Class List

Here are the classes, structs, unions and interfaces with brief descriptions:

[detail level 1234567]

▼Ndag
Cdag_vector
Crank_vector
▼Ngatb
▼Ncore	Core package of the GATP project
▼Nbank	Package for genomic databases management
►Nimpl	Implementation for genomic databases management
CAbstractBank	Abstract implementation of IBank for factorizing common behavior
CBank	Front end for managing IBank objects
CBankAlbum	Genomic bank file made of a list of other bank files URI
►CBankBinary	Implementation of IBank for compressed format
CIterator	Specific Iterator impl for BankBinary class
CBankComposite	IBank implementation for composite banks
CBankConverterAlgorithm	Algorithm implementation that converts a bank into a binary one
CBankDelegate	Bank implementation that delegates work to a referred bank
►CBankFasta	Implementation of IBank for FASTA format
CIterator	Specific Iterator impl for Bank class
CBankFiltered	Bank that can filter sequences through a provided functor
CBankHelper	Utility class holding useful methods for bank management
CBankRandom	Implementation of IBank for random banks
CBankSplitter	Split a given bank in pieces
CBankStrings	IBank defined by constant strings
CIBank	Interface for what we need to read genomic databases
CIBankFactory	Factory for IBank
CSequence	Structure holding genomic information
▼Ndebruijn	Package for De Bruijn graph management
►Nimpl	Implementation package for De Bruijn graph management
CBranchingAlgorithm	Computation of the branching nodes of a Graph
CBranchingEdge_t	Specific Edge structure representing a transition between two branching nodes
CBranchingNode_t	Specific Node structure representing a branching node in the De Bruijn graph
CBranchingTerminatorTemplate	Implementation of Terminator that marks branching nodes
CContainerNode	IContainerNode implementation with a Bloom filter and a cFP set
CContainerNodeCascading	IContainerNode implementation with cascading Bloom filters
CContainerNodeNoCFP	IContainerNode implementation with a Bloom filter
CEdge_t	Definition of an Edge, ie a transition between two nodes in the De Bruijn graph
CFunctorSetVariant
CGraphTemplate	Class representing a De Bruijn graph
CGraphUnitigsTemplate	Class representing a De Bruijn graph based on unitigs
CIterativeExtensions	Class providing helpers for graph traversal
CMonumentTraversalTemplate	Implementation of Traversal that produces contigs
CMPHFTerminatorTemplate	MPHF implementation of Terminator
CNode_t	Node structure representing a node in the De Bruijn graph
CNullTerminatorTemplate	Null implementation of Terminator
CNullTraversalTemplate	Null implementation of Traversal
CPath_t	Structure representing a path in the De Bruijn graph
CSimpleNode	Specific Node structure representing a simple node in the De Bruijn graph
CSimplePathsTraversalTemplate	Implementation of Traversal that produces unitigs
CTerminatorTemplate	Interface that allows to mark certain nodes in a graph. Note: It is on the verge of becoming deprecated
CTraversalTemplate	Class that traverse nodes of a Graph
CUnitigsConstructionAlgorithm	Computation of the unitigs of a Graph, using BCALM 2
CIContainerNode	Container interface
▼Nkmer	Package for genomic databases management
►Nimpl	Implementation for genomic databases management
CBankKmers	Bank whose sequences are all the possible kmers of a kmer model
CBankStats	Statistics about banks
CBloomBuilder	Helper that builds a Bloom filter from an iterator of kmers
CCounterBuilder	Class that counts the number of occurrences of a kmer in several banks
CCountProcessorAbstract
CCountProcessorChain
CCountProcessorCustomProxy
CCountProcessorCutoff
CCountProcessorDump
CCountProcessorDumpKff
CCountProcessorHistogram
CCountProcessorSolidityAbstract
CDebloomAlgorithm	Construction of the set of critical false positives nodes
►CKmer	Entry point for kmer management
CCount	Structure associating a kmer value with an abundance value
CKmerCanonical	Kmer type for the ModelCanonical class
CKmerDirect	Kmer type for the ModelDirect class
CKmerMinimizer	Kmer type for the ModelMinimizer class
CModelAbstract
CModelCanonical	Model that handles "canonical" kmers, ie the minimum value of the direct kmer and its reverse complement
CModelDirect	Model that handles "direct" kmers, ie sequences of nucleotides. The associated value of such a kmer is computed as a polynom P(X) with X=4 and where the coefficients are in [0..3]. By convention, we use A=0, C=1, T=2 and G=3
CModelMinimizer	Model that handles kmers of the Model type + a minimizer
CMPHFAlgorithm	Algorithm that builds a hash table whose keys are kmers and values are kmer abundances
CPartiInfo
CRepartitor
CSortingCountAlgorithm	Class performing the kmer counting (also known as 'DSK')
CICountProcessor	Interface that uses kmer counting information
▼Nsystem	Operating System abstraction layer
►Nimpl	Implementation of Operating System abstraction layer
CCommonFile	Default implementation of IFile interface
CCpuInfoCommon	Interface providing a way to get CPU usage information
