BitMagic-C++: CSeqClusters Class Reference

BitMagic-C++

Public Types
typedef std::vector< std::unique_ptr< CSeqGroup > >	groups_vector_type

Public Member Functions
	CSeqClusters ()

	CSeqClusters (const CSeqClusters &)=delete

void	add_group (CSeqGroup *sg)
	More...

void	take_group (bm::bvector<> &bv_members)
	memebers moved into their own group More...

void	merge_from (CSeqClusters &sc)
	Acquire all groups from another cluster collection. More...

void	clear_empty_groups ()
	Remove groups which turned empty after clusterization. More...

const bm::bvector &	union_all_groups ()
	Compute union of all cluster group members. More...

void	resolve_duplicates (const CSequenceColl &seq_coll)
	Resolve duplicate membership between groups. More...

void	elect_leaders (const CSequenceColl &seq_coll, unsigned concurrency)
	Find the best representatives in all cluster groups the criteria is maximum absolute similarity to all members. More...

bm::id64_t	compute_avg_count () const
	calculate avg cluster population count More...

size_t	groups_size () const
	More...

CSeqGroup *	get_group (size_t idx)
	More...

void	print_summary (const char *title) const
	print clusterization report More...

Detailed Description

Examples: xsample07a.cpp.

Definition at line 757 of file xsample07a.cpp.

Member Function Documentation

◆ add_group()

void CSeqClusters::add_group ( CSeqGroup * sg )

inline

Examples: xsample07a.cpp.

Definition at line 766 of file xsample07a.cpp.

Referenced by compute_random_clusters(), and take_group().

◆ clear_empty_groups()

void CSeqClusters::clear_empty_groups ( )

Remove groups which turned empty after clusterization.

Examples: xsample07a.cpp.

Definition at line 807 of file xsample07a.cpp.

References bm::bvector< Alloc >::count(), and CSeqGroup::get_members().

Referenced by compute_jaccard_clusters().

◆ compute_avg_count()

bm::id64_t CSeqClusters::compute_avg_count ( ) const

calculate avg cluster population count

Examples: xsample07a.cpp.

Definition at line 847 of file xsample07a.cpp.

References bm::bvector< Alloc >::count(), and CSeqGroup::get_members().

Referenced by compute_jaccard_clusters().

◆ elect_leaders()

void CSeqClusters::elect_leaders	(	const CSequenceColl &	seq_coll,
		unsigned	concurrency
	)

Find the best representatives in all cluster groups the criteria is maximum absolute similarity to all members.

Examples: xsample07a.cpp.

Definition at line 994 of file xsample07a.cpp.

References bm::bvector< Alloc >::clear(), compute_and_sim(), compute_seq_group_union(), bm::bvector< Alloc >::count(), bm::bvector< Alloc >::count_range(), bm::deserialize(), bm::bvector< Alloc >::first(), CSequenceColl::get_buf(), CSeqGroup::get_lead(), CSeqGroup::get_members(), CSeqGroup::get_rep(), bm::random_subset< BV >::sample(), bm::bvector< Alloc >::set(), CSeqGroup::set_lead(), bm::bvector< Alloc >::test(), and bm::bvector< Alloc >::iterator_base::valid().

Referenced by compute_jaccard_clusters().

◆ get_group()

CSeqGroup* CSeqClusters::get_group ( size_t idx )

inline

Examples: xsample07a.cpp.

Definition at line 796 of file xsample07a.cpp.

Referenced by assign_to_best_cluster(), and assign_to_best_cluster_union().

◆ groups_size()

size_t CSeqClusters::groups_size ( ) const

inline

Examples: xsample07a.cpp.

Definition at line 795 of file xsample07a.cpp.

Referenced by assign_to_best_cluster(), and assign_to_best_cluster_union().

◆ merge_from()

void CSeqClusters::merge_from ( CSeqClusters & sc )

Acquire all groups from another cluster collection.

Examples: xsample07a.cpp.

Definition at line 861 of file xsample07a.cpp.

Referenced by compute_jaccard_clusters().

◆ print_summary()

void CSeqClusters::print_summary ( const char * title ) const

print clusterization report

Examples: xsample07a.cpp.

Definition at line 1087 of file xsample07a.cpp.

References bm::bvector< Alloc >::count(), CSeqGroup::get_lead(), and CSeqGroup::get_members().

Referenced by compute_jaccard_clusters().

◆ resolve_duplicates()

void CSeqClusters::resolve_duplicates ( const CSequenceColl & seq_coll )

Resolve duplicate membership between groups.

Examples: xsample07a.cpp.

Definition at line 873 of file xsample07a.cpp.

References resolve_duplicates().

Referenced by compute_jaccard_clusters(), and resolve_duplicates().

◆ take_group()

void CSeqClusters::take_group ( bm::bvector<> & bv_members )

memebers moved into their own group

Examples: xsample07a.cpp.

Definition at line 822 of file xsample07a.cpp.

References add_group(), bm::bvector< Alloc >::get_first(), CSeqGroup::get_members(), and bm::bvector< Alloc >::swap().

Referenced by compute_jaccard_clusters().

◆ union_all_groups()

const bm::bvector & CSeqClusters::union_all_groups ( )

Compute union of all cluster group members.

Examples: xsample07a.cpp.

Definition at line 830 of file xsample07a.cpp.

References bm::aggregator< BV >::add(), bm::bvector< Alloc >::clear(), bm::aggregator< BV >::combine_or(), CSeqGroup::get_members(), bm::aggregator< BV >::reset(), and bm::aggregator< BV >::set_optimization().

Referenced by compute_jaccard_clusters().

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

xsample07a.cpp