ED4_search.cxx File Reference

#include <ed4_extern.hxx>
#include "ed4_awars.hxx"
#include "ed4_class.hxx"
#include "ed4_tools.hxx"
#include "ed4_edit_string.hxx"
#include <fast_aligner.hxx>
#include <awt_config_manager.hxx>
#include <aw_awars.hxx>
#include <aw_file.hxx>
#include <aw_msg.hxx>
#include <aw_root.hxx>
#include <aw_question.hxx>
#include <arbdbt.h>
#include <climits>
#include <cctype>
#include <cerrno>
#include <map>

Include dependency graph for ED4_search.cxx:

Go to the source code of this file.

Classes
struct	SearchAwarList
class	SearchSettings
class	SearchTreeNode
class	SearchTree
struct	LoadSaveSearchParam
struct	search_windows

Macros
#define	INSERT_ROOT_PATTERN(tok, com)
#define	AWAR_NAME(t, s)   ED4_AWAR_##t##_SEARCH_##s
#define	AWAR_LIST(t)
#define	cb(action)   add_callback(makeRootCallback(searchParamsChanged, ED4_SearchPositionType(i), search_params_changed_action(action)));
#define	ESC   '\\'

Typedefs
typedef void(*	reportMatch )(int start, int end, GB_CSTR comment, int mismatches[MAX_MISMATCHES])
typedef std::map< ED4_window *, SmartPtr< search_windows > >	search_window_map

Enumerations
enum	search_params_changed_action {   REFRESH_IF_SHOWN = 1, REFRESH_ALWAYS = 2, RECALC_SEARCH_TREE = 4, TEST_MIN_MISMATCH = 8,   TEST_MAX_MISMATCH = 16, DO_AUTO_JUMP = 32 }

Functions
static char *	shortenString (char *s)
static void	splitTokComment (char **tok, char **commentP)
static char *	appendComment (const char *s1, int l1, const char *s2)
static int	resultsAreShown (ED4_SearchPositionType type)
static void	searchParamsChanged (AW_root *root, ED4_SearchPositionType type, search_params_changed_action action)
void	ED4_create_search_awars (AW_root *root)
static void	reportSearchPosition (int start, int end, GB_CSTR comment, int mismatches[MAX_MISMATCHES])
void	decodeSearchDescriptor (int descriptor, int *direction, ED4_SearchPositionType *pattern)
GB_ERROR	ED4_repeat_last_search (ED4_window *ed4w)
void	ED4_search_cb (UNFIXED, int searchDescriptor, ED4_window *ed4w)
static void	ED4_mark_matching_species (AW_window *, ED4_SearchPositionType pattern)
static char *	pattern2str (GB_CSTR p)
static void	str2pattern (char *s)
static void	save_search_paras_to_file (AW_window *aw, ED4_SearchPositionType type)
static void	load_search_paras_from_file (AW_window *aw, ED4_SearchPositionType type)
static void	aws_init_localized (AW_root *root, AW_window_simple *aws, GB_CSTR id_format, GB_CSTR title_format, GB_CSTR typeId, int winNum)
static AW_window *	loadsave_search_parameters (AW_root *root, const LoadSaveSearchParam *param, bool load)
static void	setup_search_config (AWT_config_definition &cdef, ED4_SearchPositionType search_type)
void	ED4_popup_search_window (AW_window *aww, ED4_SearchPositionType type)

Variables
const char *	ED4_SearchPositionTypeId [SEARCH_PATTERNS+1]
static struct SearchAwarList	awar_list [SEARCH_PATTERNS]
static SearchSettings *	settings [SEARCH_PATTERNS]
static SearchTree *	tree [SEARCH_PATTERNS]
static ED4_SearchResults *	reportToResult = NULp
static ED4_SearchPositionType	reportType
static int	last_searchDescriptor = -1

Macro Definition Documentation

#define INSERT_ROOT_PATTERN	(		tok,
			com
	)

Value:

do {                                                    \
        if (root) {                                         \
            root = root->insert_unified_pattern(tok, com);  \
        }                                                   \
        else {                                              \
            root = new SearchTreeNode(tok, com);            \
        }                                                   \
    } while (0)

Referenced by SearchTree::SearchTree().

