Iterator over FASTA file. More...
#include <OpenMS/FORMAT/FastaIterator.h>
 
  
 | Public Types | |
| typedef std::pair< String, String > | FASTAEntry | 
|  Public Types inherited from PepIterator | |
| typedef std::pair< String, String > | FASTAEntry | 
| Public Member Functions | |
| FastaIterator () | |
| constructor  More... | |
| virtual | ~FastaIterator () | 
| destructor  More... | |
| virtual FASTAEntry | operator* () | 
| * operator for getting the iterator's value  More... | |
| virtual PepIterator & | operator++ () | 
| pre-increment Operator for the iterator  More... | |
| virtual PepIterator * | operator++ (int i) | 
| post-increment Operator for the iterator  More... | |
| virtual void | setFastaFile (const String &f) | 
| setter for FASTAfile  More... | |
| virtual String | getFastaFile () | 
| getter for FASTA file  More... | |
| virtual void | setSpectrum (const std::vector< DoubleReal > &) | 
| setter for spectrum  More... | |
| virtual const std::vector < DoubleReal > & | getSpectrum () | 
| getter for spectrum  More... | |
| virtual void | setTolerance (DoubleReal) | 
| setter for tolerance  More... | |
| virtual DoubleReal | getTolerance () | 
| getter for tolerance  More... | |
| virtual bool | begin () | 
| initializing of 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 PepIterator * | create () | 
| 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_ () | 
| gets the next string  More... | |
| Protected Attributes | |
| bool | is_at_end_ | 
| bool indicated whether iterator is at end  More... | |
| std::ifstream | input_file_ | 
| input file  More... | |
| String | fasta_file_ | 
| fasta file location  More... | |
| std::string | actual_seq_ | 
| actual sequence  More... | |
| std::string | header_ | 
| actual fasta header  More... | |
| std::string | last_header_ | 
| last fasta header  More... | |
| Private Member Functions | |
| FastaIterator (const FastaIterator &) | |
| copy constructor  More... | |
| FastaIterator & | operator= (const FastaIterator &) | 
| Assignment.  More... | |
Iterator over FASTA file.
Iterates over FASTA file without loading it into memory. It holds just one entry in memory.
| typedef std::pair<String, String> FASTAEntry | 
| FastaIterator | ( | ) | 
constructor
| 
 | virtual | 
destructor
| 
 | private | 
copy constructor
| 
 | virtual | 
initializing of iterator
| Exception::InvalidIterator | if fastaFile was not set | 
Implements PepIterator.
| 
 | inlinestatic | 
needed by Factory
| 
 | virtual | 
| 
 | inlinestatic | 
needed by Factory
| 
 | inlinevirtual | 
getter for spectrum
| Exception::NotImplemented | 
Implements PepIterator.
| 
 | inlinevirtual | 
getter for tolerance
| Exception::NotImplemented | 
Implements PepIterator.
| 
 | virtual | 
| 
 | protectedvirtual | 
gets the next string
| 
 | virtual | 
* operator for getting the iterator's value
| InvalidIterator | if iterator was not initialized | 
Implements PepIterator.
| 
 | virtual | 
pre-increment Operator for the iterator
| Exception::InvalidIterator | if iterator was not initialized | 
Implements PepIterator.
| 
 | virtual | 
post-increment Operator for the iterator
| Exception::InvalidIterator | if iterator was not initialized | 
Implements PepIterator.
| 
 | private | 
Assignment.
| 
 | virtual | 
setter for FASTAfile
| f | Name of the fasta file | 
| Exception::FileNotFound | |
| ParseError | is thrown if the file could not be parsed | 
Implements PepIterator.
| 
 | inlinevirtual | 
setter for spectrum
| Exception::NotImplemented | 
Implements PepIterator.
| 
 | inlinevirtual | 
setter for tolerance
| Exception::NotImplemented | 
Implements PepIterator.
| 
 | protected | 
actual sequence
| 
 | protected | 
fasta file location
| 
 | protected | 
actual fasta header
| 
 | protected | 
input file
| 
 | protected | 
bool indicated whether iterator is at end
| 
 | protected | 
last fasta header
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:30 using doxygen 1.8.5 |