Changeset 7801

Timestamp:

07/08/11 18:41:16 (10 months ago)

Author:

westram

Message:

merge from dev [7710]

• resolve some nesting in library dependencies
  • allows unit tests in GENOM and GENOM_IMPORT

Location:

trunk

Files:

• ARB_GDE/GDE_event.cxx (modified) (1 diff)
• AWT/AWT_asciiprint.cxx (modified) (1 diff)
• AWT/AWT_changekey.cxx (deleted)
• AWT/AWT_config_manager.cxx (modified) (1 diff)
• AWT/AWT_db_browser.cxx (modified) (1 diff)
• AWT/AWT_item_sel_list.cxx (deleted)
• AWT/AWT_nds.cxx (deleted)
• AWT/AWT_query_and_functions.cxx (deleted)
• AWT/AWT_sel_boxes.cxx (modified) (2 diffs)
• AWT/AWT_tables.cxx (modified) (1 diff)
• AWT/AWT_www.cxx (modified) (1 diff)
• AWT/Makefile (modified) (5 diffs)
• AWT/awt.hxx (modified) (2 diffs)
• AWT/awt_input_mask.hxx (modified) (3 diffs)
• AWT/awt_input_mask_internal.hxx (modified) (1 diff)
• AWT/awt_item_sel_list.hxx (deleted)
• AWT/awt_nds.hxx (deleted)
• AWT/awt_sel_boxes.hxx (modified) (1 diff)
• AWT/awtlocal.hxx (modified) (2 diffs)
• AWT/refentries.cxx (deleted)
• AWT/refentries.h (deleted)
• AWTC/AWTC_submission.cxx (modified) (1 diff)
• AWTC/Makefile (modified) (1 diff)
• AWTI/AWTI_export.cxx (modified) (1 diff)
• AWTI/AWTI_import.cxx (modified) (1 diff)
• AWTI/Makefile (modified) (1 diff)
• DIST/DI_save_matr.cxx (modified) (1 diff)
• DIST/Makefile (modified) (1 diff)
• EDIT4/ED4_naligner.cxx (modified) (1 diff)
• EDIT4/ED4_no_class.cxx (modified) (1 diff)
• EDIT4/ED4_visualizeSAI.cxx (modified) (1 diff)
• EDIT4/Makefile (modified) (4 diffs)
• EDIT4/needs_libs (modified) (1 diff)
• GENOM/EXP_interface.cxx (modified) (5 diffs)
• GENOM/EXP_main.cxx (modified) (4 diffs)
• GENOM/GEN_graphic.cxx (modified) (1 diff)
• GENOM/GEN_interface.cxx (modified) (5 diffs)
• GENOM/GEN_map.cxx (modified) (4 diffs)
• GENOM/GEN_nds.cxx (modified) (1 diff)
• GENOM/Makefile (modified) (8 diffs)
• GENOM/needs_libs (modified) (1 diff)
• GENOM_IMPORT/Location.cxx (modified) (1 diff)
• GENOM_IMPORT/Makefile (modified) (1 diff)
• MERGE/MG_checkfield.cxx (modified) (1 diff)
• MERGE/MG_configs.cxx (modified) (1 diff)
• MERGE/MG_extendeds.cxx (modified) (2 diffs)
• MERGE/MG_gene_species.cxx (modified) (1 diff)
• MERGE/MG_preserves.cxx (modified) (1 diff)
• MERGE/MG_species.cxx (modified) (1 diff)
• MERGE/Makefile (modified) (6 diffs)
• MERGE/needs_libs (modified) (1 diff)
• MULTI_PROBE/MP_noclass.cxx (modified) (1 diff)
• MULTI_PROBE/Makefile (modified) (1 diff)
• Makefile (modified) (10 diffs)
• NTREE/Makefile (modified) (20 diffs)
• NTREE/NT_cb.cxx (modified) (1 diff)
• NTREE/NT_concatenate.cxx (modified) (1 diff)
• NTREE/NT_dbrepair.cxx (modified) (1 diff)
• NTREE/NT_extern.cxx (modified) (9 diffs)
• NTREE/NT_import.cxx (modified) (2 diffs)
• NTREE/NT_join.cxx (modified) (1 diff)
• NTREE/NT_main.cxx (modified) (3 diffs)
• NTREE/NT_sort.cxx (modified) (1 diff)
• NTREE/NT_validManual.cxx (modified) (1 diff)
• NTREE/NT_validNames.cxx (modified) (1 diff)
• NTREE/ad_ext.cxx (modified) (1 diff)
• NTREE/ad_fields.cxx (modified) (1 diff)
• NTREE/ad_spec.cxx (modified) (5 diffs)
• NTREE/ad_spec.hxx (deleted)
• NTREE/map_viewer.hxx (modified) (1 diff)
• NTREE/needs_libs (modified) (2 diffs)
• NTREE/nt_cb.hxx (modified) (1 diff)
• NTREE/nt_internal.h (modified) (2 diffs)
• PARSIMONY/GA_window.cxx (modified) (1 diff)
• PARSIMONY/Makefile (modified) (2 diffs)
• PARSIMONY/PARS_main.cxx (modified) (1 diff)
• PROBE_DESIGN/Makefile (modified) (1 diff)
• PROBE_DESIGN/SaiProbeVisualization.cxx (modified) (1 diff)
• SECEDIT/Makefile (modified) (1 diff)
• SECEDIT/SEC_main.cxx (modified) (1 diff)
• SEQ_QUALITY/Makefile (modified) (2 diffs)
• SEQ_QUALITY/SQ_functions.cxx (modified) (1 diff)
• SEQ_QUALITY/SQ_main.cxx (modified) (2 diffs)
• SL/AW_NAME/AW_names_admin.cxx (modified) (1 diff)
• SL/AW_NAME/Makefile (modified) (1 diff)
• SL/DB_QUERY (copied) (copied from branches/dev/SL/DB_QUERY)
• SL/DB_SCANNER/Makefile (modified) (3 diffs)
• SL/DB_SCANNER/db_scanner.cxx (modified) (4 diffs)
• SL/DB_SCANNER/db_scanner.hxx (modified) (1 diff)
• SL/DB_SCANNER/needs_libs (modified) (1 diff)
• SL/DB_UI (copied) (copied from branches/dev/SL/DB_UI)
• SL/GUI_ALIVIEW/AWT_filter.cxx (modified) (4 diffs)
• SL/GUI_ALIVIEW/ColumnStat.cxx (modified) (3 diffs)
• SL/GUI_ALIVIEW/GUI_aliview.cxx (modified) (1 diff)
• SL/GUI_ALIVIEW/Makefile (modified) (3 diffs)
• SL/GUI_ALIVIEW/awt_filter.hxx (modified) (1 diff)
• SL/GUI_ALIVIEW/ga_local.h (copied) (copied from branches/dev/SL/GUI_ALIVIEW/ga_local.h)
• SL/ITEMS (copied) (copied from branches/dev/SL/ITEMS)
• SL/Makefile (modified) (2 diffs)
• SL/NDS (copied) (copied from branches/dev/SL/NDS)
• SL/REFENTRIES (copied) (copied from branches/dev/SL/REFENTRIES)
• SL/TREEDISP/Makefile (modified) (3 diffs)
• SL/TREEDISP/TreeCallbacks.cxx (modified) (14 diffs)
• SL/TREEDISP/TreeDisplay.cxx (modified) (15 diffs)
• SL/TREEDISP/TreeDisplay.hxx (modified) (1 diff)
• SL/TREEDISP/irstree_display.cxx (modified) (1 diff)
• SL/TREEDISP/needs_libs (modified) (1 diff)
• SL/TREE_WRITE/Makefile (modified) (1 diff)
• SL/TREE_WRITE/TreeWrite.h (modified) (1 diff)
• SOURCE_TOOLS/generate_all_links.sh (modified) (3 diffs)
• STAT/Makefile (modified) (1 diff)
• STAT/ST_window.cxx (modified) (1 diff)
• TOOLS/Makefile (modified) (1 diff)
• WETC/WETC_main.cxx (modified) (1 diff)
• WINDOW/AW_edit.cxx (modified) (1 diff)
• WINDOW/aw_detach.hxx (modified) (1 diff)
• WINDOW/aw_root.hxx (modified) (1 diff)

trunk/ARB_GDE/GDE_event.cxx

@@ -487 +487 @@
 
     GapCompression  compress          = static_cast<GapCompression>(aw_root->awar(AWAR_GDE_COMPRESSION)->read_int());
-    AP_filter      *filter2           = awt_get_filter(aw_root, agde_filtercd);
+    AP_filter      *filter2           = awt_get_filter(agde_filtercd);
     char           *filter_name       = 0; /* aw_root->awar(AWAR_GDE_FILTER_NAME)->read_string() */
     char           *alignment_name    = strdup("ali_unknown");

trunk/AWT/AWT_asciiprint.cxx

@@ -12 +12 @@
 #include "awt.hxx"
 
+#include <aw_window.hxx>
 #include <aw_root.hxx>
 #include <aw_awar.hxx>

trunk/AWT/AWT_config_manager.cxx

@@ -15 +15 @@
 #include "awt_config_manager.hxx"
 #include "awt.hxx"
+#include <aw_window.hxx>
 #include <aw_root.hxx>
 #include <aw_awar.hxx>

trunk/AWT/AWT_db_browser.cxx

@@ -16 +16 @@
 #include <arb_str.h>
 #include <AP_Tree.hxx>
+#include <aw_window.hxx>
 #include <aw_awar.hxx>
 #include <aw_msg.hxx>

trunk/AWT/AWT_sel_boxes.cxx

@@ -11 +11 @@
 #include "awt.hxx"
 #include "awt_sel_boxes.hxx"
-#include "awt_item_sel_list.hxx"
+
+#include <item_sel_list.h>
 
 #include <aw_awars.hxx>
@@ -763 +764 @@
 }
 
-void AWT_popup_select_species_field_window(AW_window *aww, AW_CL cl_awar_name, AW_CL cl_gb_main)
-{
-    static AW_window_simple *aws = 0;
-
-    // everytime map selection awar to latest user awar:
-    AW_root    *aw_root   = aww->get_root();
-    const char *awar_name = (const char *)cl_awar_name;
-    aw_root->awar("tmp/viewkeys/key_text_select")->map(awar_name);
-
-    if (!aws) {
-        aws = new AW_window_simple;
-
-        aws->init(aw_root, "SELECT_SPECIES_FIELD", "Select species field");
-        aws->load_xfig("awt/nds_sel.fig");
-        aws->button_length(13);
-
-        aws->callback(AW_POPDOWN);
-        aws->at("close");
-        aws->create_button("CLOSE", "CLOSE", "C");
-
-        awt_create_selection_list_on_itemfields((GBDATA *)cl_gb_main,
-                                                aws,
-                                                "tmp/viewkeys/key_text_select",
-                                                AWT_NDS_FILTER,
-                                                "scandb", "rescandb", &AWT_species_selector, 20, 10);
-        aws->recalc_pos_atShow(AW_REPOS_TO_MOUSE);
-    }
-    aws->activate();
-}
-
-
+
+

trunk/AWT/AWT_tables.cxx

@@ -13 +13 @@
 #include "awt_sel_boxes.hxx"
 
+#include <aw_window.hxx>
 #include <aw_awars.hxx>
 #include <aw_file.hxx>

trunk/AWT/AWT_www.cxx

@@ -12 +12 @@
 #include "awt.hxx"
 
+#include <aw_window.hxx>
 #include <aw_global_awars.hxx>
 #include <aw_awars.hxx>

trunk/AWT/Makefile

@@ -128 +128 @@
 AWT_canvas.o: $(ARBHOME)/INCLUDE/smartptr.h
 AWT_canvas.o: $(ARBHOME)/INCLUDE/test_global.h
-
-AWT_changekey.o: awt.hxx
-AWT_changekey.o: awt_item_sel_list.hxx
-AWT_changekey.o: $(ARBHOME)/INCLUDE/ad_prot.h
-AWT_changekey.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
-AWT_changekey.o: $(ARBHOME)/INCLUDE/arb_assert.h
-AWT_changekey.o: $(ARBHOME)/INCLUDE/arb_core.h
-AWT_changekey.o: $(ARBHOME)/INCLUDE/arb_error.h
-AWT_changekey.o: $(ARBHOME)/INCLUDE/arb_msg.h
-AWT_changekey.o: $(ARBHOME)/INCLUDE/arb_strarray.h
-AWT_changekey.o: $(ARBHOME)/INCLUDE/arb_string.h
-AWT_changekey.o: $(ARBHOME)/INCLUDE/arbdb.h
-AWT_changekey.o: $(ARBHOME)/INCLUDE/arbdb_base.h
-AWT_changekey.o: $(ARBHOME)/INCLUDE/arbdbt.h
-AWT_changekey.o: $(ARBHOME)/INCLUDE/arbtools.h
-AWT_changekey.o: $(ARBHOME)/INCLUDE/attributes.h
-AWT_changekey.o: $(ARBHOME)/INCLUDE/aw_awar.hxx
-AWT_changekey.o: $(ARBHOME)/INCLUDE/aw_awars.hxx
-AWT_changekey.o: $(ARBHOME)/INCLUDE/aw_base.hxx
-AWT_changekey.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
-AWT_changekey.o: $(ARBHOME)/INCLUDE/aw_select.hxx
-AWT_changekey.o: $(ARBHOME)/INCLUDE/aw_window.hxx
-AWT_changekey.o: $(ARBHOME)/INCLUDE/cb.h
-AWT_changekey.o: $(ARBHOME)/INCLUDE/dupstr.h
-AWT_changekey.o: $(ARBHOME)/INCLUDE/smartptr.h
-AWT_changekey.o: $(ARBHOME)/INCLUDE/test_global.h
 
 AWT_config_manager.o: awt.hxx
@@ -241 +215 @@
 AWT_input_mask.o: $(ARBHOME)/INCLUDE/test_global.h
 
-AWT_item_sel_list.o: awt.hxx
-AWT_item_sel_list.o: awt_item_sel_list.hxx
-AWT_item_sel_list.o: $(ARBHOME)/INCLUDE/ad_prot.h
-AWT_item_sel_list.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
-AWT_item_sel_list.o: $(ARBHOME)/INCLUDE/arb_assert.h
-AWT_item_sel_list.o: $(ARBHOME)/INCLUDE/arb_core.h
-AWT_item_sel_list.o: $(ARBHOME)/INCLUDE/arb_error.h
-AWT_item_sel_list.o: $(ARBHOME)/INCLUDE/arb_msg.h
-AWT_item_sel_list.o: $(ARBHOME)/INCLUDE/arb_string.h
-AWT_item_sel_list.o: $(ARBHOME)/INCLUDE/arbdb.h
-AWT_item_sel_list.o: $(ARBHOME)/INCLUDE/arbdb_base.h
-AWT_item_sel_list.o: $(ARBHOME)/INCLUDE/arbdbt.h
-AWT_item_sel_list.o: $(ARBHOME)/INCLUDE/arbtools.h
-AWT_item_sel_list.o: $(ARBHOME)/INCLUDE/attributes.h
-AWT_item_sel_list.o: $(ARBHOME)/INCLUDE/aw_awar.hxx
-AWT_item_sel_list.o: $(ARBHOME)/INCLUDE/aw_awars.hxx
-AWT_item_sel_list.o: $(ARBHOME)/INCLUDE/aw_base.hxx
-AWT_item_sel_list.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
-AWT_item_sel_list.o: $(ARBHOME)/INCLUDE/aw_select.hxx
-AWT_item_sel_list.o: $(ARBHOME)/INCLUDE/aw_window.hxx
-AWT_item_sel_list.o: $(ARBHOME)/INCLUDE/cb.h
-AWT_item_sel_list.o: $(ARBHOME)/INCLUDE/dupstr.h
-AWT_item_sel_list.o: $(ARBHOME)/INCLUDE/smartptr.h
-AWT_item_sel_list.o: $(ARBHOME)/INCLUDE/test_global.h
-
 AWT_macro.o: awt_macro.hxx
 AWT_macro.o: $(ARBHOME)/INCLUDE/ad_prot.h
@@ -307 +256 @@
 AWT_map_key.o: $(ARBHOME)/INCLUDE/test_global.h
 
-AWT_nds.o: awt.hxx
-AWT_nds.o: awt_config_manager.hxx
-AWT_nds.o: awt_nds.hxx
-AWT_nds.o: awt_sel_boxes.hxx
-AWT_nds.o: $(ARBHOME)/INCLUDE/ad_prot.h
-AWT_nds.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
-AWT_nds.o: $(ARBHOME)/INCLUDE/arb_assert.h
-AWT_nds.o: $(ARBHOME)/INCLUDE/arb_core.h
-AWT_nds.o: $(ARBHOME)/INCLUDE/arb_error.h
-AWT_nds.o: $(ARBHOME)/INCLUDE/arb_msg.h
-AWT_nds.o: $(ARBHOME)/INCLUDE/arb_string.h
-AWT_nds.o: $(ARBHOME)/INCLUDE/arbdb.h
-AWT_nds.o: $(ARBHOME)/INCLUDE/arbdb_base.h
-AWT_nds.o: $(ARBHOME)/INCLUDE/arbdbt.h
-AWT_nds.o: $(ARBHOME)/INCLUDE/arbtools.h
-AWT_nds.o: $(ARBHOME)/INCLUDE/attributes.h
-AWT_nds.o: $(ARBHOME)/INCLUDE/aw_awar.hxx
-AWT_nds.o: $(ARBHOME)/INCLUDE/aw_awars.hxx
-AWT_nds.o: $(ARBHOME)/INCLUDE/aw_base.hxx
-AWT_nds.o: $(ARBHOME)/INCLUDE/aw_file.hxx
-AWT_nds.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
-AWT_nds.o: $(ARBHOME)/INCLUDE/aw_msg.hxx
-AWT_nds.o: $(ARBHOME)/INCLUDE/aw_root.hxx
-AWT_nds.o: $(ARBHOME)/INCLUDE/aw_window.hxx
-AWT_nds.o: $(ARBHOME)/INCLUDE/cb.h
-AWT_nds.o: $(ARBHOME)/INCLUDE/dupstr.h
-AWT_nds.o: $(ARBHOME)/INCLUDE/smartptr.h
-AWT_nds.o: $(ARBHOME)/INCLUDE/test_global.h
-
-AWT_query_and_functions.o: awt.hxx
-AWT_query_and_functions.o: awt_config_manager.hxx
-AWT_query_and_functions.o: awt_item_sel_list.hxx
-AWT_query_and_functions.o: awtlocal.hxx
-AWT_query_and_functions.o: $(ARBHOME)/INCLUDE/ad_prot.h
-AWT_query_and_functions.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
-AWT_query_and_functions.o: $(ARBHOME)/INCLUDE/arb_assert.h
-AWT_query_and_functions.o: $(ARBHOME)/INCLUDE/arb_core.h
-AWT_query_and_functions.o: $(ARBHOME)/INCLUDE/arb_error.h
-AWT_query_and_functions.o: $(ARBHOME)/INCLUDE/arb_msg.h
-AWT_query_and_functions.o: $(ARBHOME)/INCLUDE/arb_progress.h
-AWT_query_and_functions.o: $(ARBHOME)/INCLUDE/arb_sort.h
-AWT_query_and_functions.o: $(ARBHOME)/INCLUDE/arb_strbuf.h
-AWT_query_and_functions.o: $(ARBHOME)/INCLUDE/arb_string.h
-AWT_query_and_functions.o: $(ARBHOME)/INCLUDE/arbdb.h
-AWT_query_and_functions.o: $(ARBHOME)/INCLUDE/arbdb_base.h
-AWT_query_and_functions.o: $(ARBHOME)/INCLUDE/arbdbt.h
-AWT_query_and_functions.o: $(ARBHOME)/INCLUDE/arbtools.h
-AWT_query_and_functions.o: $(ARBHOME)/INCLUDE/attributes.h
-AWT_query_and_functions.o: $(ARBHOME)/INCLUDE/aw_advice.hxx
-AWT_query_and_functions.o: $(ARBHOME)/INCLUDE/aw_awar.hxx
-AWT_query_and_functions.o: $(ARBHOME)/INCLUDE/aw_awars.hxx
-AWT_query_and_functions.o: $(ARBHOME)/INCLUDE/aw_base.hxx
-AWT_query_and_functions.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx
-AWT_query_and_functions.o: $(ARBHOME)/INCLUDE/aw_file.hxx
-AWT_query_and_functions.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
-AWT_query_and_functions.o: $(ARBHOME)/INCLUDE/aw_msg.hxx
-AWT_query_and_functions.o: $(ARBHOME)/INCLUDE/aw_root.hxx
-AWT_query_and_functions.o: $(ARBHOME)/INCLUDE/aw_select.hxx
-AWT_query_and_functions.o: $(ARBHOME)/INCLUDE/aw_window.hxx
-AWT_query_and_functions.o: $(ARBHOME)/INCLUDE/cb.h
-AWT_query_and_functions.o: $(ARBHOME)/INCLUDE/dupstr.h
-AWT_query_and_functions.o: $(ARBHOME)/INCLUDE/smartptr.h
-AWT_query_and_functions.o: $(ARBHOME)/INCLUDE/test_global.h
-
 AWT_sel_boxes.o: awt.hxx
-AWT_sel_boxes.o: awt_item_sel_list.hxx
 AWT_sel_boxes.o: awt_sel_boxes.hxx
 AWT_sel_boxes.o: $(ARBHOME)/INCLUDE/ad_config.h
@@ -400 +284 @@
 AWT_sel_boxes.o: $(ARBHOME)/INCLUDE/cb.h
 AWT_sel_boxes.o: $(ARBHOME)/INCLUDE/dupstr.h
+AWT_sel_boxes.o: $(ARBHOME)/INCLUDE/item_sel_list.h
+AWT_sel_boxes.o: $(ARBHOME)/INCLUDE/items.h
 AWT_sel_boxes.o: $(ARBHOME)/INCLUDE/smartptr.h
 AWT_sel_boxes.o: $(ARBHOME)/INCLUDE/test_global.h
@@ -485 +371 @@
 AWT_www.o: $(ARBHOME)/INCLUDE/static_assert.h
 AWT_www.o: $(ARBHOME)/INCLUDE/test_global.h
-
-refentries.o: awt.hxx
-refentries.o: refentries.h
-refentries.o: $(ARBHOME)/INCLUDE/ad_prot.h
-refentries.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
-refentries.o: $(ARBHOME)/INCLUDE/arb_assert.h
-refentries.o: $(ARBHOME)/INCLUDE/arb_core.h
-refentries.o: $(ARBHOME)/INCLUDE/arb_error.h
-refentries.o: $(ARBHOME)/INCLUDE/arb_msg.h
-refentries.o: $(ARBHOME)/INCLUDE/arb_strarray.h
-refentries.o: $(ARBHOME)/INCLUDE/arb_string.h
-refentries.o: $(ARBHOME)/INCLUDE/arbdb.h
-refentries.o: $(ARBHOME)/INCLUDE/arbdb_base.h
-refentries.o: $(ARBHOME)/INCLUDE/arbdbt.h
-refentries.o: $(ARBHOME)/INCLUDE/arbtools.h
-refentries.o: $(ARBHOME)/INCLUDE/attributes.h
-refentries.o: $(ARBHOME)/INCLUDE/aw_awar.hxx
-refentries.o: $(ARBHOME)/INCLUDE/aw_awars.hxx
-refentries.o: $(ARBHOME)/INCLUDE/aw_base.hxx
-refentries.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
-refentries.o: $(ARBHOME)/INCLUDE/aw_msg.hxx
-refentries.o: $(ARBHOME)/INCLUDE/aw_root.hxx
-refentries.o: $(ARBHOME)/INCLUDE/aw_window.hxx
-refentries.o: $(ARBHOME)/INCLUDE/cb.h
-refentries.o: $(ARBHOME)/INCLUDE/dbitem_set.h
-refentries.o: $(ARBHOME)/INCLUDE/dupstr.h
-refentries.o: $(ARBHOME)/INCLUDE/smartptr.h
-refentries.o: $(ARBHOME)/INCLUDE/test_global.h

