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 |