KISES< GENOME_TYPE > Class Template Reference

#include <kises.h>

List of all members.

Public Member Functions
	KISES ()
	~KISES ()
vector< KIS< GENOME_TYPE > > &	find_KISes (const vector< SEQ< GENOME_TYPE > > &a, const vector< SEQ< GENOME_TYPE > > &b, const char *resFile)
Private Member Functions
int	binary_search (const match< SEQ< GENOME_TYPE > > *arr, const SEQ< GENOME_TYPE > &elm, int len) const
int *	find (const vector< SEQ< GENOME_TYPE > > &a, const vector< SEQ< GENOME_TYPE > > &b) const
Private Attributes
vector< KIS< GENOME_TYPE > > *	res

template<class GENOME_TYPE>
class KISES< GENOME_TYPE >

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Constructor & Destructor Documentation

template<class GENOME_TYPE> KISES< GENOME_TYPE >::KISES (   )

Default constructor.

template<class GENOME_TYPE> KISES< GENOME_TYPE >::~KISES (   )

Destructor.

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Member Function Documentation

template<class GENOME_TYPE> int KISES< GENOME_TYPE >::binary_search (  const match< SEQ< GENOME_TYPE > > *  arr, const SEQ< GENOME_TYPE > &  elm, int  len )  const [private]

Binary search for elm in arr and returns the index of the suitable cell. Parameters: arr,:  An array of match< SEQ<GENOME_TYPE> > objects (look in match.h). elm,:  The SEQ<GENOME_TYPE> object we look for. len,:  The length of arr. Returns: int: In case of success, the index of the suitable cell, -1 otherwise.

template<class GENOME_TYPE> int * KISES< GENOME_TYPE >::find (  const vector< SEQ< GENOME_TYPE > > &  a, const vector< SEQ< GENOME_TYPE > > &  b )  const [private]

This method maps between vector "a" and vector "b" by returning an array of indexes where the i'th cell holds the index (j) of the cell in "b" which tells us that the i'th element of "a" is the j'th element of "b". Parameters: a,:  A vector of SEQ<GENOME_TYPE> objects. b,:  A vector of SEQ<GENOME_TYPE> objects.

template<class GENOME_TYPE> vector< KIS< GENOME_TYPE > > & KISES< GENOME_TYPE >::find_KISes (  const vector< SEQ< GENOME_TYPE > > &  a, const vector< SEQ< GENOME_TYPE > > &  b, const char *  resFile )

Extract the KISs out of the intersection result (we get it from CleanFile's method) to the file resFile. Parameters: a,:  A vector of SEQ<GENOME_TYPE> objects. b,:  A vector of SEQ<GENOME_TYPE> objects. resFile,:  The name of the output file. Returns: A vector of KIS objects, the KIS table (the same result that was copied to the file).

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Member Data Documentation

template<class GENOME_TYPE> vector< KIS<GENOME_TYPE> >* KISES< GENOME_TYPE >::res [private]

A vector of KISs.

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

• C:/cygwin/doc/kises.h

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