ARB
Classes | Macros | Enumerations | Functions | Variables
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 <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 const charPD_probe_pt_look_for_server (int serverNumber, GB_ERROR &error)
 
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 charbond_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 charreadableUnknownNames (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_windowcreate_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_windowcreate_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_windowcreate_IUPAC_resolve_window (AW_root *root, GBDATA *gb_main)
 
static void popupSaiProbeMatchWindow (AW_window *aw, GBDATA *gb_main)
 
AW_windowcreate_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 charptserver_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_windowcreate_probe_admin_window (AW_root *root, GBDATA *gb_main)
 
static AW_windowcreate_probe_match_specificity_control_window (AW_root *root)
 
static void probe_match_update_probe_list (ArbPM_Context *pContext)
 
static AW_windowcreate_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_windowcreate_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_windowprobe_collection_load_prompt (AW_root *root, ArbPC_Context *pContext)
 
static AW_windowprobe_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 saiProbeDatag_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 charauto_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"
#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"

Definition at line 59 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 60 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 61 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 62 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"
#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"

Definition at line 87 of file probe_design.cxx.

Referenced by bond_awar_name().

#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"

Definition at line 93 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 94 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 95 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"
#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"

Definition at line 107 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"
#define AWAR_PC_MATCH_NHITS   "tmp/probe_collection/nhits"
#define AWAR_PC_MISMATCH_THRESHOLD   "probe_collection/mismatch_threshold"
#define REPLACE_TARGET_CONTROL_CHARS   ":#=_:\\:=_"

Definition at line 115 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 1664 of file probe_design.cxx.

Function Documentation

static void probe_match_event_using_awars ( AW_root root,
ProbeMatchEventParam event_param 
)
static
static void auto_match_cb ( AW_root root)
static
static void auto_match_changed ( AW_root root)
static
static void enable_auto_match_cb ( AW_root root,
ProbeMatchEventParam event_param 
)
static
static void popup_match_window_cb ( AW_window aww,
GBDATA gb_main 
)
static
static void popup_probe_design_result_window ( AW_window aww,
GBDATA gb_main 
)
static
static int init_local_com_struct ( )
static

Definition at line 276 of file probe_design.cxx.

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

Referenced by probe_design_event(), and probe_match_event().

static const char* PD_probe_pt_look_for_server ( int  serverNumber,
GB_ERROR error 
)
static
static GB_ERROR species_requires ( GBDATA gb_species,
const char whats_required 
)
static

Definition at line 307 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
static GB_ERROR pd_get_the_names ( GBDATA gb_main,
bytestring bs,
bytestring checksum 
)
static
static GB_ERROR pd_get_the_gene_names ( GBDATA gb_main,
bytestring bs,
bytestring checksum 
)
static
const char* bond_awar_name ( int  i)
inline
static int probe_common_send_data ( const ProbeCommonSettings commonSettings)
static
static int probe_design_send_data ( AW_root root,
const T_PT_PDC &  pdc 
)
static
static int probe_match_send_data ( const ProbeMatchSettings matchSettings)
static
static int ecolipos2int ( const char awar_val)
static

Definition at line 501 of file probe_design.cxx.

Referenced by probe_design_event().

static char* readableUnknownNames ( const ConstStrArray unames)
static
static void probe_design_event ( AW_window aww,
GBDATA gb_main 
)
static
static __ATTR__USERESULT GB_ERROR probe_match_event ( const ProbeMatchSettings matchSettings,
ProbeMatchEventParam event_param 
)
static

Definition at line 756 of file probe_design.cxx.

References aisc_close(), aisc_get(), AISC_MAGIC_NUMBER, aisc_nput(), aisc_open(), allow_probe_match_event, ProbeMatchSettings::alsoRevcompl, 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, PD_probe_pt_look_for_server(), 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
static void resolved_probe_chosen ( AW_root root)
static
static void selected_match_changed_cb ( AW_root root)
static
static void probelength_changed_cb ( AW_root root,
bool  maxChanged 
)
static
static void minmax_awar_pair_changed_cb ( AW_root root,
bool  maxChanged,
const char minAwarName,
const char maxAwarName 
)
static
static void gc_minmax_changed_cb ( AW_root root,
bool  maxChanged 
)
static
static void temp_minmax_changed_cb ( AW_root root,
bool  maxChanged 
)
static
void create_probe_design_variables ( AW_root root,
AW_default  props,
AW_default  db 
)

Definition at line 1247 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(), 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
static void setup_probe_config ( AWT_config_definition cdef,
const AWT_config_mapping_def mapping 
)
static
AW_window* create_probe_design_window ( AW_root root,
GBDATA gb_main 
)
void my_strupr ( char s)
inline

Definition at line 1529 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
static void modify_target_string ( AW_window aww,
GBDATA gb_main,
ModMode  mod_mode 
)
static
static void clear_itarget ( AW_window aww)
static
static AW_window* create_IUPAC_resolve_window ( AW_root root,
GBDATA gb_main 
)
static
static void popupSaiProbeMatchWindow ( AW_window aw,
GBDATA gb_main 
)
static
AW_window* create_probe_match_window ( AW_root root,
GBDATA gb_main 
)
static void pd_start_pt_server ( AW_window aww)
static
static void pd_kill_pt_server ( AW_window aww,
bool  kill_all 
)
static
static const char* ptserver_directory_info_command ( const char dirname,
const char directory 
)
static

