ARB
Classes | Macros | Functions | Variables
ED4_block.cxx File Reference
#include "ed4_awars.hxx"
#include "ed4_class.hxx"
#include "ed4_tools.hxx"
#include "ed4_block.hxx"
#include "ed4_edit_string.hxx"
#include "ed4_list.hxx"
#include <awt_sel_boxes.hxx>
#include <fast_aligner.hxx>
#include <aw_awars.hxx>
#include <aw_msg.hxx>
#include <aw_root.hxx>
#include <aw_select.hxx>
#include <arbdbt.h>
#include <arb_defs.h>
#include <gb_aci.h>
#include <climits>
#include <cctype>
#include <map>
Include dependency graph for ED4_block.cxx:

Go to the source code of this file.

Classes

class  ED4_block
 
class  SeqPart
 
class  replace_op
 
class  case_op
 
class  revcomp_op
 
class  unalign_op
 
class  shift_op
 

Macros

#define AWAR_MOD_SAI_SCRIPT   "modsai/script"
 

Functions

static void col_block_refresh_on_seq_term (ED4_sequence_terminal *seq_term)
 
static void refresh_highlighted (bool refresh_name_terminals)
 
static GB_ERROR perform_block_operation_on_whole_sequence (const ED4_block_operator&block_operator, ED4_sequence_terminal *term)
 
static GB_ERROR perform_block_operation_on_part_of_sequence (const ED4_block_operator&block_operator, ED4_sequence_terminal *term)
 
static void ED4_with_whole_block (const ED4_block_operator&block_operator)
 
bool ED4_get_highlighted_range (ED4_terminal *term, PosRange &range)
 
ED4_blocktype ED4_getBlocktype ()
 
void ED4_setBlocktype (ED4_blocktype bt)
 
void ED4_toggle_block_type ()
 
void ED4_correctBlocktypeAfterModification ()
 
static void highlight_and_update (ED4_sequence_terminal *term1, ED4_sequence_terminal *term2, ED4_index pos1, ED4_index pos2, int initial_call)
 
void ED4_setColumnblockCorner (AW_event *event, ED4_sequence_terminal *seq_term)
 
bool matchesUsingWildcard (GB_CSTR s1, GB_CSTR s2, int len)
 
static void replace_in_block (AW_window *)
 
AW_window * ED4_create_replace_window (AW_root *root)
 
char * dont_return_unchanged (char *result, int &new_len, const SeqPart &part)
 
void ED4_perform_block_operation (ED4_blockoperation_type operationType)
 
static void modsai_cb (AW_window *aww)
 
AW_window * ED4_create_modsai_window (AW_root *root)
 

Variables

static ED4_block block
 

Macro Definition Documentation

#define AWAR_MOD_SAI_SCRIPT   "modsai/script"

Definition at line 918 of file ED4_block.cxx.

Referenced by ED4_create_modsai_window(), and modsai_cb().

Function Documentation

static void col_block_refresh_on_seq_term ( ED4_sequence_terminal *  seq_term)
static

Definition at line 113 of file ED4_block.cxx.

References ED4_sequence_terminal::corresponding_columnStat_terminal(), and ED4_terminal::request_refresh().

Referenced by highlight_and_update(), and refresh_highlighted().

static void refresh_highlighted ( bool  refresh_name_terminals)
static

Definition at line 119 of file ED4_block.cxx.

References col_block_refresh_on_seq_term(), ED4_ROOT, ED4_list_elem< T >::elem(), ED4_list< T >::head(), ED4_root::highlighted_objects, ED4_list_elem< T >::next(), and ED4_terminal::request_refresh().

Referenced by highlight_and_update(), and ED4_block::set_type().

static GB_ERROR perform_block_operation_on_whole_sequence ( const ED4_block_operator&  block_operator,
ED4_sequence_terminal *  term 
)
static

Definition at line 196 of file ED4_block.cxx.

References ED4_is_gap_character(), error(), GB_read_string(), GB_read_string_count(), GB_write_string(), ED4_block_operator::get_error(), ED4_base::get_species_pointer(), NULp, ED4_block_operator::operate(), ED4_terminal::request_refresh(), and seq.

Referenced by ED4_with_whole_block().

static GB_ERROR perform_block_operation_on_part_of_sequence ( const ED4_block_operator&  block_operator,
ED4_sequence_terminal *  term 
)
static

Definition at line 247 of file ED4_block.cxx.

