Abstract base class for different peptide iterators. More...
#include <OpenMS/CHEMISTRY/PepIterator.h>
Public Types | |
| typedef std::pair< String, String > | FASTAEntry |
Public Member Functions | |
| PepIterator () | |
| constructor | |
| virtual | ~PepIterator () |
| destructor | |
| PepIterator (const PepIterator &source) | |
| copy constructor | |
| virtual FASTAEntry | operator* ()=0 |
| * operator for accessing the value of the iterator | |
| virtual PepIterator & | operator++ ()=0 |
| operator ++ for pre-increment | |
| virtual PepIterator * | operator++ (int)=0 |
| operator ++ for post-increment | |
| virtual void | setFastaFile (const String &f)=0 |
| setter for FASTA file | |
| virtual String | getFastaFile ()=0 |
| getter for FASTA file | |
| virtual void | setSpectrum (const std::vector< DoubleReal > &s)=0 |
| setter for spectrum | |
| virtual const std::vector < DoubleReal > & | getSpectrum ()=0 |
| getter for spectrum | |
| virtual void | setTolerance (DoubleReal t)=0 |
| setter for tolerance | |
| virtual DoubleReal | 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 | |
Detailed Description
Abstract base class for different peptide iterators.
- Note:
- every derived class has to implement the static functions "PepIterator * create()" and "const String getProductName()" (see Factory for details)
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 bool begin | ( | ) | [pure virtual] |
initializing iterator
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 const std::vector<DoubleReal>& getSpectrum | ( | ) | [pure virtual] |
getter for spectrum
- Returns:
- the used spectrum
Implemented in EdwardsLippertIterator, TrypticIterator, FastaIterator, and FastaIteratorIntern.
| virtual DoubleReal getTolerance | ( | ) | [pure virtual] |
getter for tolerance
- Returns:
- tolerance
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.
| virtual FASTAEntry operator* | ( | ) | [pure virtual] |
* operator for accessing the value of the iterator
- Returns:
- FASTAEntry representing a peptide
- Exceptions:
-
InvalidIterator if iterator has not been initialized
Implemented in EdwardsLippertIterator, TrypticIterator, FastaIterator, and FastaIteratorIntern.
| virtual PepIterator& operator++ | ( | ) | [pure virtual] |
operator ++ for pre-increment
- Returns:
- Reference to PepIterator
- Exceptions:
-
InvalidIterator if iterator has not been initialized
Implemented in EdwardsLippertIterator, TrypticIterator, FastaIterator, and FastaIteratorIntern.
| virtual PepIterator* operator++ | ( | int | ) | [pure virtual] |
operator ++ for post-increment
- Returns:
- pointer to PepIterator
- Exceptions:
-
Exception::InvalidIterator if iterator has not been initialized
Implemented in EdwardsLippertIterator, TrypticIterator, FastaIterator, and FastaIteratorIntern.
| static void registerChildren | ( | ) | [static] |
all children has to be registered here
- See also:
- Factory
| virtual void setFastaFile | ( | const String & | f | ) | [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 void setSpectrum | ( | const std::vector< DoubleReal > & | s | ) | [pure virtual] |
setter for spectrum
- Parameters:
-
s ms spectrum given as vector of DoubleReals
- Exceptions:
-
Exception::InvalidValue if spectrum is not sorted acendingly
Implemented in EdwardsLippertIterator, TrypticIterator, FastaIterator, and FastaIteratorIntern.
| virtual void setTolerance | ( | DoubleReal | t | ) | [pure virtual] |
setter for tolerance
- Parameters:
-
t tolerance value
- Exceptions:
-
Exception::InvalidValue if tolerance is negative
Implemented in EdwardsLippertIterator, TrypticIterator, FastaIterator, and FastaIteratorIntern.
| OpenMS / TOPP release 1.10.0 | Documentation generated on Thu Mar 7 2013 09:42:50 using doxygen 1.7.1 |