CSeqGroup Class Reference

Group (clustrer) of sequences. More...

Public Member Functions
	CSeqGroup (bm::id64_t lead_id=~0ull)
	More...
void	set_lead (bm::id64_t lead_id)
	set id for the group representative More...
bm::id64_t	get_lead () const
	Get lead id. More...
bool	is_assigned ()
	check is cluster is non-empty More...
void	add_member (bm::id64_t id)
	add a member to the group More...
void	add_member (bm::id64_t id, const bm::bvector<> &bv_kmer)
	More...
void	add_member_sync (bm::id64_t id, const bm::bvector<> &bv_kmer)
	More...
void	merge_member_sync (bm::bvector<> &bv_seq, bm::bvector<> &bv_kmer)
	More...
bm::id64_t	count_and_union_sync (const bm::bvector<> &bv)
	More...
void	clear_member (bm::id64_t id)
	More...
bm::bvector &	get_rep ()
	More...
const bm::bvector &	get_rep () const
const bm::bvector &	get_members () const
	More...
bm::bvector &	get_members ()
bm::bvector &	get_kmer_union ()
	More...
const bm::bvector &	get_kmer_union () const

Friends
class	CSeqClusters

Detailed Description

Group (clustrer) of sequences.

Examples

xsample07a.cpp.

Definition at line 686 of file xsample07a.cpp.

Member Function Documentation

add_member() [1/2]

void CSeqGroup::add_member ( bm::id64_t  id )

inline

add a member to the group

Examples

xsample07a.cpp.

Definition at line 705 of file xsample07a.cpp.

References bm::bvector< Alloc >::set_bit_no_check().

Referenced by compute_group(), and set_lead().

add_member() [2/2]

void CSeqGroup::add_member ( bm::id64_t  id, const bm::bvector<> &  bv_kmer  )

inline

Definition at line 706 of file xsample07a.cpp.

References bm::bvector< Alloc >::set_bit_no_check().

add_member_sync()

void CSeqGroup::add_member_sync ( bm::id64_t  id, const bm::bvector<> &  bv_kmer  )

inline

Examples

xsample07a.cpp.

Definition at line 711 of file xsample07a.cpp.

References bm::bvector< Alloc >::set_bit_no_check().

Referenced by assign_to_best_cluster_union().

clear_member()

void CSeqGroup::clear_member ( bm::id64_t  id )

inline

Examples

xsample07a.cpp.

Definition at line 731 of file xsample07a.cpp.

References bm::bvector< Alloc >::set().

Referenced by compute_group(), and resolve_duplicates().

count_and_union_sync()

bm::id64_t CSeqGroup::count_and_union_sync ( const bm::bvector<> &  bv )

inline

Examples

xsample07a.cpp.

Definition at line 725 of file xsample07a.cpp.

References bm::count_and().

Referenced by assign_to_best_cluster_union().

get_kmer_union()

bm::bvector& CSeqGroup::get_kmer_union ( )

inline

Examples

xsample07a.cpp.

Definition at line 739 of file xsample07a.cpp.

Referenced by compute_seq_group_union().

get_lead()

bm::id64_t CSeqGroup::get_lead ( ) const

inline

Get lead id.

Examples

xsample07a.cpp.

Definition at line 699 of file xsample07a.cpp.

Referenced by compute_group(), CSeqClusters::elect_leaders(), CSeqClusters::print_summary(), and resolve_duplicates().

get_members()

const bm::bvector& CSeqGroup::get_members ( ) const

inline

Examples

xsample07a.cpp.

Definition at line 736 of file xsample07a.cpp.

Referenced by CSeqClusters::clear_empty_groups(), CSeqClusters::compute_avg_count(), compute_seq_group_union(), CSeqClusters::elect_leaders(), CSeqClusters::print_summary(), resolve_duplicates(), CSeqClusters::take_group(), and CSeqClusters::union_all_groups().

get_rep()

bm::bvector& CSeqGroup::get_rep ( )

inline

Examples

xsample07a.cpp.

Definition at line 733 of file xsample07a.cpp.

Referenced by assign_to_best_cluster(), compute_group(), CSeqClusters::elect_leaders(), and resolve_duplicates().

is_assigned()

bool CSeqGroup::is_assigned ( )

inline

check is cluster is non-empty

Examples

xsample07a.cpp.

Definition at line 702 of file xsample07a.cpp.

Referenced by compute_group().

merge_member_sync()

void CSeqGroup::merge_member_sync ( bm::bvector<> &  bv_seq, bm::bvector<> &  bv_kmer  )

inline

Examples

xsample07a.cpp.

Definition at line 718 of file xsample07a.cpp.

References bm::bvector< Alloc >::merge().

Referenced by assign_to_best_cluster().

set_lead()

void CSeqGroup::set_lead ( bm::id64_t  lead_id )

inline

set id for the group representative

Examples

xsample07a.cpp.

Definition at line 696 of file xsample07a.cpp.

References add_member().

Referenced by CSeqClusters::elect_leaders().

---

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

• xsample07a.cpp