An integer to integer mapping structure that is used to detect the presence of genes in a dataset. More...

#include <seekmap.h>

Public Member Functions
	CSeekIntIntMap (const utype &)
	Constructor.
	CSeekIntIntMap (const vector< char > &, const bool=false)
	Constructor.
	CSeekIntIntMap (const char *, const utype &, const bool=false)
	Constructor.
	CSeekIntIntMap (CSeekIntIntMap *)
	Copy constructor.
void	Initialize (const utype &)
	Helper function that is used by constructor.
	~CSeekIntIntMap ()
	Destructor.
utype	GetForward (const utype &) const
	Get an element from the forward array.
utype	GetReverse (const utype &) const
	Get an element from the reverse array.
const vector< utype > &	GetAllForward () const
	Get the entire forward array.
const vector< utype > &	GetAllReverse () const
	Get the entire reverse array.
void	Add (const utype &)
	Add an available gene to the map.
void	Clear ()
	Clear the member arrays in the structure.
void	Reset (const vector< char > &, const bool=false)
	Reset function.
void	Reset (const char *, const bool=false)
	Reset function.
utype	GetNumSet () const
	Get the number of present genes that are currently contained in the map.
utype	GetSize () const
	Get the genome size.

Detailed Description

An integer to integer mapping structure that is used to detect the presence of genes in a dataset.

This map is used to conveniently get a set of available genes in a dataset, and to quickly check if a given gene is present in the dataset. Normally, a user needs to create two separate arrays for this purpose:

The first array is the presence vector (0 or 1) that is used to track the presence (1) or absence (0) of each gene in a given dataset. But this array cannot be used to efficiently get all available genes in the datasets, because it requires scanning through the entire presence vector.

The second array contains only available genes in the dataset. But it cannot be used to efficiently check whether a gene is present, because again it requires a scan-through.

The solution is to use this int-int mapping structure.

CSeekIntIntMap encapsulates the two arrays that we want: forward and reverse.

As an example, let us consider a simple scenario where we have a genome of 5 genes {0, 1, 2, 3, 4}. We want to use CSeekIntIntMap to capture the gene-presence for a dataset d which contains the following genes: {1, 3, 4}. Then the two arrays would be:

The forward array: f = [-1, 0, -1, 1, 2], where -1 means that the gene is absent; a non -1 value, n, means that the gene is present, and it is the n-th present gene in the array.
So: the absent genes {0, 2} => f[0] = -1, f[2] = -1.
the present genes {1, 3, 4} => f[1] = 0, f[3] = 1, f[4] = 2.

The reverse array: r = [1, 3, 4]. (ie., only the available genes).

These arrays are automatically updated as genes are added to the map.

Definition at line 64 of file seekmap.h.

Constructor & Destructor Documentation

Sleipnir::CSeekIntIntMap::CSeekIntIntMap ( const utype & iSize )

Constructor.

Parameters:

iSize The number of genes in the gene-database

Definition at line 35 of file seekmap.cpp.

References Initialize().

Sleipnir::CSeekIntIntMap::CSeekIntIntMap	(	const vector< char > &	cP,
		const bool	bReverse = `false`
	)

Constructor.

Parameters:

cP	The gene presence vector (char type)
bReverse	When creating the map, whether or not to follow the reverse logic. (eg 1 means absent, 0 means present)

Remarks:: If bReverse is true, then this map captures only the absent genes in the dataset. By default, bReverse is false.

Definition at line 47 of file seekmap.cpp.

References Initialize(), and Reset().

Sleipnir::CSeekIntIntMap::CSeekIntIntMap	(	const char *	cP,
		const utype &	iSize,
		const bool	bReverse = `false`
	)

Constructor.

Parameters:

cP	The gene presence array (char* type)
iSize	The size of the gene-presence array
bReverse	When creating the map, whether or not to follow the reverse logic. (eg 1 means absent, 0 means present)

Remarks:: If bReverse is true, then this map captures only the absent genes in the dataset. By default, bReverse is false.

Definition at line 53 of file seekmap.cpp.

References Initialize(), and Reset().

Sleipnir::CSeekIntIntMap::CSeekIntIntMap ( CSeekIntIntMap * a )

Copy constructor.

Parameters:

a	A map instance

Definition at line 59 of file seekmap.cpp.

Member Function Documentation

void Sleipnir::CSeekIntIntMap::Add ( const utype & i )

Add an available gene to the map.

Parameters:

i	The gene ID to be added

Remarks:: The gene ID is a number between 0 and 21000 (the genome size). It is specified by the gene ID mapping file gene_map.txt.

Definition at line 84 of file seekmap.cpp.

Referenced by Sleipnir::CSeekDataset::InitializeGeneMap(), Sleipnir::CSeekDataset::InitializeQuery(), Sleipnir::CSeekDataset::InitializeQueryBlock(), and Reset().

void Sleipnir::CSeekIntIntMap::Clear ( )

Clear the member arrays in the structure.

This is used by the destructor.

Definition at line 91 of file seekmap.cpp.

Referenced by Initialize().

const vector< utype > & Sleipnir::CSeekIntIntMap::GetAllForward ( ) const

Get the entire forward array.

Returns:: The forward array

Definition at line 39 of file seekmap.cpp.

const vector< utype > & Sleipnir::CSeekIntIntMap::GetAllReverse ( ) const

Get the entire reverse array.

Returns:: The reverse array

Definition at line 43 of file seekmap.cpp.

Referenced by Sleipnir::CSeekDataset::InitializeDataMatrix().

utype Sleipnir::CSeekIntIntMap::GetForward ( const utype & i ) const

Get an element from the forward array.

Parameters:

i	Element index

Returns:: The item at the index

Definition at line 76 of file seekmap.cpp.

Referenced by Sleipnir::CSeekWeighter::CVWeighting(), Sleipnir::CSeekDataset::InitializeQuery(), Sleipnir::CSeekDataset::InitializeQueryBlock(), Sleipnir::CSeekWeighter::LinearCombine(), Sleipnir::CSeekWeighter::OneGeneWeighting(), and Sleipnir::CSeekTools::ReadDatabaselets().

utype Sleipnir::CSeekIntIntMap::GetNumSet ( ) const

Get the number of present genes that are currently contained in the map.

Returns:: The number of genes that are present

Definition at line 102 of file seekmap.cpp.

Referenced by Sleipnir::CSeekCentral::GetMaxGenomeCoverage(), Sleipnir::CSeekDataset::InitializeDataMatrix(), Sleipnir::CSeekDataset::InitializeQueryBlock(), and Sleipnir::CSeekPerformanceMeasure::SortRankVector().

utype Sleipnir::CSeekIntIntMap::GetReverse ( const utype & i ) const

Get an element from the reverse array.

Parameters:

i	Element index

Returns:: The item at the index

Definition at line 80 of file seekmap.cpp.

Referenced by Sleipnir::CSeekDataset::InitializeDataMatrix().

utype Sleipnir::CSeekIntIntMap::GetSize ( ) const

Get the genome size.

Returns:: The genome size

Definition at line 106 of file seekmap.cpp.

void Sleipnir::CSeekIntIntMap::Initialize ( const utype & iSize )

Helper function that is used by constructor.

Parameters:

iSize The genome size

Definition at line 29 of file seekmap.cpp.

References Clear().

Referenced by CSeekIntIntMap().

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

src/seekmap.h
src/seekmap.cpp

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation