Detailed Description

A class to store the clusters generated during hierarchical clustering.

Definition at line 35 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

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 93 of file hierarchical_clustering.h.

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