trunk/AWT/awt.hxx

@@ -12 +12 @@
 #define AWT_HXX
 
-#ifndef AW_WINDOW_HXX
-#include <aw_window.hxx>
+#ifndef AW_BASE_HXX
+#include <aw_base.hxx>
+#endif
+#ifndef ARBDB_BASE_H
+#include <arbdb_base.h>
 #endif
 
-#define awt_assert(bed) arb_assert(bed)
+
+#define awt_assert(cond) arb_assert(cond)
 
 // ------------------------------------------------------------
@@ -22 +26 @@
 // holds all stuff needed to make ad_.. functions work with species _and_ genes (and more..)
 
-typedef enum {
-    AWT_QUERY_ITEM_SPECIES,
-    AWT_QUERY_ITEM_GENES,
-    AWT_QUERY_ITEM_EXPERIMENTS,
-
-    AWT_QUERY_ITEM_TYPES // how many different types do we have
-
-} AWT_QUERY_ITEM_TYPE;
-
-typedef enum {
-    QUERY_CURRENT_ITEM,
-    QUERY_MARKED_ITEMS,
-    QUERY_ALL_ITEMS
-} AWT_QUERY_RANGE;
-
-typedef enum {
-    AWT_QUERY_SORT_NONE = 0,
-
-    // "real" criteria:
-    AWT_QUERY_SORT_BY_1STFIELD_CONTENT = 1,         // by content of first selected search field
-    AWT_QUERY_SORT_BY_ID               = 2,         // by item id (not by parent)
-    AWT_QUERY_SORT_BY_NESTED_PID       = 4,         // by nested parent id
-    AWT_QUERY_SORT_BY_MARKED           = 8,         // marked items first
-    AWT_QUERY_SORT_BY_HIT_DESCRIPTION  = 16,        // by hit description
-    AWT_QUERY_SORT_REVERSE             = 32,        // revert following (may occur multiple times)
-
-} AWT_QUERY_RESULT_ORDER;
-
-#define AWT_QUERY_SORT_CRITERIA_BITS 6              // number of "real" sort criteria
-#define AWT_QUERY_SORT_CRITERIA_MASK ((1<<AWT_QUERY_SORT_CRITERIA_BITS)-1)
-
-struct ad_item_selector { // @@@ remove AW_root arguments!
-    AWT_QUERY_ITEM_TYPE type;
-
-    // if user selects an item in the result list,
-    // this callback sets the appropriate AWARs
-    // - for species: AWAR_SPECIES_NAME is changed (item_name = 'species_name')
-    // - for genes: AWAR_GENE_NAME and AWAR_SPECIES_NAME are changed (item_name = 'species_name/gene_name')
-    void (*update_item_awars)(GBDATA* gb_main, AW_root *aw_root, const char *item_name);
-    char *(*generate_item_id)(GBDATA *gb_main, GBDATA *gb_item); // @@@ remove parameter 'gb_main'
-    GBDATA *(*find_item_by_id)(GBDATA *gb_main, const char *id);
-    AW_CB selection_list_rescan_cb;
-    int   item_name_length; // -1 means "unknown" (might be long)
-
-    const char *change_key_path;
-    const char *item_name;                          // "species" or "gene" or "experiment" or "organism"
-    const char *items_name;                         // "species" or "genes" or "experiments" or "organisms"
-    const char *id_field;                           // e.g. "name" for species, genes
-
-    GBDATA *(*get_first_item_container)(GBDATA *, AW_root *, AWT_QUERY_RANGE); // AW_root may be NULL for QUERY_ALL_ITEMS and QUERY_MARKED_ITEMS
-    GBDATA *(*get_next_item_container)(GBDATA *, AWT_QUERY_RANGE); // use same AWT_QUERY_RANGE as in get_first_item_container()
-
-    GBDATA *(*get_first_item)(GBDATA *, AWT_QUERY_RANGE);
-    GBDATA *(*get_next_item)(GBDATA *, AWT_QUERY_RANGE);
-
-    GBDATA *(*get_selected_item)(GBDATA *gb_main, AW_root *aw_root); // searches the currently selected item
-
-    struct ad_item_selector *parent_selector;       // selector of parent item (or NULL if item has no parents)
-    GBDATA *(*get_parent)(GBDATA *gb_item);         // if 'parent_selector' is defined, this function returns the parent of the item
-};
-
-char   *AWT_get_item_id(GBDATA *gb_main, const ad_item_selector *sel, GBDATA *gb_item);
-GBDATA *AWT_get_item_with_id(GBDATA *gb_main, const ad_item_selector *sel, const char *id);
-
-extern ad_item_selector AWT_species_selector;
-extern ad_item_selector AWT_organism_selector;
-
-// ------------------
-//      query box
-
-typedef AW_window *(*awt_create_viewer_window_cb)(AW_root *aw_root, AW_CL cl_gb_main);
-
-#define IS_QUERIED(gb_species, cbs)   (cbs->select_bit & GB_read_usr_private(gb_species))
-class awt_query_struct {
-public:
-    awt_query_struct();
-
-    GBDATA *gb_main;                                // the main database (in merge tool: source db in left query; dest db in right query)
-    GBDATA *gb_ref;                                 // second reference database (only used by merge tool; dest db in left query; source db in right query)
-    bool    expect_hit_in_ref_list;                 // merge-tool: when searching dups in fields: match only if hit exists in other DBs hitlist (true for DBII-query)
-    AWAR    species_name;                           // AWAR containing current species name
-    AWAR    tree_name;                              // AWAR containing current tree name
-
-    const ad_item_selector *selector;               // which kind of item do we handle?
-
-    int select_bit;                                 // one of 1 2 4 8 .. 128 (one for each query box)
-    int use_menu;                                   // put additional commands in menu
-
-    const char *ere_pos_fig;                        // rebuild enlarge reduce
-    const char *where_pos_fig;                      // current, marked or all species (used for sub-items of species)
-    const char *by_pos_fig;                         // fit query don't fit, marked
-
-    const char *qbox_pos_fig;                       // key box for queries
-    const char *rescan_pos_fig;                     // rescan label
-    const char *key_pos_fig;                        // the key
-    const char *query_pos_fig;                      // the query
-
-
-    const char *result_pos_fig;                     // the result box
-    const char *count_pos_fig;
-
-    const char *do_query_pos_fig;
-    const char *config_pos_fig;
-    const char *do_mark_pos_fig;
-    const char *do_unmark_pos_fig;
-    const char *do_delete_pos_fig;
-    const char *do_set_pos_fig;                     // multi set a key
-    const char *open_parser_pos_fig;
-    const char *do_refresh_pos_fig;
-
-    awt_create_viewer_window_cb create_view_window;
-
-    const char *info_box_pos_fig;
-
-};
-
-struct DbQuery;
-void awt_copy_selection_list_2_queried_species(DbQuery *cbs, AW_selection_list *id, const char *hit_description);
-DbQuery *awt_create_query_box(AW_window *aws, awt_query_struct *awtqs, const char *query_id); // create the query box
-void awt_search_equal_entries(AW_window *dummy, DbQuery *cbs, bool tokenize);
-long awt_count_queried_items(DbQuery *cbs, AWT_QUERY_RANGE range);
-void awt_unquery_all(void *dummy, DbQuery *cbs);
 
 // ------------------------------------------------------------
-
-AW_window *awt_create_item_colorizer(AW_root *aw_root, GBDATA *gb_main, const ad_item_selector *sel);
 
 void awt_set_long(AW_window *aws, AW_CL varname, AW_CL value);      // set an awar

trunk/AWT/awt_input_mask.hxx

@@ -1 +1 @@
 //  ==================================================================== //
 //                                                                       //
-//    File      : AWT_input_mask.h                                       //
+//    File      : awt_input_mask.hxx                                     //
 //    Purpose   : General input masks                                    //
 //                                                                       //
@@ -19 +19 @@
 #include <string>
 #endif
-#ifndef AWT_HXX
-#include <awt.hxx>
+#ifndef AW_BASE_HXX
+#include <aw_base.hxx>
 #endif
 
@@ -74 +74 @@
 
 awt_item_type AWT_getItemType(const std::string& itemtype_name);
-void          AWT_create_mask_submenu(AW_window_menu_modes *awm, awt_item_type wanted_item_type, AWT_OpenMaskWindowCallback open_mask_window_cb, AW_CL cl_user);
+void          AWT_create_mask_submenu(class AW_window_menu_modes *awm, awt_item_type wanted_item_type, AWT_OpenMaskWindowCallback open_mask_window_cb, AW_CL cl_user);
 void          AWT_destroy_input_masks();
 

trunk/AWT/awt_input_mask_internal.hxx

@@ -28 +28 @@
 #include <aw_root.hxx>
 #endif
+#ifndef AW_WINDOW_HXX
+#include <aw_window.hxx>
+#endif
+#ifndef AWT_HXX
+#include "awt.hxx"
+#endif
+
 
 #ifndef _GLIBCXX_MAP

trunk/AWT/awt_sel_boxes.hxx

@@ -48 +48 @@
                                void (*callback)(AW_window*), AW_window* (*create_popup)(AW_root *, AW_default));
 
-void AWT_popup_select_species_field_window(AW_window *aww, AW_CL cl_awar_name, AW_CL cl_gb_main);
-
 // -------------------------------
 

trunk/AWT/awtlocal.hxx

@@ -12 +12 @@
 #define AWTLOCAL_HXX
 
-typedef enum {
-    AWT_QUERY_GENERATE,
-    AWT_QUERY_ENLARGE,
-    AWT_QUERY_REDUCE
-} AWT_QUERY_MODES;
+#ifndef ARBTOOLS_H
+#include <arbtools.h>
+#endif
 
-typedef enum {
-    AWT_QUERY_MARKED,
-    AWT_QUERY_MATCH,
-    AWT_QUERY_DONT_MATCH
-} AWT_QUERY_TYPES;
-
-#define AWT_QUERY_SEARCHES 3 // no of search-lines in search tool
-
-struct DbQuery {
-    AW_window         *aws;
-    GBDATA            *gb_main;                     // the main database (in merge tool: source db in left query; dest db in right query)
-    GBDATA            *gb_ref;                      // second reference database (only used by merge tool; dest db in left query; source db in right query)
-    bool               expect_hit_in_ref_list;      // merge-tool: when searching dups in fields: match only if hit exists in other DBs hitlist (true for DBII-query)
-    AWAR               species_name;
-    const char        *tree_name;
-    AWAR               awar_keys[AWT_QUERY_SEARCHES];
-    AWAR               awar_setkey;
-    AWAR               awar_setprotection;
-    AWAR               awar_setvalue;
-    AWAR               awar_parskey;
-    AWAR               awar_parsvalue;
-    AWAR               awar_parspredefined;
-    AWAR               awar_queries[AWT_QUERY_SEARCHES];
-    AWAR               awar_not[AWT_QUERY_SEARCHES]; // not flags for queries
-    AWAR               awar_operator[AWT_QUERY_SEARCHES]; // not flags for queries
-    AWAR               awar_ere;
-    AWAR               awar_where;
-    AWAR               awar_by;
-    AWAR               awar_use_tag;
-    AWAR               awar_double_pars;
-    AWAR               awar_deftag;
-    AWAR               awar_tag;
-    AWAR               awar_count;
-    AWAR               awar_sort;
-    unsigned long      sort_mask;                   // contains several cascading sort criteria (AWT_QUERY_SORT_CRITERIA_BITS each)
-    AW_selection_list *result_id;
-    int                select_bit;                  // one of 1 2 4 8 .. 128 (one for each query box)
-
-    const ad_item_selector *selector;
-
-    GB_HASH *hit_description; // key = char* (hit item name), value = char* (description of hit - allocated!)
-};
 
 #define AWAR_TABLE_FIELD_REORDER_SOURCE_TEMPLATE "tmp/table/%s/field/reorder_source"
@@ -87 +43 @@
 #define AWAR_TABLE_IMPORT "tmp/ad_table/import_table"
 
-long awt_query_update_list(void *dummy, DbQuery *cbs);
-
 
 #else

trunk/AWTC/AWTC_submission.cxx

@@ -9 +9 @@
 // ================================================================ //
 
-#include <awt.hxx>
-
+#include <aw_window.hxx>
 #include <aw_awars.hxx>
 #include <aw_edit.hxx>

trunk/AWTC/Makefile

@@ -81 +81 @@
 AWTC_submission.o: $(ARBHOME)/INCLUDE/aw_root.hxx
 AWTC_submission.o: $(ARBHOME)/INCLUDE/aw_window.hxx
-AWTC_submission.o: $(ARBHOME)/INCLUDE/awt.hxx
 AWTC_submission.o: $(ARBHOME)/INCLUDE/cb.h
 AWTC_submission.o: $(ARBHOME)/INCLUDE/dupstr.h

trunk/AWTI/AWTI_export.cxx

@@ -53 +53 @@
     char *real_outname = 0;     // with suffix (name of first file if multiple)
 
-    AP_filter *filter = awt_get_filter(awr, acbs);
+    AP_filter *filter = awt_get_filter(acbs);
     char *db_name = awr->awar(AWAR_DB_NAME)->read_string();
 

trunk/AWTI/AWTI_import.cxx

@@ -13 +13 @@
 #include <seqio.hxx>
 #include <awt.hxx>
-#include <awt_item_sel_list.hxx>
+#include <item_sel_list.h>
 #include <aw_advice.hxx>
 #include <aw_file.hxx>

trunk/AWTI/Makefile

@@ -92 +92 @@
 AWTI_import.o: $(ARBHOME)/INCLUDE/aw_window.hxx
 AWTI_import.o: $(ARBHOME)/INCLUDE/awt.hxx
-AWTI_import.o: $(ARBHOME)/INCLUDE/awt_item_sel_list.hxx
 AWTI_import.o: $(ARBHOME)/INCLUDE/cb.h
 AWTI_import.o: $(ARBHOME)/INCLUDE/dupstr.h
 AWTI_import.o: $(ARBHOME)/INCLUDE/GEN.hxx
 AWTI_import.o: $(ARBHOME)/INCLUDE/GenomeImport.h
+AWTI_import.o: $(ARBHOME)/INCLUDE/item_sel_list.h
+AWTI_import.o: $(ARBHOME)/INCLUDE/items.h
 AWTI_import.o: $(ARBHOME)/INCLUDE/seqio.hxx
 AWTI_import.o: $(ARBHOME)/INCLUDE/smartptr.h

trunk/DIST/DI_save_matr.cxx

@@ -10 +10 @@
 
 #include "di_matr.hxx"
-#include <awt_nds.hxx>
+#include <nds.h>
 
 const char *DI_MATRIX::save(char *filename, enum DI_SAVE_TYPE type)

trunk/DIST/Makefile

@@ -316 +316 @@
 DI_save_matr.o: $(ARBHOME)/INCLUDE/aw_base.hxx
 DI_save_matr.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx
-DI_save_matr.o: $(ARBHOME)/INCLUDE/awt_nds.hxx
 DI_save_matr.o: $(ARBHOME)/INCLUDE/downcast.h
 DI_save_matr.o: $(ARBHOME)/INCLUDE/dupstr.h
+DI_save_matr.o: $(ARBHOME)/INCLUDE/nds.h
 DI_save_matr.o: $(ARBHOME)/INCLUDE/smartptr.h
 DI_save_matr.o: $(ARBHOME)/INCLUDE/test_global.h

trunk/EDIT4/ED4_naligner.cxx

@@ -11 +11 @@
 #include "ed4_naligner.hxx"
 
+#include <aw_window.hxx>
 #include <aw_awars.hxx>
 #include <aw_root.hxx>
-#include <awt.hxx>
 #include <awt_sel_boxes.hxx>
 #include <arbdbt.h>

trunk/EDIT4/ED4_no_class.cxx

@@ -22 +22 @@
 #include <AW_rename.hxx>
 #include <awt.hxx>
-#include <awt_item_sel_list.hxx>
+#include <item_sel_list.h>
 #include <awt_sel_boxes.hxx>
 #include <awt_seq_colors.hxx>

trunk/EDIT4/ED4_visualizeSAI.cxx

@@ -16 +16 @@
 
 #include <aw_awars.hxx>
-#include <awt.hxx>
 #include <awt_canvas.hxx>
 #include <awt_sel_boxes.hxx>

trunk/EDIT4/Makefile

@@ -457 +457 @@
 ED4_naligner.o: $(ARBHOME)/INCLUDE/aw_root.hxx
 ED4_naligner.o: $(ARBHOME)/INCLUDE/aw_window.hxx
-ED4_naligner.o: $(ARBHOME)/INCLUDE/awt.hxx
 ED4_naligner.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx
 ED4_naligner.o: $(ARBHOME)/INCLUDE/cb.h
@@ -535 +534 @@
 ED4_no_class.o: $(ARBHOME)/INCLUDE/aw_window.hxx
 ED4_no_class.o: $(ARBHOME)/INCLUDE/awt.hxx
-ED4_no_class.o: $(ARBHOME)/INCLUDE/awt_item_sel_list.hxx
 ED4_no_class.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx
 ED4_no_class.o: $(ARBHOME)/INCLUDE/awt_seq_colors.hxx
@@ -542 +540 @@
 ED4_no_class.o: $(ARBHOME)/INCLUDE/cb.h
 ED4_no_class.o: $(ARBHOME)/INCLUDE/dupstr.h
+ED4_no_class.o: $(ARBHOME)/INCLUDE/item_sel_list.h
+ED4_no_class.o: $(ARBHOME)/INCLUDE/items.h
 ED4_no_class.o: $(ARBHOME)/INCLUDE/smartptr.h
 ED4_no_class.o: $(ARBHOME)/INCLUDE/st_window.hxx
@@ -895 +895 @@
 ED4_visualizeSAI.o: $(ARBHOME)/INCLUDE/aw_root.hxx
 ED4_visualizeSAI.o: $(ARBHOME)/INCLUDE/aw_window.hxx
-ED4_visualizeSAI.o: $(ARBHOME)/INCLUDE/awt.hxx
 ED4_visualizeSAI.o: $(ARBHOME)/INCLUDE/awt_canvas.hxx
 ED4_visualizeSAI.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx

trunk/EDIT4/needs_libs

@@ -7 +7 @@
 SL/FAST_ALIGNER/FAST_ALIGNER.a
 SL/TRANSLATE/TRANSLATE.a
+SL/ITEMS/ITEMS.a
 STAT/STAT.a
 

trunk/GENOM/EXP_interface.cxx

@@ -17 +17 @@
 #include "GEN_local.hxx"
 #include "GEN_interface.hxx"
-#include "../NTREE/ad_spec.hxx"
-#include <../NTREE/nt_internal.h>
-
+
+#include <db_query.h>
 #include <db_scanner.hxx>
+#include <dbui.h>
 #include <awt_sel_boxes.hxx>
-#include <awt_item_sel_list.hxx>
+#include <item_sel_list.h>
 #include <aw_awars.hxx>
 #include <aw_detach.hxx>
@@ -207 +207 @@
 }
 
