gatb.core-API-1.4.2
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< CountNumberCountRange
 

Enumerations

Detailed Description

Misc interfaces.

Typedef Documentation

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

We define a type for a range of kmer counts.

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

Enumeration Type Documentation

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.

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.

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.

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.

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.

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

Provide different modes of graph traversal for building extensions.

Enumerator
SearchMode_Breadth 

Breadth first traversal.

SearchMode_Depth 

Depth first traversal.

Enumeration of different kinds of graph traversal.

Enumerator
TRAVERSAL_NONE 

Undefined

TRAVERSAL_UNITIG 

Path are unitigs

TRAVERSAL_CONTIG 

Path are contigs