string actual_pep_
 actual peptide More...
 
std::vector< doublespec_
 given spectrum More...
 
double tol_
 tolerance More...
 
double masse_ [255]
 mass table More...
 
bool is_at_end_
 indicates if iterator is at end More...
 
PepIteratorf_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...
 
double m_
 
double massMax_
 mass and maximum masse More...
 

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

Constructor & Destructor Documentation

Constructor.

Copy Constructor.

virtual ~EdwardsLippertIterator ( )
virtual

Destructor.

Member Function Documentation

virtual bool begin ( )
virtual

initializing iterator

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

Implements PepIterator.

static PepIterator* create ( )
inlinestatic

needed by Factory

Returns
pointer to new object
virtual String getFastaFile ( )
virtual

getter for FASTA file

Returns
String with file location

Implements PepIterator.

static const String getProductName ( )
inlinestatic

needed by Factory

Returns
const string name of class
virtual const std::vector<double>& getSpectrum ( )
virtual

getter for spectrum

Returns
the used spectrum

Implements PepIterator.

virtual double 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 digesting enzyme cuts the sequence

Reimplemented in EdwardsLippertIteratorTryptic.

virtual bool isInSpectrum_ ( double mass)
protectedvirtual

indicates if a mass is in spectrum

Returns
true if a given mass is in spectrum
virtual std::string next_ ( )
protectedvirtual

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
InvalidIteratorif iterator has not been initialized

Implements PepIterator.

virtual PepIterator& operator++ ( )
virtual

operator ++ for postincrement

Returns
Reference to PepIterator
Exceptions
InvalidIteratorif iterator has not been initialized

Implements PepIterator.

virtual PepIterator* operator++ ( int  i)
virtual

operator ++ for preincrement

Returns
pointer to PepIterator
Exceptions
InvalidIteratorif iterator has not been initialized

Implements PepIterator.

virtual void setFastaFile ( const String f)
virtual

setter for fasta file

Parameters
fString with fasta file location
Exceptions
FileNotFoundif file could not be found

Implements PepIterator.

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

setter for spectrum

Parameters
sspectrum as a vector of doubles
Exceptions
InvalidValueif spectrum is not sorted

Implements PepIterator.

virtual void setTolerance ( double  t)
virtual

setter for tolerance

Parameters
ttolerance
Exceptions
InvalidValueif 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
bool is_at_end_
protected

indicates if iterator is at end

double m_
protected
double masse_[255]
protected

mass table

double massMax_
protected

mass and maximum masse

std::vector<double> spec_
protected

given spectrum

double tol_
protected

tolerance


OpenMS / TOPP release 2.0.0 Documentation generated on Tue Aug 25 2015 05:54:00 using doxygen 1.8.9.1