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< double > &) |
setter for spectrum More... | |
virtual const std::vector< double > & | getSpectrum () |
getter for spectrum More... | |
virtual void | setTolerance (double) |
setter for tolerance More... | |
virtual double | 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
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virtual |
destructor
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private |
copy constructor
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virtual |
initializing of iterator
Exception::InvalidIterator | if fastaFile was not set |
Implements PepIterator.
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inlinestatic |
needed by Factory
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virtual |
|
inlinestatic |
needed by Factory
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inlinevirtual |
getter for spectrum
Exception::NotImplemented |
Implements PepIterator.
|
inlinevirtual |
getter for tolerance
Exception::NotImplemented |
Implements PepIterator.
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virtual |
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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.
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private |
Assignment.
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virtual |
setter for FASTAfile
f | Name of the fasta file |
Exception::FileNotFound | |
ParseError | is thrown if the file could not be parsed |
Implements PepIterator.
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inlinevirtual |
setter for spectrum
Exception::NotImplemented |
Implements PepIterator.
|
inlinevirtual |
setter for tolerance
Exception::NotImplemented |
Implements PepIterator.
|
protected |
actual sequence
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protected |
fasta file location
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protected |
actual fasta header
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protected |
input file
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protected |
bool indicated whether iterator is at end
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protected |
last fasta header
OpenMS / TOPP release 2.3.0 | Documentation generated on Tue Jan 9 2018 18:22:08 using doxygen 1.8.13 |