ARB
|
#include <cstdio>
#include <cstdlib>
#include <unistd.h>
#include <memory.h>
#include <attributes.h>
#include <arbtools.h>
Go to the source code of this file.
Macros | |
#define | ALI_A_CODE 0 |
#define | ALI_C_CODE 1 |
#define | ALI_G_CODE 2 |
#define | ALI_U_CODE 3 |
#define | ALI_GAP_CODE 4 |
#define | ALI_N_CODE 5 |
#define | ALI_DOT_CODE 6 |
#define | ALI_UNDEF_CODE 200 |
#define ALI_A_CODE 0 |
Definition at line 34 of file ali_misc.hxx.
#define ALI_C_CODE 1 |
Definition at line 35 of file ali_misc.hxx.
#define ALI_G_CODE 2 |
Definition at line 36 of file ali_misc.hxx.
#define ALI_U_CODE 3 |
Definition at line 37 of file ali_misc.hxx.
#define ALI_GAP_CODE 4 |
Definition at line 38 of file ali_misc.hxx.
Referenced by ali_prealigner_mask::delete_expensive(), ALI_MAP::sequence(), and ALI_MAP::sequence_without_inserts().
#define ALI_N_CODE 5 |
Definition at line 39 of file ali_misc.hxx.
#define ALI_DOT_CODE 6 |
Definition at line 40 of file ali_misc.hxx.
Referenced by ALI_MAP::sequence(), and ALI_MAP::sequence_without_inserts().
#define ALI_UNDEF_CODE 200 |
Definition at line 41 of file ali_misc.hxx.
|
inline |
Definition at line 46 of file ali_misc.hxx.
Referenced by ALI_ALIGNER::ALI_ALIGNER(), ALI_PREALIGNER::ALI_PREALIGNER(), ALI_PROFILE::ALI_PROFILE(), ALI_PT::ALI_PT(), ARB_main(), ALI_PT::find_family(), and ALI_GLOBAL::init().
|
inline |
Definition at line 47 of file ali_misc.hxx.
Referenced by ali_base_to_number(), ali_number_to_base(), ali_sequence_to_postree_sequence(), ARB_main(), ALI_TLIST< T >::delete_element(), ALI_GLOBAL::init(), ALI_PROFILE::is_in_helix(), and ALI_PROFILE::is_outside_helix().
Definition at line 90 of file ali_main.cxx.
Referenced by ALI_PROFILE::ALI_PROFILE(), ARB_main(), convert_for_back_write(), ALI_PT::find_family(), and ALI_GLOBAL::init().
Definition at line 85 of file ali_main.cxx.
Referenced by ali_number_to_base(), ali_out_of_memory_if(), ALI_PT::ALI_PT(), ALI_TARRAY< ali_pathmap_up_pointer >::ALI_TARRAY(), ARB_main(), ALI_PROFILE::base_weight(), ALI_SEQUENCE::check(), convert_for_back_write(), ali_prealigner_mask::delete_expensive(), ALI_PT::find_family(), ALI_PATHMAP::get(), ALI_TARRAY< ali_pathmap_up_pointer >::get(), ALI_TSTACK< T >::get(), ALI_PATHMAP::get_value(), ali_prealigner_mask::insert(), ALI_MAP::is_inserted(), ALI_MAP::is_undefined(), ALI_SUB_SOLUTION::make_one_map(), ALI_TLIST< ali_pt_member * >::marked(), ALI_TSTACK< T >::pop(), ALI_MAP::position(), ALI_TSTACK< T >::push(), ALI_PATHMAP::set(), ALI_TARRAY< ali_pathmap_up_pointer >::set(), ALI_MAP::set(), ALI_TSTACK< T >::top(), ALI_MAP::undefine(), and ALI_MAP::unundefine().
|
inline |
Definition at line 52 of file ali_misc.hxx.
References ali_fatal_error().
Referenced by ali_aligner_column::ali_aligner_column(), ALI_MAP::ALI_MAP(), ALI_NORM_SEQUENCE::ALI_NORM_SEQUENCE(), ALI_PATHMAP::ALI_PATHMAP(), ali_prealigner_column::ali_prealigner_column(), ALI_SEQUENCE::ALI_SEQUENCE(), ALI_TARRAY< ali_pathmap_up_pointer >::ALI_TARRAY(), ALI_PROFILE::borders_sequence(), CALLOC(), ALI_PROFILE::cheapest_sequence(), ALI_PT::find_family(), ALI_PATHMAP::optimize(), ALI_MAP::sequence(), ALI_MAP::sequence_without_inserts(), ALI_PATHMAP::set(), and ALI_NORM_SEQUENCE::string().
Definition at line 56 of file ali_misc.hxx.
References ali_out_of_memory_if().
Referenced by ALI_MAP::ALI_MAP(), ALI_NORM_SEQUENCE::ALI_NORM_SEQUENCE(), ALI_PATHMAP::ALI_PATHMAP(), ALI_PROFILE::cheapest_sequence(), ALI_MAP::insert_marker(), ALI_PATHMAP::optimize(), ALI_MAP::sequence(), ALI_MAP::sequence_without_inserts(), ALI_PATHMAP::set(), ALI_SEQUENCE::string(), and ALI_NORM_SEQUENCE::string().
Definition at line 66 of file ali_misc.hxx.
Referenced by ALI_NORM_SEQUENCE::ALI_NORM_SEQUENCE(), ali_sequence_to_postree_sequence(), ali_string_to_sequence(), and check_base_invariance().
Definition at line 72 of file ali_misc.hxx.
Definition at line 76 of file ali_misc.hxx.
Definition at line 82 of file ali_misc.hxx.
Definition at line 86 of file ali_misc.hxx.
Referenced by ALI_PROFILE::w_bind().
Definition at line 92 of file ali_misc.hxx.
Definition at line 96 of file ali_misc.hxx.
Referenced by ALI_NORM_SEQUENCE::ALI_NORM_SEQUENCE(), and convert_for_back_write().
Definition at line 100 of file ali_misc.hxx.
Definition at line 104 of file ali_misc.hxx.
Referenced by ali_sequence_to_postree_sequence().
Definition at line 108 of file ali_misc.hxx.
Definition at line 112 of file ali_misc.hxx.
Referenced by convert_for_back_write().
Definition at line 116 of file ali_misc.hxx.
Definition at line 120 of file ali_misc.hxx.
References ali_warning(), and FALLTHROUGH.
Referenced by ALI_NORM_SEQUENCE::ALI_NORM_SEQUENCE(), and ali_string_to_sequence().
Definition at line 134 of file ali_misc.hxx.
References ali_fatal_error(), and ali_warning().
Referenced by ali_sequence_to_string(), and ALI_PROFILE::cheapest_sequence().
|
inline |
Definition at line 150 of file ali_misc.hxx.
References ali_base_to_number(), and ali_is_base().
Referenced by ALI_SEQUENCE::ALI_SEQUENCE().
Definition at line 158 of file ali_misc.hxx.
References ali_number_to_base().
Referenced by ALI_SEQUENCE::string(), and ALI_NORM_SEQUENCE::string().
Definition at line 163 of file ali_misc.hxx.
References ali_is_base(), ali_is_nbase(), and ali_warning().
Definition at line 175 of file ali_misc.hxx.