Iterator over FASTA file. More...
#include <OpenMS/FORMAT/FastaIterator.h>
Inheritance diagram for FastaIterator:
Public Types | |
| typedef std::pair< String, String > | FASTAEntry |
Public Member Functions | |
| FastaIterator () | |
| constructor | |
| virtual | ~FastaIterator () |
| destructor | |
| virtual FASTAEntry | operator* () |
| * operator for getting the iterator's value | |
| virtual PepIterator & | operator++ () |
| pre-increment Operator for the iterator | |
| virtual PepIterator * | operator++ (int i) |
| post-increment Operator for the iterator | |
| virtual void | setFastaFile (const String &f) |
| setter for FASTAfile | |
| virtual String | getFastaFile () |
| getter for FASTA file | |
| virtual void | setSpectrum (const std::vector< DoubleReal > &) |
| setter for spectrum | |
| virtual const std::vector < DoubleReal > & | getSpectrum () |
| getter for spectrum | |
| virtual void | setTolerance (DoubleReal) |
| setter for tolerance | |
| virtual DoubleReal | getTolerance () |
| getter for tolerance | |
| virtual bool | begin () |
| initializing of iterator | |
| virtual bool | isAtEnd () |
| indicates whether iterator is at end | |
Static Public Member Functions | |
| static const String | getProductName () |
| needed by Factory | |
| static PepIterator * | create () |
| needed by Factory | |
Protected Member Functions | |
| virtual std::string | next_ () |
| gets the next string | |
Protected Attributes | |
| bool | is_at_end_ |
| bool indicated whether iterator is at end | |
| std::ifstream | input_file_ |
| input file | |
| String | fasta_file_ |
| fasta file location | |
| std::string | actual_seq_ |
| actual sequence | |
| std::string | header_ |
| actual fasta header | |
| std::string | last_header_ |
| last fasta header | |
Private Member Functions | |
| FastaIterator (const FastaIterator &) | |
| copy constructor | |
| FastaIterator & | operator= (const FastaIterator &) |
| Assignment. | |
Detailed Description
Iterator over FASTA file.
Iterates over FASTA file without loading it into memory. It holds just one entry in memory.
- See also:
- FastaIteratorIntern.h
Member Typedef Documentation
| typedef std::pair<String, String> FASTAEntry |
Reimplemented from PepIterator.
Constructor & Destructor Documentation
| FastaIterator | ( | ) |
constructor
| virtual ~FastaIterator | ( | ) | [virtual] |
destructor
| FastaIterator | ( | const FastaIterator & | ) | [private] |
copy constructor
Member Function Documentation
| virtual bool begin | ( | ) | [virtual] |
initializing of iterator
- Returns:
- true if everything went right
- Exceptions:
-
Exception::InvalidIterator if fastaFile was not set
Implements PepIterator.
| static PepIterator* create | ( | ) | [inline, static] |
needed by Factory
- Returns:
- pointer 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
- Note:
- note available for FastaIterator
- Exceptions:
-
Exception::NotImplemented
Implements PepIterator.
| virtual DoubleReal getTolerance | ( | ) | [inline, virtual] |
getter for tolerance
- Note:
- note available for FastaIterator
- Returns:
- tolerance
- Exceptions:
-
Exception::NotImplemented
Implements PepIterator.
| virtual bool isAtEnd | ( | ) | [virtual] |
indicates whether iterator is at end
- Returns:
- bool true if iterator is at end
Implements PepIterator.
| virtual std::string next_ | ( | ) | [protected, virtual] |
gets the next string
- Returns:
- string
| virtual FASTAEntry operator* | ( | ) | [virtual] |
* operator for getting the iterator's value
- Returns:
- FASTAEntry
- Exceptions:
-
InvalidIterator if iterator was not initialized
Implements PepIterator.
| virtual PepIterator& operator++ | ( | ) | [virtual] |
pre-increment Operator for the iterator
- Returns:
- reference to PepIterator
- Exceptions:
-
Exception::InvalidIterator if iterator was not initialized
Implements PepIterator.
| virtual PepIterator* operator++ | ( | int | i | ) | [virtual] |
post-increment Operator for the iterator
- Returns:
- pointer to PepIterator
- Exceptions:
-
Exception::InvalidIterator if iterator was not initialized
Implements PepIterator.
| FastaIterator& operator= | ( | const FastaIterator & | ) | [private] |
Assignment.
| virtual void setFastaFile | ( | const String & | f | ) | [virtual] |
setter for FASTAfile
- Parameters:
-
f Name of the fasta file
- Exceptions:
-
Exception::FileNotFound ParseError is thrown if the file could not be parsed
Implements PepIterator.
| virtual void setSpectrum | ( | const std::vector< DoubleReal > & | ) | [inline, virtual] |
setter for spectrum
- Note:
- note available for FastaIterator
- Exceptions:
-
Exception::NotImplemented
Implements PepIterator.
| virtual void setTolerance | ( | DoubleReal | ) | [inline, virtual] |
setter for tolerance
- Note:
- note available for FastaIterator
- Exceptions:
-
Exception::NotImplemented
Implements PepIterator.
Member Data Documentation
std::string actual_seq_ [protected] |
actual sequence
String fasta_file_ [protected] |
fasta file location
std::string header_ [protected] |
actual fasta header
std::ifstream input_file_ [protected] |
input file
bool is_at_end_ [protected] |
bool indicated whether iterator is at end
std::string last_header_ [protected] |
last fasta header
| OpenMS / TOPP release 1.10.0 | Documentation generated on Thu Mar 7 2013 09:42:53 using doxygen 1.7.1 |