References ED4_is_gap_character(), error(), GB_read_string(), GB_read_string_count(), GB_write_autoconv_string(), ED4_block::get_colblock_range(), ED4_block_operator::get_error(), ED4_base::get_species_pointer(), NULp, ED4_block_operator::operate(), ED4_terminal::request_refresh(), seq, and PosRange::size().

Referenced by ED4_with_whole_block().

static void ED4_with_whole_block ( const ED4_block_operator&  block_operator)
static

Definition at line 302 of file ED4_block.cxx.

References aw_message(), ED4_window::cursor, ED4_BT_COLUMNBLOCK, ED4_BT_LINEBLOCK, ED4_BT_MODIFIED_COLUMNBLOCK, ED4_BT_NOBLOCK, ED4_JUMP_KEEP_VISIBLE, ED4_ROOT, ED4_list_elem< T >::elem(), error(), ED4_root::first_window, GB_begin_transaction(), GB_end_transaction_show_error(), gb_main, GBS_global_string(), ED4_cursor::get_base_position(), ED4_root::get_gb_main(), ED4_block::get_type(), ED4_list< T >::head(), ED4_root::highlighted_objects, ED4_cursor::jump_base_pos(), ED4_list_elem< T >::next(), ED4_cursor::owner_of_cursor, perform_block_operation_on_part_of_sequence(), perform_block_operation_on_whole_sequence(), ED4_root::root_group_man, ED4_root_group_manager::update_remap(), and win.

Referenced by ED4_perform_block_operation(), and replace_in_block().

bool ED4_get_highlighted_range ( ED4_terminal *  term,
PosRange &  range 
)

Definition at line 355 of file ED4_block.cxx.

References ED4_base::containing_species_manager(), ED4_BT_NOBLOCK, ED4_block::get_range_according_to_type(), and ED4_block::get_type().

Referenced by get_selected_range().

ED4_blocktype ED4_getBlocktype ( )

Definition at line 363 of file ED4_block.cxx.

References ED4_block::get_type().

Referenced by ED4_menu_highlight().

void ED4_setBlocktype ( ED4_blocktype  bt)

Definition at line 364 of file ED4_block.cxx.

References ED4_block::set_type().

Referenced by ED4_root::deselect_all().

void ED4_toggle_block_type ( )

Definition at line 365 of file ED4_block.cxx.

References ED4_block::toggle_type().

Referenced by ED4_menu_highlight().

void ED4_correctBlocktypeAfterModification ( )

Definition at line 366 of file ED4_block.cxx.

References ED4_block::autocorrect_type().

Referenced by ED4_menu_highlight(), ED4_terminal::event_sent_by_parent(), and ED4_multi_species_manager::toggle_selected_species().

static void highlight_and_update ( ED4_sequence_terminal *  term1,
ED4_sequence_terminal *  term2,
ED4_index  pos1,
ED4_index  pos2,
int  initial_call 
)
static

Definition at line 368 of file ED4_block.cxx.

References ED4_root::add_to_highlighted(), ED4_root::aw_root, AW_root::awar(), AWAR_RANGE, ED4_base::calc_world_coords(), col_block_refresh_on_seq_term(), ED4_base::containing_species_manager(), ED4_abstract_sequence_terminal::corresponding_species_name_terminal(), ED4_BT_MODIFIED_COLUMNBLOCK, ED4_ROOT, PosRange::end(), GBS_global_string(), ED4_base::get_next_terminal(), ED4_block::get_range_according_to_type(), ED4_block::get_type(), info2bio(), ED4_base::is_sequence_terminal(), ED4_base::is_species_name_terminal(), refresh_highlighted(), ED4_root::remove_from_highlighted(), ED4_block::set_range(), PosRange::start(), AW_awar::write_string(), and y.

Referenced by ED4_setColumnblockCorner().

void ED4_setColumnblockCorner ( AW_event *  event,
ED4_sequence_terminal *  seq_term 
)

Definition at line 474 of file ED4_block.cxx.

References abs, AW_Mouse_Drag, AW_Mouse_Press, AW_Mouse_Release, ED4_abstract_sequence_terminal::calc_interval_displayed_in_rectangle(), ED4_base::calc_world_coords(), ED4_remap::clip_screen_range(), current_ed4w(), e4_assert, ED4_BT_COLUMNBLOCK, ED4_BT_LINEBLOCK, ED4_BT_MODIFIED_COLUMNBLOCK, ED4_BT_NOBLOCK, ED4_R_OK, ED4_ROOT, PosRange::end(), ED4_root::get_area_rectangle(), ED4_block::get_colblock_range(), ED4_block::get_type(), ED4_list< T >::head(), highlight_and_update(), ED4_root::highlighted_objects, intersection(), ED4_base::is_consensus_terminal(), PosRange::is_empty(), MAXSEQUENCECHARACTERLENGTH, NULp, ED4_root::pixel2pos(), ED4_root_group_manager::remap(), ED4_root::root_group_man, ED4_remap::screen_to_sequence(), ED4_remap::sequence_to_screen(), ED4_block::set_type(), PosRange::start(), AW_event::type, ED4_foldable::world_to_win_coords(), and AW_event::x.

