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EdwardsLippertIteratorTryptic Class Reference

EdwardsLippertIterator that only retrieves tryptic seqences. More...

#include <OpenMS/CHEMISTRY/EdwardsLippertIteratorTryptic.h>

Inheritance diagram for EdwardsLippertIteratorTryptic:
EdwardsLippertIterator PepIterator

Public Member Functions

 EdwardsLippertIteratorTryptic ()
 default constructor More...
 
 EdwardsLippertIteratorTryptic (const EdwardsLippertIteratorTryptic &rhs)
 copy constructor More...
 
virtual ~EdwardsLippertIteratorTryptic ()
 destructor More...
 
EdwardsLippertIteratorTrypticoperator= (const EdwardsLippertIteratorTryptic &rhs)
 assignment operator More...
 
virtual bool isDigestingEnd (char aa1, char aa2)
 indicates if trypsin will cat between the two amino acids More...
 
- Public Member Functions inherited from EdwardsLippertIterator
 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++ ()
 opperator ++ for postincrement More...
 
virtual PepIteratoroperator++ (int i)
 opperator ++ 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 (DoubleReal t)
 setter for tolerance More...
 
virtual DoubleReal getTolerance ()
 getter for tolerance More...
 
virtual void setSpectrum (const std::vector< DoubleReal > &s)
 setter for spectrum More...
 
virtual const std::vector
< DoubleReal > & 
getSpectrum ()
 getter for spectrum More...
 
virtual bool begin ()
 initializing iterator More...
 
virtual bool isAtEnd ()
 indicates whether iterator is at end 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 EdwardsLippertIterator
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...
 

Additional Inherited Members

- Public Types inherited from EdwardsLippertIterator
typedef std::pair< String, StringFASTAEntry
 
- Public Types inherited from PepIterator
typedef std::pair< String, StringFASTAEntry
 
- Protected Member Functions inherited from EdwardsLippertIterator
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_ (DoubleReal &mass)
 indicates if a mass is in spectrum More...
 
- Protected Attributes inherited from EdwardsLippertIterator
String f_file_
 fasta file location More...
 
std::string actual_pep_
 actual peptide More...
 
std::vector< DoubleRealspec_
 given spectrum More...
 
DoubleReal tol_
 tolerance More...
 
DoubleReal 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...
 
DoubleReal m_
 
DoubleReal massMax_
 mass and maximum masse More...
 

Detailed Description

EdwardsLippertIterator that only retrieves tryptic seqences.

Constructor & Destructor Documentation

default constructor

copy constructor

virtual ~EdwardsLippertIteratorTryptic ( )
virtual

destructor

Member Function Documentation

static PepIterator* create ( )
inlinestatic

needed by Factory

Returns
poiter to new object
static const String getProductName ( )
inlinestatic

needed by Factory

Returns
const string name of class
virtual bool isDigestingEnd ( char  aa1,
char  aa2 
)
virtual

indicates if trypsin will cat between the two amino acids

Parameters
aa1first amino acid
aa2second amino acid

Reimplemented from EdwardsLippertIterator.

assignment operator


OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:27 using doxygen 1.8.5