IMP::em2d::ClusterSet Class Reference

A class to store the clusters generated during hierarchical clustering. More...

#include <IMP/em2d/hierarchical_clustering.h>

Detailed Description

A class to store the clusters generated during hierarchical clustering.

Definition at line 34 of file hierarchical_clustering.h.

Public Member Functions
	ClusterSet (unsigned int N)
void	do_join_clusters (unsigned int cluster_id1, unsigned int cluster_id2, double distance_between_clusters)
	join operation More...
Ints	get_cluster_elements (unsigned int id) const
	Returns a vector with the ids of the elements that are in a cluster. More...
Ints	get_cluster_formed_at_step (unsigned int step) const
	Return the elements of the cluster formed at a given step. More...
Ints	get_clusters_below_cutoff (double cutoff) const
	Get the biggest clusters that have distances below a given cutoff. More...
double	get_distance_at_step (unsigned int step) const
	Distance in the linkage matrix at a given step. More...
unsigned int	get_id_for_cluster_at_step (unsigned int step) const
FloatsList	get_linkage_matrix () const
	Returns the linkage matrix. More...
FloatsList	get_linkage_matrix_in_matlab_format () const
	Returns the linkage matrix compatible with Matlab format. More...
unsigned int	get_number_of_steps () const
	Returns the number of steps of clustering recorded. More...
void	show (std::ostream &out) const

Constructor & Destructor Documentation

IMP::em2d::ClusterSet::ClusterSet

(

unsigned int

N

)

Parameters

[in]

N

Number of elements to be clustered

Member Function Documentation

void IMP::em2d::ClusterSet::do_join_clusters	(	unsigned int	cluster_id1,
		unsigned int	cluster_id2,
		double	distance_between_clusters
	)

join operation

Parameters

[in]	cluster_id1	id of the 1st cluster joined
[in]	cluster_id2	id of the 2nd cluster merged
[in]	distance_between_clusters	distance between the merged clusters

Ints IMP::em2d::ClusterSet::get_cluster_elements

(

unsigned int

id

)

const

Returns a vector with the ids of the elements that are in a cluster.

Does not contain any hierarchical information, just the members

Parameters

[in]

id

of the cluster

Ints IMP::em2d::ClusterSet::get_cluster_formed_at_step

(

unsigned int

step

)

const

Return the elements of the cluster formed at a given step.

Ints IMP::em2d::ClusterSet::get_clusters_below_cutoff

(

double

cutoff

)

const

Get the biggest clusters that have distances below a given cutoff.

Parameters

[in]

cutoff

distance

Returns

A vector of Ints: Each Ints has the ids of all elements of the cluster

double IMP::em2d::ClusterSet::get_distance_at_step

(

unsigned int

step

)

const

Distance in the linkage matrix at a given step.

FloatsList IMP::em2d::ClusterSet::get_linkage_matrix

(

)

const

Returns the linkage matrix.

Note

Linkage matrix is a matrix A[N-1][3]. A[i][0] - id of the first cluster merged at step i A[i][1] - id of the second cluster merged at step i A[i][2] - distance between the clusters

FloatsList IMP::em2d::ClusterSet::get_linkage_matrix_in_matlab_format

(

)

const

Returns the linkage matrix compatible with Matlab format.

Note

This function merely adds 1 to the cluster ids, for compatibility with Matlab. Matlab format: http://www.mathworks.com/help/toolbox/stats/linkage.html

unsigned int IMP::em2d::ClusterSet::get_number_of_steps

(

)

const

Returns the number of steps of clustering recorded.

Definition at line 90 of file hierarchical_clustering.h.

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

• hierarchical_clustering.h