probe_design.cxx File Reference

#include "SaiProbeVisualization.hxx"
#include "probe_match_parser.hxx"
#include <PT_com.h>
#include <PT_server.h>
#include <client.h>
#include <servercntrl.h>
#include <probe_gui.hxx>
#include <probe_local.hxx>
#include <GEN.hxx>
#include <TreeCallbacks.hxx>
#include <iupac.h>
#include <awt_config_manager.hxx>
#include <awt_sel_boxes.hxx>
#include <awt_misc.hxx>
#include <aw_awars.hxx>
#include <aw_preset.hxx>
#include <aw_select.hxx>
#include <aw_msg.hxx>
#include <aw_root.hxx>
#include <aw_question.hxx>
#include <aw_edit.hxx>
#include <aw_global_awars.hxx>
#include <rootAsWin.h>
#include <adGene.h>
#include <arb_progress.h>
#include <arb_strbuf.h>
#include <arb_file.h>
#include <arb_misc.h>
#include "probe_collection.hxx"

Include dependency graph for probe_design.cxx:

Go to the source code of this file.

Classes
struct	ProbeMatchEventParam
struct	AutoMatchSettings
struct	ProbeCommonSettings
struct	ProbeMatchSettings
struct	ArbPM_Context
struct	ArbWriteFile_Context
class	GetMatchesContext
class	ProbeCollDisplay
struct	ArbPC_Context

Macros
#define	AWAR_PROBE_CREATE_GENE_SERVER   "tmp/probe_admin/gene_server"
#define	AWAR_ITARGET_STRING   "nt/itarget_string"
#define	AWAR_PD_SELECTED_MATCH   "tmp/probe_design/match"
#define	AWAR_PD_MATCH_RESOLVE   "tmp/probe_design/match_resolve"
#define	AWAR_PD_MATCH_SORTBY   "probe_match/sort_by"
#define	AWAR_PD_MATCH_ALSO_REVCOMP   "probe_match/complement"
#define	AWAR_PD_MATCH_MARKHITS   "probe_match/mark_hits"
#define	AWAR_PD_MATCH_WRITE2TMP   "probe_match/write_2_tmp"
#define	AWAR_PD_MATCH_AUTOMATCH   "probe_match/auto_match"
#define	AWAR_PD_MATCH_NHITS   "tmp/probe_match/nhits"
#define	AWAR_PD_DESIGN_CLIPRESULT   "probe_design/CLIPRESULT"
#define	AWAR_PD_DESIGN_MISHIT   "probe_design/MISHIT"
#define	AWAR_PD_DESIGN_MAXBOND   "probe_design/MAXBOND"
#define	AWAR_PD_DESIGN_MINTARGETS   "probe_design/MINTARGETS"
#define	AWAR_PD_DESIGN_MIN_LENGTH   "probe_design/PROBELENGTH"
#define	AWAR_PD_DESIGN_MAX_LENGTH   "probe_design/PROBEMAXLENGTH"
#define	AWAR_PD_DESIGN_MIN_TEMP   "probe_design/MINTEMP"
#define	AWAR_PD_DESIGN_MAX_TEMP   "probe_design/MAXTEMP"
#define	AWAR_PD_DESIGN_MIN_GC   "probe_design/MINGC"
#define	AWAR_PD_DESIGN_MAX_GC   "probe_design/MAXGC"
#define	AWAR_PD_DESIGN_MIN_ECOLIPOS   "probe_design/MINECOLI"
#define	AWAR_PD_DESIGN_MAX_ECOLIPOS   "probe_design/MAXECOLI"
#define	AWAR_PD_DESIGN_GENE   "probe_design/gene"
#define	AWAR_PD_COMMON_EXP_BONDS_FORMAT   "probe_design/bonds/pos%i"
#define	AWAR_PD_COMMON_EXP_SPLIT   "probe_design/SPLIT"
#define	AWAR_PD_DESIGN_EXP_DTEDGE   "probe_design/DTEDGE"
#define	AWAR_PD_DESIGN_EXP_DT   "probe_design/DT"
#define	AWAR_PD_MATCH_NMATCHES   "probe_match/nmatches"
#define	AWAR_PD_MATCH_LIM_NMATCH   "probe_match/lim_nmatch"
#define	AWAR_PD_MATCH_MAX_RES   "probe_match/maxres"
#define	AWAR_PC_TARGET_STRING   "probe_collection/target_string"
#define	AWAR_PC_TARGET_NAME   "probe_collection/target_name"
#define	AWAR_PC_MATCH_WEIGHTS   "probe_collection/match_weights/pos"
#define	AWAR_PC_MATCH_WIDTH   "probe_collection/match_weights/width"
#define	AWAR_PC_MATCH_BIAS   "probe_collection/match_weights/bias"
#define	AWAR_PC_AUTO_MATCH   "probe_collection/auto"
#define	AWAR_PC_CURRENT_COLLECTION   "probe_collection/current"
#define	AWAR_PC_SELECTED_PROBE   "tmp/probe_collection/probe"
#define	AWAR_PC_MATCH_NHITS   "tmp/probe_collection/nhits"
#define	AWAR_PC_MISMATCH_THRESHOLD   "probe_collection/mismatch_threshold"
#define	REPLACE_TARGET_CONTROL_CHARS   ":#=_:\\:=_"
#define	DISP_FORMAT   "%7i %s"

Enumerations
enum	ModMode { TS_MOD_CLEAR, TS_MOD_REV_COMPL, TS_MOD_COMPL }

Functions
static void	probe_match_event_using_awars (AW_root *root, ProbeMatchEventParam *event_param)
static void	auto_match_cb (AW_root *root)
static void	auto_match_changed (AW_root *root)
static void	enable_auto_match_cb (AW_root *root, ProbeMatchEventParam *event_param)
static void	popup_match_window_cb (AW_window *aww, GBDATA *gb_main)
static void	popup_probe_design_result_window (AW_window *aww, GBDATA *gb_main)
static int	init_local_com_struct ()
static GB_ERROR	species_requires (GBDATA *gb_species, const char *whats_required)
static GB_ERROR	gene_requires (GBDATA *gb_gene, const char *whats_required)
static GB_ERROR	pd_get_the_names (GBDATA *gb_main, bytestring &bs, bytestring &checksum)
static GB_ERROR	pd_get_the_gene_names (GBDATA *gb_main, bytestring &bs, bytestring &checksum)
const char *	bond_awar_name (int i)
static int	probe_common_send_data (const ProbeCommonSettings &commonSettings)
static int	probe_design_send_data (AW_root *root, const T_PT_PDC &pdc)
static int	probe_match_send_data (const ProbeMatchSettings &matchSettings)
static int	ecolipos2int (const char *awar_val)
static char *	readableUnknownNames (const ConstStrArray &unames)
static void	probe_design_event (AW_window *aww, GBDATA *gb_main)
static __ATTR__USERESULT GB_ERROR	probe_match_event (const ProbeMatchSettings &matchSettings, ProbeMatchEventParam *event_param)
static void	probe_match_all_event (AW_window *aww, AW_selection_list *iselection_id, GBDATA *gb_main)
static void	resolved_probe_chosen (AW_root *root)
static void	selected_match_changed_cb (AW_root *root)
static void	probelength_changed_cb (AW_root *root, bool maxChanged)
static void	minmax_awar_pair_changed_cb (AW_root *root, bool maxChanged, const char *minAwarName, const char *maxAwarName)
static void	gc_minmax_changed_cb (AW_root *root, bool maxChanged)
static void	temp_minmax_changed_cb (AW_root *root, bool maxChanged)
void	create_probe_design_variables (AW_root *root, AW_default props, AW_default db)
static AW_window *	create_probe_expert_window (AW_root *root, bool for_design)
static void	setup_probe_config (AWT_config_definition &cdef, const AWT_config_mapping_def *mapping)
AW_window *	create_probe_design_window (AW_root *root, GBDATA *gb_main)
void	my_strupr (char *s)
static void	resolve_IUPAC_target_string (AW_root *root, AW_selection_list *selection_id, GBDATA *gb_main)
static void	modify_target_string (AW_window *aww, GBDATA *gb_main, ModMode mod_mode)
static void	clear_itarget (AW_window *aww)
static AW_window *	create_IUPAC_resolve_window (AW_root *root, GBDATA *gb_main)
static void	popupSaiProbeMatchWindow (AW_window *aw, GBDATA *gb_main)
AW_window *	create_probe_match_window (AW_root *root, GBDATA *gb_main)
static void	pd_start_pt_server (AW_window *aww)
static void	pd_kill_pt_server (AW_window *aww, bool kill_all)
static const char *	ptserver_directory_info_command (const char *dirname, const char *directory)
static void	pd_query_pt_server (AW_window *aww)
static void	pd_export_pt_server (AW_window *aww, GBDATA *gb_main)
static void	pd_edit_ptserver_log (AW_window *)
static void	pd_view_server_console (AW_window *)
AW_window *	create_probe_admin_window (AW_root *root, GBDATA *gb_main)
static AW_window *	create_probe_match_specificity_control_window (AW_root *root)
static void	probe_match_update_probe_list (ArbPM_Context *pContext)
static AW_window *	create_probe_collection_window (AW_root *root, ArbPM_Context *pContext)
static bool	probe_match_with_specificity_enum_callback (void *pVoidContext, const char *pResult, bool bIsComment, int nItem, int nItems)
static void	probe_match_with_specificity_edit_event ()
bool	displays_probeColl_markers (MarkerDisplay *md)
static void	refresh_matchedProbesDisplay_cb (AW_root *root, TREE_canvas *ntw)
static void	probe_match_with_specificity_event (AW_root *root, TREE_canvas *ntw)
static void	auto_match_cb (AW_root *root, TREE_canvas *ntw)
static void	trigger_auto_match (AW_root *root)
static void	probe_forget_matches_event (AW_window *aww, ArbPM_Context *pContext)
static void	selected_probe_changed_cb (AW_root *root)
static void	target_string_changed_cb (AW_root *root)
static void	match_changed_cb (AW_root *root)
AW_window *	create_probe_match_with_specificity_window (AW_root *root, TREE_canvas *ntw)
static void	save_probe_list_to_DB (const ArbProbePtrList &rProbeList, AW_root *root)
static void	show_probes_in_sellist (const ArbProbePtrList &rProbeList, AW_selection_list *sellist)
static void	load_probe_collection (AW_window *aww, ArbPC_Context *Context, const char *const *awar_filename)
static void	probe_collection_update_parameters ()
static void	save_probe_collection (AW_window *aww, const char *const *awar_filename)
static void	add_probe_to_collection_event (AW_window *aww, ArbPC_Context *pContext)
static void	modify_probe_event (AW_window *aww, ArbPC_Context *pContext)
static void	remove_probe_from_collection_event (AW_window *aww, ArbPC_Context *pContext)
static AW_window *	probe_collection_load_prompt (AW_root *root, ArbPC_Context *pContext)
static AW_window *	probe_collection_save_prompt (AW_root *root)
static void	clear_probe_collection_event (AW_window *aww, ArbPC_Context *pContext)
static void	probe_collection_close (AW_window *aww)

