HistogramCache Class Reference

Cached implementation of the IHistogram interface. More...

#include <Histogram.hpp>

Inheritance diagram for HistogramCache:

Public Member Functions
	HistogramCache (IHistogram *ref, system::ISynchronizer *synchro=0)
	~HistogramCache ()
void	inc (u_int16_t index)
void	inc2D (u_int16_t index1, u_int16_t index2)
void	save (tools::storage::impl::Group &group)
void	compute_threshold (int min_auto_threshold)
u_int16_t	get_solid_cutoff ()
u_int64_t	get_nbsolids_auto ()
float	get_ratio_weak ()
u_int16_t	get_first_peak ()
size_t	getLength ()
size_t	getLength2 ()
u_int64_t &	get (u_int16_t idx)
u_int64_t &	get2D (u_int16_t idx1, u_int16_t idx2)
Public Member Functions inherited from IHistogram
virtual	~IHistogram ()
Public Member Functions inherited from ISmartPointer
virtual	~ISmartPointer ()
Public Member Functions inherited from SmartPointer
void	use ()
void	forget ()

Additional Inherited Members
Protected Member Functions inherited from SmartPointer
	SmartPointer ()
virtual	~SmartPointer ()

Detailed Description

Cached implementation of the IHistogram interface.

This implementation is a Proxy design pattern. It allows to modify a IHistogram instance by several threads at the same time. Actually, each thread has a local copy and at the end, all the local copies are merged into the referred instance.

Constructor & Destructor Documentation

HistogramCache ( IHistogram *  ref, system::ISynchronizer *  synchro = 0  )

inline

Constructor.

Parameters

[in]	ref	: the referred instance.
[in]	synchro	: used for synchronization

~HistogramCache ( )

inline

Destructor.

Member Function Documentation

void compute_threshold ( int  min_auto_threshold )

inlinevirtual

Compute first minimum at x0 and firt maximum at x1 (x1>x0).

Implements IHistogram.

u_int64_t& get ( u_int16_t  idx )

inlinevirtual

Retrieve the value for x.

Parameters

[in]

idx

: x value.

Returns

y(x).

Implements IHistogram.

u_int64_t& get2D ( u_int16_t  idx1, u_int16_t  idx2  )

inlinevirtual

Retrieve the value for x and y of histo2D.

Parameters

[in]	idx1	: x value.
[in]	idx2	: y value.

Returns

cpt(x,y).

Implements IHistogram.

u_int16_t get_first_peak ( )

inlinevirtual

Get the x1 value at the first maximum after x0.

Implements IHistogram.

u_int64_t get_nbsolids_auto ( )

inlinevirtual

Get the number of kmers for x>x0, aka solid kmers for x0 threshold

Returns

number of kmers.

Implements IHistogram.

float get_ratio_weak ( )

inlinevirtual

Get the ratio of weak kmers in total volume

Returns

ratio

Implements IHistogram.

u_int16_t get_solid_cutoff ( )

inlinevirtual

Get the solid cutoff, ie the x0 at first minimum.

Returns

x0

Implements IHistogram.

size_t getLength ( )

inlinevirtual

Return the maximum allowed for X.

Returns

the max X value.

Implements IHistogram.

size_t getLength2 ( )

inlinevirtual

Return the maximum allowed for Y in case of 2D histogram.

Returns

the max Y value.

Implements IHistogram.

void inc ( u_int16_t  index )

inlinevirtual

Increase the number of kmers occurring X time

Parameters

[in]

index

: the X value.

Implements IHistogram.

void inc2D ( u_int16_t  index1, u_int16_t  index2  )

inlinevirtual

Increase the number of kmers occurring X time in genome and Y times in read

Parameters

[in]	index1	: the X value.
[in]	index2	: the Y value.

Implements IHistogram.

void save ( tools::storage::impl::Group &  group )

inlinevirtual

Save the distribution. It is saved into the bag provided at construction.

Implements IHistogram.

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The documentation for this class was generated from the following file:

• /builds/workspace/publish-doc-api-gitlab/gatb-core/src/gatb/tools/misc/impl/Histogram.hpp