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Classes | |
| class | PH_root |
| class | PHDATA |
Macros | |
| #define | ph_assert(cond) arb_assert(cond) |
| #define | AWAR_PHYLO_ALIGNMENT "tmp/phyl/alignment" |
| #define | AWAR_PHYLO_FILTER_FILTER "phyl/filter/filter" |
| #define | AWAR_PHYLO_FILTER_STARTCOL "phyl/filter/startcol" |
| #define | AWAR_PHYLO_FILTER_STOPCOL "phyl/filter/stopcol" |
| #define | AWAR_PHYLO_FILTER_MINHOM "phyl/filter/minhom" |
| #define | AWAR_PHYLO_FILTER_MAXHOM "phyl/filter/maxhom" |
| #define | AWAR_PHYLO_FILTER_DOT "phyl/filter/point" |
| #define | AWAR_PHYLO_FILTER_MINUS "phyl/filter/minus" |
| #define | AWAR_PHYLO_FILTER_AMBIG "phyl/filter/rest" |
| #define | AWAR_PHYLO_FILTER_LOWER "phyl/filter/lower" |
| #define | AWAR_PHYLO_FILTER_AUTOCALC "phyl/filter/autocalc" |
| #define | AWAR_PHYLO_MARKERLINENAME "tmp/phylo/markerlinename" |
| #define | PH_DB_CACHE_SIZE 2000000 |
Enumerations | |
| enum | FilterMode { DONT_COUNT, SKIP_COLUMN_IF_MAX, SKIP_COLUMN_IF_OCCUR, COUNT_DONT_USE_MAX, TREAT_AS_UPPERCASE, TREAT_AS_REGULAR } |
| enum | { PH_GC_SEQUENCE, PH_GC_MARKER, PH_GC_NOT_MARKER, PH_GC_DRAG } |
| enum | { PH_GC_BOTTOM_TEXT, PH_GC_BOTTOM_DRAG } |
| enum | display_type { DISP_NONE, DISP_SPECIES, DISP_FILTER } |
Functions | |
| void | PH_create_filter_variables (AW_root *aw_root, AW_default default_file, GBDATA *gb_main) |
| AW_window * | PH_create_filter_window (AW_root *aw_root) |
Variables | |
| const int | FILTER_MODES = TREAT_AS_REGULAR+1 |
Macro Definition Documentation
| #define ph_assert | ( | cond | ) | arb_assert(cond) |
Definition at line 24 of file phylo.hxx.
Referenced by PH_filter::calculate_column_homology(), gc_changed_cb(), PH_root::get_gb_main(), PHDATA::load(), PH_create_filter_variables(), PH_create_ml_multiline_SAI(), PH_root::PH_root(), and PH_root::~PH_root().
| #define AWAR_PHYLO_ALIGNMENT "tmp/phyl/alignment" |
Definition at line 26 of file phylo.hxx.
Referenced by ARB_main(), create_select_alignment_window(), create_variables(), startup_sequence_cb(), and valid_alignment_selected().
| #define AWAR_PHYLO_FILTER_FILTER "phyl/filter/filter" |
Definition at line 27 of file phylo.hxx.
Referenced by PH_filter::calculate_column_homology(), and create_variables().
| #define AWAR_PHYLO_FILTER_STARTCOL "phyl/filter/startcol" |
Definition at line 29 of file phylo.hxx.
Referenced by PH_filter::calculate_column_homology(), correct_startstop_cb(), PH_display::display(), display_status_cb(), PH_create_filter_variables(), PH_create_filter_window(), PH_create_ml_multiline_SAI(), PH_save_ml_cb(), and startup_sequence_cb().
| #define AWAR_PHYLO_FILTER_STOPCOL "phyl/filter/stopcol" |
Definition at line 30 of file phylo.hxx.
Referenced by PH_filter::calculate_column_homology(), correct_startstop_cb(), PH_display::display(), display_status_cb(), PH_create_filter_variables(), PH_create_filter_window(), PH_create_ml_multiline_SAI(), PH_save_ml_cb(), and startup_sequence_cb().
| #define AWAR_PHYLO_FILTER_MINHOM "phyl/filter/minhom" |
Definition at line 31 of file phylo.hxx.
Referenced by PH_filter::calculate_column_homology(), correct_minmaxhom_cb(), PH_display::display(), display_status_cb(), PH_create_filter_variables(), PH_create_filter_window(), PH_create_ml_multiline_SAI(), and PH_save_ml_cb().
| #define AWAR_PHYLO_FILTER_MAXHOM "phyl/filter/maxhom" |
Definition at line 32 of file phylo.hxx.