Variables
static saiProbeData *	g_spd = NULp
struct {
aisc_com *   link
T_PT_LOCS   locs
T_PT_MAIN   com
AW_window_simple *   win
AW_selection_list *   resultList
}	PD
static AutoMatchSettings	auto_match_cb_settings
static const char *	auto_match_sensitive_awars []
static bool	allow_probe_match_event = true
static AWT_config_mapping_def	probe_design_mapping_def []
static AWT_config_mapping_def	probe_match_mapping_def []
static ArbPM_Context	PM_Context
static SmartPtr < GetMatchesContext >	getMatchesContext
static ArbPC_Context	PC_Context

Macro Definition Documentation

#define AWAR_PROBE_CREATE_GENE_SERVER   "tmp/probe_admin/gene_server"

Definition at line 50 of file probe_design.cxx.

Referenced by create_probe_admin_window(), create_probe_design_variables(), and pd_export_pt_server().

#define AWAR_ITARGET_STRING   "nt/itarget_string"

Definition at line 52 of file probe_design.cxx.

Referenced by clear_itarget(), create_IUPAC_resolve_window(), create_probe_design_variables(), and resolve_IUPAC_target_string().

#define AWAR_PD_SELECTED_MATCH   "tmp/probe_design/match"

Definition at line 57 of file probe_design.cxx.

Referenced by create_probe_design_variables(), create_probe_match_window(), and selected_match_changed_cb().

#define AWAR_PD_MATCH_RESOLVE   "tmp/probe_design/match_resolve"

Definition at line 58 of file probe_design.cxx.

Referenced by create_IUPAC_resolve_window(), create_probe_design_variables(), and resolved_probe_chosen().

#define AWAR_PD_MATCH_SORTBY   "probe_match/sort_by"

Definition at line 60 of file probe_design.cxx.

Referenced by create_probe_design_variables(), and create_probe_match_window().

#define AWAR_PD_MATCH_ALSO_REVCOMP   "probe_match/complement"

Definition at line 61 of file probe_design.cxx.

Referenced by create_probe_design_variables(), and create_probe_match_window().

#define AWAR_PD_MATCH_MARKHITS   "probe_match/mark_hits"

Definition at line 62 of file probe_design.cxx.

Referenced by create_probe_design_variables(), and create_probe_match_window().

#define AWAR_PD_MATCH_WRITE2TMP   "probe_match/write_2_tmp"

Definition at line 63 of file probe_design.cxx.

Referenced by create_probe_design_variables(), and create_probe_match_window().

#define AWAR_PD_MATCH_AUTOMATCH   "probe_match/auto_match"

Definition at line 64 of file probe_design.cxx.

Referenced by auto_match_changed(), create_probe_design_variables(), create_probe_match_window(), and popup_probe_design_result_window().

#define AWAR_PD_MATCH_NHITS   "tmp/probe_match/nhits"

Definition at line 66 of file probe_design.cxx.

Referenced by create_probe_design_variables(), create_probe_match_window(), and probe_match_event_using_awars().

#define AWAR_PD_DESIGN_CLIPRESULT   "probe_design/CLIPRESULT"

Definition at line 70 of file probe_design.cxx.

Referenced by create_probe_design_variables(), create_probe_design_window(), and probe_design_send_data().

#define AWAR_PD_DESIGN_MISHIT   "probe_design/MISHIT"

Definition at line 71 of file probe_design.cxx.

Referenced by create_probe_design_variables(), create_probe_design_window(), and probe_design_event().

#define AWAR_PD_DESIGN_MAXBOND   "probe_design/MAXBOND"

Definition at line 72 of file probe_design.cxx.

Referenced by create_probe_design_variables(), create_probe_design_window(), and probe_design_event().

#define AWAR_PD_DESIGN_MINTARGETS   "probe_design/MINTARGETS"

Definition at line 73 of file probe_design.cxx.

Referenced by create_probe_design_variables(), create_probe_design_window(), and probe_design_event().

#define AWAR_PD_DESIGN_MIN_LENGTH   "probe_design/PROBELENGTH"

Definition at line 75 of file probe_design.cxx.

Referenced by create_probe_design_variables(), create_probe_design_window(), probe_design_event(), and probelength_changed_cb().

#define AWAR_PD_DESIGN_MAX_LENGTH   "probe_design/PROBEMAXLENGTH"

Definition at line 76 of file probe_design.cxx.

Referenced by create_probe_design_variables(), create_probe_design_window(), probe_design_event(), and probelength_changed_cb().

#define AWAR_PD_DESIGN_MIN_TEMP   "probe_design/MINTEMP"

Definition at line 78 of file probe_design.cxx.

Referenced by create_probe_design_variables(), create_probe_design_window(), probe_design_event(), and temp_minmax_changed_cb().

#define AWAR_PD_DESIGN_MAX_TEMP   "probe_design/MAXTEMP"

Definition at line 79 of file probe_design.cxx.

Referenced by create_probe_design_variables(), create_probe_design_window(), probe_design_event(), and temp_minmax_changed_cb().

#define AWAR_PD_DESIGN_MIN_GC   "probe_design/MINGC"

Definition at line 80 of file probe_design.cxx.

Referenced by create_probe_design_variables(), create_probe_design_window(), gc_minmax_changed_cb(), and probe_design_event().

#define AWAR_PD_DESIGN_MAX_GC   "probe_design/MAXGC"

Definition at line 81 of file probe_design.cxx.

Referenced by create_probe_design_variables(), create_probe_design_window(), gc_minmax_changed_cb(), and probe_design_event().

#define AWAR_PD_DESIGN_MIN_ECOLIPOS   "probe_design/MINECOLI"

Definition at line 82 of file probe_design.cxx.

Referenced by create_probe_design_variables(), create_probe_design_window(), and probe_design_event().

#define AWAR_PD_DESIGN_MAX_ECOLIPOS   "probe_design/MAXECOLI"

Definition at line 83 of file probe_design.cxx.

Referenced by create_probe_design_variables(), create_probe_design_window(), and probe_design_event().

#define AWAR_PD_DESIGN_GENE   "probe_design/gene"

Definition at line 85 of file probe_design.cxx.

Referenced by create_probe_design_variables(), create_probe_design_window(), and probe_design_event().

#define AWAR_PD_COMMON_EXP_BONDS_FORMAT   "probe_design/bonds/pos%i"

Definition at line 88 of file probe_design.cxx.

Referenced by bond_awar_name().

#define AWAR_PD_COMMON_EXP_SPLIT   "probe_design/SPLIT"

Definition at line 89 of file probe_design.cxx.

Referenced by create_probe_design_variables(), create_probe_expert_window(), and setup_probe_config().

#define AWAR_PD_DESIGN_EXP_DTEDGE   "probe_design/DTEDGE"

Definition at line 91 of file probe_design.cxx.

