OpenMS
2.6.0
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This class serves for reading in and writing FASTA files. More...
#include <OpenMS/FORMAT/FASTAFile.h>
Classes | |
struct | FASTAEntry |
FASTA entry type (identifier, description and sequence) More... | |
Public Member Functions | |
FASTAFile () | |
Default constructor. More... | |
virtual | ~FASTAFile () |
Destructor. More... | |
void | readStart (const String &filename) |
Prepares a FASTA file given by 'filename' for streamed reading using readNext(). More... | |
bool | readNext (FASTAEntry &protein) |
Reads the next FASTA entry from file. More... | |
std::streampos | position () const |
current stream position More... | |
bool | atEnd () const |
is stream at EOF? More... | |
bool | setPosition (const std::streampos &pos) |
seek stream to pos More... | |
void | writeStart (const String &filename) |
Prepares a FASTA file given by 'filename' for streamed writing using writeNext(). More... | |
void | writeNext (const FASTAEntry &protein) |
Stores the data given by protein . Call writeStart() once before calling writeNext(). More... | |
void | writeEnd () |
Closes the file (flush). Called implicitly when FASTAFile object does out of scope. More... | |
Static Public Member Functions | |
static void | load (const String &filename, std::vector< FASTAEntry > &data) |
loads a FASTA file given by 'filename' and stores the information in 'data' More... | |
static void | store (const String &filename, const std::vector< FASTAEntry > &data) |
stores the data given by 'data' at the file 'filename' More... | |
Protected Attributes | |
std::fstream | infile_ |
filestream for reading; init using FastaFile::readStart() More... | |
std::ofstream | outfile_ |
filestream for writing; init using FastaFile::writeStart() More... | |
std::unique_ptr< void, std::function< void(void *) > > | reader_ |
filestream for reading; init using FastaFile::readStart(); needs to be a pointer, since its not copy-constructable; we use void* here, to avoid pulling in seqan includes More... | |
Size | entries_read_ |
some internal book-keeping during reading More... | |
This class serves for reading in and writing FASTA files.
If the protein/gene sequence contains unusual symbols (such as translation end (*)), they will be kept!
You can use aggregate methods load() and store() to read/write a set of protein sequences at the cost of memory.
Or use single read/write of protein sequences using readStart(), readNext() and writeStart(), writeNext(), writeEnd() for more memory efficiency. Reading from one and writing to another FASTA file can be handled by one single FASTAFile instance.
FASTAFile | ( | ) |
Default constructor.
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virtual |
Destructor.
bool atEnd | ( | ) | const |
is stream at EOF?
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static |
loads a FASTA file given by 'filename' and stores the information in 'data'
This uses more RAM than readStart() and readNext().
Exception::FileNotFound | is thrown if the file does not exists. |
Exception::ParseError | is thrown if the file does not suit to the standard. |
Referenced by NucleicAcidSearchEngine::main_().
std::streampos position | ( | ) | const |
current stream position
bool readNext | ( | FASTAEntry & | protein | ) |
Reads the next FASTA entry from file.
If you want to read all entries in one go, use load().
Exception::FileNotFound | is thrown if the file does not exists. |
Exception::ParseError | is thrown if the file does not suit to the standard. |
void readStart | ( | const String & | filename | ) |
Prepares a FASTA file given by 'filename' for streamed reading using readNext().
Exception::FileNotFound | is thrown if the file does not exists. |
Exception::ParseError | is thrown if the file does not suit to the standard. |
bool setPosition | ( | const std::streampos & | pos | ) |
seek stream to pos
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static |
stores the data given by 'data' at the file 'filename'
This uses more RAM than writeStart() and writeNext().
Exception::UnableToCreateFile | is thrown if the process is not able to write the file. |
void writeEnd | ( | ) |
Closes the file (flush). Called implicitly when FASTAFile object does out of scope.
void writeNext | ( | const FASTAEntry & | protein | ) |
Stores the data given by protein
. Call writeStart() once before calling writeNext().
Call writeEnd() when done to close the file!
Exception::UnableToCreateFile | is thrown if the process is not able to write the file. |
void writeStart | ( | const String & | filename | ) |
Prepares a FASTA file given by 'filename' for streamed writing using writeNext().
Exception::UnableToCreateFile | is thrown if the process is not able to write to the file (disk full?). |
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protected |
some internal book-keeping during reading
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protected |
filestream for reading; init using FastaFile::readStart()
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protected |
filestream for writing; init using FastaFile::writeStart()
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protected |
filestream for reading; init using FastaFile::readStart(); needs to be a pointer, since its not copy-constructable; we use void* here, to avoid pulling in seqan includes