CSeqClusters Class Reference

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)
void	take_group (bm::bvector<> &bv_members)
	memebers moved into their own group
void	merge_from (CSeqClusters &sc)
	Acquire all groups from another cluster collection.
void	clear_empty_groups ()
	Remove groups which turned empty after clusterization.
const bm::bvector &	union_all_groups ()
	Compute union of all cluster group members.
void	resolve_duplicates (const CSequenceColl &seq_coll)
	Resolve duplicate membership between groups.
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.
bm::id64_t	compute_avg_count () const
	calculate avg cluster population count
size_t	groups_size () const
CSeqGroup *	get_group (size_t idx)
void	print_summary (const char *title) const
	print clusterization report

Detailed Description

Examples

xsample07a.cpp.

Definition at line 757 of file xsample07a.cpp.

Member Typedef Documentation

groups_vector_type

typedef std::vector<std::unique_ptr<CSeqGroup> > CSeqClusters::groups_vector_type

Examples

xsample07a.cpp.

Definition at line 760 of file xsample07a.cpp.

Constructor & Destructor Documentation

CSeqClusters() [1/2]

CSeqClusters::CSeqClusters ( )

inline

Examples

xsample07a.cpp.

Definition at line 762 of file xsample07a.cpp.

Referenced by CSeqClusters(), and merge_from().

CSeqClusters() [2/2]

CSeqClusters::CSeqClusters ( const CSeqClusters & )

delete

References CSeqClusters().

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.

References CSeqClusters().

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::bvector< Alloc >::clear(), and CSeqGroup::get_members().

Referenced by compute_jaccard_clusters().

---

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

• xsample07a.cpp