Referenced by create_probe_design_variables(), create_probe_expert_window(), and probe_design_send_data().

#define AWAR_PD_DESIGN_EXP_DT   "probe_design/DT"

Definition at line 92 of file probe_design.cxx.

Referenced by create_probe_design_variables(), create_probe_expert_window(), and probe_design_send_data().

#define AWAR_PD_MATCH_NMATCHES   "probe_match/nmatches"

Definition at line 94 of file probe_design.cxx.

Referenced by create_probe_design_variables(), and create_probe_expert_window().

#define AWAR_PD_MATCH_LIM_NMATCH   "probe_match/lim_nmatch"

Definition at line 95 of file probe_design.cxx.

Referenced by create_probe_design_variables(), and create_probe_expert_window().

#define AWAR_PD_MATCH_MAX_RES   "probe_match/maxres"

Definition at line 96 of file probe_design.cxx.

Referenced by create_probe_design_variables(), and create_probe_expert_window().

#define AWAR_PC_TARGET_STRING   "probe_collection/target_string"

Definition at line 102 of file probe_design.cxx.

Referenced by add_probe_to_collection_event(), create_probe_collection_window(), create_probe_design_variables(), create_probe_match_with_specificity_window(), match_changed_cb(), modify_probe_event(), selected_probe_changed_cb(), and target_string_changed_cb().

#define AWAR_PC_TARGET_NAME   "probe_collection/target_name"

Definition at line 103 of file probe_design.cxx.

Referenced by add_probe_to_collection_event(), create_probe_collection_window(), create_probe_design_variables(), match_changed_cb(), modify_probe_event(), and selected_probe_changed_cb().

#define AWAR_PC_MATCH_WEIGHTS   "probe_collection/match_weights/pos"

Definition at line 104 of file probe_design.cxx.

Referenced by create_probe_collection_window(), create_probe_design_variables(), load_probe_collection(), and probe_collection_update_parameters().

#define AWAR_PC_MATCH_WIDTH   "probe_collection/match_weights/width"

Definition at line 105 of file probe_design.cxx.

Referenced by create_probe_collection_window(), create_probe_design_variables(), load_probe_collection(), and probe_collection_update_parameters().

#define AWAR_PC_MATCH_BIAS   "probe_collection/match_weights/bias"

Definition at line 106 of file probe_design.cxx.

Referenced by create_probe_collection_window(), create_probe_design_variables(), load_probe_collection(), and probe_collection_update_parameters().

#define AWAR_PC_AUTO_MATCH   "probe_collection/auto"

Definition at line 107 of file probe_design.cxx.

Referenced by auto_match_cb(), create_probe_design_variables(), create_probe_match_with_specificity_window(), and trigger_auto_match().

#define AWAR_PC_CURRENT_COLLECTION   "probe_collection/current"

Definition at line 108 of file probe_design.cxx.

Referenced by create_probe_design_variables(), and save_probe_list_to_DB().

#define AWAR_PC_SELECTED_PROBE   "tmp/probe_collection/probe"

Definition at line 110 of file probe_design.cxx.

Referenced by add_probe_to_collection_event(), create_probe_collection_window(), create_probe_design_variables(), create_probe_match_with_specificity_window(), ProbeCollDisplay::handle_click(), modify_probe_event(), remove_probe_from_collection_event(), selected_probe_changed_cb(), and target_string_changed_cb().

#define AWAR_PC_MATCH_NHITS   "tmp/probe_collection/nhits"

Definition at line 111 of file probe_design.cxx.

Referenced by create_probe_design_variables(), create_probe_match_with_specificity_window(), probe_forget_matches_event(), and probe_match_with_specificity_event().

#define AWAR_PC_MISMATCH_THRESHOLD   "probe_collection/mismatch_threshold"

Definition at line 114 of file probe_design.cxx.

Referenced by create_probe_design_variables(), create_probe_match_specificity_control_window(), create_probe_match_with_specificity_window(), probe_match_with_specificity_event(), and refresh_matchedProbesDisplay_cb().

#define REPLACE_TARGET_CONTROL_CHARS   ":#=_:\\:=_"

Definition at line 116 of file probe_design.cxx.

Referenced by create_probe_design_variables().

#define DISP_FORMAT   "%7i %s"

Referenced by probe_match_all_event().

Enumeration Type Documentation

enum ModMode

Enumerator
TS_MOD_CLEAR
TS_MOD_REV_COMPL
TS_MOD_COMPL

Definition at line 1657 of file probe_design.cxx.

Function Documentation

static void probe_match_event_using_awars ( AW_root *  root, ProbeMatchEventParam *  event_param  )

static

Definition at line 1110 of file probe_design.cxx.

References allow_probe_match_event, aw_message_if(), AW_root::awar(), AWAR_PD_MATCH_NHITS, AWAR_SPV_DB_FIELD_NAME, AWAR_TREE_REFRESH, error(), ProbeMatchEventParam::hits_summary, probe_match_event(), ProbeMatchEventParam::refresh_sai_display, ProbeMatchEventParam::selection_id, AW_awar::touch(), and AW_awar::write_string().

Referenced by auto_match_cb(), and create_probe_match_window().

static void auto_match_cb ( AW_root *  root )

static

Definition at line 167 of file probe_design.cxx.

References AW_root::awar(), AWAR_TARGET_STRING, AutoMatchSettings::disable, AutoMatchSettings::event_param, probe_match_event_using_awars(), and AW_awar::read_string().

Referenced by auto_match_changed(), and create_probe_match_with_specificity_window().

static void auto_match_changed ( AW_root *  root )

static

Definition at line 186 of file probe_design.cxx.

References AW_awar::add_callback(), auto_match_cb(), AW_root::awar(), AWAR_PD_MATCH_AUTOMATCH, AW_awar::read_int(), and AW_awar::remove_callback().

Referenced by create_probe_design_variables(), and enable_auto_match_cb().

static void enable_auto_match_cb ( AW_root *  root, ProbeMatchEventParam *  event_param  )

static

Definition at line 207 of file probe_design.cxx.

References auto_match_changed(), and AutoMatchSettings::initialized().

Referenced by create_probe_match_window(), and popup_probe_design_result_window().

static void popup_match_window_cb ( AW_window *  aww, GBDATA *  gb_main  )

static

Definition at line 218 of file probe_design.cxx.

References AW_window::activate(), AW_root::awar(), AWAR_TARGET_STRING, create_probe_match_window(), AW_window::get_root(), and AW_awar::touch().

Referenced by popup_probe_design_result_window().

static void popup_probe_design_result_window ( AW_window *  aww, GBDATA *  gb_main  )

static

Definition at line 227 of file probe_design.cxx.

References AW_POPDOWN(), AWAR_PD_MATCH_AUTOMATCH, AWAR_TARGET_STRING, awt_clear_selection_list_cb(), create_load_box_for_selection_lists(), create_print_box_for_selection_lists(), create_save_box_for_selection_lists(), enable_auto_match_cb(), AW_window::get_root(), StorableSelectionList::get_typedsellist(), makeHelpCallback(), NULp, PD, and popup_match_window_cb().

Referenced by create_probe_design_window(), and probe_design_event().

static int init_local_com_struct ( )

static

Definition at line 277 of file probe_design.cxx.

References aisc_create(), GB_getenvUSER(), NULp, and PD.

Referenced by probe_design_event(), and probe_match_event().

static GB_ERROR species_requires ( GBDATA *  gb_species, const char *  whats_required  )

static

Definition at line 289 of file probe_design.cxx.

References GBS_global_string(), and GBT_get_name_or_description().

Referenced by pd_get_the_gene_names(), and pd_get_the_names().

static GB_ERROR gene_requires ( GBDATA *  gb_gene, const char *  whats_required  )

static

Definition at line 293 of file probe_design.cxx.

References GB_get_grandfather(), GBS_global_string(), GBT_get_name_or_description(), and pd_assert.

Referenced by pd_get_the_gene_names().

static GB_ERROR pd_get_the_names ( GBDATA *  gb_main, bytestring &  bs, bytestring &  checksum  )

static

Definition at line 299 of file probe_design.cxx.

References GBS_strstruct::cat(), GBS_strstruct::cut_tail(), bytestring::data, error(), GB_await_error(), GB_begin_transaction(), GB_end_transaction(), GB_entry(), GB_read_char_pntr(), GBS_checksum(), GBS_global_string(), GBT_find_sequence(), GBT_first_marked_species(), GBT_get_default_alignment(), GBT_next_marked_species(), GBS_strstruct::get_position(), names, GBS_strstruct::put(), GBS_strstruct::putlong(), GBS_strstruct::release(), bytestring::size, and species_requires().

Referenced by probe_design_event().

static GB_ERROR pd_get_the_gene_names ( GBDATA *  gb_main, bytestring &  bs, bytestring &  checksum  )

static

Definition at line 342 of file probe_design.cxx.