-static AW_CL    ad_global_scannerid   = 0;
-static AW_root *ad_global_scannerroot = 0;
+static AW_CL    EXP_global_scannerid        = 0;
+static AW_root *EXP_global_scannerroot      = 0;
 AW_CL           experiment_query_global_cbs = 0;
 
@@ -458 +458 @@
 
 static void EXP_create_field_items(AW_window *aws, GBDATA *gb_main) {
-    aws->insert_menu_topic("exp_reorder_fields", "Reorder fields ...",    "R", "spaf_reorder.hlp", AD_F_ALL, AW_POPUP, (AW_CL)NT_create_ad_list_reorder, (AW_CL)&EXP_item_selector);
-    aws->insert_menu_topic("exp_delete_field",   "Delete/Hide Field ...", "D", "spaf_delete.hlp",  AD_F_ALL, AW_POPUP, (AW_CL)NT_create_ad_field_delete, (AW_CL)&EXP_item_selector);
-    aws->insert_menu_topic("exp_create_field",   "Create fields ...",     "C", "spaf_create.hlp",  AD_F_ALL, AW_POPUP, (AW_CL)NT_create_ad_field_create, (AW_CL)&EXP_item_selector);
+    static bound_item_selector *bis = 0;
+
+    exp_assert(!bis);
+    bis = new bound_item_selector(gb_main, EXP_item_selector);
+
+    aws->insert_menu_topic("exp_reorder_fields", "Reorder fields ...",    "R", "spaf_reorder.hlp", AD_F_ALL, AW_POPUP, (AW_CL)DBUI::NT_create_ad_list_reorder, (AW_CL)&bis);
+    aws->insert_menu_topic("exp_delete_field",   "Delete/Hide Field ...", "D", "spaf_delete.hlp",  AD_F_ALL, AW_POPUP, (AW_CL)DBUI::NT_create_ad_field_delete, (AW_CL)&bis);
+    aws->insert_menu_topic("exp_create_field",   "Create fields ...",     "C", "spaf_create.hlp",  AD_F_ALL, AW_POPUP, (AW_CL)DBUI::NT_create_ad_field_create, (AW_CL)&bis);
     aws->insert_separator();
     aws->insert_menu_topic("exp_unhide_fields", "Show all hidden fields", "S", "scandb.hlp", AD_F_ALL, (AW_CB)awt_experiment_field_selection_list_unhide_all_cb, (AW_CL)gb_main, AWT_NDS_FILTER);
@@ -494 +499 @@
 
 
-        AW_CL scannerid       = create_db_scanner(gb_main, aws, "box", 0, "field", "enable", DB_VIEWER, 0, "mark", AWT_NDS_FILTER, &EXP_item_selector);
-        ad_global_scannerid   = scannerid;
-        ad_global_scannerroot = aws->get_root();
+        AW_CL scannerid        = create_db_scanner(gb_main, aws, "box", 0, "field", "enable", DB_VIEWER, 0, "mark", AWT_NDS_FILTER, &EXP_item_selector);
+        EXP_global_scannerid   = scannerid;
+        EXP_global_scannerroot = aws->get_root();
 
         aws->create_menu("EXPERIMENT", "E", AD_F_ALL);
@@ -514 +519 @@
 
             aws->at("detach");
-            aws->callback(NT_detach_information_window, (AW_CL)&aws, (AW_CL)cb_info);
+            aws->callback(DBUI::NT_detach_information_window, (AW_CL)&aws, (AW_CL)cb_info);
             aws->create_button("DETACH", "DETACH", "D");
 

trunk/GENOM/EXP_main.cxx

@@ -16 +16 @@
 #include "EXP_interface.hxx"
 
+#include <awt.hxx>
 #include <awt_input_mask.hxx>
 #include <aw_awars.hxx>
@@ -21 +22 @@
 #include <arbdbt.h>
 #include <ntree.hxx>
+#include <db_query.h>
 
 class AWT_canvas;
@@ -113 +115 @@
 }
 
+static void EXP_run_pgt(AW_window *aww, AW_CL cl_gb_main, AW_CL) {
+    AW_system(aww, (GBDATA*)cl_gb_main, "arb_pgt &", 0);
+}
+
 #define AWMIMT awm->insert_menu_topic
 
@@ -131 +137 @@
         AWMIMT("experiment_colors",     "Colors ...",           "C",    "mark_colors.hlp", AWM_ALL, AW_POPUP,  (AW_CL)EXP_create_experiment_colorize_window, (AW_CL)gb_main);
 
-#if defined(DEBUG)
         awm->insert_separator();
-        AWMIMT("pgt", "[debug-only] Proteom Genome Toolkit (PGT)", "P", "pgt.hlp", AWM_ALL, NT_system_cb, (AW_CL)"arb_pgt &", 0);
-#endif // DEVEL_KAI
+        AWMIMT("pgt", "Proteom Genome Toolkit (PGT)", "P", "pgt.hlp", AWM_ALL, EXP_run_pgt, (AW_CL)gb_main, 0);
     }
     if (submenu) awm->close_sub_menu();

trunk/GENOM/GEN_graphic.cxx

@@ -18 +18 @@
 #include <aw_preset.hxx>
 #include <awt_attributes.hxx>
-#include <awt.hxx>
 #include <aw_msg.hxx>
 #include <aw_root.hxx>

trunk/GENOM/GEN_interface.cxx

@@ -12 +12 @@
 #include "GEN_local.hxx"
 
-#include <ntree.hxx>
-#include <../NTREE/ad_spec.hxx>
-#include <../NTREE/nt_internal.h>
-
 #include <db_scanner.hxx>
-#include <awt_item_sel_list.hxx>
+#include <db_query.h>
+#include <dbui.h>
+#include <item_sel_list.h>
 #include <awt_sel_boxes.hxx>
 #include <aw_awars.hxx>
@@ -365 +363 @@
 
 
-static AW_CL    ad_global_scannerid   = 0;
-static AW_root *ad_global_scannerroot = 0;
+static AW_CL    GEN_global_scannerid   = 0;
+static AW_root *GEN_global_scannerroot = 0;
 AW_CL           gene_query_global_cbs = 0;
 
@@ -590 +588 @@
 
 static void GEN_create_field_items(AW_window *aws, GBDATA *gb_main) {
-    aws->insert_menu_topic("gen_reorder_fields", "Reorder fields ...",    "R", "spaf_reorder.hlp", AD_F_ALL, AW_POPUP, (AW_CL)NT_create_ad_list_reorder, (AW_CL)&GEN_item_selector);
-    aws->insert_menu_topic("gen_delete_field",   "Delete/Hide field ...", "D", "spaf_delete.hlp",  AD_F_ALL, AW_POPUP, (AW_CL)NT_create_ad_field_delete, (AW_CL)&GEN_item_selector);
-    aws->insert_menu_topic("gen_create_field",   "Create fields ...",     "C", "spaf_create.hlp",  AD_F_ALL, AW_POPUP, (AW_CL)NT_create_ad_field_create, (AW_CL)&GEN_item_selector);
+    static bound_item_selector *bis = 0;
+
+    gen_assert(!bis);
+    bis = new bound_item_selector(gb_main, GEN_item_selector);
+
+    aws->insert_menu_topic("gen_reorder_fields", "Reorder fields ...",    "R", "spaf_reorder.hlp", AD_F_ALL, AW_POPUP, (AW_CL)DBUI::NT_create_ad_list_reorder, (AW_CL)&bis);
+    aws->insert_menu_topic("gen_delete_field",   "Delete/Hide field ...", "D", "spaf_delete.hlp",  AD_F_ALL, AW_POPUP, (AW_CL)DBUI::NT_create_ad_field_delete, (AW_CL)&bis);
+    aws->insert_menu_topic("gen_create_field",   "Create fields ...",     "C", "spaf_create.hlp",  AD_F_ALL, AW_POPUP, (AW_CL)DBUI::NT_create_ad_field_create, (AW_CL)&bis);
     aws->insert_separator();
     aws->insert_menu_topic("gen_unhide_fields", "Show all hidden fields", "S", "scandb.hlp", AD_F_ALL, (AW_CB)awt_gene_field_selection_list_unhide_all_cb, (AW_CL)gb_main, AWT_NDS_FILTER);
@@ -625 +628 @@
 
 
-        AW_CL scannerid       = create_db_scanner(gb_main, aws, "box", 0, "field", "enable", DB_VIEWER, 0, "mark", AWT_NDS_FILTER, &GEN_item_selector);
-        ad_global_scannerid   = scannerid;
-        ad_global_scannerroot = aws->get_root();
+        AW_CL scannerid        = create_db_scanner(gb_main, aws, "box", 0, "field", "enable", DB_VIEWER, 0, "mark", AWT_NDS_FILTER, &GEN_item_selector);
+        GEN_global_scannerid   = scannerid;
+        GEN_global_scannerroot = aws->get_root();
 
         aws->create_menu("GENE", "G", AD_F_ALL);
@@ -646 +649 @@
 
             aws->at("detach");
-            aws->callback(NT_detach_information_window, (AW_CL)&aws, (AW_CL)detach_info);
+            aws->callback(DBUI::NT_detach_information_window, (AW_CL)&aws, (AW_CL)detach_info);
             aws->create_button("DETACH", "DETACH", "D");
 

trunk/GENOM/GEN_map.cxx

@@ -17 +17 @@
 #include "EXP_interface.hxx"
 #include "EXP_local.hxx"
-#include "../NTREE/ad_spec.hxx" // needed for species query window
-
+
+#include <dbui.h>
 #include <aw_preset.hxx>
 #include <aw_awars.hxx>
 #include <aw_question.hxx>
 #include <AW_rename.hxx>
+#include <awt.hxx>
 #include <awt_input_mask.hxx>
 #include <aw_msg.hxx>
@@ -28 +29 @@
 #include <aw_root.hxx>
 #include <adGene.h>
+#include <db_query.h>
 
 #include <map>
@@ -1444 +1446 @@
 void GEN_popup_organism_window(AW_window *aww, AW_CL cl_gb_main, AW_CL) {
     // used to avoid that the organisms info window is stored in a menu (or with a button)
-    AW_window *aws = NTX_create_organism_window(aww->get_root(), cl_gb_main);
+    AW_window *aws = DBUI::NTX_create_organism_window(aww->get_root(), cl_gb_main);
     aws->activate();
 }
@@ -1682 +1684 @@
     at(gene_x, first_line_y);
     help_text("organism_search.hlp");
-    callback(AW_POPUP, (AW_CL)NTX_create_query_window, 0);  // @@@ hier sollte eine Art "Organism-Search" verwendet werden (AWT_organism_selector anpassen)
+    callback(AW_POPUP, (AW_CL)DBUI::NTX_create_query_window, (AW_CL)gb_main); // @@@ should use an organism search (using AWT_organism_selector) 
     create_button("SEARCH_ORGANISM", AWAR_LOCAL_ORGANISM_NAME(window_nr));
 

trunk/GENOM/GEN_nds.cxx

@@ -12 +12 @@
 #include "GEN_interface.hxx"
 
-#include <awt.hxx>
-#include <awt_nds.hxx>
-#include <awt_item_sel_list.hxx>
+#include <nds.h>
+#include <item_sel_list.h>
 #include <awt_sel_boxes.hxx>
 #include <aw_msg.hxx>

trunk/GENOM/Makefile

@@ -43 +43 @@
 # For formatting issues see SOURCE_TOOLS/fix_depends.pl
 
-EXP_interface.o: ../NTREE/ad_spec.hxx
-EXP_interface.o: ../NTREE/nt_internal.h
 EXP_interface.o: EXP.hxx
 EXP_interface.o: EXP_interface.hxx
@@ -72 +70 @@
 EXP_interface.o: $(ARBHOME)/INCLUDE/aw_select.hxx
 EXP_interface.o: $(ARBHOME)/INCLUDE/aw_window.hxx
-EXP_interface.o: $(ARBHOME)/INCLUDE/awt.hxx
-EXP_interface.o: $(ARBHOME)/INCLUDE/awt_item_sel_list.hxx
 EXP_interface.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx
 EXP_interface.o: $(ARBHOME)/INCLUDE/cb.h
+EXP_interface.o: $(ARBHOME)/INCLUDE/db_query.h
 EXP_interface.o: $(ARBHOME)/INCLUDE/db_scanner.hxx
+EXP_interface.o: $(ARBHOME)/INCLUDE/dbui.h
 EXP_interface.o: $(ARBHOME)/INCLUDE/dupstr.h
+EXP_interface.o: $(ARBHOME)/INCLUDE/item_sel_list.h
+EXP_interface.o: $(ARBHOME)/INCLUDE/items.h
 EXP_interface.o: $(ARBHOME)/INCLUDE/smartptr.h
 EXP_interface.o: $(ARBHOME)/INCLUDE/test_global.h
@@ -106 +106 @@
 EXP_main.o: $(ARBHOME)/INCLUDE/awt_input_mask.hxx
 EXP_main.o: $(ARBHOME)/INCLUDE/cb.h
+EXP_main.o: $(ARBHOME)/INCLUDE/db_query.h
 EXP_main.o: $(ARBHOME)/INCLUDE/dupstr.h
+EXP_main.o: $(ARBHOME)/INCLUDE/items.h
 EXP_main.o: $(ARBHOME)/INCLUDE/ntree.hxx
 EXP_main.o: $(ARBHOME)/INCLUDE/smartptr.h
@@ -165 +167 @@
 GEN_graphic.o: $(ARBHOME)/INCLUDE/aw_root.hxx
 GEN_graphic.o: $(ARBHOME)/INCLUDE/aw_window.hxx
-GEN_graphic.o: $(ARBHOME)/INCLUDE/awt.hxx
 GEN_graphic.o: $(ARBHOME)/INCLUDE/awt_attributes.hxx
 GEN_graphic.o: $(ARBHOME)/INCLUDE/awt_canvas.hxx
@@ -173 +174 @@
 GEN_graphic.o: $(ARBHOME)/INCLUDE/test_global.h
 
-GEN_interface.o: ../NTREE/ad_spec.hxx
-GEN_interface.o: ../NTREE/nt_internal.h
 GEN_interface.o: GEN.hxx
 GEN_interface.o: GEN_local.hxx
@@ -199 +198 @@
 GEN_interface.o: $(ARBHOME)/INCLUDE/aw_select.hxx
 GEN_interface.o: $(ARBHOME)/INCLUDE/aw_window.hxx
-GEN_interface.o: $(ARBHOME)/INCLUDE/awt.hxx
-GEN_interface.o: $(ARBHOME)/INCLUDE/awt_item_sel_list.hxx
 GEN_interface.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx
 GEN_interface.o: $(ARBHOME)/INCLUDE/cb.h
+GEN_interface.o: $(ARBHOME)/INCLUDE/db_query.h
 GEN_interface.o: $(ARBHOME)/INCLUDE/db_scanner.hxx
+GEN_interface.o: $(ARBHOME)/INCLUDE/dbui.h
 GEN_interface.o: $(ARBHOME)/INCLUDE/dupstr.h
-GEN_interface.o: $(ARBHOME)/INCLUDE/ntree.hxx
+GEN_interface.o: $(ARBHOME)/INCLUDE/item_sel_list.h
+GEN_interface.o: $(ARBHOME)/INCLUDE/items.h
 GEN_interface.o: $(ARBHOME)/INCLUDE/smartptr.h
 GEN_interface.o: $(ARBHOME)/INCLUDE/test_global.h
 
-GEN_map.o: ../NTREE/ad_spec.hxx
 GEN_map.o: EXP.hxx
 GEN_map.o: EXP_interface.hxx
@@ -250 +249 @@
 GEN_map.o: $(ARBHOME)/INCLUDE/awt_input_mask.hxx
 GEN_map.o: $(ARBHOME)/INCLUDE/cb.h
+GEN_map.o: $(ARBHOME)/INCLUDE/db_query.h
+GEN_map.o: $(ARBHOME)/INCLUDE/dbui.h
 GEN_map.o: $(ARBHOME)/INCLUDE/dupstr.h
+GEN_map.o: $(ARBHOME)/INCLUDE/items.h
 GEN_map.o: $(ARBHOME)/INCLUDE/smartptr.h
 GEN_map.o: $(ARBHOME)/INCLUDE/test_global.h
@@ -272 +274 @@
 GEN_nds.o: $(ARBHOME)/INCLUDE/aw_select.hxx
 GEN_nds.o: $(ARBHOME)/INCLUDE/aw_window.hxx
-GEN_nds.o: $(ARBHOME)/INCLUDE/awt.hxx
-GEN_nds.o: $(ARBHOME)/INCLUDE/awt_item_sel_list.hxx
-GEN_nds.o: $(ARBHOME)/INCLUDE/awt_nds.hxx
 GEN_nds.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx
 GEN_nds.o: $(ARBHOME)/INCLUDE/cb.h
 GEN_nds.o: $(ARBHOME)/INCLUDE/dupstr.h
+GEN_nds.o: $(ARBHOME)/INCLUDE/item_sel_list.h
+GEN_nds.o: $(ARBHOME)/INCLUDE/items.h
+GEN_nds.o: $(ARBHOME)/INCLUDE/nds.h
 GEN_nds.o: $(ARBHOME)/INCLUDE/smartptr.h
 GEN_nds.o: $(ARBHOME)/INCLUDE/test_global.h

trunk/GENOM/needs_libs

@@ -3 +3 @@
 # depends on NTREE/NTREE.a # fix this
 
-SL/DB_SCANNER/DB_SCANNER.a
+SL/DB_UI/DB_UI.a
+#SL/DB_SCANNER/DB_SCANNER.a
+#SL/DB_QUERY/DB_QUERY.a
+SL/NDS/NDS.a
 SL/TRANSLATE/TRANSLATE.a
 

trunk/GENOM_IMPORT/Location.cxx

@@ -265 +265 @@
 
 
+// --------------------------------------------------------------------------------
+
+#ifdef UNIT_TESTS
+#include <test_unit.h>
+
+void TEST_gene_location() {
+    // TEST_ASSERT(0); // @@@ works - keep it
+}
+
+#endif // UNIT_TESTS

trunk/GENOM_IMPORT/Makefile

@@ -170 +170 @@
 Location.o: $(ARBHOME)/INCLUDE/smartptr.h
 Location.o: $(ARBHOME)/INCLUDE/test_global.h
+Location.o: $(ARBHOME)/INCLUDE/test_unit.h
 
 MetaInfo.o: defs.h

trunk/MERGE/MG_checkfield.cxx

@@ -11 +11 @@
 #include "merge.hxx"
 
-#include <awt.hxx>
-#include <awt_item_sel_list.hxx>
+#include <item_sel_list.h>
 #include <awt_sel_boxes.hxx>
 

trunk/MERGE/MG_configs.cxx

@@ -16 +16 @@
 
 #include <ad_config.h>
-#include <awt.hxx>
 #include <awt_sel_boxes.hxx>
 #include <aw_root.hxx>

trunk/MERGE/MG_extendeds.cxx

@@ -10 +10 @@
 
 #include "merge.hxx"
+
 #include <db_scanner.hxx>
-#include <awt.hxx>
 #include <awt_sel_boxes.hxx>
 #include <aw_awars.hxx>
@@ -17 +17 @@
 #include <aw_root.hxx>
 #include <arbdbt.h>
+#include <items.h>
 
 #define AWAR_EX_NAME1 "tmp/merge1/extended_name"

trunk/MERGE/MG_gene_species.cxx

@@ -16 +16 @@
 #include "merge.hxx"
 
-#include <awt.hxx>
 #include <awt_config_manager.hxx>
 #include <aw_awars.hxx>

trunk/MERGE/MG_preserves.cxx

@@ -16 +16 @@
 #include "MG_adapt_ali.hxx"
 
