Sleipnir::CSeekQuery Class Reference

Representation of a query gene-set that is used by Seek. More...

#include <seekquery.h>

Public Types
enum	PartitionMode { LEAVE_ONE_IN = 0, LEAVE_ONE_OUT = LEAVE_ONE_IN + 1, CUSTOM_PARTITION = LEAVE_ONE_OUT + 1 }
	Query partitioning mode. More...
Public Member Functions
	CSeekQuery ()
	Constructor.
	~CSeekQuery ()
	Destructor.
bool	Reset ()
	The reset function.
bool	InitializeQuery (const vector< char > &)
	Initialize with a 0-1 query presence vector.
bool	InitializeQuery (const vector< utype > &, const utype &)
	Initialize with a vector of query genes' ID.
utype	GetNumFold () const
	Get the number of query partitions.
const vector< utype > &	GetQuery () const
	Get the query genes as a vector.
const vector< char > &	GetQueryPresence () const
	Get the query presence as a char vector.
const vector< utype > &	GetCVQuery (utype &) const
	Get the i-th query partition.
bool	CreateCVPartitions (const gsl_rng *, const enum PartitionMode &, const utype=-1)
	Create N random query partitions.

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Detailed Description

Representation of a query gene-set that is used by Seek.

Includes vectors for storing the query genes, and utilities for partitioning query genes into specified number of groups

There are two ways to represent a query.

• A presence char vector, with number of elements = size of genome. All elements are 0 except the elements indexed by the query genes, which have a value of 1.

• A utype vector, with number of elements = size of query. A compact representation which only stores the query genes' ID.

Definition at line 45 of file seekquery.h.

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Member Enumeration Documentation

enum Sleipnir::CSeekQuery::PartitionMode

Query partitioning mode.

Let us consider a query of size N.

LEAVE_ONE_IN : create N partitions, where each partition is one of the query genes

LEAVE_ONE_OUT : create N partitions, where each partition is everything excluding one of the query genes

CUSTOM_PARTITION : create X equally sized partitions, where each partition is N / X number of genes. X is a user-given parameter.

Definition at line 65 of file seekquery.h.

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Member Function Documentation

bool Sleipnir::CSeekQuery::CreateCVPartitions	(	const gsl_rng *	,
		const enum PartitionMode &	,
		const utype	= -1
	)

Create N random query partitions.

Parameters:

rnd	A random number generator
p	The partitioning mode
iFold	The number of partitions to be created

Remarks:

The parameter iFold is not used if the partitioning mode is LEAVE_ONE_IN or LEAVE_ONE_OUT, because the number of partitions in this case is the size of the query.

Definition at line 93 of file seekquery.cpp.

References Sleipnir::CSeekTools::IsNaN().

const vector< utype > & Sleipnir::CSeekQuery::GetCVQuery

(

utype &

i

)

const

Get the i-th query partition.

Parameters:

i	The index of partition to return

Returns:

The vector of genes in i-th partition

Remarks:

No bound checking on i.

Definition at line 89 of file seekquery.cpp.

Referenced by Sleipnir::CSeekWeighter::CVWeighting(), and Sleipnir::CSeekWeighter::OneGeneWeighting().

utype Sleipnir::CSeekQuery::GetNumFold

(

)

const

Get the number of query partitions.

Returns:

The number of query partitions

Definition at line 77 of file seekquery.cpp.

Referenced by Sleipnir::CSeekWeighter::CVWeighting().

const vector< utype > & Sleipnir::CSeekQuery::GetQuery

(

)

const

Get the query genes as a vector.

Returns:

The query genes as a utype vector

Definition at line 85 of file seekquery.cpp.

Referenced by Sleipnir::CSeekWeighter::CVWeighting(), Sleipnir::CSeekWeighter::OneGeneWeighting(), and Sleipnir::CSeekCentral::VarianceWeightSearch().

const vector< char > & Sleipnir::CSeekQuery::GetQueryPresence

(

)

const

Get the query presence as a char vector.

Returns:

The query genes as a presence char vector

Definition at line 81 of file seekquery.cpp.

bool Sleipnir::CSeekQuery::InitializeQuery

(

const vector< char > &

query

)

Initialize with a 0-1 query presence vector.

Parameters:

query

A char vector (0 or 1) that specifies the location of the query genes,

Remarks:

The parameter query: based on the gene_map.txt, all genes are mapped to integers between 0 to 21000 (or whatever the upper limit is). In the char vector query, query[q] = 1 for q in Q. All other genes: query[g] = 0.

Definition at line 50 of file seekquery.cpp.

References Reset().

bool Sleipnir::CSeekQuery::InitializeQuery	(	const vector< utype > &	query,
		const utype &	iGenes
	)

Initialize with a vector of query genes' ID.

Parameters:

query	A utype-vector that stores the query genes' ID
iGenes	The number of genes in the genome

Remarks:

This is an alternative way of defining query input. An example of a valid query parameter is <201, 242, 42>, and iGenes is 21000 (if there are 21000 genes).

Definition at line 63 of file seekquery.cpp.

References Reset().

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

• src/seekquery.h
• src/seekquery.cpp