References GBS_strstruct::cat(), GBS_strstruct::cut_tail(), bytestring::data, error(), GB_await_error(), GB_begin_transaction(), GB_end_transaction(), GB_entry(), GB_FIND, GB_read_char_pntr(), GB_search(), GBS_checksum(), GBS_global_string(), GBT_find_sequence(), GBT_read_gene_sequence(), GEN_first_marked_gene(), GEN_first_organism(), GEN_next_marked_gene(), GEN_next_organism(), gene_requires(), GENOM_ALIGNMENT, GBS_strstruct::get_position(), names, NULp, GBS_strstruct::put(), GBS_strstruct::putlong(), GBS_strstruct::release(), bytestring::size, and species_requires().

Referenced by probe_design_event().

const char* bond_awar_name ( int  i )

inline

Definition at line 402 of file probe_design.cxx.

References AWAR_PD_COMMON_EXP_BONDS_FORMAT, and GBS_global_string().

Referenced by create_probe_design_variables(), create_probe_expert_window(), ProbeCommonSettings::ProbeCommonSettings(), and setup_probe_config().

static int probe_common_send_data ( const ProbeCommonSettings &  commonSettings )

static

Definition at line 419 of file probe_design.cxx.

References aisc_put(), ProbeCommonSettings::bonds, NULp, PD, and ProbeCommonSettings::split.

Referenced by probe_design_send_data(), and probe_match_send_data().

static int probe_design_send_data ( AW_root *  root, const T_PT_PDC &  pdc  )

static

Definition at line 435 of file probe_design.cxx.

References aisc_put(), AW_root::awar(), AWAR_PD_DESIGN_CLIPRESULT, AWAR_PD_DESIGN_EXP_DT, AWAR_PD_DESIGN_EXP_DTEDGE, long, NULp, PD, probe_common_send_data(), AW_awar::read_float(), and AW_awar::read_int().

Referenced by probe_design_event().

static int probe_match_send_data ( const ProbeMatchSettings &  matchSettings )

static

Definition at line 474 of file probe_design.cxx.

References aisc_put(), ProbeMatchSettings::maxhits, ProbeMatchSettings::nlimit, ProbeMatchSettings::nmatches, NULp, PD, and probe_common_send_data().

Referenced by probe_match_event().

static int ecolipos2int ( const char *  awar_val )

static

Definition at line 485 of file probe_design.cxx.

Referenced by probe_design_event().

static char* readableUnknownNames ( const ConstStrArray &  unames )

static

Definition at line 490 of file probe_design.cxx.

References GBS_strstruct::cat(), GBS_strstruct::nprintf(), arb_test::readable(), GBS_strstruct::release(), and CharPtrArray::size().

Referenced by probe_design_event().

static void probe_design_event ( AW_window *  aww, GBDATA *  gb_main  )

static

Definition at line 505 of file probe_design.cxx.

References aisc_close(), aisc_create(), aisc_get(), AISC_MAGIC_NUMBER, aisc_open(), aisc_put(), arb_look_and_start_ptserver(), ARB_strdup(), aw_message(), aw_question(), AW_root::awar(), AWAR_PD_DESIGN_GENE, AWAR_PD_DESIGN_MAX_ECOLIPOS, AWAR_PD_DESIGN_MAX_GC, AWAR_PD_DESIGN_MAX_LENGTH, AWAR_PD_DESIGN_MAX_TEMP, AWAR_PD_DESIGN_MAXBOND, AWAR_PD_DESIGN_MIN_ECOLIPOS, AWAR_PD_DESIGN_MIN_GC, AWAR_PD_DESIGN_MIN_LENGTH, AWAR_PD_DESIGN_MIN_TEMP, AWAR_PD_DESIGN_MINTARGETS, AWAR_PD_DESIGN_MISHIT, AWAR_PT_SERVER, bytestring::data, ecolipos2int(), error(), GB_await_error(), GB_export_errorf(), GB_read_char_pntr(), GB_read_string_count(), GBS_global_string(), GBT_find_sequence(), GBT_find_species(), GBT_get_default_alignment(), GBT_split_string(), GEN_is_genome_db(), AW_window::get_root(), init_local_com_struct(), long, NULp, PD, pd_get_the_gene_names(), pd_get_the_names(), popup_probe_design_result_window(), probe_design_send_data(), AW_awar::read_char_pntr(), AW_awar::read_float(), AW_awar::read_int(), readableUnknownNames(), s, bytestring::size, CharPtrArray::size(), arb_test::space(), SPLIT_DROPEMPTY, arb_progress::subtitle(), and ta.

Referenced by create_probe_design_window().

static __ATTR__USERESULT GB_ERROR probe_match_event ( const ProbeMatchSettings &  matchSettings, ProbeMatchEventParam *  event_param  )

static

Definition at line 744 of file probe_design.cxx.

References aisc_close(), aisc_get(), AISC_MAGIC_NUMBER, aisc_nput(), aisc_open(), allow_probe_match_event, ProbeMatchSettings::alsoRevcompl, arb_look_and_start_ptserver(), aw_message(), AW_selection_list::clear(), ProbeMatchEventParam::counter, bytestring::data, AW_awar::deny_read, AW_awar::deny_write, error(), flags, g_spd, GB_await_error(), GB_delete(), GB_entry(), GB_FIND, gb_main, ProbeMatchEventParam::gb_main, GB_pop_transaction(), GB_push_transaction(), GB_read_flag(), GB_read_string(), GB_search(), gb_species_data, GB_STRING, GB_write_flag(), GB_write_string(), GBS_global_string(), GBS_static_string(), GBT_find_species_rel_species_data(), GBT_first_marked_species_rel_species_data(), GBT_first_species_rel_species_data(), GBT_get_species_data(), GBT_next_marked_species(), GBT_next_species(), GEN_find_gene(), GEN_find_gene_data(), GEN_first_gene(), GEN_first_marked_gene(), GEN_is_genome_db(), GEN_next_gene(), GEN_next_marked_gene(), gene_flag, ParsedProbeMatch::get_column_content(), ProbeMatchParser::get_error(), ProbeMatchParser::get_probe_region_offset(), ProbeMatchEventParam::hits_summary, init_local_com_struct(), AW_selection_list::insert(), AW_selection_list::insert_default(), ProbeMatchParser::is_gene_result(), ProbeMatchSettings::markHits, ProbeMatchSettings::maxMismatches, NULp, PD, pd_assert, probe_match_send_data(), saiProbeData::probeSeq, saiProbeData::probeSpecies, ProbeMatchEventParam::refresh_sai_display, result, ProbeMatchEventParam::selection_id, ProbeMatchSettings::serverNumber, saiProbeData::setHeadline(), saiProbeData::setProbeTarget(), ProbeMatchSettings::sortBy, string(), arb_progress::subtitle(), ProbeMatchSettings::targetString, transferProbeData(), AW_selection_list::update(), and ProbeMatchSettings::write2tmp.

Referenced by probe_match_all_event(), probe_match_event_using_awars(), and probe_match_with_specificity_event().

static void probe_match_all_event ( AW_window *  aww, AW_selection_list *  iselection_id, GBDATA *  gb_main  )

static

Definition at line 1129 of file probe_design.cxx.

References DISP_FORMAT, error(), GBS_global_string(), AW_window::get_root(), AW_scalar::get_string(), AW_selection_list_iterator::get_value(), probe_match_event(), AW_selection_list_iterator::set_displayed(), AW_selection_list::size(), AW_selection_list::sort(), and AW_selection_list::update().

Referenced by create_IUPAC_resolve_window().

static void resolved_probe_chosen ( AW_root *  root )

static

Definition at line 1167 of file probe_design.cxx.

References AW_root::awar(), AWAR_PD_MATCH_RESOLVE, AWAR_TARGET_STRING, AW_awar::read_string(), and AW_awar::write_string().

Referenced by create_probe_design_variables().

static void selected_match_changed_cb ( AW_root *  root )

static

Definition at line 1172 of file probe_design.cxx.

References allow_probe_match_event, AW_root::awar(), AWAR_GENE_NAME, AWAR_PD_SELECTED_MATCH, AWAR_SPECIES_NAME, AWAR_TARGET_STRING, NULp, AW_awar::read_string(), AW_awar::touch(), and AW_awar::write_string().

Referenced by create_probe_design_variables().

static void probelength_changed_cb ( AW_root *  root, bool  maxChanged  )

static

Definition at line 1195 of file probe_design.cxx.

References AW_root::awar(), AWAR_PD_DESIGN_MAX_LENGTH, AWAR_PD_DESIGN_MIN_LENGTH, AW_awar::read_int(), and AW_awar::write_int().

Referenced by create_probe_design_variables().

static void minmax_awar_pair_changed_cb ( AW_root *  root, bool  maxChanged, const char *  minAwarName, const char *  maxAwarName  )

static

Definition at line 1211 of file probe_design.cxx.

References AW_root::awar(), AW_awar::read_float(), and AW_awar::write_float().

