ARB
Public Member Functions | List of all members
ALI_PROFILE Class Reference

#include <ali_profile.hxx>

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Public Member Functions

 ALI_PROFILE (ALI_SEQUENCE *sequence, ALI_PROFILE_CONTEXT *context)
 
 ~ALI_PROFILE ()
 
void print (int start=-1, int end=-1)
 
int is_in_helix (unsigned long pos, unsigned long *first, unsigned long *last)
 
int is_outside_helix (unsigned long pos, unsigned long *first, unsigned long *last)
 
int complement_position (unsigned long pos)
 
int is_in_helix (unsigned long pos)
 
int is_internal_last (unsigned long pos)
 
char * cheapest_sequence ()
 
char * borders_sequence ()
 
unsigned long length ()
 
ALI_NORM_SEQUENCE * sequence ()
 
unsigned long sequence_length ()
 
float base_weight (unsigned long pos, unsigned char c)
 
float w_sub (unsigned long positiony, unsigned long positionx)
 
float w_sub_gap (unsigned long positiony)
 
float w_sub_gap_cheap (unsigned long positiony)
 
float w_sub_multi_gap_cheap (unsigned long start, unsigned long end)
 
float w_sub_maximum ()
 
float w_del (unsigned long begin, unsigned long end)
 
float w_del_cheap (unsigned long position)
 
float w_del_multi (unsigned long start, unsigned long end)
 
float w_del_multi_cheap (unsigned long start, unsigned long end)
 
float w_del_multi_unweighted (unsigned long start, unsigned long end)
 
float w_ins (unsigned long, unsigned long)
 
float w_ins_cheap (unsigned long, unsigned long)
 
float w_ins_multi_unweighted (unsigned long startx, unsigned long endx)
 
float w_ins_multi (unsigned long startx, unsigned long endx)
 
float w_ins_multi_cheap (unsigned long startx, unsigned long endx)
 
float gap_percent (unsigned long begin, unsigned long end)
 
float w_bind (unsigned long pos_1, unsigned char base_1, unsigned long pos_2, unsigned char base_2)
 
float w_binding (unsigned long first_position_of_sequence, ALI_SEQUENCE *sequence)
 

Detailed Description

Definition at line 68 of file ali_profile.hxx.

Constructor & Destructor Documentation

ALI_PROFILE::ALI_PROFILE ( ALI_SEQUENCE *  sequence,
ALI_PROFILE_CONTEXT *  context 
)

Definition at line 412 of file ali_profile.cxx.

References ali_error(), ali_message(), ALI_TLIST< T >::first(), ALI_TLIST< T >::has_next(), ALI_PROFILE_CONTEXT::insert_factor, ALI_TLIST< T >::is_empty(), ALI_PROFILE_CONTEXT::multi_gap_factor, ALI_PROFILE_CONTEXT::multi_insert_factor, ALI_TLIST< T >::next(), and ali_family_member::sequence.

ALI_PROFILE::~ALI_PROFILE ( )

Definition at line 454 of file ali_profile.cxx.

Member Function Documentation

void ALI_PROFILE::print ( int  start = -1,
int  end = -1 
)
inline

Definition at line 117 of file ali_profile.hxx.

References start.

int ALI_PROFILE::is_in_helix ( unsigned long  pos,
unsigned long *  first,
unsigned long *  last 
)

Definition at line 479 of file ali_profile.cxx.

References ALI_PROFILE_BORDER_LEFT, ALI_PROFILE_BORDER_RIGHT, ali_warning(), and long.

Referenced by ali_prealigner_mask::delete_expensive().

int ALI_PROFILE::is_outside_helix ( unsigned long  pos,
unsigned long *  first,
unsigned long *  last 
)

Definition at line 527 of file ali_profile.cxx.

References ALI_PROFILE_BORDER_LEFT, ALI_PROFILE_BORDER_RIGHT, ali_warning(), and long.

int ALI_PROFILE::complement_position ( unsigned long  pos)
inline

Definition at line 161 of file ali_profile.hxx.

Referenced by ali_prealigner_mask::delete_expensive().

int ALI_PROFILE::is_in_helix ( unsigned long  pos)
inline

Definition at line 167 of file ali_profile.hxx.

References ALI_PROFILE_BORDER_LEFT, ALI_PROFILE_BORDER_RIGHT, and long.

int ALI_PROFILE::is_internal_last ( unsigned long  pos)
inline

Definition at line 189 of file ali_profile.hxx.

References ALI_NORM_SEQUENCE::is_begin().

char * ALI_PROFILE::cheapest_sequence ( )

Definition at line 571 of file ali_profile.cxx.

References ali_number_to_base(), ali_out_of_memory_if(), CALLOC(), min, and seq.

Referenced by ARB_main().

char* ALI_PROFILE::borders_sequence ( )
inline

Definition at line 194 of file ali_profile.hxx.

References ali_out_of_memory_if(), ALI_PROFILE_BORDER_LEFT, and ALI_PROFILE_BORDER_RIGHT.

Referenced by ARB_main().

unsigned long ALI_PROFILE::length ( )
inline

Definition at line 211 of file ali_profile.hxx.