Definition at line 1915 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
static void pd_export_pt_server ( AW_window aww,
GBDATA gb_main 
)
static
static void pd_edit_ptserver_log ( AW_window )
static

Definition at line 2047 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 2050 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 
)
static AW_window* create_probe_match_specificity_control_window ( AW_root root)
static
static void probe_match_update_probe_list ( ArbPM_Context pContext)
static
static AW_window * create_probe_collection_window ( AW_root root,
ArbPM_Context pContext 
)
static
static bool probe_match_with_specificity_enum_callback ( void *  pVoidContext,
const char pResult,
bool  bIsComment,
int  nItem,
int  nItems 
)
static
static void probe_match_with_specificity_edit_event ( )
static

Definition at line 2213 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 2285 of file probe_design.cxx.

References md.

Referenced by refresh_matchedProbesDisplay_cb().

static void refresh_matchedProbesDisplay_cb ( AW_root root,
TREE_canvas ntw 
)
static
static void probe_match_with_specificity_event ( AW_root root,
TREE_canvas ntw 
)
static
static void auto_match_cb ( AW_root root,
TREE_canvas ntw 
)
static
static void trigger_auto_match ( AW_root root)
static
static void probe_forget_matches_event ( AW_window aww,
ArbPM_Context pContext 
)
static
static void selected_probe_changed_cb ( AW_root root)
static
static void target_string_changed_cb ( AW_root root)
static
static void match_changed_cb ( AW_root root)
static
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
static void show_probes_in_sellist ( const ArbProbePtrList rProbeList,
AW_selection_list sellist 
)
static
static void load_probe_collection ( AW_window aww,
ArbPC_Context Context,
const char *const *  awar_filename 
)
static
static void probe_collection_update_parameters ( )
static
static void save_probe_collection ( AW_window aww,
const char *const *  awar_filename 
)
static
static void add_probe_to_collection_event ( AW_window aww,
ArbPC_Context pContext 
)
static
static void modify_probe_event ( AW_window aww,
ArbPC_Context pContext 
)
static
static void remove_probe_from_collection_event ( AW_window aww,
ArbPC_Context pContext 
)
static
static AW_window* probe_collection_load_prompt ( AW_root root,
ArbPC_Context pContext 
)
static

Definition at line 2860 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 2866 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
static void probe_collection_close ( AW_window aww)
static

Variable Documentation

saiProbeData* g_spd = NULp
static

Definition at line 119 of file probe_design.cxx.

Referenced by probe_match_event().

aisc_com* link
T_PT_LOCS locs
T_PT_MAIN com

Definition at line 124 of file probe_design.cxx.

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

AW_window_simple* win
AW_selection_list* resultList
struct { ... } PD
AutoMatchSettings auto_match_cb_settings
static

Definition at line 161 of file probe_design.cxx.

const char* auto_match_sensitive_awars[]
static
Initial value:
= {
}
#define AWAR_PD_MATCH_ALSO_REVCOMP
#define AWAR_MAX_MISMATCHES
#define AWAR_PT_SERVER
#define AWAR_TARGET_STRING
#define NULp
Definition: cxxforward.h:97
#define AWAR_PD_MATCH_SORTBY

Definition at line 176 of file probe_design.cxx.

bool allow_probe_match_event = true
static
AWT_config_mapping_def probe_design_mapping_def[]
static
Initial value:
= {
{ 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" },
{ NULp, NULp }
}
#define AWAR_PD_DESIGN_MINTARGETS
#define AWAR_PD_DESIGN_EXP_DT
#define AWAR_PD_DESIGN_MIN_TEMP
#define AWAR_PD_DESIGN_CLIPRESULT
#define AWAR_PD_DESIGN_MISHIT
#define AWAR_PD_DESIGN_MIN_LENGTH
#define AWAR_PD_DESIGN_MAXBOND
#define AWAR_PD_DESIGN_MAX_GC
#define AWAR_PD_DESIGN_MAX_LENGTH
#define AWAR_PD_DESIGN_MIN_ECOLIPOS
#define AWAR_PD_DESIGN_MAX_ECOLIPOS
#define AWAR_PD_DESIGN_EXP_DTEDGE
#define NULp
Definition: cxxforward.h:97
#define AWAR_PD_DESIGN_MAX_TEMP
#define AWAR_PD_DESIGN_MIN_GC
#define AWAR_PD_DESIGN_GENE

Definition at line 1429 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 }
}
#define AWAR_PD_MATCH_LIM_NMATCH
#define AWAR_PD_MATCH_ALSO_REVCOMP
#define AWAR_PD_MATCH_AUTOMATCH
#define AWAR_PD_MATCH_MAX_RES
#define AWAR_PD_MATCH_WRITE2TMP
#define AWAR_TARGET_STRING
#define AWAR_PD_MATCH_NMATCHES
#define AWAR_PD_MATCH_MARKHITS
#define NULp
Definition: cxxforward.h:97

Definition at line 1755 of file probe_design.cxx.

ArbPM_Context PM_Context
static

Definition at line 2173 of file probe_design.cxx.

SmartPtr<GetMatchesContext> getMatchesContext
static

Definition at line 2248 of file probe_design.cxx.

ArbPC_Context PC_Context
static

Definition at line 2614 of file probe_design.cxx.