-#include <awt.hxx>
 #include <aw_awars.hxx>
 #include <aw_root.hxx>

trunk/MERGE/MG_species.cxx

@@ -13 +13 @@
 
 #include <AW_rename.hxx>
+#include <db_query.h>
 #include <db_scanner.hxx>
-#include <awt.hxx>
-#include <awt_item_sel_list.hxx>
+#include <item_sel_list.h>
 #include <aw_awars.hxx>
 #include <aw_msg.hxx>

trunk/MERGE/Makefile

@@ -118 +118 @@
 MG_checkfield.o: $(ARBHOME)/INCLUDE/aw_select.hxx
 MG_checkfield.o: $(ARBHOME)/INCLUDE/aw_window.hxx
-MG_checkfield.o: $(ARBHOME)/INCLUDE/awt.hxx
-MG_checkfield.o: $(ARBHOME)/INCLUDE/awt_item_sel_list.hxx
 MG_checkfield.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx
 MG_checkfield.o: $(ARBHOME)/INCLUDE/cb.h
 MG_checkfield.o: $(ARBHOME)/INCLUDE/dupstr.h
+MG_checkfield.o: $(ARBHOME)/INCLUDE/item_sel_list.h
+MG_checkfield.o: $(ARBHOME)/INCLUDE/items.h
 MG_checkfield.o: $(ARBHOME)/INCLUDE/smartptr.h
 MG_checkfield.o: $(ARBHOME)/INCLUDE/test_global.h
@@ -145 +145 @@
 MG_configs.o: $(ARBHOME)/INCLUDE/aw_root.hxx
 MG_configs.o: $(ARBHOME)/INCLUDE/aw_window.hxx
-MG_configs.o: $(ARBHOME)/INCLUDE/awt.hxx
 MG_configs.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx
 MG_configs.o: $(ARBHOME)/INCLUDE/cb.h
@@ -173 +172 @@
 MG_extendeds.o: $(ARBHOME)/INCLUDE/aw_root.hxx
 MG_extendeds.o: $(ARBHOME)/INCLUDE/aw_window.hxx
-MG_extendeds.o: $(ARBHOME)/INCLUDE/awt.hxx
 MG_extendeds.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx
 MG_extendeds.o: $(ARBHOME)/INCLUDE/cb.h
 MG_extendeds.o: $(ARBHOME)/INCLUDE/db_scanner.hxx
 MG_extendeds.o: $(ARBHOME)/INCLUDE/dupstr.h
+MG_extendeds.o: $(ARBHOME)/INCLUDE/items.h
 MG_extendeds.o: $(ARBHOME)/INCLUDE/smartptr.h
 MG_extendeds.o: $(ARBHOME)/INCLUDE/test_global.h
@@ -204 +203 @@
 MG_gene_species.o: $(ARBHOME)/INCLUDE/aw_root.hxx
 MG_gene_species.o: $(ARBHOME)/INCLUDE/aw_window.hxx
-MG_gene_species.o: $(ARBHOME)/INCLUDE/awt.hxx
 MG_gene_species.o: $(ARBHOME)/INCLUDE/awt_config_manager.hxx
 MG_gene_species.o: $(ARBHOME)/INCLUDE/cb.h
@@ -293 +291 @@
 MG_preserves.o: $(ARBHOME)/INCLUDE/aw_root.hxx
 MG_preserves.o: $(ARBHOME)/INCLUDE/aw_window.hxx
-MG_preserves.o: $(ARBHOME)/INCLUDE/awt.hxx
 MG_preserves.o: $(ARBHOME)/INCLUDE/cb.h
 MG_preserves.o: $(ARBHOME)/INCLUDE/dupstr.h
@@ -327 +324 @@
 MG_species.o: $(ARBHOME)/INCLUDE/aw_select.hxx
 MG_species.o: $(ARBHOME)/INCLUDE/aw_window.hxx
-MG_species.o: $(ARBHOME)/INCLUDE/awt.hxx
-MG_species.o: $(ARBHOME)/INCLUDE/awt_item_sel_list.hxx
 MG_species.o: $(ARBHOME)/INCLUDE/cb.h
+MG_species.o: $(ARBHOME)/INCLUDE/db_query.h
 MG_species.o: $(ARBHOME)/INCLUDE/db_scanner.hxx
 MG_species.o: $(ARBHOME)/INCLUDE/dupstr.h
+MG_species.o: $(ARBHOME)/INCLUDE/item_sel_list.h
+MG_species.o: $(ARBHOME)/INCLUDE/items.h
 MG_species.o: $(ARBHOME)/INCLUDE/smartptr.h
 MG_species.o: $(ARBHOME)/INCLUDE/test_global.h

trunk/MERGE/needs_libs

@@ -1 +1 @@
 # libraries needed to link against MERGE/MERGE.a
 
-AWT/libAWT.so
-SL/DB_SCANNER/DB_SCANNER.a
+SL/DB_UI/DB_UI.a
+#SL/DB_QUERY/DB_QUERY.a
+#SL/DB_SCANNER/DB_SCANNER.a
 

trunk/MULTI_PROBE/MP_noclass.cxx

@@ -14 +14 @@
 #include "MP_probe.hxx"
 
-#include <awt.hxx>
 #include <aw_select.hxx>
 #include <aw_msg.hxx>

trunk/MULTI_PROBE/Makefile

@@ -178 +178 @@
 MP_noclass.o: $(ARBHOME)/INCLUDE/aw_select.hxx
 MP_noclass.o: $(ARBHOME)/INCLUDE/aw_window.hxx
-MP_noclass.o: $(ARBHOME)/INCLUDE/awt.hxx
 MP_noclass.o: $(ARBHOME)/INCLUDE/awt_canvas.hxx
 MP_noclass.o: $(ARBHOME)/INCLUDE/bytestring.h

trunk/Makefile

@@ -682 +682 @@
 endif
 
-# ------------------------------- 
-#     List of all Directories
+# ---------------------------------------
+#     List of all top level directories
 
 ARCHS = \
@@ -790 +790 @@
                 SERVERCNTRL/SERVERCNTRL.a \
                 SL/AW_NAME/AW_NAME.a \
+                SL/DB_UI/DB_UI.a \
                 SL/DB_SCANNER/DB_SCANNER.a \
+                SL/DB_QUERY/DB_QUERY.a \
                 SL/SEQIO/SEQIO.a \
                 SL/FILE_BUFFER/FILE_BUFFER.a \
@@ -796 +798 @@
                 SL/HELIX/HELIX.a \
                 SL/REGEXPR/REGEXPR.a \
+                SL/REFENTRIES/REFENTRIES.a \
+                SL/NDS/NDS.a \
+                SL/ITEMS/ITEMS.a \
                 SL/TRANSLATE/TRANSLATE.a \
                 SL/TREEDISP/TREEDISP.a \
@@ -835 +840 @@
                 SL/FAST_ALIGNER/FAST_ALIGNER.a \
                 SL/FILE_BUFFER/FILE_BUFFER.a \
+                SL/ITEMS/ITEMS.a \
                 SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
                 SL/HELIX/HELIX.a \
@@ -896 +902 @@
                 SL/HELIX/HELIX.a \
                 SL/MATRIX/MATRIX.a \
+                SL/NDS/NDS.a \
+                SL/ITEMS/ITEMS.a \
                 SL/NEIGHBOURJOIN/NEIGHBOURJOIN.a \
                 XML/XML.a \
@@ -916 +924 @@
                 SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
                 SL/HELIX/HELIX.a \
+                SL/NDS/NDS.a \
+                SL/ITEMS/ITEMS.a \
                 SL/TRANSLATE/TRANSLATE.a \
                 SL/TREEDISP/TREEDISP.a \
@@ -1651 +1661 @@
 
 UNITS_WORKING = \
+        $(RNA3D_TEST) \
+        ALIV3/ALIV3.test \
+        ARB_GDE/ARB_GDE.test \
+        AWT/AWT.test \
+        CONSENSUS_TREE/CONSENSUS_TREE.test \
+        DBSERVER/DBSERVER.test \
+        DIST/DIST.test \
+        EISPACK/EISPACK.test \
+        GENOM/GENOM.test \
+        GL/glAW/libglAW.test \
+        GL/glpng/libglpng_arb.test \
         ISLAND_HOPPING/ISLAND_HOPPING.test \
+        NALIGNER/NALIGNER.test \
+        NAMES/NAMES.test \
+        PARSIMONY/PARSIMONY.test \
+        PGT/PGT.test \
+        PHYLO/PHYLO.test \
+        PRIMER_DESIGN/PRIMER_DESIGN.test \
+        PROBE/PROBE.test \
+        PROBE_DESIGN/PROBE_DESIGN.test \
+        ptpan/PROBE.test \
+        SECEDIT/SECEDIT.test \
+        SEQ_QUALITY/SEQ_QUALITY.test \
+        SERVERCNTRL/SERVERCNTRL.test \
         SL/ALIVIEW/ALIVIEW.test \
         SL/AP_TREE/AP_TREE.test \
@@ -1657 +1690 @@
         SL/AW_HELIX/AW_HELIX.test \
         SL/AW_NAME/AW_NAME.test \
+        SL/DB_QUERY/DB_QUERY.test \
         SL/DB_SCANNER/DB_SCANNER.test \
         SL/FILE_BUFFER/FILE_BUFFER.test \
         SL/FILTER/FILTER.test \
         SL/GUI_ALIVIEW/GUI_ALIVIEW.test \
-        ARB_GDE/ARB_GDE.test \
         SL/HELIX/HELIX.test \
+        SL/ITEMS/ITEMS.test \
         SL/MATRIX/MATRIX.test \
+        SL/NDS/NDS.test \
         SL/NEIGHBOURJOIN/NEIGHBOURJOIN.test \
+        SL/REFENTRIES/REFENTRIES.test \
         SL/REGEXPR/REGEXPR.test \
         SL/SEQUENCE/SEQUENCE.test \
         SL/TRANSLATE/TRANSLATE.test \
         SL/TREE_READ/TREE_READ.test \
+        SL/TREE_WRITE/TREE_WRITE.test \
+        STAT/STAT.test \
+        TREEGEN/TREEGEN.test \
+        WETC/WETC.test \
         XML/XML.test \
-        SL/TREE_WRITE/TREE_WRITE.test \
-        ALIV3/ALIV3.test \
-        CONSENSUS_TREE/CONSENSUS_TREE.test \
-        EISPACK/EISPACK.test \
-        DIST/DIST.test \
-        NALIGNER/NALIGNER.test \
-        GL/glAW/libglAW.test \
-        GL/glpng/libglpng_arb.test \
-        SEQ_QUALITY/SEQ_QUALITY.test \
-        STAT/STAT.test \
-        WETC/WETC.test \
-        ptpan/PROBE.test \
-        PHYLO/PHYLO.test \
-        PROBE_DESIGN/PROBE_DESIGN.test \
-        PRIMER_DESIGN/PRIMER_DESIGN.test \
-        PGT/PGT.test \
-        PARSIMONY/PARSIMONY.test \
-        TREEGEN/TREEGEN.test \
-        NAMES/NAMES.test \
-        PROBE/PROBE.test \
-        DBSERVER/DBSERVER.test \
-        SECEDIT/SECEDIT.test \
-        $(RNA3D_TEST) \
-        SERVERCNTRL/SERVERCNTRL.test \
-        AWT/AWT.test \
 
 # untestable units
@@ -1701 +1716 @@
 
 UNITS_NEED_FIX = \
-        GENOM_IMPORT/GENOM_IMPORT.test \
-        GENOM/GENOM.test \
         AWTI/AWTI.test \
 
@@ -1711 +1724 @@
 # for the moment, put all units containing tests into UNITS_TESTED:
 UNITS_TESTED = \
+        GENOM_IMPORT/GENOM_IMPORT.test \
         CORE/CORE.test \
         SL/TREEDISP/TREEDISP.test \

trunk/NTREE/Makefile

@@ -111 +111 @@
 ad_ext.o: $(ARBHOME)/INCLUDE/aw_root.hxx
 ad_ext.o: $(ARBHOME)/INCLUDE/aw_window.hxx
-ad_ext.o: $(ARBHOME)/INCLUDE/awt.hxx
 ad_ext.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx
 ad_ext.o: $(ARBHOME)/INCLUDE/cb.h
 ad_ext.o: $(ARBHOME)/INCLUDE/db_scanner.hxx
 ad_ext.o: $(ARBHOME)/INCLUDE/dupstr.h
+ad_ext.o: $(ARBHOME)/INCLUDE/items.h
 ad_ext.o: $(ARBHOME)/INCLUDE/smartptr.h
 ad_ext.o: $(ARBHOME)/INCLUDE/test_global.h
 
-ad_spec.o: ad_spec.hxx
 ad_spec.o: map_viewer.hxx
 ad_spec.o: nt_internal.h
@@ -134 +133 @@
 ad_spec.o: $(ARBHOME)/INCLUDE/arb_msg.h
 ad_spec.o: $(ARBHOME)/INCLUDE/arb_progress.h
-ad_spec.o: $(ARBHOME)/INCLUDE/arb_strbuf.h
 ad_spec.o: $(ARBHOME)/INCLUDE/arb_string.h
 ad_spec.o: $(ARBHOME)/INCLUDE/ARB_Tree.hxx
@@ -147 +145 @@
 ad_spec.o: $(ARBHOME)/INCLUDE/aw_base.hxx
 ad_spec.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx
-ad_spec.o: $(ARBHOME)/INCLUDE/aw_detach.hxx
 ad_spec.o: $(ARBHOME)/INCLUDE/aw_device.hxx
 ad_spec.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
 ad_spec.o: $(ARBHOME)/INCLUDE/aw_msg.hxx
 ad_spec.o: $(ARBHOME)/INCLUDE/aw_position.hxx
-ad_spec.o: $(ARBHOME)/INCLUDE/AW_rename.hxx
 ad_spec.o: $(ARBHOME)/INCLUDE/aw_root.hxx
-ad_spec.o: $(ARBHOME)/INCLUDE/aw_select.hxx
 ad_spec.o: $(ARBHOME)/INCLUDE/aw_window.hxx
-ad_spec.o: $(ARBHOME)/INCLUDE/awt.hxx
 ad_spec.o: $(ARBHOME)/INCLUDE/awt_canvas.hxx
-ad_spec.o: $(ARBHOME)/INCLUDE/awt_item_sel_list.hxx
-ad_spec.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx
 ad_spec.o: $(ARBHOME)/INCLUDE/awt_www.hxx
-ad_spec.o: $(ARBHOME)/INCLUDE/awtc_next_neighbours.hxx
-ad_spec.o: $(ARBHOME)/INCLUDE/awtlocal.hxx
 ad_spec.o: $(ARBHOME)/INCLUDE/cb.h
-ad_spec.o: $(ARBHOME)/INCLUDE/db_scanner.hxx
+ad_spec.o: $(ARBHOME)/INCLUDE/dbui.h
 ad_spec.o: $(ARBHOME)/INCLUDE/downcast.h
 ad_spec.o: $(ARBHOME)/INCLUDE/dupstr.h
-ad_spec.o: $(ARBHOME)/INCLUDE/probe_design.hxx
 ad_spec.o: $(ARBHOME)/INCLUDE/smartptr.h
 ad_spec.o: $(ARBHOME)/INCLUDE/test_global.h
@@ -228 +217 @@
 ad_trees.o: $(ARBHOME)/INCLUDE/aw_root.hxx
 ad_trees.o: $(ARBHOME)/INCLUDE/aw_window.hxx
-ad_trees.o: $(ARBHOME)/INCLUDE/awt_nds.hxx
 ad_trees.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx
 ad_trees.o: $(ARBHOME)/INCLUDE/cb.h
 ad_trees.o: $(ARBHOME)/INCLUDE/dupstr.h
+ad_trees.o: $(ARBHOME)/INCLUDE/nds.h
 ad_trees.o: $(ARBHOME)/INCLUDE/smartptr.h
 ad_trees.o: $(ARBHOME)/INCLUDE/test_global.h
@@ -433 +422 @@
 NT_concatenate.o: $(ARBHOME)/INCLUDE/aw_select.hxx
 NT_concatenate.o: $(ARBHOME)/INCLUDE/aw_window.hxx
-NT_concatenate.o: $(ARBHOME)/INCLUDE/awt.hxx
-NT_concatenate.o: $(ARBHOME)/INCLUDE/awt_item_sel_list.hxx
 NT_concatenate.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx
 NT_concatenate.o: $(ARBHOME)/INCLUDE/cb.h
 NT_concatenate.o: $(ARBHOME)/INCLUDE/dupstr.h
+NT_concatenate.o: $(ARBHOME)/INCLUDE/item_sel_list.h
+NT_concatenate.o: $(ARBHOME)/INCLUDE/items.h
 NT_concatenate.o: $(ARBHOME)/INCLUDE/smartptr.h
 NT_concatenate.o: $(ARBHOME)/INCLUDE/test_global.h
@@ -464 +453 @@
 NT_dbrepair.o: $(ARBHOME)/INCLUDE/aw_root.hxx
 NT_dbrepair.o: $(ARBHOME)/INCLUDE/aw_window.hxx
-NT_dbrepair.o: $(ARBHOME)/INCLUDE/awt.hxx
 NT_dbrepair.o: $(ARBHOME)/INCLUDE/cb.h
 NT_dbrepair.o: $(ARBHOME)/INCLUDE/dupstr.h
 NT_dbrepair.o: $(ARBHOME)/INCLUDE/EXP.hxx
 NT_dbrepair.o: $(ARBHOME)/INCLUDE/GEN.hxx
+NT_dbrepair.o: $(ARBHOME)/INCLUDE/items.h
 NT_dbrepair.o: $(ARBHOME)/INCLUDE/smartptr.h
 NT_dbrepair.o: $(ARBHOME)/INCLUDE/test_global.h
@@ -501 +490 @@
 NT_edconf.o: $(ARBHOME)/INCLUDE/test_global.h
 
-NT_extern.o: ad_spec.hxx
 NT_extern.o: ad_trees.hxx
 NT_extern.o: ap_consensus.hxx
@@ -549 +537 @@
 NT_extern.o: $(ARBHOME)/INCLUDE/awt_input_mask.hxx
 NT_extern.o: $(ARBHOME)/INCLUDE/awt_macro.hxx
-NT_extern.o: $(ARBHOME)/INCLUDE/awt_nds.hxx
 NT_extern.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx
 NT_extern.o: $(ARBHOME)/INCLUDE/awt_www.hxx
@@ -555 +542 @@
 NT_extern.o: $(ARBHOME)/INCLUDE/awti_export.hxx
 NT_extern.o: $(ARBHOME)/INCLUDE/cb.h
+NT_extern.o: $(ARBHOME)/INCLUDE/db_query.h
 NT_extern.o: $(ARBHOME)/INCLUDE/dbitem_set.h
+NT_extern.o: $(ARBHOME)/INCLUDE/dbui.h
 NT_extern.o: $(ARBHOME)/INCLUDE/downcast.h
 NT_extern.o: $(ARBHOME)/INCLUDE/dupstr.h
@@ -561 +550 @@
 NT_extern.o: $(ARBHOME)/INCLUDE/gde.hxx
 NT_extern.o: $(ARBHOME)/INCLUDE/GEN.hxx
+NT_extern.o: $(ARBHOME)/INCLUDE/items.h
 NT_extern.o: $(ARBHOME)/INCLUDE/multi_probe.hxx
+NT_extern.o: $(ARBHOME)/INCLUDE/nds.h
 NT_extern.o: $(ARBHOME)/INCLUDE/primer_design.hxx
 NT_extern.o: $(ARBHOME)/INCLUDE/probe_design.hxx
@@ -573 +564 @@
 NT_extern.o: $(ARBHOME)/INCLUDE/TreeDisplay.hxx
 
-NT_import.o: ad_spec.hxx
 NT_import.o: nt_internal.h
 NT_import.o: $(ARBHOME)/INCLUDE/ad_prot.h
@@ -598 +588 @@
 NT_import.o: $(ARBHOME)/INCLUDE/awti_import.hxx
 NT_import.o: $(ARBHOME)/INCLUDE/cb.h
+NT_import.o: $(ARBHOME)/INCLUDE/dbui.h
 NT_import.o: $(ARBHOME)/INCLUDE/dupstr.h
 NT_import.o: $(ARBHOME)/INCLUDE/GEN.hxx
@@ -650 +641 @@
 NT_join.o: $(ARBHOME)/INCLUDE/aw_select.hxx
 NT_join.o: $(ARBHOME)/INCLUDE/aw_window.hxx
-NT_join.o: $(ARBHOME)/INCLUDE/awt.hxx
-NT_join.o: $(ARBHOME)/INCLUDE/awt_item_sel_list.hxx
 NT_join.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx
 NT_join.o: $(ARBHOME)/INCLUDE/cb.h
 NT_join.o: $(ARBHOME)/INCLUDE/dupstr.h
+NT_join.o: $(ARBHOME)/INCLUDE/item_sel_list.h
+NT_join.o: $(ARBHOME)/INCLUDE/items.h
 NT_join.o: $(ARBHOME)/INCLUDE/smartptr.h
 NT_join.o: $(ARBHOME)/INCLUDE/test_global.h
 