Referenced by PH_filter::calculate_column_homology(), correct_minmaxhom_cb(), PH_display::display(), display_status_cb(), PH_create_filter_variables(), PH_create_filter_window(), PH_create_ml_multiline_SAI(), and PH_save_ml_cb().
| #define AWAR_PHYLO_FILTER_DOT "phyl/filter/point" |
Definition at line 33 of file phylo.hxx.
Referenced by PH_filter::calculate_column_homology(), display_status_cb(), PH_create_filter_variables(), and PH_create_filter_window().
| #define AWAR_PHYLO_FILTER_MINUS "phyl/filter/minus" |
Definition at line 34 of file phylo.hxx.
Referenced by PH_filter::calculate_column_homology(), display_status_cb(), PH_create_filter_variables(), and PH_create_filter_window().
| #define AWAR_PHYLO_FILTER_AMBIG "phyl/filter/rest" |
Definition at line 35 of file phylo.hxx.
Referenced by PH_filter::calculate_column_homology(), display_status_cb(), PH_create_filter_variables(), and PH_create_filter_window().
| #define AWAR_PHYLO_FILTER_LOWER "phyl/filter/lower" |
Definition at line 36 of file phylo.hxx.
Referenced by PH_filter::calculate_column_homology(), display_status_cb(), PH_create_filter_variables(), and PH_create_filter_window().
| #define AWAR_PHYLO_FILTER_AUTOCALC "phyl/filter/autocalc" |
Definition at line 37 of file phylo.hxx.
Referenced by PH_create_filter_variables(), PH_create_filter_window(), ph_view_species_cb(), and update_on_config_change_cb().
| #define AWAR_PHYLO_MARKERLINENAME "tmp/phylo/markerlinename" |
Definition at line 39 of file phylo.hxx.
Referenced by PH_save_markerline(), PH_save_ml_cb(), and PH_save_ml_multiline_cb().
| #define PH_DB_CACHE_SIZE 2000000 |
Definition at line 55 of file phylo.hxx.
Referenced by startup_sequence_cb().
Enumeration Type Documentation
| enum FilterMode |
| anonymous enum |
| anonymous enum |
| enum display_type |
Function Documentation
| void PH_create_filter_variables | ( | AW_root * | aw_root, |
| AW_default | default_file, | ||
| GBDATA * | gb_main | ||
| ) |
Definition at line 371 of file PH_filt.cxx.
References AW_awar::add_callback(), aw_message_if(), AW_root::awar_int(), AWAR_PHYLO_FILTER_AMBIG, AWAR_PHYLO_FILTER_AUTOCALC, AWAR_PHYLO_FILTER_DOT, AWAR_PHYLO_FILTER_LOWER, AWAR_PHYLO_FILTER_MAXHOM, AWAR_PHYLO_FILTER_MINHOM, AWAR_PHYLO_FILTER_MINUS, AWAR_PHYLO_FILTER_STARTCOL, AWAR_PHYLO_FILTER_STOPCOL, correct_minmaxhom_cb(), correct_startstop_cb(), DONT_COUNT, GB_await_error(), GBT_get_alignment_len(), GBT_get_default_alignment(), ph_assert, AW_awar::set_minmax(), ta, and update_on_config_change_cb().
Referenced by create_variables().
Definition at line 416 of file PH_filt.cxx.
References AW_POPDOWN(), AW_ROOT_DEFAULT, AWAR_PHYLO_FILTER_AMBIG, AWAR_PHYLO_FILTER_AUTOCALC, AWAR_PHYLO_FILTER_DOT, AWAR_PHYLO_FILTER_LOWER, AWAR_PHYLO_FILTER_MAXHOM, AWAR_PHYLO_FILTER_MINHOM, AWAR_PHYLO_FILTER_MINUS, AWAR_PHYLO_FILTER_STARTCOL, AWAR_PHYLO_FILTER_STOPCOL, AWT_insert_config_manager(), COUNT_DONT_USE_MAX, DONT_COUNT, filter_text, AW_window::load_xfig(), SKIP_COLUMN_IF_MAX, SKIP_COLUMN_IF_OCCUR, TREAT_AS_REGULAR, and TREAT_AS_UPPERCASE.
Referenced by create_phyl_main_window().
Variable Documentation
| const int FILTER_MODES = TREAT_AS_REGULAR+1 |