CFileSystemCommon	Default implementation
CFileSystemLinux	Default implementation
CFileSystemMacos	Default implementation
CMemoryAllocatorStdlib	Implementation of IMemoryAllocator interface using standard system functions
CMemoryBounded	Implementation of IMemory interface with bounded memory usage
CMemoryCommon	Common implementation of IMemory interface
CMemoryOperationsCommon	Implementation of IMemoryOperations interface using standard system functions
CMemorySizeStore	Implementation of IMemory interface with Proxy design pattern
CSystem	Entry point providing access to operating system resources
CSystemInfoCommon	Abstract class for ISystemInfo interface
CSystemInfoLinux	Linux implementation for ISystemInfo interface
CSystemInfoMacos	MacOs implementation for ISystemInfo interface
CSystemInfoWindows	Windows implementation for ISystemInfo interface
CThreadFactoryLinux	Factory that creates IThread instances
CThreadFactoryMacos	Factory that creates IThread instances
CThreadGroup	Implementation of IThreadGroup
CThreadObject	Facility to share a common resource between several threads
CTimeAbstract	Abstract implementation of ITime interface
CTimeCycle	Implementation of ITime interface
CTimeSystem	Implementation of ITime interface
CException	Exception class for operating system failures
CExceptionComposite	Composite exception
CExceptionErrno	Exception class with information got from strerror_r
CExceptionNotImplemented	Exception class for lack of implementation
CIFile	Abstraction of what we need about file
CIFileSystem	Interface for some operations at file system level
CIMemory	Interface providing methods for dynamic allocation and memory statistics
CIMemoryAllocator	Interface providing methods for dynamic allocation
CIMemoryComponent	Interface providing methods for getting memory usage by a component
CIMemoryOperations	Interface providing methods for manipulating memory blocks
CISmartPointer	Tool for managing instances life cycle
CISynchronizer	Define a synchronization abstraction
►CISystemInfo	Interface providing some general information about the system
CCpuInfo	Interface providing a way to get CPU usage information
CIThread	Define what a thread is
CIThreadFactory	Factory that creates IThread instances
CIThreadGroup	Interface that defines a group of threads
CITime	Interface that provides methods returning time information
CLocalObject	Local usage of SmartPointer instance
CLocalSynchronizer	Tool for locally managing synchronization
CSmartPointer	Implementation of the ISmartPointer interface
▼Ntools	Tools package
►Ncollections	Collections interfaces
►Nimpl
CAdaptatorDefault
CBagCache	Bag implementation as a cache to a referred Bag instance
CBagCacheSorted	Bag implementation as a cache to a referred Bag instance
CBagCacheSortedBuffered	Bag implementation as a cache to a referred Bag instance
CBagFile	Bag implementation for file
CBloom	Bloom filter implementation
CBloomCacheCoherent	Bloom filter implementation with CPU cache consideration
CBloomContainer	Bloom filter implementation
CBloomExtendedNeighborCoherent	Bloom filter implementation with cache consideration
CBloomFactory	Factory that creates IBloom instances
CBloomNeighborCoherent	Bloom filter implementation with cache consideration
CBloomNull	Bloom filter null implementation
CBloomSynchronized	Bloom filter implementation with synchronization
CBooPHF	Minimal Perfect Hash Function
CCollectionAbstract	Abstract implementation of the Collection interface
CCollectionCache	Cache implementation of the Collection interface
CCollectionCacheSorted	Cache implementation of the Collection interface
CContainerSet	Implementation of the Container interface
CHash16	Class providing hash table service with a given memory max usage
CHashFunctors	Define a set of hash functions
CIBloom	Bloom interface
CIterableAdaptor	Adaptor of an Iterable<T1> into an Iterable<T2>
CIterableFile	Implementation of the Iterable interface as a file
CIterableHelpers	Some helper methods for Iterable objects
CIteratorFile	Iterator implementation for file
CMapMPHF	Hash table implementation
COAHash	Hash table implementation
CProgressIterator	Iterator with progress information
CBag	Bag interface
CCollection	Collection interface
CContainer	Container interface
CIterable	Iterable interface
►Ndp	Design Patterns concepts
►Nimpl
CAbstractSubjectIterator	Factorization of code for the subject part of the Observer pattern
CCancellableIterator	Iterator that can be cancelled at some point during iteration
CCompositeIterator	Composite iterator
CCompoundIterator	Iterator that gather two iterators in a single loop
CDispatcher	Launches commands in different threads
CFilterIterator	Iterator that filters out some iterated items
CIteratorAdaptor	Iterator adaptation from one type to another one
CListIterator	Iterator that loops over std::list
CNullIterator	Null implementation of the Iterator interface
CPairedIterator	Iterator over two iterators
CProductIterator	Iterator over two iterators
CSerialDispatcher	Launches commands in current thread
CSTLIterator	TO BE DONE..
