AW_helix.cxx File Reference

#include "AW_helix.hxx"
#include <awt_config_manager.hxx>
#include <aw_root.hxx>
#include <aw_window.hxx>
#include <aw_awar.hxx>
#include <aw_device.hxx>
#include <arbdbt.h>
#include <arb_strbuf.h>
#include <cctype>

Include dependency graph for AW_helix.cxx:

Go to the source code of this file.

Classes
struct	helix_pair_def

Macros
#define	AWAR_HELIX_REFRESH   "tmp/Helix/refresh"
#define	AWAR_HELIX_ENABLE   "Helix/enable"
#define	HELIX_AWAR_SYMBOL_TEMPLATE   "Helix/symbols/%s"
#define	HELIX_AWAR_PAIR_TEMPLATE   "Helix/pairs/%s"

Functions
const char *	helix_symbol_awar (int idx)
const char *	helix_pair_awar (int idx)
static void	helix_setup_changed_cb (AW_root *aw_root, AW_helix *helix)
static void	helix_pairs_changed_cb (AW_root *aw_root, int changed_idx)
static void	setup_helix_config (AWT_config_definition &cdef)
AW_window *	create_helix_props_window (AW_root *awr)

Variables
static helix_pair_def	helix_awars []
static AWT_predefined_config	predefined_helix_configs []

Macro Definition Documentation

#define AWAR_HELIX_REFRESH   "tmp/Helix/refresh"

Definition at line 28 of file AW_helix.cxx.

Referenced by AW_helix::AW_helix(), and AW_helix::setup_changed_cb().

#define AWAR_HELIX_ENABLE   "Helix/enable"

Definition at line 29 of file AW_helix.cxx.

Referenced by AW_helix::AW_helix(), create_helix_props_window(), helix_pairs_changed_cb(), AW_helix::setup_changed_cb(), and setup_helix_config().

#define HELIX_AWAR_SYMBOL_TEMPLATE   "Helix/symbols/%s"

Definition at line 30 of file AW_helix.cxx.

Referenced by helix_symbol_awar().

#define HELIX_AWAR_PAIR_TEMPLATE   "Helix/pairs/%s"

Definition at line 31 of file AW_helix.cxx.

Referenced by helix_pair_awar().

Function Documentation

const char* helix_symbol_awar ( int  idx )

inline

Definition at line 53 of file AW_helix.cxx.

References GBS_global_string(), and HELIX_AWAR_SYMBOL_TEMPLATE.

Referenced by AW_helix::AW_helix(), create_helix_props_window(), AW_helix::setup_changed_cb(), and setup_helix_config().

const char* helix_pair_awar ( int  idx )

inline

Definition at line 54 of file AW_helix.cxx.

References GBS_global_string(), and HELIX_AWAR_PAIR_TEMPLATE.

Referenced by AW_helix::AW_helix(), create_helix_props_window(), helix_pairs_changed_cb(), AW_helix::setup_changed_cb(), and setup_helix_config().

static void helix_setup_changed_cb ( AW_root *  aw_root, AW_helix *  helix  )

static

Definition at line 82 of file AW_helix.cxx.

References AW_helix::setup_changed_cb().

Referenced by AW_helix::AW_helix().

static void helix_pairs_changed_cb ( AW_root *  aw_root, int  changed_idx  )

static

Definition at line 96 of file AW_helix.cxx.

References arb_assert, helix_pair_def::awar, AW_root::awar(), AWAR_HELIX_ENABLE, GBS_strstruct::cut(), GBS_strstruct::empty(), GBS_strstruct::get_data(), GBS_strstruct::get_position(), helix_pair_awar(), GBS_strstruct::put(), AW_awar::read_char_pntr(), AW_awar::read_string(), swap(), AW_awar::touch(), and AW_awar::write_string().

Referenced by AW_helix::AW_helix().

static void setup_helix_config ( AWT_config_definition &  cdef )

static

Definition at line 213 of file AW_helix.cxx.

References AWT_config_definition::add(), helix_pair_def::awar, AWAR_HELIX_ENABLE, GBS_global_string(), HELIX_DEFAULT, helix_pair_awar(), helix_symbol_awar(), and helix_pair_def::pair_type.

Referenced by create_helix_props_window().

AW_window* create_helix_props_window

(

AW_root *

awr

)

Definition at line 246 of file AW_helix.cxx.

References arb_assert, AW_POPDOWN(), AW_ROOT_DEFAULT, helix_pair_def::awar, AWAR_HELIX_ENABLE, AWT_insert_config_manager(), HELIX_DEFAULT, helix_pair_awar(), helix_symbol_awar(), makeHelpCallback(), NULp, helix_pair_def::pair_type, AW_window::reset_layout(), setup_helix_config(), and y.

