7 #ifndef PATTERN_ITERATOR_HPP_ 8 #define PATTERN_ITERATOR_HPP_ 9 #include "boost/assert.hpp" 24 const boost::string_ref suff,
26 ) : t_(t), patt_(suff), curr_(bid)
35 bool at_end()
const {
return at_end_;}
40 unsigned index()
const {
return pi_;}
Branch_id next_id() const
Definition: pattern_iterator.hpp:37
bool has_next() const
Definition: pattern_iterator.hpp:45
bool mismatch_
Definition: pattern_iterator.hpp:67
Branch_id current() const
Definition: pattern_iterator.hpp:32
const boost::string_ref patt_
Definition: pattern_iterator.hpp:62
bool at_end_
Definition: pattern_iterator.hpp:64
Pattern_iter(Gdst const &t, const boost::string_ref suff, const Branch_id bid)
Definition: pattern_iterator.hpp:22
Branch_id next_
Definition: pattern_iterator.hpp:65
Nucleotide
Definition: nucleotide_index.hpp:24
bool at_end() const
Definition: pattern_iterator.hpp:35
Branch_id curr_
Definition: pattern_iterator.hpp:63
Nucleotide edge_char() const
Definition: pattern_iterator.hpp:42
unsigned index() const
Definition: pattern_iterator.hpp:40
Gdst const & t_
Definition: pattern_iterator.hpp:61
Nucleotide nc_
Definition: pattern_iterator.hpp:70
Navigate suffix tree according to pattern.
Definition: pattern_iterator.hpp:20
Main namespace of vdj_pipe library.
Definition: keywords_variable.hpp:11
void next()
Definition: pattern_iterator.hpp:54
Nucleotide ec_
Definition: pattern_iterator.hpp:69
#define VDJ_PIPE_DECL
Definition: config.hpp:23
unsigned pi_
Definition: pattern_iterator.hpp:68
bool at_mismatch() const
Definition: pattern_iterator.hpp:39
Nucleotide pattern_char() const
Definition: pattern_iterator.hpp:41
bool at_pattern_end_
Definition: pattern_iterator.hpp:66
bool has_next(Parser const &p1, Parser const &p2)
Definition: pipe_paired_read.cpp:109
Nucleotide nucleotide_index(const char c)
Definition: nucleotide_index.hpp:45
Generalized DNA suffix tree.
Definition: gdst.hpp:66
bool at_pattern_end() const
Definition: pattern_iterator.hpp:38
Nucleotide node_char() const
Definition: pattern_iterator.hpp:43