Referenced by ARB_main(), ALI_SUB_SOLUTION::free_area(), ALI_SUB_SOLUTION::insert(), and ALI_SUB_SOLUTION::is_konsistent().

ALI_NORM_SEQUENCE* ALI_PROFILE::sequence ( )
inline

Definition at line 214 of file ali_profile.hxx.

Referenced by ARB_main(), ali_prealigner_mask::delete_expensive(), ALI_PREALIGNER::sequence(), and ALI_PREALIGNER::sequence_without_inserts().

unsigned long ALI_PROFILE::sequence_length ( )
inline

Definition at line 217 of file ali_profile.hxx.

References ALI_NORM_SEQUENCE::length().

Referenced by ARB_main(), ALI_SUB_SOLUTION::free_area(), ALI_SUB_SOLUTION::insert(), ALI_SUB_SOLUTION::is_konsistent(), and ALI_SUB_SOLUTION::number_of_free_areas().

float ALI_PROFILE::base_weight ( unsigned long  pos,
unsigned char  c 
)
inline

Definition at line 221 of file ali_profile.hxx.

References ali_fatal_error().

float ALI_PROFILE::w_sub ( unsigned long  positiony,
unsigned long  positionx 
)
inline

Definition at line 227 of file ali_profile.hxx.

References ALI_NORM_SEQUENCE::base().

Referenced by ali_prealigner_mask::delete_expensive().

float ALI_PROFILE::w_sub_gap ( unsigned long  positiony)
inline

Definition at line 230 of file ali_profile.hxx.

Referenced by w_sub_multi_gap_cheap().

float ALI_PROFILE::w_sub_gap_cheap ( unsigned long  positiony)
inline

Definition at line 233 of file ali_profile.hxx.

float ALI_PROFILE::w_sub_multi_gap_cheap ( unsigned long  start,
unsigned long  end 
)
inline

Definition at line 236 of file ali_profile.hxx.

References w_sub_gap().

float ALI_PROFILE::w_sub_maximum ( )
inline

Definition at line 244 of file ali_profile.hxx.

Referenced by ali_prealigner_mask::delete_expensive().

float ALI_PROFILE::w_del ( unsigned long  begin,
unsigned long  end 
)
inline

Definition at line 248 of file ali_profile.hxx.

Referenced by ali_aligner_dellist::update(), w_del_multi(), and w_del_multi_unweighted().

float ALI_PROFILE::w_del_cheap ( unsigned long  position)
inline

Definition at line 258 of file ali_profile.hxx.

Referenced by w_del_multi_cheap().

float ALI_PROFILE::w_del_multi ( unsigned long  start,
unsigned long  end 
)
inline

Definition at line 261 of file ali_profile.hxx.

References w_del().

Referenced by ali_aligner_last_cell::update_border().

float ALI_PROFILE::w_del_multi_cheap ( unsigned long  start,
unsigned long  end 
)
inline

Definition at line 268 of file ali_profile.hxx.

References w_del_cheap().

Referenced by ali_aligner_last_cell::update_up().

float ALI_PROFILE::w_del_multi_unweighted ( unsigned long  start,
unsigned long  end 
)
inline

Definition at line 275 of file ali_profile.hxx.

References w_del().

float ALI_PROFILE::w_ins ( unsigned  long,
unsigned  long 
)
inline

Definition at line 283 of file ali_profile.hxx.

float ALI_PROFILE::w_ins_cheap ( unsigned  long,
unsigned  long 
)
inline

Definition at line 286 of file ali_profile.hxx.

float ALI_PROFILE::w_ins_multi_unweighted ( unsigned long  startx,
unsigned long  endx 
)
inline

Definition at line 289 of file ali_profile.hxx.

float ALI_PROFILE::w_ins_multi ( unsigned long  startx,
unsigned long  endx 
)
inline

Definition at line 292 of file ali_profile.hxx.

Referenced by ali_aligner_last_cell::update_border().

float ALI_PROFILE::w_ins_multi_cheap ( unsigned long  startx,
unsigned long  endx 
)
inline

Definition at line 295 of file ali_profile.hxx.

Referenced by ali_aligner_last_cell::update_left().

float ALI_PROFILE::gap_percent ( unsigned long  begin,
unsigned long  end 
)
inline

Definition at line 300 of file ali_profile.hxx.

Referenced by ali_aligner_dellist::optimize(), and ali_aligner_dellist::print_cont().

float ALI_PROFILE::w_bind ( unsigned long  pos_1,
unsigned char  base_1,
unsigned long  pos_2,
unsigned char  base_2 
)
inline

Definition at line 311 of file ali_profile.hxx.

References ali_is_real_base_or_gap().

Referenced by ali_prealigner_mask::delete_expensive(), and w_binding().

float ALI_PROFILE::w_binding ( unsigned long  first_position_of_sequence,
ALI_SEQUENCE *  sequence 
)

Definition at line 610 of file ali_profile.cxx.

References ALI_SEQUENCE::base(), ALI_SEQUENCE::length(), long, and w_bind().

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