finds all tryptic Peptides with every missed cleavage More...
#include <OpenMS/CHEMISTRY/TrypticIterator.h>
Public Types | |
| typedef std::pair< String, String > | FASTAEntry |
Public Member Functions | |
| TrypticIterator () | |
| Constructor. | |
| TrypticIterator (const TrypticIterator &) | |
| Copy Constructor. | |
| virtual | ~TrypticIterator () |
| 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) |
| setter for tolerance | |
| virtual DoubleReal | getTolerance () |
| getter for tolerance | |
| virtual void | setSpectrum (const std::vector< DoubleReal > &) |
| 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 aa1, char aa2) |
| 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 | |
Protected Attributes | |
| String | f_file_ |
| fasta file location | |
| std::string | actual_pep_ |
| actual peptide | |
| 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) | |
Detailed Description
finds all tryptic Peptides with every missed cleavage
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 bool begin | ( | ) | [virtual] |
initializing iterator
- Returns:
- true if everything was ok
- Exceptions:
-
throws InvalidIterator if begin iterator is not valid
Implements PepIterator.
| static PepIterator* create | ( | ) | [inline, static] |
needed by Factory
- Returns:
- poiter to new object
| virtual String getFastaFile | ( | ) | [virtual] |
| static const String getProductName | ( | ) | [inline, static] |
needed by Factory
- Returns:
- const string name of class
| virtual const std::vector<DoubleReal>& getSpectrum | ( | ) | [inline, virtual] |
getter for spectrum
- Returns:
- the used spectrum
- Exceptions:
-
NotImplemented because its not available for tryptic iterator
Implements PepIterator.
| virtual DoubleReal getTolerance | ( | ) | [inline, virtual] |
getter for tolerance
- Returns:
- tolerance
- Exceptions:
-
NotImplemented because its not available for tryptic iterator
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 | aa1, | |
| char | aa2 | |||
| ) | [virtual] |
indicated if a digesting enzyme will cut at this position
- Returns:
- true if digenting enzym cuts the sequence
| 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++ | ( | int | i | ) | [virtual] |
opperator ++ for preincrement
- Returns:
- pointer to PepIterator
- 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 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 > & | ) | [inline, virtual] |
setter for spectrum
- Exceptions:
-
NotImplemented because its not available for tryptic iterator
Implements PepIterator.
| virtual void setTolerance | ( | DoubleReal | ) | [inline, virtual] |
setter for tolerance
- Exceptions:
-
NotImplemented because its not available for tryptic iterator
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
PepIterator* f_iterator_ [protected] |
bool is_at_end_ [protected] |
indicates if iterator is at end
| OpenMS / TOPP release 1.10.0 | Documentation generated on Thu Mar 7 2013 09:42:50 using doxygen 1.7.1 |