#define AWAR_NAME	(		t,
			s
	)		ED4_AWAR_##t##_SEARCH_##s

Definition at line 584 of file ED4_search.cxx.

#define AWAR_LIST

(

t

)

Value:

AWAR_NAME(t, PATTERN),                      \
    AWAR_NAME(t, MIN_MISMATCHES),               \
    AWAR_NAME(t, MAX_MISMATCHES),               \
    AWAR_NAME(t, CASE),                         \
    AWAR_NAME(t, TU),                           \
    AWAR_NAME(t, PAT_GAPS),                     \
    AWAR_NAME(t, SEQ_GAPS),                     \
    AWAR_NAME(t, REVERSE),                      \
    AWAR_NAME(t, COMPLEMENT),                   \
    AWAR_NAME(t, EXACT),                        \
    AWAR_NAME(t, SHOW),                         \
    AWAR_NAME(t, OPEN_FOLDED),                  \
    AWAR_NAME(t, AUTO_JUMP)

Definition at line 586 of file ED4_search.cxx.

#define cb

(

action

)

add_callback(makeRootCallback(searchParamsChanged, ED4_SearchPositionType(i), search_params_changed_action(action)));

Referenced by AW_root_cblist::add(), LocationEditor::add_pos_changed_cb(), TREE_canvas::at_screen_update_call(), gb_callback_list::call(), ED4_cb_list< ED4_species_manager, ED4_species_managerCallback >::call(), gb_pending_callbacks::call_and_forget(), TrackedFile::callAll(), AW_cb::contains(), CallbackList< gb_hierarchy_callback >::contains_unremoved_callback(), CallbackList< CB >::contains_unremoved_callback(), create_config_manager_window(), ED4_seq_colors::ED4_seq_colors(), ED4_with_all_edit_windows(), free_action(), GB_ensure_callback(), GB_get_callback_info(), GBK_raises_SIGSEGV(), glwInput(), AW_cb::is_equal(), IsSpecificHierarchyCallback::operator()(), Realize(), Redraw(), CallbackList< gb_callback >::remove_callbacks_that(), Resize(), ED4_base::route_down_hierarchy(), ED4_manager::route_down_hierarchy(), AW_cb::run_callbacks(), SEC_seq_data::SEC_seq_data(), DI_GLOBAL_MATRIX::set_changed_cb(), AP_tree_root::set_node_deleted_callback(), AP_tree_root::set_root_changed_callback(), with_affected_clusters_do(), and GEN_map_manager::with_all_mapped_windows().

#define ESC   '\\'

Definition at line 1386 of file ED4_search.cxx.

Referenced by pattern2str(), and str2pattern().

Typedef Documentation

typedef void(* reportMatch)(int start, int end, GB_CSTR comment, int mismatches[MAX_MISMATCHES])

Definition at line 123 of file ED4_search.cxx.

typedef std::map<ED4_window*, SmartPtr<search_windows> > search_window_map

Definition at line 1654 of file ED4_search.cxx.

Enumeration Type Documentation

enum search_params_changed_action

Enumerator
REFRESH_IF_SHOWN
REFRESH_ALWAYS
RECALC_SEARCH_TREE
TEST_MIN_MISMATCH
TEST_MAX_MISMATCH
DO_AUTO_JUMP

Definition at line 617 of file ED4_search.cxx.

Function Documentation

static char* shortenString ( char *  s )

static

Definition at line 307 of file ED4_search.cxx.

References s.

Referenced by splitTokComment().

static void splitTokComment ( char **  tok, char **  commentP  )

static

Definition at line 320 of file ED4_search.cxx.

References NULp, and shortenString().

Referenced by SearchTree::SearchTree().

static char* appendComment ( const char *  s1, int  l1, const char *  s2  )

static

Definition at line 334 of file ED4_search.cxx.

References NULp, and s.

Referenced by SearchTree::SearchTree().

static int resultsAreShown ( ED4_SearchPositionType  type )

inlinestatic

Definition at line 613 of file ED4_search.cxx.

References ED4_root::aw_root, AW_root::awar(), ED4_ROOT, AW_awar::read_int(), and SearchAwarList::show.

