#include <OpenMS/FORMAT/FastaIteratorIntern.h>
In comparision to FastaIterator the FASTA file will be loaded first and stored to RAM, while the FastaIterator just iterates over the FASTA file without loading it completly to memory.
Public Types | |
typedef std::pair< String, String > | FASTAEntry |
Public Member Functions | |
FastaIteratorIntern () | |
constructor | |
FastaIteratorIntern (const FastaIteratorIntern &) | |
copy constructor | |
virtual | ~FastaIteratorIntern () |
constructor | |
virtual FASTAEntry | operator * () throw (Exception::InvalidIterator) |
* Operator for derefering of iterator | |
virtual PepIterator & | operator++ () throw (Exception::InvalidIterator) |
++ Operator for the iterator | |
virtual PepIterator * | operator++ (int i) throw (Exception::InvalidIterator) |
++ Operator for the iterator | |
virtual void | setFastaFile (const String &f) throw (Exception::FileNotFound,Exception::ParseError) |
setter for FASTA file | |
virtual String | getFastaFile () |
getter for FASTA file | |
virtual void | setSpectrum (const std::vector< float > &) throw (Exception::NotImplemented) |
setter for spectrum | |
virtual const std::vector < float > & | getSpectrum () throw (Exception::NotImplemented) |
getter for spectrum | |
virtual void | setTolerance (float) throw (Exception::NotImplemented) |
setter for tolerance | |
virtual float | getTolerance () throw (Exception::NotImplemented) |
getter for tolerance | |
virtual bool | begin () throw (Exception::InvalidIterator) |
initializing of iterator | |
virtual bool | isAtEnd () |
indicates whether iterator is at end | |
Static Public Member Functions | |
static const std::string | getName () |
needed by FactoryProduct | |
static PepIterator * | create () |
needed by FactoryProduct | |
Protected Attributes | |
String | fasta_file_ |
location of the fasta file | |
std::vector< FASTAEntry > | entrys_ |
content of fasta file | |
std::vector< FASTAEntry >::iterator | it_ |
iterator over fasta file content |
typedef std::pair<String,String> FASTAEntry |
Reimplemented from PepIterator.
constructor
FastaIteratorIntern | ( | const FastaIteratorIntern & | ) |
copy constructor
virtual ~FastaIteratorIntern | ( | ) | [virtual] |
constructor
virtual FASTAEntry operator * | ( | ) | throw (Exception::InvalidIterator) [virtual] |
* Operator for derefering of iterator
Exception::InvalidIterator | if iterator has not been initialized |
Implements PepIterator.
virtual PepIterator& operator++ | ( | ) | throw (Exception::InvalidIterator) [virtual] |
++ Operator for the iterator
Exception::InvalidIterator | if iterator has not been initialized |
Implements PepIterator.
virtual PepIterator* operator++ | ( | int | i | ) | throw (Exception::InvalidIterator) [virtual] |
++ Operator for the iterator
Exception::InvalidIterator | if iterator has not been initialized |
Implements PepIterator.
virtual void setFastaFile | ( | const String & | f | ) | throw (Exception::FileNotFound,Exception::ParseError) [virtual] |
setter for FASTA file
f | const String reference representing file location |
Exception::FileNotFound | ||
Exception::ParseError |
Implements PepIterator.
virtual String getFastaFile | ( | ) | [virtual] |
virtual void setSpectrum | ( | const std::vector< float > & | ) | throw (Exception::NotImplemented) [inline, virtual] |
setter for spectrum
Exception::NotImplemented |
Implements PepIterator.
virtual const std::vector<float>& getSpectrum | ( | ) | throw (Exception::NotImplemented) [inline, virtual] |
getter for spectrum
Exception::NotImplemented |
Implements PepIterator.
virtual void setTolerance | ( | float | ) | throw (Exception::NotImplemented) [inline, virtual] |
setter for tolerance
t | tolerance value |
Exception::NotImplemented |
Implements PepIterator.
virtual float getTolerance | ( | ) | throw (Exception::NotImplemented) [inline, virtual] |
getter for tolerance
Exception::NotImplemented |
Implements PepIterator.
virtual bool begin | ( | ) | throw (Exception::InvalidIterator) [virtual] |
initializing of iterator
Exception::InvalidIterator | if fastaFile was not set |
Implements PepIterator.
virtual bool isAtEnd | ( | ) | [virtual] |
indicates whether iterator is at end
Implements PepIterator.
static const std::string getName | ( | ) | [inline, static] |
static PepIterator* create | ( | ) | [inline, static] |
String fasta_file_ [protected] |
location of the fasta file
std::vector<FASTAEntry > entrys_ [protected] |
content of fasta file
std::vector<FASTAEntry >::iterator it_ [protected] |
iterator over fasta file content
Generated Tue Apr 1 15:36:44 2008 -- using doxygen 1.5.4 | OpenMS / TOPP 1.1 |