KIS< GENOME_TYPE > Class Template Reference

#include <kis.h>

List of all members.

Public Member Functions
	KIS ()
	KIS (char ORI)
	KIS (const KIS< GENOME_TYPE > &K)
	~KIS ()
void	print (FILE *whereTo)
KIS< GENOME_TYPE > &	operator= (const KIS< GENOME_TYPE > &K)
void	insert_seg (const SEQ< GENOME_TYPE > &segment1, const SEQ< GENOME_TYPE > &segment2)
KIS< GENOME_TYPE > &	unionKis (const KIS< GENOME_TYPE > &K)
char	get_Orientation () const
void	get_Coords (GENOME_TYPE &start1, GENOME_TYPE &start2, GENOME_TYPE &end1, GENOME_TYPE &end2) const
Private Types
typedef std::vector< SEQ< GENOME_TYPE > >::iterator	itr
Private Attributes
vector< SEQ< GENOME_TYPE > > *	seg1
vector< SEQ< GENOME_TYPE > > *	seg2
char	orientation

template<class GENOME_TYPE>
class KIS< GENOME_TYPE >

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Member Typedef Documentation

template<class GENOME_TYPE> typedef std::vector< SEQ<GENOME_TYPE> >::iterator KIS< GENOME_TYPE >::itr [private]

An auxiliary declaration of a vector iterator.

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Constructor & Destructor Documentation

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

Default constructor.

template<class GENOME_TYPE> KIS< GENOME_TYPE >::KIS (  char  ORI  )

Secondary constructor. Parameters: ORI,:  The orientation of the KIS.

template<class GENOME_TYPE> KIS< GENOME_TYPE >::KIS (  const KIS< GENOME_TYPE > &  K  )

Copy constructor. Parameters: K,:  KIS<GENOME_TYPE> object reference.

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

Destructor.

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Member Function Documentation

template<class GENOME_TYPE> void KIS< GENOME_TYPE >::get_Coords (  GENOME_TYPE &  start1, GENOME_TYPE &  start2, GENOME_TYPE &  end1, GENOME_TYPE &  end2 )  const

Returns the details of both segments held by the calling KIS object. Parameters: start1,:  A reference to the variable which will save the beginning value of the segment in the first genome. start2,:  A reference to the variable which will save the beginning value of the segment in the second genome. end1,:  A reference to the variable which will save the ending value of the segment in the first genome. end2,:  A reference to the variable which will save the ending value of the segment in the second genome.

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

Returns the orientation of the KIS. Returns: char

template<class GENOME_TYPE> void KIS< GENOME_TYPE >::insert_seg (  const SEQ< GENOME_TYPE > &  segment1, const SEQ< GENOME_TYPE > &  segment2 )

Adds segment1 to the end of seg1 vector, and segment2 to the end of seg2. Parameters: segment1,:  The first desired segment for insertion. segment2,:  The second desired segment for insertion.

template<class GENOME_TYPE> KIS< GENOME_TYPE > & KIS< GENOME_TYPE >::operator= (  const KIS< GENOME_TYPE > &  K  )

Assignment operator. Copies K's fields to the calling object fields. Parameters: K,:  const KIS<GENOME_TYPE>& Returns: KIS<GENOME_TYPE>&

template<class GENOME_TYPE> void KIS< GENOME_TYPE >::print (  FILE *  whereTo  )

Prints the coordinates of both segments in the KIS along with their orientation to the given file. Parameters: whereTo,:  FILE*

template<class GENOME_TYPE> KIS< GENOME_TYPE > & KIS< GENOME_TYPE >::unionKis (  const KIS< GENOME_TYPE > &  K  )

Combines between the calling object and K by adding both segments of K to the end of both current object's segments, respectively. Parameters: K,:  The KIS we want to put together with the calling KIS object.

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Member Data Documentation

template<class GENOME_TYPE> char KIS< GENOME_TYPE >::orientation [private]

The orientation of the KIS (+/-).

template<class GENOME_TYPE> vector< SEQ<GENOME_TYPE> >* KIS< GENOME_TYPE >::seg1 [private]

Two vectors of SEQ objects that define both segments of a KIS.

template<class GENOME_TYPE> vector< SEQ<GENOME_TYPE> > * KIS< GENOME_TYPE >::seg2 [private]

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

• C:/cygwin/doc/kis.h

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