File List

Here is a list of all documented files with brief descriptions:

[detail level 12345678910]

▼ builds
▼ workspace
▼ publish-doc-api-gitlab
▼ gatb-core
▼ src
▼ gatb
▼ bank
▼ api
IAlphabet.hpp	Interface definition for genomic alphabets
IBank.hpp	Interface definition for genomic databases management
Sequence.hpp	Definition of what a genomic sequence is
▼ impl
AbstractBank.hpp	Abstract implementation of the IBank interface
Alphabet.hpp	Implementation for genomic alphabets
Bank.hpp	User front end for opening genomic banks in a generic way
BankAlbum.hpp	Bank format that holds other banks URI
BankBinary.hpp	Binary bank format
BankComposite.hpp	Composite bank, ie. a bank made of other banks
BankConverterAlgorithm.hpp	Bank conversion from one IBank to another IBank
BankFasta.hpp	FASTA bank format
BankHelpers.hpp	Helpers for managing IBank objects
BankRandom.hpp	Random bank format
Banks.hpp	Include all IBank implementations
BankSplitter.hpp	Interface definition for genomic databases management
BankStrings.hpp	Hard coded genomic bank (mainly for tests)
▼ debruijn
▼ api
IContainerNode.hpp	Container interface
▼ impl
BranchingAlgorithm.hpp	Algorithm that computes the branching nodes of a De Bruijn graph
ContainerNode.hpp	Container implementation
Graph.hpp	Graph class
▼ kmer
▼ api
IModel.hpp	Interface definition for the kmer model
▼ impl
BankKmerIterator.hpp	Kmer iterator on sequences of a bank
BankKmers.hpp	Kmer iterator on sequences of a bank
BloomAlgorithm.hpp	Bloom algorithm, ie. compute a Bloom filter from a set of reads
BloomBuilder.hpp	Build bloom filter from an iterator of kmers
DebloomAlgorithm.hpp	Debloom algorithm, ie. compute false positive sets for a Bloom filter
DebloomAlgorithmFactory.hpp	Factory for Debloom algorithms
DebloomMinimizerAlgorithm.hpp	Debloom algorithm, ie. compute false positive sets for a Bloom filter
LinearCounter.hpp	Linear counter for kmers using a bloom
Model.hpp	Kmer management
RepartitionAlgorithm.hpp	Repartition algorithm, ie. compute statistics on kmers
Sequence2SuperKmer.hpp
SortingCountAlgorithm.hpp	Counting kmers from a set of sequences
▼ system
▼ api
Exception.hpp	Operating System common abstraction
IFileSystem.hpp	Operating System abstraction for file system management
IMemory.hpp	Implementation of an abstraction for dynamic memory allocation
ISmartPointer.hpp	Smart Pointer Design Pattern interface
ISystemInfo.hpp	Interface providing information about the operating system
IThread.hpp	Interface for threads
ITime.hpp	Interface for time retrieval
types.hpp	Types definition for GATB
▼ impl
FileSystemCommon.hpp	Implementations common to various OS
FileSystemLinux.hpp	Implementation for Linux
FileSystemMacos.hpp	Implementation for MacOs
MemoryCommon.hpp	Implementations common to various OS
System.hpp	Entry point class for accessing operating system operations
SystemInfoCommon.hpp	Implementations common to various OS
ThreadLinux.hpp	Thread management for Linux
ThreadMacos.hpp	Thread management for Macos
TimeCommon.hpp	Implementations common to various OS
▼ tools
▼ collections
► api
Bag.hpp	Bag interface
Collection.hpp	Collection interface
Container.hpp	Container interface
Iterable.hpp	Iterable interface
► impl
BagCache.hpp	Bag implementation as a cache for a referred Bag
BagFile.hpp	Bag implementation for file
BagPartition.hpp	Bag partition implementation for file
Bloom.hpp	Bloom implementation
BloomGroup.hpp	Bloom Group implementation
BooPHF.hpp	Minimal Perfect Hash Function from Guillaume
CollectionAbstract.hpp	Collection interface
CollectionCache.hpp	Collection interface
ContainerSet.hpp	Container implementation
Hash16.hpp	Hash function
IterableHelpers.hpp	Helpers class for iterable concept
IteratorFile.hpp	Iterator implementation for file
MapMPHF.hpp	Minimal Perfect Hash Function
OAHash.hpp	Container implementation
▼ designpattern
► api
ICommand.hpp	Interface for command concept
IObserver.hpp	Smart Pointer Design Pattern definition
Iterator.hpp	Smart Pointer Design Pattern definition
► impl
Command.hpp	Implementation of ICommand and IDispatcher
IteratorHelpers.hpp	Some helper classes for iteration
Observer.hpp	Implementation of INode interface
▼ math
FastMinimizer.hpp	Fast computation of lexicographical minimizers wtih no-AA-inside constraint
Integer.hpp	Entry point class for large integer usage
LargeInt.hpp	Class that manages large integers
NativeInt128.hpp	Integer class relying on native 128 bits integer type
NativeInt16.hpp	Integer class relying on native u_int16_t type
NativeInt32.hpp	Integer class relying on native u_int32_t type
NativeInt64.hpp	Integer class relying on native u_int64_t type
NativeInt8.hpp	Integer class relying on native u_int8_t type
▼ misc
► api
Abundance.hpp	Abundance definition
Data.hpp	Data structure
Enums.hpp	Enumerations
IHistogram.hpp	Interface for histogram (something counting abundances)
IOptionsParser.hpp	Tool for parsing command line arguments
IProperty.hpp	Interface for properties, ie. list of tag values with hierarchical feature
Macros.hpp	Several macros for every day work
Range.hpp	Iterable interface
StringsRepository.hpp	Pool of strings providing information to end users
Vector.hpp	Vector implementation
► impl
Algorithm.hpp	Tool framework
Histogram.hpp	Histogram feature
HostInfo.hpp
LibraryInfo.hpp
OptionsParser.hpp	Tool for parsing command line arguments
Pool.hpp	Tool for pooling objects
Progress.hpp	Progress feature
Property.hpp	Progress feature
Stringify.hpp	Tool framework
StringLine.hpp	Tool framework
TimeInfo.hpp	Tool for time measurement feature
Tokenizer.hpp	String Tokenizer
Tool.hpp	Tool framework
XmlReader.hpp	XML parsing
▼ storage
► api
ICell.hpp	Node
► impl
Cell.hpp	Implementation of INode interface
CollectionFile.hpp	Collection interface
CollectionHDF5.hpp	Collection interface
CollectionHDF5Patch.hpp	Collection interface
Storage.hpp	Storage interface
StorageFile.hpp	Collection interface
StorageHDF5.hpp	Collection interface
StorageTools.hpp	Collection interface
gatb_core.hpp	Global header file