Logo Search packages:      
Sourcecode: fastx-toolkit version File versions  Download package

Public Member Functions | Protected Types | Protected Member Functions | Protected Attributes

SequenceAlignment Class Reference

Inheritance diagram for SequenceAlignment:
Inheritance graph
[legend]
Collaboration diagram for SequenceAlignment:
Collaboration graph
[legend]

List of all members.

Public Member Functions

const SequenceAlignmentResultsalign (const std::string &query, const std::string &target)
score_type gap_panelty () const
char match (const size_t query_index, const size_t target_index) const
score_type match_panelty () const
char match_value (const char q, const char t) const
size_t matrix_height () const
size_t matrix_width () const
score_type mismatch_panelty () const
score_type neutral_panelty () const
score_type nucleotide_match_score (const size_t query_index, const size_t target_index) const
DIRECTION origin (const size_t query_index, const size_t target_index) const
void print_matrix (std::ostream &strm=std::cout) const
char query_nucleotide (size_t query_index) const
const std::string & query_sequence () const
const SequenceAlignmentResultsresults () const
score_type safe_score (const ssize_t query_index, const ssize_t target_index) const
score_type score (const size_t query_index, const size_t target_index) const
char target_nucleotide (size_t target_index) const
const std::string & target_sequence () const

Protected Types

enum  DIRECTION { FROM_UPPER = 1, FROM_LEFT = 2, FROM_UPPER_LEFT = 3, FROM_NOWHERE = 4 }
typedef float score_type

Protected Member Functions

virtual void find_optimal_alignment ()=0
void populate_match_matrix ()
virtual void populate_matrix ()=0
virtual void post_process ()
virtual void reset_alignment_results ()
virtual void reset_matrix (size_t width, size_t height)=0
void resize_matrix (size_t width, size_t height)
virtual void set_sequences (const std::string &_query, const std::string &target)

Protected Attributes

SequenceAlignmentResults _alignment_results
score_type _gap_panelty
score_type _match_panelty
score_type _mismatch_panelty
score_type _neutral_panelty
std::string _query_sequence
std::string _target_sequence
std::vector< std::vector< char > > match_matrix
std::vector< std::vector
< DIRECTION > > 
origin_matrix
std::vector< score_type > query_border
std::vector< std::vector
< score_type > > 
score_matrix
std::vector< score_type > target_border

Detailed Description

Definition at line 73 of file sequence_alignment.h.


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

Generated by  Doxygen 1.6.0   Back to index