Referenced by ED4_SearchResults::ED4_SearchResults(), ED4_SearchResults::get_first_starting_after(), ED4_SearchResults::get_last_starting_before(), searchParamsChanged(), and ED4_SearchResults::setNewSearch().

static void searchParamsChanged ( AW_root *  root, ED4_SearchPositionType  type, search_params_changed_action  action  )

static

Definition at line 633 of file ED4_search.cxx.

References abs, aw_message(), AW_root::awar(), current_cursor(), current_ed4w(), DO_AUTO_JUMP, ED4_AWAR_SEARCH_RESULT_CHANGED, ED4_encodeSearchDescriptor(), ED4_JUMP_KEEP_POSITION, ED4_ROOT, ED4_search_cb(), ED4_root::first_window, GBS_global_string(), ED4_SearchResults::get_first_starting_after(), ED4_SearchResults::get_last_starting_before(), ED4_cursor::get_sequence_pos(), SearchTree::get_shortestPattern(), ED4_SearchPosition::get_start_pos(), ED4_base::is_sequence_terminal(), SearchAwarList::max_mismatches, SearchAwarList::min_mismatches, NULp, ED4_cursor::owner_of_cursor, AW_awar::read_int(), RECALC_SEARCH_TREE, REFRESH_ALWAYS, REFRESH_IF_SHOWN, ED4_root::request_refresh_for_sequence_terminals(), result, ED4_sequence_terminal::results(), resultsAreShown(), ED4_SearchResults::search(), ED4_terminal::setCursorTo(), ED4_SearchResults::setNewSearch(), TEST_MAX_MISMATCH, TEST_MIN_MISMATCH, AW_awar::touch(), type, SearchSettings::update(), win, and AW_awar::write_int().

void ED4_create_search_awars

(

AW_root *

root

)

Definition at line 735 of file ED4_search.cxx.

References ARB_strdup(), SearchAwarList::autoJump, AW_create_fileselection_awars(), AW_root::awar(), AW_root::awar_int(), AW_root::awar_string(), SearchAwarList::complement, DO_AUTO_JUMP, ED4_AWAR_SEARCH_RESULT_CHANGED, ED4_ROOT, ED4_SC_CASE_INSENSITIVE, ED4_SEARCH_SAVE_BASE, ED4_SG_IGNORE_GAPS, ED4_ST_T_EQUAL_U, SearchAwarList::exact, gb_main, GB_path_in_arbprop(), ED4_root::get_gb_main(), SearchAwarList::max_mismatches, SearchAwarList::min_mismatches, NULp, SearchAwarList::openFolded, SearchAwarList::pat_gaps, RECALC_SEARCH_TREE, REFRESH_ALWAYS, REFRESH_IF_SHOWN, SearchAwarList::reverse, SEARCH_PATTERNS, SearchAwarList::seq_gaps, SearchAwarList::show, TEST_MAX_MISMATCH, TEST_MIN_MISMATCH, SearchAwarList::tu, and AW_awar::write_string().

Referenced by ed4_create_all_awars().

static void reportSearchPosition ( int  start, int  end, GB_CSTR  comment, int  mismatches[MAX_MISMATCHES]  )

static

Definition at line 920 of file ED4_search.cxx.

References ED4_SearchResults::addSearchPosition().

Referenced by ED4_SearchResults::search().

void decodeSearchDescriptor ( int  descriptor, int *  direction, ED4_SearchPositionType *  pattern  )

inline

Definition at line 1248 of file ED4_search.cxx.

Referenced by ED4_search_cb().

GB_ERROR ED4_repeat_last_search

(

ED4_window *

ed4w

)

Definition at line 1255 of file ED4_search.cxx.

References ED4_search_cb(), GBS_global_string(), and NULp.

void ED4_search_cb	(	UNFIXED	,
		int	searchDescriptor,
		ED4_window *	ed4w
	)

Definition at line 1264 of file ED4_search.cxx.