-NT_main.o: map_viewer.hxx
 NT_main.o: nt_cb.hxx
 NT_main.o: nt_internal.h
@@ -665 +655 @@
 NT_main.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
 NT_main.o: $(ARBHOME)/INCLUDE/adGene.h
-NT_main.o: $(ARBHOME)/INCLUDE/AliView.hxx
-NT_main.o: $(ARBHOME)/INCLUDE/AP_sequence.hxx
-NT_main.o: $(ARBHOME)/INCLUDE/AP_Tree.hxx
 NT_main.o: $(ARBHOME)/INCLUDE/arb_assert.h
 NT_main.o: $(ARBHOME)/INCLUDE/arb_build.h
@@ -675 +662 @@
 NT_main.o: $(ARBHOME)/INCLUDE/arb_progress.h
 NT_main.o: $(ARBHOME)/INCLUDE/arb_string.h
-NT_main.o: $(ARBHOME)/INCLUDE/ARB_Tree.hxx
 NT_main.o: $(ARBHOME)/INCLUDE/arb_version.h
 NT_main.o: $(ARBHOME)/INCLUDE/arbdb.h
@@ -686 +672 @@
 NT_main.o: $(ARBHOME)/INCLUDE/aw_awars.hxx
 NT_main.o: $(ARBHOME)/INCLUDE/aw_base.hxx
-NT_main.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx
-NT_main.o: $(ARBHOME)/INCLUDE/aw_device.hxx
 NT_main.o: $(ARBHOME)/INCLUDE/aw_edit.hxx
 NT_main.o: $(ARBHOME)/INCLUDE/aw_file.hxx
 NT_main.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
 NT_main.o: $(ARBHOME)/INCLUDE/aw_msg.hxx
-NT_main.o: $(ARBHOME)/INCLUDE/aw_position.hxx
 NT_main.o: $(ARBHOME)/INCLUDE/aw_question.hxx
 NT_main.o: $(ARBHOME)/INCLUDE/aw_root.hxx
 NT_main.o: $(ARBHOME)/INCLUDE/aw_window.hxx
 NT_main.o: $(ARBHOME)/INCLUDE/awt.hxx
-NT_main.o: $(ARBHOME)/INCLUDE/awt_canvas.hxx
 NT_main.o: $(ARBHOME)/INCLUDE/awt_macro.hxx
 NT_main.o: $(ARBHOME)/INCLUDE/awti_import.hxx
 NT_main.o: $(ARBHOME)/INCLUDE/cb.h
-NT_main.o: $(ARBHOME)/INCLUDE/downcast.h
 NT_main.o: $(ARBHOME)/INCLUDE/dupstr.h
 NT_main.o: $(ARBHOME)/INCLUDE/mg_merge.hxx
@@ -707 +688 @@
 NT_main.o: $(ARBHOME)/INCLUDE/svn_revision.h
 NT_main.o: $(ARBHOME)/INCLUDE/test_global.h
-NT_main.o: $(ARBHOME)/INCLUDE/TreeDisplay.hxx
 
 NT_sort.o: nt_cb.hxx
@@ -732 +712 @@
 NT_sort.o: $(ARBHOME)/INCLUDE/aw_select.hxx
 NT_sort.o: $(ARBHOME)/INCLUDE/aw_window.hxx
-NT_sort.o: $(ARBHOME)/INCLUDE/awt.hxx
-NT_sort.o: $(ARBHOME)/INCLUDE/awt_item_sel_list.hxx
 NT_sort.o: $(ARBHOME)/INCLUDE/cb.h
 NT_sort.o: $(ARBHOME)/INCLUDE/dupstr.h
+NT_sort.o: $(ARBHOME)/INCLUDE/item_sel_list.h
+NT_sort.o: $(ARBHOME)/INCLUDE/items.h
 NT_sort.o: $(ARBHOME)/INCLUDE/smartptr.h
 NT_sort.o: $(ARBHOME)/INCLUDE/test_global.h
@@ -810 +790 @@
 NT_validManual.o: $(ARBHOME)/INCLUDE/aw_root.hxx
 NT_validManual.o: $(ARBHOME)/INCLUDE/aw_window.hxx
-NT_validManual.o: $(ARBHOME)/INCLUDE/awt.hxx
 NT_validManual.o: $(ARBHOME)/INCLUDE/cb.h
 NT_validManual.o: $(ARBHOME)/INCLUDE/dupstr.h
@@ -838 +817 @@
 NT_validNames.o: $(ARBHOME)/INCLUDE/aw_awars.hxx
 NT_validNames.o: $(ARBHOME)/INCLUDE/aw_base.hxx
-NT_validNames.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
 NT_validNames.o: $(ARBHOME)/INCLUDE/aw_msg.hxx
-NT_validNames.o: $(ARBHOME)/INCLUDE/aw_window.hxx
-NT_validNames.o: $(ARBHOME)/INCLUDE/awt.hxx
 NT_validNames.o: $(ARBHOME)/INCLUDE/awt_www.hxx
 NT_validNames.o: $(ARBHOME)/INCLUDE/cb.h

trunk/NTREE/NT_cb.cxx

@@ -118 +118 @@
 }
 
-void NT_system_cb(AW_window *aww, AW_CL command, AW_CL auto_help_file)
-{
-    char *sys = (char *)command;
-    if (auto_help_file) {
-        AW_POPUP_HELP(aww, auto_help_file);
-    }
-    GBCMC_system(GLOBAL_gb_main, sys);
+void NT_system_cb(AW_window *aww, AW_CL cl_command, AW_CL cl_auto_help_file) {
+    AW_system(aww, GLOBAL_gb_main, (const char *)cl_command, (const char *)cl_auto_help_file);
 }
 

trunk/NTREE/NT_concatenate.cxx

@@ -13 +13 @@
 #include "nt_internal.h"
 
-#include <awt.hxx>
-#include <awt_item_sel_list.hxx>
+#include <items.h>
+#include <item_sel_list.h>
 #include <awt_sel_boxes.hxx>
 #include <AW_rename.hxx>

trunk/NTREE/NT_dbrepair.cxx

@@ -15 +15 @@
 #include <adGene.h>
 
-#include <awt.hxx>                                  // for ad_item_selector only
+#include <items.h>
 #include <GEN.hxx>
 #include <EXP.hxx>

trunk/NTREE/NT_extern.cxx

@@ -12 +12 @@
 #include "nt_internal.h"
 #include "ntree.hxx"
-#include "ad_spec.hxx"
 #include "ad_trees.hxx"
 #include "ap_consensus.hxx"
@@ -32 +31 @@
 #include <awti_export.hxx>
 
+#include <awt.hxx>
 #include <awt_macro.hxx>
 #include <awt_config_manager.hxx>
@@ -37 +37 @@
 #include <awt_sel_boxes.hxx>
 #include <awt_www.hxx>
-#include <awt_nds.hxx>
+#include <nds.h>
+
+#include <items.h>
+#include <db_query.h>
+#include <dbui.h>
 
 #include <aw_advice.hxx>
@@ -206 +210 @@
     create_primer_design_variables(awr, def, GLOBAL_gb_main);
     create_trees_var(awr, def);
-    NT_create_species_var(awr, def);
+    DBUI::NT_create_species_var(awr, def);
     create_consensus_var(awr, def);
     GDE_create_var(awr, def, GLOBAL_gb_main);
@@ -788 +792 @@
 {
     AWT_canvas *canvas = (AWT_canvas*)cd1;
-    AW_window  *aws    = NT_create_species_window(aww->get_root(), (AW_CL)canvas->gb_main);
+    AW_window  *aws    = DBUI::NT_create_species_window(aww->get_root(), (AW_CL)canvas->gb_main);
     aws->activate();
     nt_mode_event(aww, canvas, (AWT_COMMAND_MODE)cd2);
@@ -991 +995 @@
 void NT_popup_species_window(AW_window *aww, AW_CL cl_gb_main, AW_CL) {
     // used to avoid that the species info window is stored in a menu (or with a button)
-    NT_create_species_window(aww->get_root(), cl_gb_main)->activate();
+    DBUI::NT_create_species_window(aww->get_root(), cl_gb_main)->activate();
 }
 
@@ -1242 +1246 @@
         awm->create_menu("Species", "c", AWM_ALL);
         {
-            AWMIMT("species_search", "Search and query",    "q", "sp_search.hlp", AWM_ALL, AW_POPUP,                (AW_CL)NTX_create_query_window, 0);
+            AWMIMT("species_search", "Search and query",    "q", "sp_search.hlp", AWM_ALL, AW_POPUP,                (AW_CL)DBUI::NTX_create_query_window, (AW_CL)GLOBAL_gb_main);
             AWMIMT("species_info",   "Species information", "i", "sp_info.hlp",   AWM_ALL, NT_popup_species_window, (AW_CL)GLOBAL_gb_main,         0);
 
@@ -1255 +1259 @@
 
             awm->insert_sub_menu("Database fields admin", "f");
-            NT_spec_create_field_items(awm);
+            DBUI::NT_spec_create_field_items(awm, GLOBAL_gb_main);
             awm->close_sub_menu();
             NT_create_mask_submenu(awm);
@@ -1771 +1775 @@
 
     awm->at(db_searchx, first_liney);
-    awm->callback(AW_POPUP, (AW_CL)NTX_create_query_window, 0);
+    awm->callback(AW_POPUP, (AW_CL)DBUI::NTX_create_query_window, (AW_CL)GLOBAL_gb_main);
     awm->help_text("sp_search.hlp");
     awm->create_button("SEARCH",  "Search");

trunk/NTREE/NT_import.cxx

@@ -10 +10 @@
 
 #include "nt_internal.h"
-#include "ad_spec.hxx"
 
+#include <awt.hxx>
+#include <dbui.h>
 #include <GEN.hxx>
 #include <awti_import.hxx>
@@ -26 +27 @@
 void nt_seq_load_cb(AW_root *awr, AW_CL, AW_CL) {
     GLOBAL_gb_dest    = GLOBAL_gb_main;
-    AW_window *aww    = NTX_create_query_window(awr);
-    NT_unquery_all();
+    AW_window *aww    = DBUI::NTX_create_query_window(awr, (AW_CL)GLOBAL_gb_main);
+    DBUI::NT_unquery_all();
     GB_ERROR   error  = MG_simple_merge(awr);
     if (!error) error = NT_format_all_alignments(GLOBAL_gb_main);
-    NT_query_update_list();
+    DBUI::NT_query_update_list();
     if (!error) aww->activate();
 }

trunk/NTREE/NT_join.cxx

@@ -9 +9 @@
 // =============================================================== //
 
-#include <awt.hxx>
-#include <awt_item_sel_list.hxx>
+#include <item_sel_list.h>
 #include <awt_sel_boxes.hxx>
 #include <aw_awars.hxx>

trunk/NTREE/NT_main.cxx

@@ -9 +9 @@
 // =============================================================== //
 
-#include "map_viewer.hxx"
 #include "nt_internal.h"
 #include "ntree.hxx"
@@ -29 +28 @@
 #include <aw_root.hxx>
 
+#include <arbdbt.h>
 #include <adGene.h>
 #include <arb_version.h>
@@ -527 +527 @@
 
     GLOBAL_NT.awr = aw_root;
-    MapViewer_set_default_root(aw_root);            // set default for launch_MapViewer_cb (as long as no info-box was opened)
 
     // create some early awars

trunk/NTREE/NT_sort.cxx

@@ -12 +12 @@
 #include "nt_cb.hxx"
 
-#include <awt_item_sel_list.hxx>
-#include <awt.hxx>
+#include <item_sel_list.h>
 #include <aw_awar.hxx>
 #include <arb_progress.h>

trunk/NTREE/NT_validManual.cxx

@@ -9 +9 @@
 // =============================================================== //
 
-#include <arbdbt.h>
+#include <aw_window.hxx>
 #include <aw_awars.hxx>
 #include <aw_root.hxx>
-#include <awt.hxx>
 #include <aw_msg.hxx>
+#include <arbdbt.h>
 
 #include <string>

trunk/NTREE/NT_validNames.cxx

@@ -14 +14 @@
 #include <aw_awars.hxx>
 #include <aw_msg.hxx>
-#include <awt.hxx>
 #include <awt_www.hxx>
 

trunk/NTREE/ad_ext.cxx

@@ -10 +10 @@
 
 #include <db_scanner.hxx>
-#include <awt.hxx>
+#include <items.h>
 #include <awt_sel_boxes.hxx>
 #include <aw_awars.hxx>

trunk/NTREE/ad_fields.cxx

@@ -10 +10 @@
 
 #include <arbdbt.h>
-#include <awt.hxx>
 
 extern GBDATA *GLOBAL_gb_main;

trunk/NTREE/ad_spec.cxx

@@ -10 +10 @@
 
 #include "map_viewer.hxx"
-#include "ad_spec.hxx"
 #include "nt_internal.h"
 #include "ntree.hxx"
 
-#include <awtc_next_neighbours.hxx>
-#include <AW_rename.hxx>
-#include <db_scanner.hxx>
-#include <awt_item_sel_list.hxx>
-#include <awtlocal.hxx>
+#include <dbui.h>
+
 #include <awt_www.hxx>
-#include <awt_sel_boxes.hxx>
+#include <awt_canvas.hxx>
+
 #include <aw_awars.hxx>
-#include <aw_detach.hxx>
 #include <aw_msg.hxx>
+#include <aw_root.hxx>
+
 #include <arb_progress.h>
-#include <arb_strbuf.h>
 #include <arb_defs.h>
-#include <probe_design.hxx>
 
 #include <cctype>
@@ -35 +31 @@
 
 extern GBDATA *GLOBAL_gb_main;
-
-// next neighbours of listed and selected:
-#define AWAR_NN_COMPLEMENT  AWAR_NN_BASE "complement"
-
-// next neighbours of selected only:
-#define AWAR_NN_MAX_HITS  AWAR_NN_BASE "max_hits"
-#define AWAR_NN_HIT_COUNT "tmp/" AWAR_NN_BASE "hit_count"
-
-// next neighbours of listed only:
-#define AWAR_NN_DEST_FIELD     AWAR_NN_BASE "dest_field"
-#define AWAR_NN_WANTED_ENTRIES AWAR_NN_BASE "wanted_entries"
-#define AWAR_NN_SCORED_ENTRIES AWAR_NN_BASE "scored_entries"
-#define AWAR_NN_MIN_SCORE      AWAR_NN_BASE "min_score"
-#define AWAR_NN_RANGE_START    AWAR_NN_BASE "range_start"
-#define AWAR_NN_RANGE_END      AWAR_NN_BASE "range_end"
-
-enum ReorderMode {
-    // real orders
-    ORDER_ALPHA,
-    ORDER_TYPE,
-    ORDER_FREQ,
-    
-    // special modes
-    RIGHT_BEHIND_LEFT,
-    REVERSE_ORDER,
-};
-
-void NT_create_species_var(AW_root *aw_root, AW_default aw_def) {
-    aw_root->awar_string(AWAR_SPECIES_DEST,         "",          aw_def);
-    aw_root->awar_string(AWAR_SPECIES_INFO,         "",          aw_def);
-    aw_root->awar_string(AWAR_SPECIES_KEY,          "",          aw_def);
-    aw_root->awar_string(AWAR_FIELD_REORDER_SOURCE, "",          aw_def);
-    aw_root->awar_string(AWAR_FIELD_REORDER_DEST,   "",          aw_def);
-    aw_root->awar_int   (AWAR_FIELD_REORDER_ORDER,  ORDER_ALPHA, aw_def);
-    aw_root->awar_string(AWAR_FIELD_CREATE_NAME,    "",          aw_def);
-    aw_root->awar_int   (AWAR_FIELD_CREATE_TYPE,    GB_STRING,   aw_def);
-    aw_root->awar_string(AWAR_FIELD_DELETE,         "",          aw_def);
-    aw_root->awar_string(AWAR_FIELD_CONVERT_SOURCE, "",          aw_def);
-    aw_root->awar_int   (AWAR_FIELD_CONVERT_TYPE,   GB_STRING,   aw_def);
-    aw_root->awar_string(AWAR_FIELD_CONVERT_NAME,   "",          aw_def);
-}
-
-static void move_species_to_extended(AW_window *aww) {
-    char     *source = aww->get_root()->awar(AWAR_SPECIES_NAME)->read_string();
-    GB_ERROR  error  = GB_begin_transaction(GLOBAL_gb_main);
-
-    if (!error) {
-        GBDATA *gb_sai_data     = GBT_get_SAI_data(GLOBAL_gb_main);
-        if (!gb_sai_data) error = GB_await_error();
-        else {
-            GBDATA *gb_species = GBT_find_species(GLOBAL_gb_main, source);
-            GBDATA *gb_dest    = GBT_find_SAI_rel_SAI_data(gb_sai_data, source);
-
-            if (gb_dest) error = GBS_global_string("SAI '%s' already exists", source);
-            else if (gb_species) {
-                gb_dest             = GB_create_container(gb_sai_data, "extended");
-                if (!gb_dest) error = GB_await_error();
-                else {
-                    error = GB_copy(gb_dest, gb_species);
-                    if (!error) {
-                        error = GB_delete(gb_species);
-                        if (!error) aww->get_root()->awar(AWAR_SPECIES_NAME)->write_string("");
-                    }
-                }
-            }
-            else error = "Please select a species";
-        }
-    }
-    GB_end_transaction_show_error(GLOBAL_gb_main, error, aw_message);
-    free(source);
-}
 
 static const char * const SAI_COUNTED_CHARS = "COUNTED_CHARS";
@@ -320 +245 @@
 }
 
-static void species_create_cb(AW_window * aww) {
-    char     *dest  = aww->get_root()->awar(AWAR_SPECIES_DEST)->read_string();
-    GB_ERROR  error = GB_begin_transaction(GLOBAL_gb_main);
-
-    if (!error) {
-        GBDATA *gb_species_data     = GB_search(GLOBAL_gb_main, "species_data", GB_CREATE_CONTAINER);
-        if (!gb_species_data) error = GB_await_error();
-        else {
-            GBDATA *gb_dest = GBT_find_species_rel_species_data(gb_species_data, dest);
-
-            if (gb_dest) error = GBS_global_string("Species '%s' already exists", dest);
-            else {
-                gb_dest             = GBT_find_or_create_species_rel_species_data(gb_species_data, dest);
-                if (!gb_dest) error = GB_await_error();
-                else aww->get_root()->awar(AWAR_SPECIES_NAME)->write_string(dest);
-            }
-        }
-    }
-    GB_end_transaction_show_error(GLOBAL_gb_main, error, aw_message);
-    free(dest);
-}
-
-static AW_window *create_species_create_window(AW_root *root)
-{
-    AW_window_simple *aws = new AW_window_simple;
-    aws->init(root, "CREATE_SPECIES", "SPECIES CREATE");
-    aws->load_xfig("ad_al_si.fig");
-
-    aws->callback((AW_CB0)AW_POPDOWN);
-    aws->at("close");
-    aws->create_button("CLOSE", "CLOSE", "C");
-
-    aws->at("label");
-    aws->create_autosize_button(0, "Please enter the name\nof the new species");
-
-    aws->at("input");
-    aws->create_input_field(AWAR_SPECIES_DEST, 15);
-
-    aws->at("ok");
-    aws->callback(species_create_cb);
-    aws->create_button("GO", "GO", "G");
-
-    return (AW_window *)aws;
-}
-
-static GBDATA *expect_species_selected(AW_root *aw_root, char **give_name = 0) {
-    GB_transaction  ta(GLOBAL_gb_main);
-    char           *name       = aw_root->awar(AWAR_SPECIES_NAME)->read_string();
-    GBDATA         *gb_species = GBT_find_species(GLOBAL_gb_main, name);
-
-    if (!gb_species) {
-        if (name && name[0]) aw_message(GBS_global_string("Species '%s' does not exist.", name));
-        else aw_message("Please select a species first");
-    }
-
-    if (give_name) *give_name = name;
-    else free(name);
-
-    return gb_species;
-}
-
-static void ad_species_copy_cb(AW_window *aww, AW_CL, AW_CL) {
-    AW_root *aw_root    = aww->get_root();
-    char    *name;
-    GBDATA  *gb_species = expect_species_selected(aw_root, &name);
-
-    if (gb_species) {
-        GB_transaction      ta(GLOBAL_gb_main);
-        GBDATA             *gb_species_data = GB_get_father(gb_species);
-        UniqueNameDetector  und(gb_species_data);
-        GB_ERROR            error           = 0;
-        char               *copy_name       = AWTC_makeUniqueShortName(GBS_global_string("c%s", name), und);
-
-        if (!copy_name) error = GB_await_error();
-        else {
-            GBDATA *gb_new_species = GB_create_container(gb_species_data, "species");
-
-            if (!gb_new_species) error = GB_await_error();
-            else {
-                error = GB_copy(gb_new_species, gb_species);
-                if (!error) {
-                    error = GBT_write_string(gb_new_species, "name", copy_name);
-                    if (!error) aw_root->awar(AWAR_SPECIES_NAME)->write_string(copy_name); // set focus
-                }
-            }
-
-            free(copy_name);
-        }
-        if (error) {
-            error = ta.close(error);
-            aw_message(error);
-        }
-    }
-}
-
-static void ad_species_rename_cb(AW_window *aww, AW_CL, AW_CL) {
-    AW_root *aw_root    = aww->get_root();
-    GBDATA  *gb_species = expect_species_selected(aw_root);
-    if (gb_species) {
-        GB_transaction  ta(GLOBAL_gb_main);
-        GBDATA         *gb_full_name  = GB_search(gb_species, "full_name", GB_STRING);
-        const char     *full_name     = gb_full_name ? GB_read_char_pntr(gb_full_name) : "";
-        char           *new_full_name = aw_input("Enter new 'full_name' of species:", full_name);
-
-        if (new_full_name) {
-            GB_ERROR error = 0;
-
-            if (strcmp(full_name, new_full_name) != 0) {
-                error = GB_write_string(gb_full_name, new_full_name);
-            }
-            if (!error) {
-                if (aw_ask_sure("Do you want to re-create the 'name' field?")) {
-                    arb_progress progress("Recreating species name", 1);
-                    error = AWTC_recreate_name(gb_species);
-                    if (!error) aw_root->awar(AWAR_SPECIES_NAME)->write_string(GBT_read_name(gb_species)); // set focus
-                }
-            }
-
-            if (error) {
-                error = ta.close(error);
-                aw_message(error);
-            }
-        }
-    }
-}
-
-static void ad_species_delete_cb(AW_window *aww, AW_CL, AW_CL) {
-    AW_root  *aw_root    = aww->get_root();
-    char     *name;
-    GBDATA   *gb_species = expect_species_selected(aw_root, &name);
-    GB_ERROR  error      = 0;
-
-    if (!gb_species) {
-        error = "Please select a species first";
-    }
-    else if (aw_ask_sure(GBS_global_string("Are you sure to delete the species '%s'?", name))) {
-        GB_transaction ta(GLOBAL_gb_main);
-        error = GB_delete(gb_species);
-        error = ta.close(error);
-        if (!error) aw_root->awar(AWAR_SPECIES_NAME)->write_string("");
-    }
-
-    if (error) aw_message(error);
-    free(name);
-}
-
-static AW_CL    ad_global_scannerid      = 0;
-static AW_root *ad_global_scannerroot    = 0;
-static AW_root *ad_global_default_awroot = 0;
-
-void MapViewer_set_default_root(AW_root *aw_root) {
-    ad_global_default_awroot = aw_root;
-}
-
-static void AD_map_species(AW_root *aw_root, AW_CL scannerid, AW_CL mapOrganism)
-{
-    GB_push_transaction(GLOBAL_gb_main);
-    char *source = aw_root->awar((bool)mapOrganism ? AWAR_ORGANISM_NAME : AWAR_SPECIES_NAME)->read_string();
-    GBDATA *gb_species = GBT_find_species(GLOBAL_gb_main, source);
-    if (gb_species) {
-        map_db_scanner(scannerid, gb_species, CHANGE_KEY_PATH);
-    }
-    GB_pop_transaction(GLOBAL_gb_main);
-    free(source);
-}
-
 void launch_MapViewer_cb(GBDATA *gbd, AD_MAP_VIEWER_TYPE type) {
     GB_ERROR error = GB_push_transaction(GLOBAL_gb_main);
@@ -497 +256 @@
         }
 
