FASTAContainer.h File Reference

#include <OpenMS/CONCEPT/Exception.h>
#include <OpenMS/CONCEPT/LogStream.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/DATASTRUCTURES/ListUtils.h>
#include <OpenMS/DATASTRUCTURES/StringUtilsSimple.h>
#include <OpenMS/FORMAT/FASTAFile.h>
#include <functional>
#include <fstream>
#include <unordered_map>
#include <memory>
#include <utility>
#include <vector>
#include <boost/regex.hpp>

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Classes
class	FASTAContainer< TFI_File >
	FASTAContainer<TFI_File> will make FASTA entries available chunk-wise from start to end by loading it from a FASTA file. This avoids having to load the full file into memory. While loading, the container will memorize the file offsets of each entry, allowing to read an arbitrary i'th entry again from disk. If possible, only entries from the currently cached chunk should be queried, otherwise access will be slow. More...
class	FASTAContainer< TFI_Vector >
	FASTAContainer<TFI_Vector> simply takes an existing vector of FASTAEntries and provides the same interface with a potentially huge speed benefit over FASTAContainer<TFI_File> since it does not need disk access, but at the cost of memory. More...
class	DecoyHelper
	Helper class for calculations on decoy proteins. More...
struct	DecoyHelper::Result

Namespaces
	OpenMS
	Main OpenMS namespace.

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Class Documentation

OpenMS::DecoyHelper::Result

struct OpenMS::DecoyHelper::Result

Collaboration diagram for DecoyHelper::Result:

Class Members
bool	is_prefix	on success, was it a prefix or suffix
String	name	on success, what was the decoy string?
bool	success	did more than 40% of proteins have the *same* prefix or suffix