Referenced by gc_minmax_changed_cb(), and temp_minmax_changed_cb().

static void gc_minmax_changed_cb ( AW_root *  root, bool  maxChanged  )

static

Definition at line 1228 of file probe_design.cxx.

References AWAR_PD_DESIGN_MAX_GC, AWAR_PD_DESIGN_MIN_GC, and minmax_awar_pair_changed_cb().

Referenced by create_probe_design_variables().

static void temp_minmax_changed_cb ( AW_root *  root, bool  maxChanged  )

static

Definition at line 1231 of file probe_design.cxx.

References AWAR_PD_DESIGN_MAX_TEMP, AWAR_PD_DESIGN_MIN_TEMP, and minmax_awar_pair_changed_cb().

Referenced by create_probe_design_variables().

void create_probe_design_variables	(	AW_root *	root,
		AW_default	props,
		AW_default	db
	)

Definition at line 1235 of file probe_design.cxx.

References ArbProbeCollection::add(), AW_awar::add_callback(), ARB_strpartdup(), auto_match_changed(), aw_message(), AW_root::awar_float(), AW_root::awar_int(), AWAR_ITARGET_STRING, AWAR_MAX_MISMATCHES, AWAR_PC_AUTO_MATCH, AWAR_PC_CURRENT_COLLECTION, AWAR_PC_MATCH_BIAS, AWAR_PC_MATCH_NHITS, AWAR_PC_MATCH_WEIGHTS, AWAR_PC_MATCH_WIDTH, AWAR_PC_MISMATCH_THRESHOLD, AWAR_PC_SELECTED_PROBE, AWAR_PC_TARGET_NAME, AWAR_PC_TARGET_STRING, AWAR_PD_COMMON_EXP_SPLIT, AWAR_PD_DESIGN_CLIPRESULT, AWAR_PD_DESIGN_EXP_DT, AWAR_PD_DESIGN_EXP_DTEDGE, AWAR_PD_DESIGN_GENE, AWAR_PD_DESIGN_MAX_ECOLIPOS, AWAR_PD_DESIGN_MAX_GC, AWAR_PD_DESIGN_MAX_LENGTH, AWAR_PD_DESIGN_MAX_TEMP, AWAR_PD_DESIGN_MAXBOND, AWAR_PD_DESIGN_MIN_ECOLIPOS, AWAR_PD_DESIGN_MIN_GC, AWAR_PD_DESIGN_MIN_LENGTH, AWAR_PD_DESIGN_MIN_TEMP, AWAR_PD_DESIGN_MINTARGETS, AWAR_PD_DESIGN_MISHIT, AWAR_PD_MATCH_ALSO_REVCOMP, AWAR_PD_MATCH_AUTOMATCH, AWAR_PD_MATCH_LIM_NMATCH, AWAR_PD_MATCH_MARKHITS, AWAR_PD_MATCH_MAX_RES, AWAR_PD_MATCH_NHITS, AWAR_PD_MATCH_NMATCHES, AWAR_PD_MATCH_RESOLVE, AWAR_PD_MATCH_SORTBY, AWAR_PD_MATCH_WRITE2TMP, AWAR_PD_SELECTED_MATCH, AWAR_PROBE_ADMIN_PT_SERVER, AWAR_PROBE_CREATE_GENE_SERVER, AWAR_PT_SERVER, AWAR_SPECIES_NAME, AWAR_SPV_ACI_COMMAND, AWAR_SPV_DB_FIELD_NAME, AWAR_SPV_DB_FIELD_WIDTH, AWAR_SPV_SAI_2_PROBE, AWAR_SPV_SELECTED_PROBE, AW_root::awar_string(), AWAR_TARGET_STRING, bond_awar_name(), buffer, ArbProbeCollection::clear(), GBS_global_string(), GBT_splitNdestroy_string(), gc_minmax_changed_cb(), get_probe_collection(), ArbProbeCollection::getParameters(), NULp, PD, probelength_changed_cb(), AW_awar::read_float(), AW_awar::read_int(), AW_awar::read_string(), REPLACE_TARGET_CONTROL_CHARS, resolved_probe_chosen(), selected_match_changed_cb(), seq, AW_awar::set_minmax(), AW_awar::set_srt(), ArbProbeCollection::setParameters(), CharPtrArray::size(), SPLIT_DROPEMPTY, and temp_minmax_changed_cb().

Referenced by nt_create_all_awars().

static AW_window* create_probe_expert_window ( AW_root *  root, bool  for_design  )

static

Definition at line 1369 of file probe_design.cxx.

References AW_POPDOWN(), AWAR_PD_COMMON_EXP_SPLIT, AWAR_PD_DESIGN_EXP_DT, AWAR_PD_DESIGN_EXP_DTEDGE, AWAR_PD_MATCH_LIM_NMATCH, AWAR_PD_MATCH_MAX_RES, AWAR_PD_MATCH_NMATCHES, AWM_ALL, AWM_EXP, bond_awar_name(), AW_window::load_xfig(), and makeHelpCallback().

Referenced by create_probe_design_window(), and create_probe_match_window().

static void setup_probe_config ( AWT_config_definition &  cdef, const AWT_config_mapping_def *  mapping  )

static

Definition at line 1440 of file probe_design.cxx.

References AWT_config_definition::add(), AWAR_PD_COMMON_EXP_SPLIT, and bond_awar_name().

Referenced by create_probe_design_window(), and create_probe_match_window().

AW_window* create_probe_design_window	(	AW_root *	root,
		GBDATA *	gb_main
	)

Definition at line 1450 of file probe_design.cxx.

References AW_POPDOWN(), AW_ROOT_DEFAULT, AWAR_PD_DESIGN_CLIPRESULT, AWAR_PD_DESIGN_GENE, AWAR_PD_DESIGN_MAX_ECOLIPOS, AWAR_PD_DESIGN_MAX_GC, AWAR_PD_DESIGN_MAX_LENGTH, AWAR_PD_DESIGN_MAX_TEMP, AWAR_PD_DESIGN_MAXBOND, AWAR_PD_DESIGN_MIN_ECOLIPOS, AWAR_PD_DESIGN_MIN_GC, AWAR_PD_DESIGN_MIN_LENGTH, AWAR_PD_DESIGN_MIN_TEMP, AWAR_PD_DESIGN_MINTARGETS, AWAR_PD_DESIGN_MISHIT, AWAR_PT_SERVER, AWM_ALL, AWM_EXP, awt_create_PTSERVER_selection_button(), AWT_insert_config_manager(), create_probe_expert_window(), GEN_is_genome_db(), makeHelpCallback(), popup_probe_design_result_window(), probe_design_event(), setup_probe_config(), and ta.

Referenced by popup_new_main_window().

void my_strupr ( char *  s )

inline

Definition at line 1517 of file probe_design.cxx.

References pd_assert.

Referenced by resolve_IUPAC_target_string().

static void resolve_IUPAC_target_string ( AW_root *  root, AW_selection_list *  selection_id, GBDATA *  gb_main  )

static

Definition at line 1524 of file probe_design.cxx.

References AW_root::awar(), AWAR_ITARGET_STRING, buffer, AW_selection_list::clear(), iupac::Nuc_Group::count, error(), GB_append_exportedError(), GB_AT_DNA, GB_AT_RNA, GB_await_error(), GBS_global_string(), GBT_get_alignment_type(), GBT_get_default_alignment(), AW_selection_list::insert(), AW_selection_list::insert_default(), iupac::Nuc_Group::members, my_strupr(), iupac::nuc_group, NULp, offset, pd_assert, AW_awar::read_string(), iupac::to_index(), and AW_selection_list::update().

Referenced by create_IUPAC_resolve_window().

static void modify_target_string ( AW_window *  aww, GBDATA *  gb_main, ModMode  mod_mode  )

static

Definition at line 1659 of file probe_design.cxx.

References aw_message(), AW_root::awar(), AWAR_TARGET_STRING, error(), GB_AT_UNKNOWN, GB_await_error(), GBT_complementNucSequence(), GBT_determine_T_or_U(), GBT_get_alignment_type(), GBT_get_default_alignment(), GBT_reverseComplementNucSequence(), AW_window::get_root(), NULp, GB_transaction::ok(), pd_assert, AW_awar::read_string(), ta, TS_MOD_CLEAR, TS_MOD_COMPL, TS_MOD_REV_COMPL, and AW_awar::write_string().

Referenced by create_probe_match_window().

static void clear_itarget ( AW_window *  aww )

static

Definition at line 1697 of file probe_design.cxx.

References AW_root::awar(), AWAR_ITARGET_STRING, AW_window::get_root(), and AW_awar::write_string().

Referenced by create_IUPAC_resolve_window().

static AW_window* create_IUPAC_resolve_window ( AW_root *  root, GBDATA *  gb_main  )

static

Definition at line 1701 of file probe_design.cxx.