-        if (ad_global_scannerroot) { // if we have an active info-scanner, then update its awar
-            ad_global_scannerroot->awar(AWAR_SPECIES_NAME)->write_string(species_name);
-        }
-        else if (ad_global_default_awroot) { // no active scanner -> write global awar
-            ad_global_default_awroot->awar(AWAR_SPECIES_NAME)->write_string(species_name);
-        }
+        AW_root::SINGLETON->awar(AWAR_SPECIES_NAME)->write_string(species_name);
     }
 
@@ -517 +271 @@
 }
 
-static long count_field_occurrance(const ad_item_selector *sel, const char *field_name) {
-    AWT_QUERY_RANGE RANGE = QUERY_ALL_ITEMS;
-    long            count = 0;
-
-    for (GBDATA *gb_container = sel->get_first_item_container(GLOBAL_gb_main, NULL, RANGE);
-         gb_container;
-         gb_container = sel->get_next_item_container(gb_container, RANGE))
-    {
-        for (GBDATA *gb_item = sel->get_first_item(gb_container, RANGE);
-             gb_item;
-             gb_item = sel->get_next_item(gb_item, RANGE))
-        {
-            GBDATA *gb_field = GB_entry(gb_item, field_name);
-            if (gb_field) ++count;
-        }
-    }
-    return count;
-}
-
-class KeySorter : virtual Noncopyable {
-    int      key_count;
-    GBDATA **key;
-
-    int field_count; // = key_count - container_count
-
-    bool order_changed;
-
-    // helper variables for sorting
-    static GB_HASH                *order_hash;
-    static const ad_item_selector *item_selector;
-    static arb_progress           *sort_progress;
-
-    bool legal_pos(int p) { return p >= 0 && p<key_count; }
-    bool legal_field_pos(int p) const { return p >= 0 && p<field_count; }
-    bool legal_field_pos(int p1, int p2) const { return legal_field_pos(p1) && legal_field_pos(p2); }
-
-    void swap(int p1, int p2) {
-        nt_assert(legal_pos(p1));
-        nt_assert(legal_pos(p2));
-
-        GBDATA *k = key[p1];
-        key[p1]   = key[p2];
-        key[p2]   = k;
-
-        order_changed = true;
-    }
-
-    const char *field_name(int p) const {
-        GBDATA *gb_key_name = GB_entry(key[p], "key_name");
-        if (gb_key_name) return GB_read_char_pntr(gb_key_name);
-        return NULL;
-    }
-    GB_TYPES field_type(int p) const {
-        GBDATA *gb_key_type = GB_entry(key[p], "key_type");
-        if (gb_key_type) return GB_TYPES(GB_read_int(gb_key_type));
-        return GB_NONE;
-    }
-    int field_freq(int p) const {
-        const char *name            = field_name(p);
-        if (!order_hash) order_hash = GBS_create_hash(key_count, GB_IGNORE_CASE);
-
-        long freq = GBS_read_hash(order_hash, name);
-        if (!freq) {
-            freq = 1+count_field_occurrance(item_selector, name);
-            GBS_write_hash(order_hash, name, freq);
-            if (sort_progress) sort_progress->inc();
-        }
-        return freq;
-    }
-
-    int compare(int p1, int p2, ReorderMode mode) {
-        switch (mode) {
-            case RIGHT_BEHIND_LEFT:
-            case REVERSE_ORDER: 
-                nt_assert(0); // illegal ReorderMode
-                break;
-
-            case ORDER_TYPE:  return field_type(p2)-field_type(p1);
-            case ORDER_ALPHA: return strcasecmp(field_name(p1), field_name(p2));
-            case ORDER_FREQ:  return field_freq(p2)-field_freq(p1);
-        }
-        return p2-p1; // keep order
-    }
-
-public:
-    KeySorter(GBDATA *gb_key_data) {
-        key_count   = 0;
-        field_count = 0;
-        key         = NULL;
-
-        for (GBDATA *gb_key = GB_child(gb_key_data); gb_key; gb_key = GB_nextChild(gb_key)) {
-            key_count++;
-        }
-
-        if (key_count) {
-            key = (GBDATA**)malloc(key_count*sizeof(*key));
-            
-            int container_count = 0;
-            for (GBDATA *gb_key = GB_child(gb_key_data); gb_key; gb_key = GB_nextChild(gb_key)) {
-                GBDATA   *gb_type = GB_entry(gb_key, CHANGEKEY_TYPE);
-                GB_TYPES  type    = GB_TYPES(GB_read_int(gb_type));
-
-                if (type == GB_DB) { // move containers behind fields
-                    key[key_count-1-container_count++] = gb_key;
-                }
-                else {
-                    key[field_count++] = gb_key;
-                }
-            }
-            nt_assert((container_count+field_count) == key_count);
-            reverse_order(field_count, key_count-1); // of containers
-        }
-        order_changed = false;
-    }
-    ~KeySorter() {
-        nt_assert(!order_changed); // order changed but not written
-        free(key);
-    }
-
-    int get_field_count() const { return field_count; }
-
-    void bubble_sort(int p1, int p2, ReorderMode mode, const ad_item_selector *selector) {
-        if (p1>p2) std::swap(p1, p2);
-        if (legal_field_pos(p1, p2)) {
-            if (mode == ORDER_FREQ) {
-                sort_progress = new arb_progress("Calculating field frequencies", p2-p1+1);
-            }
-            item_selector = selector;
-            while (p1<p2) {
-                bool changed = false;
-
-                int i = p2;
-                while (i>p1) {
-                    if (compare(i-1, i, mode)>0) {
-                        swap(i-1, i);
-                        changed = true;
-                    }
-                    --i;
-                }
-                if (!changed) break;
-                ++p1;
-            }
-            if (order_hash) {
-                GBS_free_hash(order_hash);
-                order_hash = NULL;
-            }
-            if (sort_progress) {
-                delete sort_progress;
-                sort_progress = NULL;
-            }
-        }
-    }
-    void reverse_order(int p1, int p2) {
-        if (p1>p2) std::swap(p1, p2);
-        if (legal_field_pos(p1, p2)) while (p1<p2) swap(p1++, p2--);
-    }
-
-    int index_of(GBDATA *gb_key) {
-        int i;
-        for (i = 0; i<key_count; i++) {
-            if (gb_key == key[i]) break;
-        }
-        if (i == key_count) {
-            nt_assert(0);
-            i = -1;
-        }
-        return i;
-    }
-
-    void move_to(int to_move, int wanted_position) {
-        if (legal_field_pos(to_move, wanted_position)) {
-            while (to_move<wanted_position) {
-                swap(to_move, to_move+1);
-                to_move++;
-            }
-            while (to_move>wanted_position) {
-                swap(to_move, to_move-1);
-                to_move--;
-            }
-        }
-    }
-
-    GB_ERROR save_changes() {
-        GB_ERROR warning = NULL;
-        if (order_changed) {
-            if (key_count) {
-                GBDATA *gb_main = GB_get_root(key[0]);
-                warning         = GB_resort_data_base(gb_main, key, key_count);
-            }
-            order_changed = false;
-        }
-        return warning;
-    }
-};
-
-GB_HASH                *KeySorter::order_hash    = NULL;
-const ad_item_selector *KeySorter::item_selector = NULL;
-arb_progress           *KeySorter::sort_progress = NULL;
-
-static void reorder_keys(AW_window *aws, ReorderMode mode, AWT_itemfield_selection *sel_left, AWT_itemfield_selection *sel_right) {
-    const ad_item_selector *selector = sel_left->get_selector();
-    nt_assert(selector == sel_right->get_selector());
-    
-    int left_index  = aws->get_index_of_selected_element(sel_left->get_sellist());
-    int right_index = aws->get_index_of_selected_element(sel_right->get_sellist());
-
-    GB_ERROR warning = 0;
-
-    GB_begin_transaction(GLOBAL_gb_main);
-
-    AW_root *awr            = aws->get_root();
-    GBDATA  *gb_left_field  = GBT_get_changekey(GLOBAL_gb_main, awr->awar(AWAR_FIELD_REORDER_SOURCE)->read_char_pntr(), selector->change_key_path);
-    GBDATA  *gb_right_field = GBT_get_changekey(GLOBAL_gb_main, awr->awar(AWAR_FIELD_REORDER_DEST)->read_char_pntr(), selector->change_key_path);
-
-    if (!gb_left_field || !gb_right_field || gb_left_field == gb_right_field) {
-        warning = "Please select different fields in both list";
-    }
-    else {
-        GBDATA    *gb_key_data = GB_search(GLOBAL_gb_main, selector->change_key_path, GB_CREATE_CONTAINER);
-        KeySorter  sorter(gb_key_data);
-
-        int left_key_idx  = sorter.index_of(gb_left_field);
-        int right_key_idx = sorter.index_of(gb_right_field);
-
-        switch (mode) {
-            case RIGHT_BEHIND_LEFT:
-                sorter.move_to(right_key_idx, left_key_idx+(left_key_idx<right_key_idx));
-                if (right_index>left_index) { left_index++; right_index++; } // make it simple to move several consecutive keys
-                break;
-            case REVERSE_ORDER:
-                sorter.reverse_order(left_key_idx, right_key_idx);
-                std::swap(left_index, right_index);
-                break;
-            default: 
-                sorter.bubble_sort(left_key_idx, right_key_idx, mode, selector);
-                break;
-        }
-
-        sorter.save_changes();
-    }
-    GB_commit_transaction(GLOBAL_gb_main);
-
-    if (warning) {
-        aw_message(warning);
-    }
-    else {
-        aws->select_element_at_index(sel_left->get_sellist(), left_index);
-        aws->select_element_at_index(sel_right->get_sellist(), right_index);
-    }
-}
-
-static void reorder_right_behind_left(AW_window *aws, AW_CL cl_selleft, AW_CL cl_selright) { reorder_keys(aws, RIGHT_BEHIND_LEFT, (AWT_itemfield_selection*)cl_selleft, (AWT_itemfield_selection*)cl_selright); }
-static void reverse_key_order        (AW_window *aws, AW_CL cl_selleft, AW_CL cl_selright) { reorder_keys(aws, REVERSE_ORDER,      (AWT_itemfield_selection*)cl_selleft, (AWT_itemfield_selection*)cl_selright); }
-static void sort_keys(AW_window *aws, AW_CL cl_selleft, AW_CL cl_selright) {
-    ReorderMode mode = ReorderMode(aws->get_root()->awar(AWAR_FIELD_REORDER_ORDER)->read_int());
-    reorder_keys(aws, mode, (AWT_itemfield_selection*)cl_selleft, (AWT_itemfield_selection*)cl_selright);
-}
-
-static void reorder_up_down(AW_window *aws, AW_CL cl_selright, AW_CL cl_dir) {
-    GB_begin_transaction(GLOBAL_gb_main);
-
-    int                      dir        = (int)cl_dir;
-    AWT_itemfield_selection *sel_right  = (AWT_itemfield_selection*)cl_selright;
-    const ad_item_selector  *selector   = sel_right->get_selector();
-    int                      list_index = aws->get_index_of_selected_element(sel_right->get_sellist());
-
-    const char *field_name = aws->get_root()->awar(AWAR_FIELD_REORDER_DEST)->read_char_pntr();
-    GBDATA     *gb_field   = GBT_get_changekey(GLOBAL_gb_main, field_name, selector->change_key_path);
-    GB_ERROR    warning    = 0;
-
-    if (!gb_field) {
-        warning = "Please select the item to move in the right box";
-    }
-    else {
-        GBDATA    *gb_key_data = GB_search(GLOBAL_gb_main, selector->change_key_path, GB_CREATE_CONTAINER);
-        KeySorter  sorter(gb_key_data);
-
-        int curr_index = sorter.index_of(gb_field);
-        int dest_index = -1;
-        if (abs(dir) == 1) {
-            dest_index = curr_index+dir;
-            list_index = -1;
-        }
-        else {
-            dest_index = dir<0 ? 0 : sorter.get_field_count()-1;
-        }
-
-        sorter.move_to(curr_index, dest_index);
-        warning = sorter.save_changes();
-
-    }
-
-    GB_commit_transaction(GLOBAL_gb_main);
-    if (list_index >= 0) aws->select_element_at_index(sel_right->get_sellist(), list_index);
-    if (warning) aw_message(warning);
-}
-
-AW_window *NT_create_ad_list_reorder(AW_root *root, AW_CL cl_item_selector) {
-    const ad_item_selector *selector = (const ad_item_selector*)cl_item_selector;
-    
-    static AW_window_simple *awsa[AWT_QUERY_ITEM_TYPES];
-    if (!awsa[selector->type]) {
-        AW_window_simple *aws = new AW_window_simple;
-        awsa[selector->type]  = aws;
-
-        aws->init(root, "REORDER_FIELDS", "REORDER FIELDS");
-        aws->load_xfig("ad_kreo.fig");
-
-        aws->callback((AW_CB0)AW_POPDOWN);
-        aws->at("close");
-        aws->create_button("CLOSE", "CLOSE", "C");
-
-        const char *HELPFILE = "spaf_reorder.hlp";
-        aws->callback(AW_POPUP_HELP, (AW_CL)HELPFILE);
-        aws->at("help");
-        aws->create_button("HELP", "HELP", "H");
-
-        AWT_itemfield_selection *sel1 = awt_create_selection_list_on_itemfields(GLOBAL_gb_main, aws, AWAR_FIELD_REORDER_SOURCE, AWT_NDS_FILTER, "source", 0, selector, 20, 10);
-        AWT_itemfield_selection *sel2 = awt_create_selection_list_on_itemfields(GLOBAL_gb_main, aws, AWAR_FIELD_REORDER_DEST,   AWT_NDS_FILTER, "dest",   0, selector, 20, 10);
-
-        aws->button_length(8);
-
-        aws->at("sort");
-        aws->callback(sort_keys, (AW_CL)sel1, (AW_CL)sel2);
-        aws->help_text(HELPFILE);
-        aws->create_button("SORT", "Sort by");
-
-        aws->at("sorttype");
-        aws->create_option_menu(AWAR_FIELD_REORDER_ORDER);
-        aws->insert_option("name",      "a", ORDER_ALPHA);
-        aws->insert_option("type",      "t", ORDER_TYPE);
-        aws->insert_option("frequency", "f", ORDER_FREQ);
-        aws->update_option_menu();
-
-        aws->at("leftright");
-        aws->callback(reorder_right_behind_left, (AW_CL)sel1, (AW_CL)sel2);
-        aws->help_text(HELPFILE);
-        aws->create_autosize_button("MOVE_RIGHT_BEHIND_LEFT", "Move right\nbehind left");
-
-        aws->at("reverse");
-        aws->callback(reverse_key_order, (AW_CL)sel1, (AW_CL)sel2);
-        aws->help_text(HELPFILE);
-        aws->create_autosize_button("REVERSE", "Reverse");
-        
-        aws->button_length(6);
-        struct {
-            const char *tag;
-            const char *macro;
-            int         dir;
-        } reorder[4] = {
-            { "Top",    "MOVE_TOP_RIGHT",  -2 },
-            { "Up",     "MOVE_UP_RIGHT",   -1 },
-            { "Down",   "MOVE_DOWN_RIGHT", +1 },
-            { "Bottom", "MOVE_BOT_RIGHT",  +2 },
-        };
-
-        for (int i = 0; i<4; ++i) {
-            aws->at(reorder[i].tag);
-            aws->callback(reorder_up_down, (AW_CL)sel2, reorder[i].dir);
-            aws->help_text(HELPFILE);
-            aws->create_button(reorder[i].macro, reorder[i].tag);
-        }
-    }
-    
-    return awsa[selector->type];
-}
-
-static void ad_hide_field(AW_window *aws, AW_CL cl_sel, AW_CL cl_hide) {
-    AWT_itemfield_selection *item_sel = (AWT_itemfield_selection*)cl_sel;
-    GB_ERROR                 error    = GB_begin_transaction(GLOBAL_gb_main);
-
-    if (!error) {
-        char                   *source    = aws->get_root()->awar(AWAR_FIELD_DELETE)->read_string();
-        const ad_item_selector *selector  = item_sel->get_selector();
-        GBDATA                 *gb_source = GBT_get_changekey(GLOBAL_gb_main, source, selector->change_key_path);
-
-        if (!gb_source) error = "Please select the field you want to (un)hide";
-        else error            = GBT_write_int(gb_source, CHANGEKEY_HIDDEN, int(cl_hide));
-
-        free(source);
-    }
-    GB_end_transaction_show_error(GLOBAL_gb_main, error, aw_message);
-    if (!error) aws->move_selection(item_sel->get_sellist(), 1);
-}
-
-static void ad_field_delete(AW_window *aws, AW_CL cl_sel) {
-    GB_ERROR error = GB_begin_transaction(GLOBAL_gb_main);
-
-    if (!error) {
-        char                    *source     = aws->get_root()->awar(AWAR_FIELD_DELETE)->read_string();
-        AWT_itemfield_selection *item_sel   = (AWT_itemfield_selection*)cl_sel;
-        const ad_item_selector  *selector   = item_sel->get_selector();
-        AW_selection_list       *sellist    = item_sel->get_sellist();
-        int                      curr_index = aws->get_index_of_selected_element(sellist);
-        GBDATA                  *gb_source  = GBT_get_changekey(GLOBAL_gb_main, source, selector->change_key_path);
-
-        if (!gb_source) error = "Please select the field you want to delete";
-        else error            = GB_delete(gb_source);
-
-        for (GBDATA *gb_item_container = selector->get_first_item_container(GLOBAL_gb_main, aws->get_root(), QUERY_ALL_ITEMS);
-             !error && gb_item_container;
-             gb_item_container = selector->get_next_item_container(gb_item_container, QUERY_ALL_ITEMS))
-        {
-            for (GBDATA * gb_item = selector->get_first_item(gb_item_container, QUERY_ALL_ITEMS);
-                 !error && gb_item;
-                 gb_item = selector->get_next_item(gb_item, QUERY_ALL_ITEMS))
-            {
-                GBDATA *gbd = GB_search(gb_item, source, GB_FIND);
-
-                if (gbd) {
-                    error = GB_delete(gbd);
-                    if (!error) {
-                        // item has disappeared, this selects the next one:
-                        aws->select_element_at_index(sellist, curr_index);
-                    }
-                }
-            }
-        }
-
-        free(source);
-    }
-
-    GB_end_transaction_show_error(GLOBAL_gb_main, error, aw_message);
-}
-
-
-AW_window *NT_create_ad_field_delete(AW_root *root, AW_CL cl_item_selector) {
-    const ad_item_selector *selector = (const ad_item_selector*)cl_item_selector;
-
-    static AW_window_simple *awsa[AWT_QUERY_ITEM_TYPES];
-    if (!awsa[selector->type]) {
-        AW_window_simple *aws = new AW_window_simple;
-        awsa[selector->type]  = aws;
-
-        aws->init(root, "DELETE_FIELD", "DELETE FIELD");
-        aws->load_xfig("ad_delof.fig");
-        aws->button_length(6);
-
-        aws->at("close"); aws->callback(AW_POPDOWN);
-        aws->create_button("CLOSE", "CLOSE", "C");
-
-        aws->at("help"); aws->callback(AW_POPUP_HELP, (AW_CL)"spaf_delete.hlp");
-        aws->create_button("HELP", "HELP", "H");
-
-        AWT_itemfield_selection *item_sel =
-            awt_create_selection_list_on_itemfields(GLOBAL_gb_main,
-                                                    aws, AWAR_FIELD_DELETE,
-                                                    -1,
-                                                    "source", 0, selector, 20, 10,
-                                                    AWT_SF_HIDDEN);
-
-        aws->button_length(13);
-        aws->at("hide");
-        aws->callback(ad_hide_field, (AW_CL)item_sel, (AW_CL)1);
-        aws->help_text("rm_field_only.hlp");
-        aws->create_button("HIDE_FIELD", "Hide field", "H");
-
-        aws->at("unhide");
-        aws->callback(ad_hide_field, (AW_CL)item_sel, (AW_CL)0);
-        aws->help_text("rm_field_only.hlp");
-        aws->create_button("UNHIDE_FIELD", "Unhide field", "U");
-
-        aws->at("delf");
-        aws->callback(ad_field_delete, (AW_CL)item_sel);
-        aws->help_text("rm_field_cmpt.hlp");
-        aws->create_button("DELETE_FIELD", "DELETE FIELD\n(DATA DELETED)", "C");
-    }
-    
-    return awsa[selector->type];
-}
-
-static void ad_field_create_cb(AW_window *aws, AW_CL cl_item_selector)
-{
-    GB_push_transaction(GLOBAL_gb_main);
-    char *name = aws->get_root()->awar(AWAR_FIELD_CREATE_NAME)->read_string();
-    GB_ERROR error = GB_check_key(name);
-    GB_ERROR error2 = GB_check_hkey(name);
-    if (error && !error2) {
-        aw_message("Warning: Your key contain a '/' character,\n"
-                   "    that means it is a hierarchical key");
-        error = 0;
-    }
-
-    int type = (int)aws->get_root()->awar(AWAR_FIELD_CREATE_TYPE)->read_int();
-
-    const ad_item_selector *selector = (const ad_item_selector*)cl_item_selector;
-    if (!error) error = GBT_add_new_changekey_to_keypath(GLOBAL_gb_main, name, type, selector->change_key_path);
-    aws->hide_or_notify(error);
-    free(name);
-    GB_pop_transaction(GLOBAL_gb_main);
-}
-
-AW_window *NT_create_ad_field_create(AW_root *root, AW_CL cl_item_selector)
-{
-    const ad_item_selector *selector = (const ad_item_selector*)cl_item_selector;
-
-    static AW_window_simple *awsa[AWT_QUERY_ITEM_TYPES];
-    if (awsa[selector->type]) return (AW_window *)awsa[selector->type];
-
-    AW_window_simple *aws = new AW_window_simple;
-    awsa[selector->type]  = aws;
-
-    aws->init(root, "CREATE_FIELD", "CREATE A NEW FIELD");
-    aws->load_xfig("ad_fcrea.fig");
-
-    aws->callback((AW_CB0)AW_POPDOWN);
-    aws->at("close");
-    aws->create_button("CLOSE", "CLOSE", "C");
-
-    aws->at("input");
-    aws->label("FIELD NAME");
-    aws->create_input_field(AWAR_FIELD_CREATE_NAME, 15);
-
-    aws->at("type");
-    aws->create_toggle_field(AWAR_FIELD_CREATE_TYPE, "FIELD TYPE", "F");
-    aws->insert_toggle("Ascii Text",        "S", (int)GB_STRING);
-    aws->insert_toggle("Link",              "L", (int)GB_LINK);
-    aws->insert_toggle("Rounded Numerical", "N", (int)GB_INT);
-    aws->insert_toggle("Numerical",         "R", (int)GB_FLOAT);
-    aws->insert_toggle("MASK = 01 Text",    "0", (int)GB_BITS);
-    aws->update_toggle_field();
-
-    aws->at("ok");
-    aws->callback(ad_field_create_cb, cl_item_selector);
-    aws->create_button("CREATE", "CREATE", "C");
-
-    return (AW_window *)aws;
-}
-
-#if defined(WARN_TODO)
-#warning GBT_convert_changekey currently only works for species fields, make it work with genes/exp/... as well (use selector)
-#endif
-
-static void ad_field_convert_commit_cb(AW_window *aws, AW_CL /*cl_item_selector*/) {
-    // const ad_item_selector *selector = (const ad_item_selector*) cl_item_selector;
-    AW_root *root = aws->get_root();
-    GB_ERROR error = NULL;
-
-    GB_push_transaction(GLOBAL_gb_main);
-    error = GBT_convert_changekey(GLOBAL_gb_main,
-                                  root->awar(AWAR_FIELD_CONVERT_SOURCE)->read_string(),
-                                  (GB_TYPES)root->awar(AWAR_FIELD_CONVERT_TYPE)->read_int());
-
-    GB_end_transaction_show_error(GLOBAL_gb_main, error, aw_message);
-}
-
-static void ad_field_convert_update_typesel_cb(AW_window *aws, AW_CL cl_item_selector) {
-    const ad_item_selector *selector = (const ad_item_selector*) cl_item_selector;
-    AW_root *root = aws->get_root();
-
-    GB_push_transaction(GLOBAL_gb_main);
-    int type = GBT_get_type_of_changekey(
-        GLOBAL_gb_main,
-        root->awar(AWAR_FIELD_CONVERT_SOURCE)->read_string(),
-        selector->change_key_path);
-    GB_pop_transaction(GLOBAL_gb_main);
-
-    root->awar(AWAR_FIELD_CONVERT_TYPE)->write_int(type);
-}
-
-AW_window *NT_create_ad_field_convert(AW_root *root, AW_CL cl_item_selector) {
-    const ad_item_selector *selector = (const ad_item_selector*) cl_item_selector;
-
-    static AW_window_simple *awsa[AWT_QUERY_ITEM_TYPES];
-    if (awsa[selector->type]) return (AW_window *)awsa[selector->type];
-
-    AW_window_simple *aws = new AW_window_simple;
-    awsa[selector->type]  = aws;
-
-    aws->init(root, "CONVERT_FIELD", "CONVERT FIELDS");
-    aws->load_xfig("ad_conv.fig");
-
-    aws->at("close");
-    aws->callback((AW_CB0)AW_POPDOWN);
-    aws->create_button("CLOSE", "CLOSE", "C");
-
-    aws->at("help");
-    aws->callback(AW_POPUP_HELP, (AW_CL)"spaf_convert.hlp");
-    aws->create_button("HELP", "HELP", "H");
-
-    aws->callback(ad_field_convert_update_typesel_cb, cl_item_selector);
-    awt_create_selection_list_on_itemfields(GLOBAL_gb_main,
-                                            aws,
-                                            AWAR_FIELD_CONVERT_SOURCE, // AWAR containing selection
-                                            -1,     // type filter
-                                            "source", // selector xfig position
-                                            0,      // rescan button xfig position
-                                            selector,
-                                            40, 20, // selector w,h
-                                            AWT_SF_HIDDEN);
-
-    aws->at("typesel");
-    aws->create_toggle_field(AWAR_FIELD_CONVERT_TYPE, NULL, "F");
-    aws->insert_toggle("Ascii Text",        "S", (int)GB_STRING);
-    aws->insert_toggle("Link",              "L", (int)GB_LINK);
-    aws->insert_toggle("Rounded Numerical", "N", (int)GB_INT);
-    aws->insert_toggle("Numerical",         "R", (int)GB_FLOAT);
-    aws->insert_toggle("MASK = 01 Text",    "0", (int)GB_BITS);
-    aws->update_toggle_field();
-
-    aws->at("convert");
