OpenMS  2.8.0
Classes | Namespaces
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.
 

Class Documentation

◆ OpenMS::DecoyHelper::Result

struct OpenMS::DecoyHelper::Result
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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