References AW_awar::add_callback(), AW_POPDOWN(), AW_root::awar(), AWAR_DEFAULT_ALIGNMENT, AWAR_ITARGET_STRING, AWAR_PD_MATCH_RESOLVE, AWT_create_IUPAC_info_window(), clear_itarget(), AW_selection_list::insert_default(), AW_window::load_xfig(), makeHelpCallback(), probe_match_all_event(), resolve_IUPAC_target_string(), and AW_awar::touch().

Referenced by create_probe_match_window().

static void popupSaiProbeMatchWindow ( AW_window *  aw, GBDATA *  gb_main  )

static

Definition at line 1748 of file probe_design.cxx.

References AW_window::activate(), createSaiProbeMatchWindow(), gb_main, AW_window::get_root(), NULp, and transferProbeData().

Referenced by create_probe_match_window().

AW_window* create_probe_match_window	(	AW_root *	root,
		GBDATA *	gb_main
	)

Definition at line 1774 of file probe_design.cxx.

References AW_POPDOWN(), AW_ROOT_DEFAULT, AW_SCALER_EXP_LOWER, AWAR_MAX_MISMATCHES, AWAR_PD_MATCH_ALSO_REVCOMP, AWAR_PD_MATCH_AUTOMATCH, AWAR_PD_MATCH_MARKHITS, AWAR_PD_MATCH_NHITS, AWAR_PD_MATCH_SORTBY, AWAR_PD_MATCH_WRITE2TMP, AWAR_PD_SELECTED_MATCH, AWAR_PT_SERVER, AWAR_TARGET_STRING, awt_create_PTSERVER_selection_button(), AWT_insert_config_manager(), create_IUPAC_resolve_window(), create_print_box_for_selection_lists(), create_probe_expert_window(), enable_auto_match_cb(), AW_selection_list::insert_default(), makeHelpCallback(), modify_target_string(), NULp, popupSaiProbeMatchWindow(), probe_match_event_using_awars(), setup_probe_config(), RootAsWindowCallback::simple(), TS_MOD_CLEAR, TS_MOD_COMPL, and TS_MOD_REV_COMPL.

Referenced by popup_match_window_cb(), and popup_new_main_window().

static void pd_start_pt_server ( AW_window *  aww )

static

Definition at line 1869 of file probe_design.cxx.

References AISC_MAGIC_NUMBER, arb_look_and_start_server(), aw_message(), AW_root::awar(), AWAR_PROBE_ADMIN_PT_SERVER, error(), GBS_ptserver_tag(), AW_window::get_root(), and AW_awar::read_int().

Referenced by create_probe_admin_window().

static void pd_kill_pt_server ( AW_window *  aww, bool  kill_all  )

static

Definition at line 1876 of file probe_design.cxx.

References AISC_MAGIC_NUMBER, arb_look_and_kill_server(), aw_ask_sure(), aw_message(), aw_message_if(), AW_root::awar(), AWAR_PROBE_ADMIN_PT_SERVER, arb_progress::done(), error(), GB_await_error(), GBS_get_arb_tcp_entries(), GBS_global_string(), GBS_ptserver_id_to_choice(), GBS_ptserver_tag(), AW_window::get_root(), arb_progress::inc_and_check_user_abort(), max, min, NULp, AW_awar::read_int(), and arb_progress::subtitle().

Referenced by create_probe_admin_window().

static const char* ptserver_directory_info_command ( const char *  dirname, const char *  directory  )

static

Definition at line 1922 of file probe_design.cxx.

References GBS_global_string().

Referenced by pd_query_pt_server().

static void pd_query_pt_server ( AW_window *  aww )

static

Definition at line 1930 of file probe_design.cxx.

References ARB_getenv_ignore_empty(), aw_message_if(), AW_root::awar(), AWAR_PROBE_ADMIN_PT_SERVER, GBS_strstruct::cat(), createCallOnSocketHost(), error(), GB_await_error(), GB_xcmd(), GBS_ptserver_tag(), GBS_read_arb_tcp(), GBS_strstruct::get_data(), AW_window::get_root(), NULp, ptserver_directory_info_command(), AW_awar::read_int(), WAIT_FOR_TERMINATION, and XCMD_ASYNC_WAITKEY.

Referenced by create_probe_admin_window().

static void pd_export_pt_server ( AW_window *  aww, GBDATA *  gb_main  )

static

Definition at line 1965 of file probe_design.cxx.

References AISC_MAGIC_NUMBER, arb_look_and_kill_server(), arb_start_server(), aw_message(), aw_question(), AW_root::awar(), AWAR_PROBE_ADMIN_PT_SERVER, AWAR_PROBE_CREATE_GENE_SERVER, AWAR_SAVED_DB_PATH, command, error(), GB_AT_AA, GB_AT_UNKNOWN, GB_await_error(), GB_mode_of_file(), GB_save_as(), GB_set_mode_of_file(), GB_supports_mapfile(), GBK_system(), GBS_add_ptserver_logentry(), GBS_global_string(), GBS_global_string_copy(), GBS_ptserver_tag(), GBS_read_arb_tcp(), GBS_scan_arb_tcp_param(), GBS_string_eval(), GBT_get_alignment(), GBT_get_alignment_type(), GBT_get_default_alignment(), GEN_is_genome_db(), GENOM_ALIGNMENT, AW_window::get_root(), NULp, pd_assert, AW_awar::read_int(), AW_awar::read_string(), arb_progress::subtitle(), and ta.

Referenced by create_probe_admin_window().

static void pd_edit_ptserver_log ( AW_window *  )

static

Definition at line 2072 of file probe_design.cxx.

References AW_edit(), and GBS_ptserver_logname().

Referenced by create_probe_admin_window().

static void pd_view_server_console ( AW_window *  )

static

Definition at line 2075 of file probe_design.cxx.

References AWT_system_in_console_cb(), and XCMD_ASYNC_WAIT_ON_ERROR.

Referenced by create_probe_admin_window().

AW_window* create_probe_admin_window	(	AW_root *	root,
		GBDATA *	gb_main
	)

Definition at line 2079 of file probe_design.cxx.

References AW_POPDOWN(), AWAR_PROBE_ADMIN_PT_SERVER, AWAR_PROBE_CREATE_GENE_SERVER, awt_create_PTSERVER_selection_list(), awt_edit_arbtcpdat_cb(), GEN_is_genome_db(), makeHelpCallback(), pd_edit_ptserver_log(), pd_export_pt_server(), pd_kill_pt_server(), pd_query_pt_server(), pd_start_pt_server(), pd_view_server_console(), and ta.

Referenced by popup_new_main_window().

static AW_window* create_probe_match_specificity_control_window ( AW_root *  root )

static

Definition at line 2148 of file probe_design.cxx.

References AWAR_DTREE_GROUP_MARKED_THRESHOLD, AWAR_DTREE_GROUP_PARTIALLY_MARKED_THRESHOLD, AWAR_PC_MISMATCH_THRESHOLD, NULp, and TREE_create_marker_settings_window().

Referenced by create_probe_match_with_specificity_window(), and probe_match_with_specificity_event().

static void probe_match_update_probe_list ( ArbPM_Context *  pContext )

static

Definition at line 2900 of file probe_design.cxx.

References get_probe_collection(), ArbPM_Context::probes_id, and show_probes_in_sellist().

Referenced by add_probe_to_collection_event(), clear_probe_collection_event(), create_probe_match_with_specificity_window(), load_probe_collection(), modify_probe_event(), and remove_probe_from_collection_event().

static AW_window * create_probe_collection_window ( AW_root *  root, ArbPM_Context *  pContext  )

static

Definition at line 2923 of file probe_design.cxx.

References AW_awar::add_callback(), add_probe_to_collection_event(), AW_root::awar(), AWAR_PC_MATCH_BIAS, AWAR_PC_MATCH_WEIGHTS, AWAR_PC_MATCH_WIDTH, AWAR_PC_SELECTED_PROBE, AWAR_PC_TARGET_NAME, AWAR_PC_TARGET_STRING, buffer, clear_probe_collection_event(), get_probe_collection(), AW_selection_list::insert_default(), makeHelpCallback(), modify_probe_event(), NULp, pd_assert, ArbPC_Context::PM_Context, probe_collection_close(), probe_collection_load_prompt(), probe_collection_save_prompt(), remove_probe_from_collection_event(), ArbPC_Context::selection_id, show_probes_in_sellist(), and trigger_auto_match().

Referenced by create_probe_match_with_specificity_window().

static bool probe_match_with_specificity_enum_callback ( void *  pVoidContext, const char *  pResult, bool  bIsComment, int  nItem, int  nItems  )

static

Definition at line 2217 of file probe_design.cxx.

References arb_progress::aborted(), arb_progress::inc(), ArbWriteFile_Context::nLastPercent, ArbWriteFile_Context::pFile, and ArbWriteFile_Context::pProgress.

Referenced by probe_match_with_specificity_event().

static void probe_match_with_specificity_edit_event ( )

static

Definition at line 2238 of file probe_design.cxx.

References AW_edit(), and get_results_manager().