-    aws->callback(ad_field_convert_commit_cb, cl_item_selector);
-    aws->create_button("CONVERT", "CONVERT", "T");
-
-    return (AW_window*)aws;
-}
-
-void NT_spec_create_field_items(AW_window *aws) {
-    aws->insert_menu_topic("spec_reorder_fields", "Reorder fields ...",     "R", "spaf_reorder.hlp", AWM_ALL, AW_POPUP, (AW_CL)NT_create_ad_list_reorder, (AW_CL)&AWT_species_selector);
-    aws->insert_menu_topic("spec_delete_field",   "Delete/Hide fields ...", "D", "spaf_delete.hlp",  AWM_EXP, AW_POPUP, (AW_CL)NT_create_ad_field_delete, (AW_CL)&AWT_species_selector);
-    aws->insert_menu_topic("spec_create_field",   "Create fields ...",      "C", "spaf_create.hlp",  AWM_ALL, AW_POPUP, (AW_CL)NT_create_ad_field_create, (AW_CL)&AWT_species_selector);
-    aws->insert_menu_topic("spec_convert_field",  "Convert fields ...",     "t", "spaf_convert.hlp", AWM_EXP, AW_POPUP, (AW_CL)NT_create_ad_field_convert, (AW_CL)&AWT_species_selector);
-    aws->insert_separator();
-    aws->insert_menu_topic("spec_unhide_fields", "Show all hidden fields", "S", "scandb.hlp", AWM_ALL, (AW_CB)awt_selection_list_unhide_all_cb, (AW_CL)GLOBAL_gb_main, AWT_NDS_FILTER);
-    aws->insert_separator();
-    aws->insert_menu_topic("spec_scan_unknown_fields", "Scan unknown fields",   "u", "scandb.hlp", AWM_ALL, (AW_CB)awt_selection_list_scan_unknown_cb,  (AW_CL)GLOBAL_gb_main, AWT_NDS_FILTER);
-    aws->insert_menu_topic("spec_del_unused_fields",   "Forget unused fields",  "e", "scandb.hlp", AWM_ALL, (AW_CB)awt_selection_list_delete_unused_cb, (AW_CL)GLOBAL_gb_main, AWT_NDS_FILTER);
-    aws->insert_menu_topic("spec_refresh_fields",      "Refresh fields (both)", "f", "scandb.hlp", AWM_ALL, (AW_CB)awt_selection_list_update_cb,        (AW_CL)GLOBAL_gb_main, AWT_NDS_FILTER);
-}
-
-inline int get_and_fix_range_from_awar(AW_awar *awar) {
-    const char *input = awar->read_char_pntr();
-    int         bpos = atoi(input);
-    int         ipos;
-
-    if (bpos>0) {
-        awar->write_string(GBS_global_string("%i", bpos));
-        ipos = bio2info(bpos);
-    }
-    else {
-        ipos = -1;
-        awar->write_string("");
-    }
-    return ipos;
-}
-
-static TargetRange get_nn_range_from_awars(AW_root *aw_root) {
-    int start = get_and_fix_range_from_awar(aw_root->awar(AWAR_NN_RANGE_START));
-    int end   = get_and_fix_range_from_awar(aw_root->awar(AWAR_NN_RANGE_END));
-
-    return TargetRange(start, end);
-}
-
-inline char *read_sequence_region(GBDATA *gb_data, const TargetRange& range) {
-    return range.dup_corresponding_part(GB_read_char_pntr(gb_data), GB_read_count(gb_data));
-}
-
-static void awtc_nn_search_all_listed(AW_window *aww, AW_CL _cbs) {
-    DbQuery *cbs = (DbQuery *)_cbs;
-
-    nt_assert(cbs->selector->type == AWT_QUERY_ITEM_SPECIES);
-
-    GB_begin_transaction(GLOBAL_gb_main);
-
-    AW_root *aw_root    = aww->get_root();
-    char    *dest_field = aw_root->awar(AWAR_NN_DEST_FIELD)->read_string();
-
-    GB_ERROR error     = 0;
-    GB_TYPES dest_type = GBT_get_type_of_changekey(GLOBAL_gb_main, dest_field, CHANGE_KEY_PATH);
-    if (!dest_type) {
-        error = GB_export_error("Please select a valid field");
-    }
-
-    if (strcmp(dest_field, "name")==0) {
-        int answer = aw_question("CAUTION! This will destroy all name-fields of the listed species.\n",
-                                 "Continue and destroy all name-fields,Abort");
-
-        if (answer==1) {
-            error = GB_export_error("Aborted by user");
-        }
-    }
-
-    long         max = awt_count_queried_items(cbs, QUERY_ALL_ITEMS);
-    arb_progress progress("Searching next neighbours", max);
-    progress.auto_subtitles("Species");
-
-    int            pts            = aw_root->awar(AWAR_PROBE_ADMIN_PT_SERVER)->read_int();
-    char          *ali_name       = aw_root->awar(AWAR_DEFAULT_ALIGNMENT)->read_string();
-    int            oligo_len      = aw_root->awar(AWAR_NN_OLIGO_LEN)->read_int();
-    int            mismatches     = aw_root->awar(AWAR_NN_MISMATCHES)->read_int();
-    bool           fast_mode      = aw_root->awar(AWAR_NN_FAST_MODE)->read_int();
-    FF_complement  compl_mode     = static_cast<FF_complement>(aw_root->awar(AWAR_NN_COMPLEMENT)->read_int());
-    bool           rel_matches    = aw_root->awar(AWAR_NN_REL_MATCHES)->read_int();
-    int            wanted_entries = aw_root->awar(AWAR_NN_WANTED_ENTRIES)->read_int();
-    bool           scored_entries = aw_root->awar(AWAR_NN_SCORED_ENTRIES)->read_int();
-    int            min_score      = aw_root->awar(AWAR_NN_MIN_SCORE)->read_int();
-
-    TargetRange org_range = get_nn_range_from_awars(aw_root);
-
-    for (GBDATA *gb_species = GBT_first_species(GLOBAL_gb_main);
-         !error && gb_species;
-         gb_species = GBT_next_species(gb_species))
-    {
-        if (!IS_QUERIED(gb_species, cbs)) continue;
-
-        GBDATA *gb_data = GBT_read_sequence(gb_species, ali_name);
-        if (gb_data) {
-            TargetRange      range    = org_range; // modified by read_sequence_region
-            char            *sequence = read_sequence_region(gb_data, range);
-            PT_FamilyFinder  ff(GLOBAL_gb_main, pts, oligo_len, mismatches, fast_mode, rel_matches);
-
-            ff.restrict_2_region(range);
-
-            error = ff.searchFamily(sequence, compl_mode, wanted_entries);
-            if (!error) {
-                const FamilyList *fm = ff.getFamilyList();
-
-                GBS_strstruct *value = NULL;
-                while (fm) {
-                    const char *thisValue = 0;
-                    if (rel_matches) {
-                        if ((fm->rel_matches*100) > min_score) {
-                            thisValue = scored_entries
-                                ? GBS_global_string("%.1f%%:%s", fm->rel_matches*100, fm->name)
-                                : fm->name;
-                        }
-                    }
-                    else {
-                        if (fm->matches > min_score) {
-                            thisValue = scored_entries
-                                ? GBS_global_string("%li:%s", fm->matches, fm->name)
-                                : fm->name;
-                        }
-                    }
-
-                    if (thisValue) {
-                        if (value == NULL) { // first entry
-                            value = GBS_stropen(1000);
-                        }
-                        else {
-                            GBS_chrcat(value, ';');
-                        }
-                        GBS_strcat(value, thisValue);
-                    }
-
-                    fm = fm->next;
-                }
-
-                if (value) {
-                    GBDATA *gb_dest = GB_search(gb_species, dest_field, dest_type);
-
-                    error = GB_write_as_string(gb_dest, GBS_mempntr(value));
-                    GBS_strforget(value);
-                }
-                else {
-                    GBDATA *gb_dest = GB_search(gb_species, dest_field, GB_FIND);
-                    if (gb_dest) error = GB_delete(gb_dest);
-                }
-            }
-            free(sequence);
-        }
-        progress.inc_and_check_user_abort(error);
-    }
-    GB_end_transaction_show_error(GLOBAL_gb_main, error, aw_message);
-    free(dest_field);
-    free(ali_name);
-}
-
-static void awtc_nn_search(AW_window *aww, AW_CL id) {
-    AW_root     *aw_root  = aww->get_root();
-    GB_ERROR     error    = 0;
-    TargetRange  range    = get_nn_range_from_awars(aw_root);
-    char        *sequence = 0;
-    {
-        GB_transaction ta(GLOBAL_gb_main);
-
-        char   *sel_species = aw_root->awar(AWAR_SPECIES_NAME)->read_string();
-        GBDATA *gb_species  = GBT_find_species(GLOBAL_gb_main, sel_species);
-
-        if (!gb_species) {
-            error = "Select a species first";
-        }
-        else {
-            char   *ali_name = aw_root->awar(AWAR_DEFAULT_ALIGNMENT)->read_string();
-            GBDATA *gb_data  = GBT_read_sequence(gb_species, ali_name);
-
-            if (gb_data) {
-                sequence = read_sequence_region(gb_data, range);
-            }
-            else {
-                error = GBS_global_string("Species '%s' has no sequence '%s'", sel_species, ali_name);
-            }
-            free(ali_name);
-        }
-        free(sel_species);
-    }
-
-    int  pts         = aw_root->awar(AWAR_PROBE_ADMIN_PT_SERVER)->read_int();
-    int  oligo_len   = aw_root->awar(AWAR_NN_OLIGO_LEN)->read_int();
-    int  mismatches  = aw_root->awar(AWAR_NN_MISMATCHES)->read_int();
-    bool fast_mode   = aw_root->awar(AWAR_NN_FAST_MODE)->read_int();
-    bool rel_matches = aw_root->awar(AWAR_NN_REL_MATCHES)->read_int();
-
-
-    PT_FamilyFinder ff(GLOBAL_gb_main, pts, oligo_len, mismatches, fast_mode, rel_matches);
-
-    ff.restrict_2_region(range);
-
-    int max_hits = 0; // max wanted hits
-
-    if (!error) {
-        FF_complement compl_mode = static_cast<FF_complement>(aw_root->awar(AWAR_NN_COMPLEMENT)->read_int());
-        max_hits                 = aw_root->awar(AWAR_NN_MAX_HITS)->read_int();
-
-        error = ff.searchFamily(sequence, compl_mode, max_hits);
-    }
-
-    // update result list
-    {
-        AW_selection_list* sel = (AW_selection_list *)id;
-        aww->clear_selection_list(sel);
-
-        int hits = 0;
-        if (error) {
-            aw_message(error);
-            aww->insert_default_selection(sel, "<Error>", "");
-        }
-        else {
-            int count    = 1;
-            int numWidth = log(max_hits)/log(10)+1;
-
-            for (const FamilyList *fm = ff.getFamilyList(); fm; fm = fm->next) {
-                const char *dis;
-                if (rel_matches) {
-                    dis = GBS_global_string("#%0*i %-12s Rel.hits: %5.1f%%", numWidth, count, fm->name, fm->rel_matches*100);
-                }
-                else {
-                    dis = GBS_global_string("#%0*i %-12s Hits: %4li", numWidth, count, fm->name, fm->matches);
-                }
-
-                aww->insert_selection(sel, dis, fm->name);
-                count++;
-            }
-
-            aww->insert_default_selection(sel, ff.hits_were_truncated() ? "<List truncated>" : "<No more hits>", "");
-            hits = ff.getRealHits();
-        }
-        aw_root->awar(AWAR_NN_HIT_COUNT)->write_int(hits);
-        aww->update_selection_list(sel);
-    }
-
-    free(sequence);
-}
-
-static void awtc_move_hits(AW_window *aww, AW_CL id, AW_CL cbs) {
-    AW_root *aw_root         = aww->get_root();
-    char    *current_species = aw_root->awar(AWAR_SPECIES_NAME)->read_string();
-
-    if (!current_species) current_species = strdup("<unknown>");
-
-    char *hit_description = GBS_global_string_copy("<neighbour of %s: %%s>", current_species);
-
-    awt_copy_selection_list_2_queried_species((DbQuery *)cbs, (AW_selection_list *)id, hit_description);
-
-    free(hit_description);
-    free(current_species);
-}
-
-static void create_next_neighbours_vars(AW_root *aw_root) {
-    static bool created = false;
-
-    if (!created) {
-        aw_root->awar_int(AWAR_PROBE_ADMIN_PT_SERVER);
-        aw_root->awar_int(AWAR_NN_COMPLEMENT,  FF_FORWARD);
-
-        aw_root->awar_int(AWAR_NN_MAX_HITS,  50);
-        aw_root->awar_int(AWAR_NN_HIT_COUNT, 0);
-
-        aw_root->awar_string(AWAR_NN_DEST_FIELD, "tmp");
-        aw_root->awar_int(AWAR_NN_WANTED_ENTRIES, 5);
-        aw_root->awar_int(AWAR_NN_SCORED_ENTRIES, 1);
-        aw_root->awar_int(AWAR_NN_MIN_SCORE,      80);
-
-        aw_root->awar_string(AWAR_NN_RANGE_START, "");
-        aw_root->awar_string(AWAR_NN_RANGE_END,   "");
-
-        AWTC_create_common_next_neighbour_vars(aw_root);
-
-        created = true;
-    }
-}
-
-static void create_common_next_neighbour_fields(AW_window *aws) {
-    aws->at("pt_server");
-    awt_create_selection_list_on_pt_servers(aws, AWAR_PROBE_ADMIN_PT_SERVER, true);
-
-    AWTC_create_common_next_neighbour_fields(aws);
-
-    aws->auto_space(5, 5);
-    
-    aws->at("range");
-    aws->create_input_field(AWAR_NN_RANGE_START, 6);
-    aws->create_input_field(AWAR_NN_RANGE_END,   6);
-    
-    aws->at("compl");
-    aws->create_option_menu(AWAR_NN_COMPLEMENT, 0, 0);
-    aws->insert_default_option("forward",            "", FF_FORWARD);
-    aws->insert_option        ("reverse",            "", FF_REVERSE);
-    aws->insert_option        ("complement",         "", FF_COMPLEMENT);
-    aws->insert_option        ("reverse-complement", "", FF_REVERSE_COMPLEMENT);
-    aws->insert_option        ("fwd + rev-compl",    "", FF_FORWARD|FF_REVERSE_COMPLEMENT);
-    aws->insert_option        ("rev + compl",        "", FF_REVERSE|FF_COMPLEMENT);
-    aws->insert_option        ("any",                "", FF_FORWARD|FF_REVERSE|FF_COMPLEMENT|FF_REVERSE_COMPLEMENT);
-    aws->update_option_menu();
-}
-
-static AW_window *ad_spec_next_neighbours_listed_create(AW_root *aw_root, AW_CL cbs) {
-    static AW_window_simple *aws = 0;
-    if (!aws) {
-        create_next_neighbours_vars(aw_root);
-
-        aws = new AW_window_simple;
-        aws->init(aw_root, "SEARCH_NEXT_RELATIVES_OF_LISTED", "Search Next Neighbours of Listed");
-        aws->load_xfig("ad_spec_nnm.fig");
-
-        aws->at("close");
-        aws->callback((AW_CB0)AW_POPDOWN);
-        aws->create_button("CLOSE", "CLOSE", "C");
-
-        aws->at("help");
-        aws->callback(AW_POPUP_HELP, (AW_CL)"next_neighbours_listed.hlp");
-        aws->create_button("HELP", "HELP", "H");
-
-        create_common_next_neighbour_fields(aws);
-
-        aws->at("entries");
-        aws->create_input_field(AWAR_NN_WANTED_ENTRIES, 3);
-
-        aws->at("add_score");
-        aws->create_toggle(AWAR_NN_SCORED_ENTRIES);
-
-        aws->at("min_score");
-        aws->create_input_field(AWAR_NN_MIN_SCORE, 5);
-
-        aws->at("field");
-        awt_create_selection_list_on_itemfields(GLOBAL_gb_main, aws, AWAR_NN_DEST_FIELD,
-                                                (1<<GB_INT) | (1<<GB_STRING), "field", 0,
-                                                &AWT_species_selector, 20, 10);
-
-        aws->at("go");
-        aws->callback(awtc_nn_search_all_listed, cbs);
-        aws->create_button("WRITE_FIELDS", "Write to field");
-    }
-    return aws;
-}
-
-static AW_window *ad_spec_next_neighbours_create(AW_root *aw_root, AW_CL cbs) {
-    static AW_window_simple *aws = 0;
-    if (!aws) {
-        create_next_neighbours_vars(aw_root);
-
-        aws = new AW_window_simple;
-        aws->init(aw_root, "SEARCH_NEXT_RELATIVE_OF_SELECTED", "Search Next Neighbours");
-        aws->load_xfig("ad_spec_nn.fig");
-
-        aws->at("close");
-        aws->callback((AW_CB0)AW_POPDOWN);
-        aws->create_button("CLOSE", "CLOSE", "C");
-
-        aws->at("help");
-        aws->callback(AW_POPUP_HELP, (AW_CL)"next_neighbours.hlp");
-        aws->create_button("HELP", "HELP", "H");
-
-        create_common_next_neighbour_fields(aws);
-
-        aws->at("results");
-        aws->create_input_field(AWAR_NN_MAX_HITS, 3);
-
-        aws->at("hit_count");
-        aws->create_button(0, AWAR_NN_HIT_COUNT, 0, "+");
-
-        aws->at("hits");
-        AW_selection_list *id = aws->create_selection_list(AWAR_SPECIES_NAME);
-        aws->insert_default_selection(id, "No hits found", "");
-        aws->update_selection_list(id);
-
-        aws->at("go");
-        aws->callback(awtc_nn_search, (AW_CL)id);
-        aws->create_button("SEARCH", "SEARCH");
-
-        aws->at("move");
-        aws->callback(awtc_move_hits, (AW_CL)id, cbs);
-        aws->create_button("MOVE_TO_HITLIST", "MOVE TO HITLIST");
-
-    }
-    return aws;
-}
-
-// -----------------------------------------------------------------------------------------------------------------
-//      void NT_detach_information_window(AW_window *aww, AW_CL cl_pointer_to_aww, AW_CL cl_Awar_Callback_Info)
-// -----------------------------------------------------------------------------------------------------------------
-
-void NT_detach_information_window(AW_window *aww, AW_CL cl_pointer_to_aww, AW_CL cl_AW_detach_information) {
-    AW_window **aww_pointer = (AW_window**)cl_pointer_to_aww;
-
-    AW_detach_information *di           = (AW_detach_information*)cl_AW_detach_information;
-    Awar_Callback_Info    *cb_info      = di->get_cb_info();
-    AW_root               *awr          = cb_info->get_root();
-    char                  *curr_species = awr->awar(cb_info->get_org_awar_name())->read_string();
-
-    if (*aww_pointer == aww) {  // first click on detach-button
-        // create unique awar :
-        static int detach_counter = 0;
-        char       new_awar[100];
-        sprintf(new_awar, "tmp/DETACHED_INFO_%i", detach_counter++);
-        awr->awar_string(new_awar, "", AW_ROOT_DEFAULT);
-
-        cb_info->remap(new_awar); // remap the callback from old awar to new unique awar
-        aww->update_label(di->get_detach_button(), "GET");
-
-        *aww_pointer = 0;       // caller window will be recreated on next open after clearing this pointer
-        // [Note : the aww_pointer points to the static window pointer]
-    }
-
-    awr->awar(cb_info->get_awar_name())->write_string(curr_species);
-    aww->set_window_title(GBS_global_string("%s INFORMATION", curr_species));
-    free(curr_species);
-}
-
-static AW_window *create_speciesOrganismWindow(AW_root *aw_root, GBDATA *gb_main, bool organismWindow) {
-    int windowIdx = (int)organismWindow;
-
-    static AW_window_simple_menu *AWS[2] = { 0, 0 };
-    if (!AWS[windowIdx]) {
-        AW_window_simple_menu *& aws = AWS[windowIdx];
-
-        aws = new AW_window_simple_menu;
-        if (organismWindow) aws->init(aw_root, "ORGANISM_INFORMATION", "ORGANISM INFORMATION");
-        else                aws->init(aw_root, "SPECIES_INFORMATION", "SPECIES INFORMATION");
-        aws->load_xfig("ad_spec.fig");
-
-        aws->button_length(8);
-
-        aws->at("close");
-        aws->callback((AW_CB0)AW_POPDOWN);
-        aws->create_button("CLOSE", "CLOSE", "C");
-
-        aws->at("search");
-        aws->callback(AW_POPUP, (AW_CL)NTX_create_query_window, 0);
-        aws->create_button("SEARCH", "SEARCH", "S");
-
-        aws->at("help");
-        aws->callback(AW_POPUP_HELP, (AW_CL)"sp_info.hlp");
-        aws->create_button("HELP", "HELP", "H");
-
-        AW_CL scannerid = create_db_scanner(gb_main, aws, "box", 0, "field", "enable", DB_VIEWER, 0, "mark", AWT_NDS_FILTER,
-                                            organismWindow ? &AWT_organism_selector : &AWT_species_selector);
-        ad_global_scannerid = scannerid;
-        ad_global_scannerroot = aws->get_root();
-
-        if (organismWindow) aws->create_menu("ORGANISM",    "O", AWM_ALL);
-        else                aws->create_menu("SPECIES",     "S", AWM_ALL);
-
-        aws->insert_menu_topic("species_delete",        "Delete",         "D", "spa_delete.hlp",  AWM_ALL, ad_species_delete_cb,            0,                                   0);
-        aws->insert_menu_topic("species_rename",        "Rename",         "R", "spa_rename.hlp",  AWM_ALL, ad_species_rename_cb,            0,                                   0);
-        aws->insert_menu_topic("species_copy",          "Copy",           "y", "spa_copy.hlp",    AWM_ALL, ad_species_copy_cb,              0,                                   0);
-        aws->insert_menu_topic("species_create",        "Create",         "C", "spa_create.hlp",  AWM_ALL, AW_POPUP,                        (AW_CL)create_species_create_window, 0);
-        aws->insert_menu_topic("species_convert_2_sai", "Convert to SAI", "S", "sp_sp_2_ext.hlp", AWM_ALL, (AW_CB)move_species_to_extended, 0,                                   0);
-        aws->insert_separator();
-
-        aws->create_menu("FIELDS", "F", AWM_ALL);
-        NT_spec_create_field_items(aws);
-
-        {
-            const char         *awar_name = (bool)organismWindow ? AWAR_ORGANISM_NAME : AWAR_SPECIES_NAME;
-            AW_root            *awr       = aws->get_root();
-            Awar_Callback_Info *cb_info   = new Awar_Callback_Info(awr, awar_name, AD_map_species, (AW_CL)scannerid, (AW_CL)organismWindow); // do not delete!
-            cb_info->add_callback();
-
-            AW_detach_information *detach_info = new AW_detach_information(cb_info); // do not delete!
-
-            aws->at("detach");
-            aws->callback(NT_detach_information_window, (AW_CL)&aws, (AW_CL)detach_info);
-            aws->create_button("DETACH", "DETACH", "D");
-
-            detach_info->set_detach_button(aws->get_last_widget());
-        }
-
-        aws->show();
-        AD_map_species(aws->get_root(), scannerid, (AW_CL)organismWindow);
-    }
-    return AWS[windowIdx]; // already created (and not detached)
-}
-
-AW_window *NT_create_species_window(AW_root *aw_root, AW_CL cl_gb_main) {
-    return create_speciesOrganismWindow(aw_root, (GBDATA*)cl_gb_main, false);
-}
-AW_window *NTX_create_organism_window(AW_root *aw_root, AW_CL cl_gb_main) {
-    return create_speciesOrganismWindow(aw_root, (GBDATA*)cl_gb_main, true);
-}
-
-AW_CL ad_query_global_cbs = 0;
-
-void NT_unquery_all() {
-    awt_unquery_all(0, (DbQuery *)ad_query_global_cbs);
-}
-
-void NT_query_update_list() {
-    awt_query_update_list(NULL, (DbQuery *)ad_query_global_cbs);
-}
-
-AW_window *NTX_create_query_window(AW_root *aw_root)
-{
-    static AW_window_simple_menu *aws = 0;
-    if (aws) {
-        return (AW_window *)aws;
-    }
-    aws = new AW_window_simple_menu;
-    aws->init(aw_root, "SPECIES_QUERY", "SEARCH and QUERY");
-    aws->create_menu("More functions", "f");
-    aws->load_xfig("ad_query.fig");
-
-
-    awt_query_struct awtqs;
-
-    awtqs.gb_main             = GLOBAL_gb_main;
-    awtqs.species_name        = AWAR_SPECIES_NAME;
-    awtqs.tree_name           = AWAR_TREE;
-    awtqs.select_bit          = 1;
-    awtqs.use_menu            = 1;
-    awtqs.ere_pos_fig         = "ere2";
-    awtqs.by_pos_fig          = "by2";
-    awtqs.qbox_pos_fig        = "qbox";
-    awtqs.rescan_pos_fig      = 0;
-    awtqs.key_pos_fig         = 0;
-    awtqs.query_pos_fig       = "content";
-    awtqs.result_pos_fig      = "result";
-    awtqs.count_pos_fig       = "count";
-    awtqs.do_query_pos_fig    = "doquery";
-    awtqs.config_pos_fig      = "doconfig";
-    awtqs.do_mark_pos_fig     = "domark";
-    awtqs.do_unmark_pos_fig   = "dounmark";
-    awtqs.do_delete_pos_fig   = "dodelete";
-    awtqs.do_set_pos_fig      = "doset";
-    awtqs.do_refresh_pos_fig  = "dorefresh";
-    awtqs.open_parser_pos_fig = "openparser";
-    awtqs.create_view_window  = NT_create_species_window;
-    awtqs.selector            = &AWT_species_selector;
-
-    AW_CL cbs           = (AW_CL)awt_create_query_box(aws, &awtqs, "spec");
-    ad_query_global_cbs = cbs;
-
-    aws->create_menu("More search",     "s");
-    aws->insert_menu_topic("spec_search_equal_fields_within_db", "Search For Equal Fields and Mark Duplicates",                "E", "search_duplicates.hlp", AWM_ALL, (AW_CB)awt_search_equal_entries, cbs,                                          0);
-    aws->insert_menu_topic("spec_search_equal_words_within_db",  "Search For Equal Words Between Fields and Mark Duplicates",  "W", "search_duplicates.hlp", AWM_ALL, (AW_CB)awt_search_equal_entries, cbs,                                          1);
-    aws->insert_menu_topic("spec_search_next_relativ_of_sel",    "Search Next Relatives of SELECTED Species in PT_Server ...", "R", 0,                       AWM_ALL, (AW_CB)AW_POPUP,                 (AW_CL)ad_spec_next_neighbours_create,        cbs);
-    aws->insert_menu_topic("spec_search_next_relativ_of_listed", "Search Next Relatives of LISTED Species in PT_Server ...",   "L", 0,                       AWM_ALL, (AW_CB)AW_POPUP,                 (AW_CL)ad_spec_next_neighbours_listed_create, cbs);
-
-    aws->button_length(7);
-
-    aws->at("close");
-    aws->callback((AW_CB0)AW_POPDOWN);
-    aws->create_button("CLOSE", "CLOSE", "C");
-
-    aws->at("help");
-    aws->callback(AW_POPUP_HELP, (AW_CL)"sp_search.hlp");
-    aws->create_button("HELP", "HELP", "H");
-
-    return (AW_window *)aws;
-}
 
