Iterator for a FASTA file. More...
#include <OpenMS/FORMAT/FastaIteratorIntern.h>
Public Types | |
| typedef std::pair< String, String > | FASTAEntry |
Public Member Functions | |
| FastaIteratorIntern () | |
| constructor | |
| FastaIteratorIntern (const FastaIteratorIntern &) | |
| copy constructor | |
| virtual | ~FastaIteratorIntern () |
| constructor | |
| virtual FASTAEntry | operator* () |
| * Operator for derefering of iterator | |
| virtual PepIterator & | operator++ () |
| ++ Operator for the iterator | |
| virtual PepIterator * | operator++ (int i) |
| ++ Operator for the iterator | |
| virtual void | setFastaFile (const String &f) |
| setter for FASTA file | |
| 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 std::string | getProductName () |
| needed by Factory | |
| static PepIterator * | create () |
| needed by Factory | |
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 | |
Detailed Description
Iterator for a FASTA file.
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.
- See also:
- FastaIterator
Member Typedef Documentation
| typedef std::pair<String, String> FASTAEntry |
Reimplemented from PepIterator.
Constructor & Destructor Documentation
constructor
| FastaIteratorIntern | ( | const FastaIteratorIntern & | ) |
copy constructor
| virtual ~FastaIteratorIntern | ( | ) | [virtual] |
constructor
Member Function Documentation
| virtual bool begin | ( | ) | [virtual] |
initializing of iterator
- Returns:
- true if everything went rigth
- Exceptions:
-
Exception::InvalidIterator if fastaFile was not set
Implements PepIterator.
| static PepIterator* create | ( | ) | [inline, static] |
needed by Factory
- Returns:
- poiter to new object
| virtual String getFastaFile | ( | ) | [virtual] |
| static const std::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 availeble for FastaIterator
- Exceptions:
-
Exception::NotImplemented
Implements PepIterator.
| virtual DoubleReal getTolerance | ( | ) | [inline, virtual] |
getter for tolerance
- Note:
- note availeble for FastaIterator
- Returns:
- tolerance
- Exceptions:
-
Exception::NotImplemented
Implements PepIterator.
| virtual bool isAtEnd | ( | ) | [virtual] |
indicates whether iterator is at end
- Returns:
- bool true if interator is at end
Implements PepIterator.
| virtual FASTAEntry operator* | ( | ) | [virtual] |
* Operator for derefering of iterator
- Returns:
- FASTEEntry iterator at actual position
- Exceptions:
-
Exception::InvalidIterator if iterator has not been initialized
Implements PepIterator.
| virtual PepIterator* operator++ | ( | int | i | ) | [virtual] |
++ Operator for the iterator
- Returns:
- pointer to PepIterator
- Exceptions:
-
Exception::InvalidIterator if iterator has not been initialized
Implements PepIterator.
| virtual PepIterator& operator++ | ( | ) | [virtual] |
++ Operator for the iterator
- Returns:
- reference to PepIterator
- Exceptions:
-
Exception::InvalidIterator if iterator has not been initialized
Implements PepIterator.
| virtual void setFastaFile | ( | const String & | f | ) | [virtual] |
setter for FASTA file
- Parameters:
-
f const String reference representing file location
- Exceptions:
-
Exception::FileNotFound Exception::ParseError
Implements PepIterator.
| virtual void setSpectrum | ( | const std::vector< DoubleReal > & | ) | [inline, virtual] |
setter for spectrum
- Note:
- note availeble for FastaIterator
- Exceptions:
-
Exception::NotImplemented
Implements PepIterator.
| virtual void setTolerance | ( | DoubleReal | ) | [inline, virtual] |
setter for tolerance
- Note:
- note availeble for FastaIterator
- Exceptions:
-
Exception::NotImplemented
Implements PepIterator.
Member Data Documentation
std::vector<FASTAEntry> entrys_ [protected] |
content of fasta file
String fasta_file_ [protected] |
location of the fasta file
std::vector<FASTAEntry>::iterator it_ [protected] |
iterator over fasta file content
| OpenMS / TOPP release 1.10.0 | Documentation generated on Thu Mar 7 2013 09:42:53 using doxygen 1.7.1 |