Referenced by create_probe_match_with_specificity_window().

bool displays_probeColl_markers ( MarkerDisplay *  md )

inline

Definition at line 2310 of file probe_design.cxx.

References md.

Referenced by refresh_matchedProbesDisplay_cb().

static void refresh_matchedProbesDisplay_cb ( AW_root *  root, TREE_canvas *  ntw  )

static

Definition at line 2312 of file probe_design.cxx.

References allow_probe_match_event, AW_root::awar(), AWAR_PC_MISMATCH_THRESHOLD, AWAR_TREE_REFRESH, displays_probeColl_markers(), DOWNCAST, MarkerDisplay::flush_cache(), AWT_graphic_tree::get_marker_display(), get_probe_collection(), get_results_manager(), AWT_canvas::gfx, ArbMatchResultsManager::hasResults(), AWT_graphic_tree::hide_marker_display(), ArbProbeCollection::probeList(), AW_awar::read_float(), AWT_graphic_tree::set_marker_display(), MarkerDisplay::size(), and AW_awar::touch().

Referenced by create_probe_match_with_specificity_window(), probe_forget_matches_event(), and probe_match_with_specificity_event().

static void probe_match_with_specificity_event ( AW_root *  root, TREE_canvas *  ntw  )

static

Definition at line 2345 of file probe_design.cxx.

References ArbMatchResultsManager::addResultSet(), allow_probe_match_event, ArbProbe::allowedMismatches(), aw_message(), AW_root::awar(), AWAR_PC_MATCH_NHITS, AWAR_PC_MISMATCH_THRESHOLD, create_probe_match_specificity_control_window(), arb_progress::done(), ArbMatchResultsManager::enumerate_results(), error(), arb_progress::error_if_aborted(), AWT_canvas::gb_main, GBS_global_string(), ProbeMatchParser::get_error(), ParsedProbeMatch::get_error(), get_probe_collection(), get_results_manager(), saiProbeData::getHeadline(), arb_progress::inc_and_check_user_abort(), ProbeMatchSettings::markHits, ArbProbeCollection::matchWeighting(), max, ArbMatchResultsManager::maximumWeight(), ProbeMatchSettings::maxMismatches, ArbWriteFile_Context::nLastPercent, NULp, ArbWriteFile_Context::pFile, ArbWriteFile_Context::pProgress, probe_match_event(), probe_match_with_specificity_enum_callback(), ArbProbeCollection::probeList(), saiProbeData::probeSeq, refresh_matchedProbesDisplay_cb(), ArbMatchResultsManager::reset(), ArbMatchResultsManager::resultsFileName(), ArbProbe::sequence(), AW_awar::set_minmax(), AW_window::show(), string(), arb_progress::subtitle(), ProbeMatchSettings::targetString, AW_awar::touch(), ArbMatchResultsManager::updateResults(), ProbeMatchSettings::write2tmp, and AW_awar::write_int().

Referenced by auto_match_cb(), and create_probe_match_with_specificity_window().

static void auto_match_cb ( AW_root *  root, TREE_canvas *  ntw  )

static

Definition at line 2494 of file probe_design.cxx.

References AW_root::awar(), AWAR_PC_AUTO_MATCH, probe_match_with_specificity_event(), and AW_awar::read_int().

static void trigger_auto_match ( AW_root *  root )

static

Definition at line 2499 of file probe_design.cxx.

References AW_root::awar(), AWAR_PC_AUTO_MATCH, and AW_awar::touch().

Referenced by add_probe_to_collection_event(), clear_probe_collection_event(), create_probe_collection_window(), load_probe_collection(), modify_probe_event(), and remove_probe_from_collection_event().

static void probe_forget_matches_event ( AW_window *  aww, ArbPM_Context *  pContext  )

static

Definition at line 2505 of file probe_design.cxx.

References AW_root::awar(), AWAR_PC_MATCH_NHITS, get_results_manager(), AW_window::get_root(), ArbPM_Context::ntw, refresh_matchedProbesDisplay_cb(), ArbMatchResultsManager::reset(), and AW_awar::write_int().

Referenced by create_probe_match_with_specificity_window().

static void selected_probe_changed_cb ( AW_root *  root )

static

Definition at line 2513 of file probe_design.cxx.

References AW_root::awar(), AWAR_PC_SELECTED_PROBE, AWAR_PC_TARGET_NAME, AWAR_PC_TARGET_STRING, AWAR_TARGET_STRING, ArbProbeCollection::find(), get_probe_collection(), ArbProbe::name(), AW_awar::read_string(), seq, ArbProbe::sequence(), and AW_awar::write_string().

Referenced by create_probe_match_with_specificity_window().

static void target_string_changed_cb ( AW_root *  root )

static

Definition at line 2528 of file probe_design.cxx.

References AW_root::awar(), AWAR_PC_SELECTED_PROBE, AWAR_PC_TARGET_STRING, ArbProbeCollection::find(), get_probe_collection(), AW_awar::read_string(), and AW_awar::write_string().

Referenced by create_probe_match_with_specificity_window().

static void match_changed_cb ( AW_root *  root )

static

Definition at line 2537 of file probe_design.cxx.

References AW_root::awar(), AWAR_PC_TARGET_NAME, AWAR_PC_TARGET_STRING, AWAR_TARGET_STRING, AW_awar::read_char_pntr(), AW_awar::read_string(), and AW_awar::write_string().

Referenced by create_probe_match_with_specificity_window().

AW_window* create_probe_match_with_specificity_window	(	AW_root *	root,
		TREE_canvas *	ntw
	)

Definition at line 2553 of file probe_design.cxx.

References AW_awar::add_callback(), auto_match_cb(), AW_POPDOWN(), AW_root::awar(), AWAR_PC_AUTO_MATCH, AWAR_PC_MATCH_NHITS, AWAR_PC_MISMATCH_THRESHOLD, AWAR_PC_SELECTED_PROBE, AWAR_PC_TARGET_STRING, AWAR_PT_SERVER, AWAR_TARGET_STRING, awt_create_PTSERVER_selection_button(), create_probe_collection_window(), create_probe_match_specificity_control_window(), AW_selection_list::insert_default(), makeHelpCallback(), match_changed_cb(), ArbPM_Context::ntw, NULp, probe_forget_matches_event(), probe_match_update_probe_list(), probe_match_with_specificity_edit_event(), probe_match_with_specificity_event(), ArbPM_Context::probes_id, refresh_matchedProbesDisplay_cb(), selected_probe_changed_cb(), RootAsWindowCallback::simple(), target_string_changed_cb(), and AW_awar::touch().

Referenced by popup_new_main_window().

static void save_probe_list_to_DB ( const ArbProbePtrList &  rProbeList, AW_root *  root  )

static

Definition at line 2643 of file probe_design.cxx.

References AW_root::awar(), AWAR_PC_CURRENT_COLLECTION, ArbProbe::name(), ArbProbe::sequence(), string(), and AW_awar::write_string().

Referenced by load_probe_collection(), and probe_collection_update_parameters().

static void show_probes_in_sellist ( const ArbProbePtrList &  rProbeList, AW_selection_list *  sellist  )

static

Definition at line 2656 of file probe_design.cxx.

References AW_selection_list::clear(), ArbProbe::displayName(), AW_selection_list::insert(), AW_selection_list::insert_default(), ArbProbe::sequence(), and AW_selection_list::update().

Referenced by clear_probe_collection_event(), create_probe_collection_window(), load_probe_collection(), and probe_match_update_probe_list().

static void load_probe_collection ( AW_window *  aww, ArbPC_Context *  Context, const char *const *  awar_filename  )

static

Definition at line 2668 of file probe_design.cxx.

References aw_message(), AW_root::awar(), AWAR_PC_MATCH_BIAS, AWAR_PC_MATCH_WEIGHTS, AWAR_PC_MATCH_WIDTH, buffer, get_probe_collection(), AW_window::get_root(), ArbProbeCollection::getParameters(), AW_window::hide(), ArbProbeCollection::openXML(), ArbPC_Context::PM_Context, probe_match_update_probe_list(), ArbProbeCollection::probeList(), AW_awar::read_string(), save_probe_list_to_DB(), ArbPC_Context::selection_id, show_probes_in_sellist(), AW_root::SINGLETON, string(), trigger_auto_match(), weights, and AW_awar::write_float().

Referenced by probe_collection_load_prompt().

static void probe_collection_update_parameters ( )

static

Definition at line 2715 of file probe_design.cxx.

References AW_root::awar(), AWAR_PC_MATCH_BIAS, AWAR_PC_MATCH_WEIGHTS, AWAR_PC_MATCH_WIDTH, buffer, get_probe_collection(), ArbProbeCollection::probeList(), AW_awar::read_float(), save_probe_list_to_DB(), ArbProbeCollection::setParameters(), AW_root::SINGLETON, and weights.

Referenced by add_probe_to_collection_event(), modify_probe_event(), probe_collection_close(), remove_probe_from_collection_event(), and save_probe_collection().

static void save_probe_collection ( AW_window *  aww, const char *const *  awar_filename  )

static

Definition at line 2739 of file probe_design.cxx.