Referenced by ED4_terminal::event_sent_by_parent().

bool matchesUsingWildcard ( GB_CSTR  s1,
GB_CSTR  s2,
int  len 
)
inline

Definition at line 618 of file ED4_block.cxx.

References cmp.

Referenced by replace_op::operate().

static void replace_in_block ( AW_window *  )
static

Definition at line 688 of file ED4_block.cxx.

References ED4_root::aw_root, AW_root::awar(), ED4_AWAR_REP_REPLACE_PATTERN, ED4_AWAR_REP_SEARCH_PATTERN, ED4_ROOT, ED4_with_whole_block(), and AW_awar::read_char_pntr().

Referenced by ED4_create_replace_window().

AW_window* ED4_create_replace_window ( AW_root *  root)

Definition at line 695 of file ED4_block.cxx.

References AW_POPDOWN(), ED4_AWAR_REP_REPLACE_PATTERN, ED4_AWAR_REP_SEARCH_PATTERN, AW_window::load_xfig(), makeHelpCallback(), and replace_in_block().

Referenced by ED4_root::generate_window().

char* dont_return_unchanged ( char *  result,
int &  new_len,
const SeqPart &  part 
)
inline

Definition at line 725 of file ED4_block.cxx.

References SeqPart::data(), SeqPart::length(), and result.

Referenced by case_op::operate(), revcomp_op::operate(), unalign_op::operate(), and shift_op::operate().

void ED4_perform_block_operation ( ED4_blockoperation_type  operationType)

Definition at line 892 of file ED4_block.cxx.

References ED4_root::alignment_type, e4_assert, ED4_BO_COMPLEMENT, ED4_BO_LOWER_CASE, ED4_BO_REVERSE, ED4_BO_REVERSE_COMPLEMENT, ED4_BO_SHIFT_LEFT, ED4_BO_SHIFT_RIGHT, ED4_BO_UNALIGN_CENTER, ED4_BO_UNALIGN_LEFT, ED4_BO_UNALIGN_RIGHT, ED4_BO_UPPER_CASE, ED4_ROOT, and ED4_with_whole_block().

Referenced by ED4_menu_perform_block_operation().

static void modsai_cb ( AW_window *  aww)
static

Definition at line 920 of file ED4_block.cxx.

References aw_message_if(), AW_root::awar(), AWAR_MOD_SAI_SCRIPT, AWAR_SAI_NAME, GB_transaction::close(), current_cursor(), PosRange::dup_corresponding_part(), ED4_BT_NOBLOCK, ED4_ROOT, error(), GB_await_error(), GB_command_interpreter_in_env(), GB_have_error(), gb_main, GB_read_string(), GB_read_string_count(), GB_write_string(), GBS_global_string(), GBT_find_SAI(), GBT_find_sequence(), ED4_root::get_alignment_name(), ED4_root::get_gb_main(), ED4_block::get_range_according_to_type(), AW_window::get_root(), ED4_block::get_type(), ED4_cursor::in_SAI_terminal(), NULp, AW_awar::read_char_pntr(), AW_awar::read_string(), result, seq, and ta.

Referenced by ED4_create_modsai_window().

AW_window* ED4_create_modsai_window ( AW_root *  root)

Definition at line 985 of file ED4_block.cxx.

References aw_message_if(), AW_POPDOWN(), AWAR_MOD_SAI_SCRIPT, AW_root::awar_string(), awt_create_selection_list_with_input_field(), error(), GB_path_in_ARBLIB(), StorableSelectionList::load(), makeHelpCallback(), modsai_cb(), and AW_awar::write_string().

Referenced by ED4_root::generate_window().

Variable Documentation

ED4_block block
static

Definition at line 74 of file ED4_block.cxx.

Referenced by dump_token_recursive(), gbm_put_memblk(), gbmFreeMemImpl(), Parser::parseTokenListBlock(), Memory::put(), ConstStrArray::set_memblock(), and TokenList::set_parent().

Generated by   doxygen 1.8.8