References aw_message(), current_cursor(), decodeSearchDescriptor(), ED4_ANY_PATTERN, ED4_JUMP_KEEP_POSITION, ED4_ROOT, ED4_SearchResults::get_first_starting_after(), ED4_manager::get_first_terminal(), ED4_SearchResults::get_last_starting_before(), ED4_manager::get_last_terminal(), ED4_base::get_next_terminal(), ED4_base::get_prev_terminal(), ED4_cursor::get_sequence_pos(), ED4_SearchPosition::get_start_pos(), ED4_base::is_in_folded_group(), ED4_base::is_sequence_terminal(), NULp, ED4_cursor::owner_of_cursor, pattern, ED4_sequence_terminal::results(), ED4_root::root_group_man, ED4_SearchResults::search(), and ED4_terminal::setCursorTo().

Referenced by ED4_popup_search_window(), ED4_repeat_last_search(), ED4_root::generate_window(), insert_search_fields(), and searchParamsChanged().

static void ED4_mark_matching_species ( AW_window *  , ED4_SearchPositionType  pattern  )

static

Definition at line 1360 of file ED4_search.cxx.

References e4_assert, ED4_ROOT, GB_write_flag(), ED4_SearchResults::get_first_starting_after(), ED4_manager::get_first_terminal(), ED4_root::get_gb_main(), ED4_base::get_next_terminal(), ED4_base::get_parent(), ED4_base::is_sequence_terminal(), LEV_SPECIES, ED4_sequence_terminal::results(), ED4_root::root_group_man, ED4_SearchResults::search(), and ta.

Referenced by ED4_popup_search_window().

static char* pattern2str ( GB_CSTR  p )

static

Definition at line 1388 of file ED4_search.cxx.

References ARB_strdup(), ESC, GB_give_buffer(), and s.

Referenced by save_search_paras_to_file().

static void str2pattern ( char *  s )

static

Definition at line 1416 of file ED4_search.cxx.

References ESC, and s.

Referenced by load_search_paras_from_file().

static void save_search_paras_to_file ( AW_window *  aw, ED4_SearchPositionType  type  )

static

Definition at line 1447 of file ED4_search.cxx.

References aw_message(), AW_POPDOWN(), aw_question(), ED4_root::aw_root, AW_root::awar(), ED4_ROOT, ED4_SEARCH_SAVE_BASE, error(), GBS_global_string(), GBS_global_string_copy(), SearchSettings::get_autoJump(), SearchSettings::get_case_sensitive(), SearchSettings::get_complement(), SearchSettings::get_exact(), SearchSettings::get_max_mismatches(), SearchSettings::get_min_mismatches(), SearchSettings::get_open_folded(), SearchSettings::get_pat_gaps(), SearchSettings::get_pattern(), SearchSettings::get_reverse(), SearchSettings::get_seq_gaps(), SearchSettings::get_tu(), NULp, pattern2str(), AW_awar::read_string(), s, and type.

Referenced by loadsave_search_parameters().

static void load_search_paras_from_file ( AW_window *  aw, ED4_SearchPositionType  type  )

static

Definition at line 1512 of file ED4_search.cxx.

References SearchAwarList::autoJump, aw_message(), AW_POPDOWN(), ED4_root::aw_root, AW_root::awar(), buffer, BUFFERSIZE, SearchAwarList::case_sensitive, SearchAwarList::complement, ED4_ROOT, ED4_SEARCH_SAVE_BASE, error(), SearchAwarList::exact, GBS_global_string(), SearchAwarList::max_mismatches, SearchAwarList::min_mismatches, NULp, SearchAwarList::openFolded, SearchAwarList::pat_gaps, SearchAwarList::pattern, AW_awar::read_string(), SearchAwarList::reverse, SearchAwarList::seq_gaps, str2pattern(), SearchAwarList::tu, type, AW_awar::write_int(), and AW_awar::write_string().

Referenced by loadsave_search_parameters().

static void aws_init_localized ( AW_root *  root, AW_window_simple *  aws, GB_CSTR  id_format, GB_CSTR  title_format, GB_CSTR  typeId, int  winNum  )

static

Definition at line 1570 of file ED4_search.cxx.

References GBS_global_string_copy(), and GBS_string_2_key().

Referenced by ED4_popup_search_window(), and loadsave_search_parameters().

static AW_window* loadsave_search_parameters ( AW_root *  root, const LoadSaveSearchParam *  param, bool  load  )

static

Definition at line 1592 of file ED4_search.cxx.

