lightKIS< GENOME_TYPE > Class Template Reference

#include <lightkis.h>

List of all members.

Public Member Functions
	lightKIS ()
	lightKIS (GENOME_TYPE start11, GENOME_TYPE end12, GENOME_TYPE start21, GENOME_TYPE end22, char orientation)
	lightKIS (const lightKIS< GENOME_TYPE > &elm)
void	nameIt (string &newName)
string	getName () const
char	get_Orientation () const
lightKIS< GENOME_TYPE > &	operator= (const lightKIS< GENOME_TYPE > &elm)
void	get_Coords (GENOME_TYPE &start11, GENOME_TYPE &end12, GENOME_TYPE &start21, GENOME_TYPE &end22) const
bool	operator< (const lightKIS< GENOME_TYPE > &elm) const
bool	operator> (const lightKIS< GENOME_TYPE > &elm) const
bool	operator== (const lightKIS< GENOME_TYPE > &elm) const
void	update (GENOME_TYPE start1, GENOME_TYPE end1, GENOME_TYPE start2, GENOME_TYPE end2)
int	getValid () const
void	setValid (int status)
Private Attributes
GENOME_TYPE	start1
GENOME_TYPE	start2
GENOME_TYPE	end1
GENOME_TYPE	end2
char	Orientation
int	valid
string	name

template<class GENOME_TYPE>
class lightKIS< GENOME_TYPE >

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Constructor & Destructor Documentation

template<class GENOME_TYPE> lightKIS< GENOME_TYPE >::lightKIS (   )  [inline]

Default constructor.

template<class GENOME_TYPE> lightKIS< GENOME_TYPE >::lightKIS (  GENOME_TYPE  start11, GENOME_TYPE  end12, GENOME_TYPE  start21, GENOME_TYPE  end22, char  orientation )  [inline]

Secondary constructor. Parameters: start11,:  The beginning coordinate of the segment of the first genome. end12,:  The ending coordinate of the segment of the first genome. start21,:  The beginning coordinate of the segment of the second genome. end22,:  The ending coordinate of the segment of the second genome. orientation,:  The orientation of the two segments.

template<class GENOME_TYPE> lightKIS< GENOME_TYPE >::lightKIS (  const lightKIS< GENOME_TYPE > &  elm  )

Copy constructor. Parameters: elm,:  lightKIS object const reference.

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Member Function Documentation

template<class GENOME_TYPE> void lightKIS< GENOME_TYPE >::get_Coords (  GENOME_TYPE &  start11, GENOME_TYPE &  end12, GENOME_TYPE &  start21, GENOME_TYPE &  end22 )  const

Returns the details of both segments held by the calling object. Parameters: start11,:  A reference to the variable which will save the beginning value of the segment in the first genome. end12,:  A reference to the variable which will save the ending value of the segment in the first genome. start21,:  A reference to the variable which will save the beginning value of the segment in the second genome. end22,:  A reference to the variable which will save the ending value of the segment in the second genome.

template<class GENOME_TYPE> char lightKIS< GENOME_TYPE >::get_Orientation (   )  const

Returns the orientation of this object. Returns: char

template<class GENOME_TYPE> string lightKIS< GENOME_TYPE >::getName (   )  const

Returns the name of this object. Returns: string

template<class GENOME_TYPE> int lightKIS< GENOME_TYPE >::getValid (   )  const

Returns the valid variable value of the calling object.

template<class GENOME_TYPE> void lightKIS< GENOME_TYPE >::nameIt (  string &  newName  )

A method which labels the object with the given string. Parameters: newName,:  string.

template<class GENOME_TYPE> bool lightKIS< GENOME_TYPE >::operator< (  const lightKIS< GENOME_TYPE > &  elm  )  const

Operator < . Compares between this and elm according to start2 field. Parameters: elm,:  const lightKIS<GENOME_TYPE>& Returns: bool

template<class GENOME_TYPE> lightKIS< GENOME_TYPE > & lightKIS< GENOME_TYPE >::operator= (  const lightKIS< GENOME_TYPE > &  elm  )

Assignment operator. Copies elm's fields to the current object fields. Parameters: elm,:  const lightKIS<GENOME_TYPE>& Returns: lightKIS<GENOME_TYPE>&

template<class GENOME_TYPE> bool lightKIS< GENOME_TYPE >::operator== (  const lightKIS< GENOME_TYPE > &  elm  )  const

Operator == . Compares between this and elm according to coordinates fields (start1,start2,end1 and end2). Parameters: elm,:  const lightKIS<GENOME_TYPE>& Returns: bool

template<class GENOME_TYPE> bool lightKIS< GENOME_TYPE >::operator> (  const lightKIS< GENOME_TYPE > &  elm  )  const

Operator > . Compares between this and elm according to start2 field. Parameters: elm,:  const lightKIS<GENOME_TYPE>& Returns: bool

template<class GENOME_TYPE> void lightKIS< GENOME_TYPE >::setValid (  int  status  )

Sets the value of the calling object valid variable to status. Parameters: status,:  int

template<class GENOME_TYPE> void lightKIS< GENOME_TYPE >::update (  GENOME_TYPE  start1, GENOME_TYPE  end1, GENOME_TYPE  start2, GENOME_TYPE  end2 )

Updates the calling object with the given values. Parameters: start1,:  The new beginning of the segment in the first genome. end1,:  The new ending of the segment in the first genome. start2,:  The new beginning of the segment in the second genome. end2,:  The new ending of the segment in the second genome.

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Member Data Documentation

template<class GENOME_TYPE> GENOME_TYPE lightKIS< GENOME_TYPE >::end1 [private]

template<class GENOME_TYPE> GENOME_TYPE lightKIS< GENOME_TYPE >::end2 [private]

template<class GENOME_TYPE> string lightKIS< GENOME_TYPE >::name [private]

name is simply the label of the lightKIS object.

template<class GENOME_TYPE> char lightKIS< GENOME_TYPE >::Orientation [private]

Orientation +/- .

template<class GENOME_TYPE> GENOME_TYPE lightKIS< GENOME_TYPE >::start1 [private]

Defines the coordinates of both segments in both genomes preserved by the object.

template<class GENOME_TYPE> GENOME_TYPE lightKIS< GENOME_TYPE >::start2 [private]

template<class GENOME_TYPE> int lightKIS< GENOME_TYPE >::valid [private]

valid is an auxiliary variable which was used in the implementation. valid is initialized with the value 1.

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

• C:/cygwin/doc/lightkis.h

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