CSubject	Class that notifies potential observers
CSubjectIterator	Iterator that notifies some listener during iteration
CTruncateIterator	Iterator that truncate the number of iterations if needed
CEventInfo	Piece of information linked to a notification
CICommand	Interface of what a command is
CIDispatcher	Dispatching of commands
CIObserver	Interface of the Observer Design Pattern
CISubject	Interface of the Subject in the Observer Design Pattern
CIterator	Definition of the Design Pattern Iterator interface
CIteratorListener	Interface for listening to iteration progress
►Nmath	Math package
CIntegerTemplate	Class for large integers calculus
CLargeIntDummy	Large integer class
►Nmisc	Misc interfaces
►Nimpl
CAlgorithm	Framework class for implementing algorithm
CArgData
CHierarchyParserVisitor	Visitor that iterates children of an OptionsParser instance
CHistogram	Basic implementation of the IHistogram interface
CHistogramCache	Cached implementation of the IHistogram interface
CHistogramNull	Null implementation of the IHistogram interface
CHostInfo	Host information
CLibraryInfo	Framework class for implementing tools (ie. binary tools)
CLocalTimeInfo	Helper for time info statistics
COption	Implementation of the IOptionsParser interface
COptionFailure	Exception class to be used for option management error
COptionNoParam	Option that has no argument
COptionOneParam	Option that has one argument
COptionsHelpVisitor	Visitor that display help
COptionsParser	Implementation of the IOptionsParser interface
CProgress	Progress information display feature
CProgressNone	Null implementation of IteratorListener
CProgressTimer	Progress information display feature with timing information
CProgressTimerAndSystem	Progress information display feature with timing and system information
CProperties	Implementation of IProperties interface
CRawDumpPropertiesVisitor	Raw dump of a IProperties instance
CStringify	String helper for using printf-like formats
CStringLine	String line formatter
CTimeInfo	Tool for time statistics
CTokenizerIterator	String tokenizer as an Iterator
CTool	Framework abstract class for implementing tools (ie. binary tools)
CVisibilityOptionsVisitor	Visitor that sets the visibility for a list of options
CXmlDumpPropertiesVisitor	XML serialization of a IProperties instance
CXmlReader	Simple implementation of an XML (SAX) parser
CAbundance	Define a type that associates a value and an abundance
CArrayData	Define a specific kind of array
►CData	Definition of a data chunk
CConvertASCII
CIHistogram	Interface for kmers distribution management
►CIOptionsParser	Parser interface that analyzes command line options
CResult
CIOptionsParserVisitor
CIProperties	Container of IProperty instances with DP Visitor capability
CIPropertiesVisitor
CIProperty	Definition of a property as a [key,value] entry with a given depth
CVector	Vector class allowing to define vectors as sub parts of referred vectors
►Nstorage
►Nimpl
CBagHDF5	Implementation of the Bag interface with a HDF5 file
CCell	Partial implementation of the INode interface
CCollectionFile	Implementation of the Collection interface with a file
CCollectionHDF5	Collection interface
CCollectionNode	Class that add some features to the Collection interface
CGroup	Group concept
CPartition	Define a set of Collection instances having the same type
CPartitionCache	Cache (with potential synchronization) of a Partition
►CStorage	Storage class
Cistream
Costream
CStorageFactory	Factory that creates instances related to the storage feature
CStorageFileFactory	Factory used for storage of kind STORAGE_FILE
CStorageHDF5Factory	Factory used for storage of kind STORAGE_HDF5
CStorageTools	Helper class for the storage feature
CICell	Interface to be used for storage feature
CunionFind