gatb::core::tools::misc Namespace Reference

Misc interfaces. More...

Namespaces
	impl

Classes
struct	Abundance
	Define a type that associates a value and an abundance. More...
struct	ArrayData
	Define a specific kind of array. More...
class	Data
	Definition of a data chunk. More...
class	IHistogram
	Interface for kmers distribution management. More...
class	IOptionsParser
	Parser interface that analyzes command line options. More...
class	IOptionsParserVisitor
class	IProperties
	Container of IProperty instances with DP Visitor capability. More...
class	IPropertiesVisitor
class	IProperty
	Definition of a property as a [key,value] entry with a given depth. More...
class	Vector
	Vector class allowing to define vectors as sub parts of referred vectors. More...

Typedefs
typedef IProperty	Property
typedef tools::misc::Range< CountNumber >	CountRange

Enumerations

Detailed Description

Misc interfaces.

Typedef Documentation

typedef tools::misc::Range<CountNumber> CountRange

We define a type for a range of kmer counts.

typedef IProperty Property

An alias here... In the future, we should replace IProperty by Property.

Enumeration Type Documentation

enum BankConvertKind

Enumeration for the different kinds of bank conversions supported in GATB.

enum BloomKind

Enumeration for the different kinds of Bloom filters supported in GATB.

Enumerator
BLOOM_NONE	No Bloom filter
BLOOM_BASIC	Trivial implementation of Bloom filters
BLOOM_CACHE	Implementation of Bloom filters improving CPU cache management.
BLOOM_NEIGHBOR	Implementation of Bloom filters improving CPU cache management.

enum BranchingKind

Enumeration for the different kinds of branching storages supported in GATB.

Enumerator
BRANCHING_NONE	Don't save branching nodes.
BRANCHING_STORED	Save branching nodes within the graph file.

enum DebloomImpl

Enumeration for the different kinds of debloom algorithms supported in GATB.

Enumerator
DEBLOOM_IMPL_BASIC	Initial debloom algorithm
DEBLOOM_IMPL_MINIMIZER	Debloom algorithm based on minimizers.

enum DebloomKind

Enumeration for the different kinds of cFP storage mechanisms supported in GATB.

Enumerator
DEBLOOM_NONE	No cFP
DEBLOOM_ORIGINAL	Save cFP in the original way (a sorted vector)
DEBLOOM_CASCADING	Save cFP with cascading Bloom filters.

enum ExtendStopMode_e

Provide different modes for graph traversal stop criteria.

Enumerator
ExtendStopMode_after_first_contig	Stop traversal after the first unitig/contig.
ExtendStopMode_until_max_depth	Stop traversal when the maximum depth is reached.

enum KmerSolidityKind

Enumeration for the different kinds of kmer solidity criteria supported in GATB.

Enumerator
KMER_SOLIDITY_MIN	min criteria
KMER_SOLIDITY_MAX	max criteria
KMER_SOLIDITY_ONE	on criteria
KMER_SOLIDITY_CUSTOM	custom criteria
KMER_SOLIDITY_ALL	all criteria
KMER_SOLIDITY_SUM	sum criteria

enum SearchMode_e

Provide different modes of graph traversal for building extensions.

Enumerator
SearchMode_Breadth	Breadth first traversal.
SearchMode_Depth	Depth first traversal.

enum TraversalKind

Enumeration of different kinds of graph traversal.

Enumerator
TRAVERSAL_NONE	Undefined
TRAVERSAL_UNITIG	Path are unitigs
TRAVERSAL_CONTIG	Path are contigs