vdj_pipe
pipeline for processing DNA sequence data
Public Member Functions | Static Public Member Functions | Private Member Functions | Private Attributes | List of all members
vdj_pipe::gdst::Ukkonen_inserter Class Reference

According to: http://www.cise.ufl.edu/~sahni/dsaaj/enrich/c16/suffix.htm http://stackoverflow.com/questions/9452701. More...

#include <gdst_ukkonen_inserter.hpp>

Collaboration diagram for vdj_pipe::gdst::Ukkonen_inserter:
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Public Member Functions

 Ukkonen_inserter (Gdst &st, const Seq_id sid)
 
void next ()
 
bool has_next () const
 
void insert ()
 

Static Public Member Functions

static void insert (Gdst &st, const Seq_id sid)
 

Private Member Functions

Nucleotide active_edge () const
 
Branch_id active_child () const
 
void active_child (const Branch_id bid)
 
void set_branch_sl (const Branch_id bid)
 
void set_leaf_sl (const Branch_id bid)
 
void add_to_leaf (const Branch_id bid)
 
Branch_id leaf_from_branch (const Branch_id bid, const Nucleotide n1)
 
void set_active_node (const Branch_id bid)
 
Branch_id split_active_edge (const unsigned i, const Nucleotide n2)
 
unsigned edge_length () const
 
Nucleotide letter (const unsigned i) const
 

Private Attributes

Gdst & st_
 
const Seq_id sid_
 
boost::string_ref suff_
 
Branch_id active_node_
 
unsigned active_length_
 
unsigned md_
 
Branch_id prev_branch_
 
Branch_id prev_leaf_
 

Detailed Description

According to: http://www.cise.ufl.edu/~sahni/dsaaj/enrich/c16/suffix.htm http://stackoverflow.com/questions/9452701.

Constructor & Destructor Documentation

vdj_pipe::gdst::Ukkonen_inserter::Ukkonen_inserter ( Gdst &  st,
const Seq_id  sid 
)
inline

Member Function Documentation

Branch_id vdj_pipe::gdst::Ukkonen_inserter::active_child ( ) const
inlineprivate
void vdj_pipe::gdst::Ukkonen_inserter::active_child ( const Branch_id  bid)
inlineprivate
Nucleotide vdj_pipe::gdst::Ukkonen_inserter::active_edge ( ) const
inlineprivate
void vdj_pipe::gdst::Ukkonen_inserter::add_to_leaf ( const Branch_id  bid)
inlineprivate
unsigned vdj_pipe::gdst::Ukkonen_inserter::edge_length ( ) const
inlineprivate
bool vdj_pipe::gdst::Ukkonen_inserter::has_next ( ) const
inline
static void vdj_pipe::gdst::Ukkonen_inserter::insert ( Gdst &  st,
const Seq_id  sid 
)
inlinestatic
void vdj_pipe::gdst::Ukkonen_inserter::insert ( )
inline
Branch_id vdj_pipe::gdst::Ukkonen_inserter::leaf_from_branch ( const Branch_id  bid,
const Nucleotide  n1 
)
inlineprivate
Nucleotide vdj_pipe::gdst::Ukkonen_inserter::letter ( const unsigned  i) const
inlineprivate
void vdj_pipe::gdst::Ukkonen_inserter::next ( )
inline
void vdj_pipe::gdst::Ukkonen_inserter::set_active_node ( const Branch_id  bid)
inlineprivate
void vdj_pipe::gdst::Ukkonen_inserter::set_branch_sl ( const Branch_id  bid)
inlineprivate
void vdj_pipe::gdst::Ukkonen_inserter::set_leaf_sl ( const Branch_id  bid)
inlineprivate
Branch_id vdj_pipe::gdst::Ukkonen_inserter::split_active_edge ( const unsigned  i,
const Nucleotide  n2 
)
inlineprivate

Member Data Documentation

unsigned vdj_pipe::gdst::Ukkonen_inserter::active_length_
private
Branch_id vdj_pipe::gdst::Ukkonen_inserter::active_node_
private
unsigned vdj_pipe::gdst::Ukkonen_inserter::md_
private
Branch_id vdj_pipe::gdst::Ukkonen_inserter::prev_branch_
private
Branch_id vdj_pipe::gdst::Ukkonen_inserter::prev_leaf_
private
const Seq_id vdj_pipe::gdst::Ukkonen_inserter::sid_
private
Gdst& vdj_pipe::gdst::Ukkonen_inserter::st_
private
boost::string_ref vdj_pipe::gdst::Ukkonen_inserter::suff_
private
The documentation for this class was generated from the following file:
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