References AW_create_standard_fileselection(), AW_POPDOWN(), aws_init_localized(), ED4_SEARCH_SAVE_BASE, load_search_paras_from_file(), makeHelpCallback(), save_search_paras_to_file(), LoadSaveSearchParam::type, and LoadSaveSearchParam::winNum.

Referenced by ED4_popup_search_window().

static void setup_search_config ( AWT_config_definition &  cdef, ED4_SearchPositionType  search_type  )

static

Definition at line 1631 of file ED4_search.cxx.

References AWT_config_definition::add(), SearchAwarList::autoJump, SearchAwarList::case_sensitive, SearchAwarList::complement, SearchAwarList::exact, SearchAwarList::max_mismatches, SearchAwarList::min_mismatches, SearchAwarList::openFolded, SearchAwarList::pat_gaps, SearchAwarList::pattern, SearchAwarList::reverse, SearchAwarList::seq_gaps, SearchAwarList::show, and SearchAwarList::tu.

Referenced by ED4_popup_search_window().

void ED4_popup_search_window	(	AW_window *	aww,
		ED4_SearchPositionType	type
	)

Definition at line 1656 of file ED4_search.cxx.

References SearchAwarList::autoJump, AW_HORIZONTAL, AW_POPDOWN(), AW_ROOT_DEFAULT, aws_init_localized(), AWT_insert_config_manager(), SearchAwarList::case_sensitive, SearchAwarList::complement, ED4_encodeSearchDescriptor(), ED4_mark_matching_species(), ED4_search_cb(), SearchAwarList::exact, ED4_WinContext::get_ed4w(), AW_window::get_root(), ED4_window::id, loadsave_search_parameters(), makeHelpCallback(), SearchAwarList::max_mismatches, SearchAwarList::min_mismatches, SearchAwarList::openFolded, SearchAwarList::pat_gaps, SearchAwarList::pattern, SearchAwarList::reverse, SearchAwarList::seq_gaps, setup_search_config(), SearchAwarList::show, SearchAwarList::tu, type, and search_windows::windows.

Referenced by ED4_root::generate_window(), and insert_search_fields().

Variable Documentation

const char* ED4_SearchPositionTypeId[SEARCH_PATTERNS+1]

Initial value:

= {
    "User1", "User2",
    "Probe",
    "Primer (local)", "Primer (region)", "Primer (global)",
    "Signature (local)", "Signature (region)", "Signature (global)",
    "Any"
}

Definition at line 35 of file ED4_search.cxx.

Referenced by ED4_root::generate_window().

struct SearchAwarList awar_list[SEARCH_PATTERNS]

static

Initial value:

= {
    { AWAR_LIST(USER1) },
    { AWAR_LIST(USER2) },
    { AWAR_LIST(PROBE) },
    { AWAR_LIST(PRIMER1) },
    { AWAR_LIST(PRIMER2) },
    { AWAR_LIST(PRIMER3) },
    { AWAR_LIST(SIG1) },
    { AWAR_LIST(SIG2) },
    { AWAR_LIST(SIG3) },
}

Definition at line 601 of file ED4_search.cxx.

Referenced by MG_create_preserves_selection_window().

SearchSettings* settings[SEARCH_PATTERNS]

static

Definition at line 628 of file ED4_search.cxx.

Referenced by ArbParsimony::optimize_tree().

SearchTree* tree[SEARCH_PATTERNS]

static

Definition at line 629 of file ED4_search.cxx.

Referenced by add_dtree_to_dtree(), add_to_dtree(), build_dict_tree(), calculate_clusters(), cut_dtree(), cut_useless_words(), DI_MATRIX::extract_from_tree(), gbt_is_invalid(), GBT_read_tree_and_size(), GBT_remove_leafs(), TreeReader::load(), new_dtree(), nt_build_conf_string_rek(), PVP_calculate(), remove_word_from_dtree(), removeSubsequentString(), single2full_dtree(), TREE_load(), and tree_of_cached_taxonomy().

ED4_SearchResults* reportToResult = NULp

static

Definition at line 917 of file ED4_search.cxx.

ED4_SearchPositionType reportType

static

Definition at line 918 of file ED4_search.cxx.

int last_searchDescriptor = -1

static

Definition at line 1253 of file ED4_search.cxx.