Referenced by ED4_popup_helix_or_pfold_window().

Variable Documentation

helix_pair_def helix_awars[]

static

Initial value:

= {
    { "Strong_Pair",      HELIX_STRONG_PAIR },
    { "Normal_Pair",      HELIX_NORMAL_PAIR },
    { "Weak_Pair",        HELIX_WEAK_PAIR },
    { "No_Pair",          HELIX_NO_PAIR },
    { "User_Pair",        HELIX_USER0 },
    { "User_Pair2",       HELIX_USER1 },
    { "User_Pair3",       HELIX_USER2 },
    { "User_Pair4",       HELIX_USER3 },
    { "User_Pair5",       HELIX_USER4 },
    { "User_Pair6",       HELIX_USER5 },
    { "Default",          HELIX_DEFAULT },
    { NULp,               BI_PAIR_TYPE(-1) },
}

Definition at line 38 of file AW_helix.cxx.

AWT_predefined_config predefined_helix_configs[]

static

Initial value:

= {
    { "*traditional",
      "Traditional helix settings used up to arb 7.0\n(GG is defined as \"No pair\" here)\n",
      "Default_symbol='';No_Pair='AA AC CC CT CU GG TU';No_Pair_symbol='#';Normal_Pair='GT GU';Normal_Pair_symbol='-';Strong_Pair='CG AT AU';Strong_Pair_symbol='~';"
      "User_Pair='.A .C .G .T .U';User_Pair2='-A -C -G -T -U';User_Pair2_symbol='#';User_Pair3='UU TT';User_Pair3_symbol='+';"
      "User_Pair4='';User_Pair4_symbol='';User_Pair5='';User_Pair5_symbol='';User_Pair6='';User_Pair6_symbol='';User_Pair_symbol='*';Weak_Pair='GA';Weak_Pair_symbol='=';enable='1'" },
    { "*IUPAC_ambiguity_best",
      "Base pairings using ambiguity codes.\nUses best case, i.e. strongest of possible bonds.\nNote: most combinations form a strong bond \nfollowing that approach. They are NOT explicitely \nlisted, instead they use the default symbol.",
      "Default_symbol='~';No_Pair='AA AC CC CT CU TT UU';No_Pair_symbol='#';Normal_Pair='GT GU';Normal_Pair_symbol='-';Strong_Pair='CG AT AU';Strong_Pair_symbol='~';"
      "User_Pair='.A .C .G .T .U .M .R .W .S .Y .K .V .H .D .B .N';User_Pair2='-A -C -G -T -U -M -R -W -S -Y -K -V -H -D -B -N';User_Pair2_symbol='#';User_Pair3='-- .. -.';User_Pair3_symbol='';"
      "User_Pair4='AM CH CM CW CY MM TY UY YY';User_Pair4_symbol='#';User_Pair5='AR AS AV GR RR';User_Pair5_symbol='=';User_Pair6='BT BU DG GK GW KK KT KU ST SU SW';User_Pair6_symbol='-';User_Pair_symbol='*';Weak_Pair='GA GG';Weak_Pair_symbol='=';enable='1'" },
    { "*IUPAC_ambiguity_mean",
      "Base pairings using ambiguity codes.\nUses mean of possible bonds.\nNote: most combinations form a normal bond \nfollowing that approach. They are NOT explicitely \nlisted, instead they use the default symbol.",
      "Default_symbol='=';No_Pair='AA AC CC CT CU TT UU';No_Pair_symbol='#';Normal_Pair='GT GU';Normal_Pair_symbol='-';Strong_Pair='CG AT AU';Strong_Pair_symbol='~';"
      "User_Pair='.A .C .G .T .U .M .R .W .S .Y .K .V .H .D .B .N';User_Pair2='-A -C -G -T -U -M -R -W -S -Y -K -V -H -D -B -N';User_Pair2_symbol='#';User_Pair3='-- .. -.';User_Pair3_symbol='';"
      "User_Pair4='AM AV CH CM CW CY HM HY MM TY UY YY';User_Pair4_symbol='#';User_Pair5='AK BG BR BS CK CR CS GH GM GN GS GV KM KR KV RT RU RY SS';User_Pair5_symbol='-';User_Pair6='GY';User_Pair6_symbol='~';User_Pair_symbol='*';Weak_Pair='GA GG';Weak_Pair_symbol='=';enable='1'" },
    { NULp, NULp, NULp }
}

Definition at line 227 of file AW_helix.cxx.