References aw_question(), AW_root::awar(), get_probe_collection(), AW_window::get_root(), AW_window::hide(), probe_collection_update_parameters(), AW_awar::read_string(), and ArbProbeCollection::saveXML().

Referenced by probe_collection_save_prompt().

static void add_probe_to_collection_event ( AW_window *  aww, ArbPC_Context *  pContext  )

static

Definition at line 2762 of file probe_design.cxx.

References add(), aw_message_if(), AW_root::awar(), AWAR_PC_SELECTED_PROBE, AWAR_PC_TARGET_NAME, AWAR_PC_TARGET_STRING, ArbProbe::displayName(), error(), get_probe_collection(), AW_window::get_root(), AW_selection_list::insert(), NULp, ArbPC_Context::PM_Context, probe_collection_update_parameters(), probe_match_update_probe_list(), AW_awar::read_string(), ArbPC_Context::selection_id, trigger_auto_match(), AW_selection_list::update(), and AW_awar::write_string().

Referenced by create_probe_collection_window().

static void modify_probe_event ( AW_window *  aww, ArbPC_Context *  pContext  )

static

Definition at line 2801 of file probe_design.cxx.

References aw_message_if(), AW_root::awar(), AWAR_PC_SELECTED_PROBE, AWAR_PC_TARGET_NAME, AWAR_PC_TARGET_STRING, ArbProbe::displayName(), error(), AW_selection_list::get_index_of_selected(), get_probe_collection(), AW_window::get_root(), NULp, ArbPC_Context::PM_Context, probe_collection_update_parameters(), probe_match_update_probe_list(), AW_awar::read_string(), ArbPC_Context::selection_id, AW_selection_list_iterator::set_displayed(), trigger_auto_match(), AW_selection_list::update(), and AW_awar::write_string().

Referenced by create_probe_collection_window().

static void remove_probe_from_collection_event ( AW_window *  aww, ArbPC_Context *  pContext  )

static

Definition at line 2855 of file probe_design.cxx.

References AW_root::awar(), AWAR_PC_SELECTED_PROBE, AW_selection_list::delete_element_at(), ArbProbeCollection::find(), AW_selection_list::get_index_of_selected(), get_probe_collection(), AW_window::get_root(), AW_selection_list::insert_default(), ArbPC_Context::PM_Context, probe_collection_update_parameters(), probe_match_update_probe_list(), AW_awar::read_string(), ArbProbeCollection::remove(), AW_selection_list::select_element_at(), ArbPC_Context::selection_id, AW_selection_list::size(), trigger_auto_match(), and AW_selection_list::update().

Referenced by create_probe_collection_window().

static AW_window* probe_collection_load_prompt ( AW_root *  root, ArbPC_Context *  pContext  )

static

Definition at line 2885 of file probe_design.cxx.

References awt_create_load_box(), load_probe_collection(), and NULp.

Referenced by create_probe_collection_window().

static AW_window* probe_collection_save_prompt ( AW_root *  root )

static

Definition at line 2891 of file probe_design.cxx.

References awt_create_load_box(), NULp, and save_probe_collection().

Referenced by create_probe_collection_window().

static void clear_probe_collection_event ( AW_window *  aww, ArbPC_Context *  pContext  )

static

Definition at line 2906 of file probe_design.cxx.

References get_probe_collection(), AW_window::get_root(), ArbPC_Context::PM_Context, probe_match_update_probe_list(), ArbPC_Context::selection_id, show_probes_in_sellist(), and trigger_auto_match().

Referenced by create_probe_collection_window().

static void probe_collection_close ( AW_window *  aww )

static

Definition at line 2916 of file probe_design.cxx.

References AW_window::hide(), and probe_collection_update_parameters().

Referenced by create_probe_collection_window().

Variable Documentation

saiProbeData* g_spd = NULp

static

Definition at line 120 of file probe_design.cxx.

Referenced by probe_match_event().

aisc_com* link

Definition at line 123 of file probe_design.cxx.

Referenced by aisc_open(), ARB_main(), check_specific_duplicates(), create_top_links(), gbcmc_open(), print_XML_Text_expanding_links(), PT_change_link_in_father(), and ED4_base::resize_requested_by_link().

T_PT_LOCS locs

Definition at line 124 of file probe_design.cxx.

Referenced by ARB_main(), get_match_overlay(), probe_match(), PT_start_design(), and PT_unknown_names().

T_PT_MAIN com

Definition at line 125 of file probe_design.cxx.

Referenced by ARB_main(), and ArbImporter::detect_format().

AW_window_simple* win

Definition at line 126 of file probe_design.cxx.

Referenced by ED4_root::announce_deletion(), ED4_root::announce_useraction_in(), ED4_root::create_hierarchy(), ED4_compression_changed_cb(), ED4_horizontal_change_cb(), ED4_popup_gc_window(), ED4_scrollbar_change_cb(), ED4_vertical_change_cb(), ED4_with_all_edit_windows(), ED4_with_whole_block(), GEN_jump_cb(), GEN_set_display_style(), jump_to_next_helix_cb(), modes_cb(), NDS_popup_select_srtaci_window(), PV_SequenceUpdate_CB(), searchParamsChanged(), and ED4_folding_line::win2world().

AW_selection_list* resultList

Definition at line 127 of file probe_design.cxx.

Referenced by awtc_mark_hits(), create_next_neighbours_selected_window(), and NN_GlobalData::get_result_list().

struct { ... } PD

Referenced by create_probe_design_variables(), init_local_com_struct(), popup_probe_design_result_window(), primer_design_event_go(), probe_common_send_data(), probe_design_event(), probe_design_send_data(), probe_match_event(), and probe_match_send_data().

AutoMatchSettings auto_match_cb_settings

static

Definition at line 162 of file probe_design.cxx.

const char* auto_match_sensitive_awars[]

static

Initial value:

= {
    AWAR_TARGET_STRING,
    AWAR_PT_SERVER,
    AWAR_PD_MATCH_ALSO_REVCOMP,
    AWAR_MAX_MISMATCHES,
    AWAR_PD_MATCH_SORTBY,
    NULp
}

Definition at line 177 of file probe_design.cxx.

bool allow_probe_match_event = true

static

Definition at line 742 of file probe_design.cxx.

Referenced by probe_match_event(), probe_match_event_using_awars(), probe_match_with_specificity_event(), refresh_matchedProbesDisplay_cb(), and selected_match_changed_cb().

AWT_config_mapping_def probe_design_mapping_def[]

static

Initial value:

= {
    
    { AWAR_PD_DESIGN_CLIPRESULT,   "clip" },
    { AWAR_PD_DESIGN_MISHIT,       "mishit" },
    { AWAR_PD_DESIGN_MAXBOND,      "maxbond" },
    { AWAR_PD_DESIGN_MINTARGETS,   "mintarget" },
    { AWAR_PD_DESIGN_MIN_LENGTH,   "probelen" },
    { AWAR_PD_DESIGN_MAX_LENGTH,   "probemaxlen" },
    { AWAR_PD_DESIGN_MIN_TEMP,     "mintemp" },
    { AWAR_PD_DESIGN_MAX_TEMP,     "maxtemp" },
    { AWAR_PD_DESIGN_MIN_GC,       "mingc" },
    { AWAR_PD_DESIGN_MAX_GC,       "maxgc" },
    { AWAR_PD_DESIGN_MIN_ECOLIPOS, "minecoli" },
    { AWAR_PD_DESIGN_MAX_ECOLIPOS, "maxecoli" },
    { AWAR_PD_DESIGN_GENE,         "gene" },

    
    { AWAR_PD_DESIGN_EXP_DTEDGE,   "dtedge" },
    { AWAR_PD_DESIGN_EXP_DT,       "dt" },

    { NULp, NULp }
}

Definition at line 1417 of file probe_design.cxx.

AWT_config_mapping_def probe_match_mapping_def[]

static

Initial value:

= {
    
    { AWAR_TARGET_STRING,         "target" },
    { AWAR_PD_MATCH_ALSO_REVCOMP, "complement" },
    { AWAR_PD_MATCH_MARKHITS,     "markhits" },
    { AWAR_PD_MATCH_WRITE2TMP,    "writetmp" },
    { AWAR_PD_MATCH_AUTOMATCH,    "automatch" },

    
    { AWAR_PD_MATCH_NMATCHES,   "nmatches" },
    { AWAR_PD_MATCH_LIM_NMATCH, "limitnmatch" },
    { AWAR_PD_MATCH_MAX_RES,    "maxresults" },

    { NULp, NULp }
}

Definition at line 1757 of file probe_design.cxx.

ArbPM_Context PM_Context

static

Definition at line 2198 of file probe_design.cxx.

SmartPtr<GetMatchesContext> getMatchesContext

static

Definition at line 2273 of file probe_design.cxx.

ArbPC_Context PC_Context

static

Definition at line 2639 of file probe_design.cxx.