 // --------------------------------------------------------------------------------

trunk/NTREE/map_viewer.hxx

@@ -17 +17 @@
 #endif
 
-void MapViewer_set_default_root(AW_root *aw_root);
 void launch_MapViewer_cb(GBDATA *gbd, enum AD_MAP_VIEWER_TYPE type);
 

trunk/NTREE/needs_libs

@@ -2 +2 @@
 
 ARB_GDE/ARB_GDE.a
-AWTC/AWTC.a
 AWTI/AWTI.a
 MERGE/MERGE.a
@@ -11 +10 @@
 SL/TREE_READ/TREE_READ.a
 SL/TREE_WRITE/TREE_WRITE.a
+SL/REFENTRIES/REFENTRIES.a
 STAT/STAT.a
 

trunk/NTREE/nt_cb.hxx

@@ -28 +28 @@
 void NT_select_last_tree(AW_window *aww, char *awar_tree);
 AW_window *NT_open_select_alignment_window(AW_root *awr);
-void NT_system_cb(AW_window *aww, AW_CL command, AW_CL auto_help_file);
+void NT_system_cb(AW_window *aww, AW_CL cl_command, AW_CL cl_auto_help_file);
 
 /* NT_extern.cxx */

trunk/NTREE/nt_internal.h

@@ -28 +28 @@
 void NT_select_last_tree(AW_window *aww, char *awar_tree);
 AW_window *NT_open_select_alignment_window(AW_root *awr);
-void NT_system_cb(AW_window *aww, AW_CL command, AW_CL auto_help_file);
+void NT_system_cb(AW_window *aww, AW_CL cl_command, AW_CL cl_auto_help_file);
 
 /* AP_consensus.cxx */
@@ -126 +126 @@
 
 /* ad_spec.cxx */
-void NT_create_species_var(AW_root *aw_root, AW_default aw_def);
 void NT_count_different_chars(AW_window *, AW_CL cl_gb_main, AW_CL dummy_1x);
 void NT_create_sai_from_pfold(AW_window *aww, AW_CL ntw, AW_CL dummy_1x);
-AW_window *NT_create_ad_list_reorder(AW_root *root, AW_CL cl_item_selector);
-AW_window *NT_create_ad_field_delete(AW_root *root, AW_CL cl_item_selector);
-AW_window *NT_create_ad_field_create(AW_root *root, AW_CL cl_item_selector);
-AW_window *NT_create_ad_field_convert(AW_root *root, AW_CL cl_item_selector);
-void NT_spec_create_field_items(AW_window *aws);
-void NT_detach_information_window(AW_window *aww, AW_CL cl_pointer_to_aww, AW_CL cl_AW_detach_information);
-AW_window *NT_create_species_window(AW_root *aw_root, AW_CL cl_gb_main);
-void NT_unquery_all(void);
-void NT_query_update_list(void);
 
 /* ad_transpro.cxx */

trunk/PARSIMONY/GA_window.cxx

@@ -11 +11 @@
 #include <aw_window.hxx>
 #include <aw_display.hxx>
-#include <awt.hxx>
-// #include <malloc.h>
 #include "AP_buffer.hxx"
 #include "ap_main.hxx"

trunk/PARSIMONY/Makefile

@@ -259 +259 @@
 PARS_main.o: $(ARBHOME)/INCLUDE/awt_canvas.hxx
 PARS_main.o: $(ARBHOME)/INCLUDE/awt_filter.hxx
-PARS_main.o: $(ARBHOME)/INCLUDE/awt_nds.hxx
 PARS_main.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx
 PARS_main.o: $(ARBHOME)/INCLUDE/cb.h
@@ -266 +265 @@
 PARS_main.o: $(ARBHOME)/INCLUDE/dupstr.h
 PARS_main.o: $(ARBHOME)/INCLUDE/gui_aliview.hxx
+PARS_main.o: $(ARBHOME)/INCLUDE/nds.h
 PARS_main.o: $(ARBHOME)/INCLUDE/smartptr.h
 PARS_main.o: $(ARBHOME)/INCLUDE/test_global.h

trunk/PARSIMONY/PARS_main.cxx

@@ -20 +20 @@
 #include <awt.hxx>
 #include <ColumnStat.hxx>
-#include <awt_nds.hxx>
+#include <nds.h>
 #include <awt_sel_boxes.hxx>
 #include <awt_filter.hxx>

trunk/PROBE_DESIGN/Makefile

@@ -123 +123 @@
 SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/aw_root.hxx
 SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/aw_window.hxx
-SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/awt.hxx
 SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/awt_canvas.hxx
 SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/awt_config_manager.hxx
-SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/awt_nds.hxx
 SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx
 SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/cb.h
 SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/dupstr.h
+SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/items.h
+SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/nds.h
 SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/smartptr.h
 SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/test_global.h

trunk/PROBE_DESIGN/SaiProbeVisualization.cxx

@@ -12 +12 @@
 #include "probe_match_parser.hxx"
 
-#include <awt.hxx>
-#include <awt_nds.hxx>
+#include <nds.h>
+#include <items.h>
 #include <awt_sel_boxes.hxx>
 #include <awt_config_manager.hxx>

trunk/SECEDIT/Makefile

@@ -268 +268 @@
 SEC_main.o: $(ARBHOME)/INCLUDE/aw_root.hxx
 SEC_main.o: $(ARBHOME)/INCLUDE/aw_window.hxx
-SEC_main.o: $(ARBHOME)/INCLUDE/awt.hxx
 SEC_main.o: $(ARBHOME)/INCLUDE/awt_canvas.hxx
 SEC_main.o: $(ARBHOME)/INCLUDE/BI_basepos.hxx

trunk/SECEDIT/SEC_main.cxx

@@ -16 +16 @@
 
 #include <FileBuffer.h>
-
-#include <awt.hxx>
 
 #include <aw_awars.hxx>

trunk/SEQ_QUALITY/Makefile

@@ -72 +72 @@
 SQ_functions.o: $(ARBHOME)/INCLUDE/aw_preset.hxx
 SQ_functions.o: $(ARBHOME)/INCLUDE/aw_window.hxx
-SQ_functions.o: $(ARBHOME)/INCLUDE/awt.hxx
 SQ_functions.o: $(ARBHOME)/INCLUDE/BI_helix.hxx
 SQ_functions.o: $(ARBHOME)/INCLUDE/downcast.h
@@ -109 +108 @@
 SQ_main.o: $(ARBHOME)/INCLUDE/aw_root.hxx
 SQ_main.o: $(ARBHOME)/INCLUDE/aw_window.hxx
-SQ_main.o: $(ARBHOME)/INCLUDE/awt.hxx
 SQ_main.o: $(ARBHOME)/INCLUDE/awt_filter.hxx
 SQ_main.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx

trunk/SEQ_QUALITY/SQ_functions.cxx

@@ -20 +20 @@
 #include <aw_preset.hxx>
 #include <arb_progress.h>
-#include <awt.hxx>
 #include <arbdbt.h>
 

trunk/SEQ_QUALITY/SQ_main.cxx

@@ -16 +16 @@
 #include "SQ_functions.h"
 
-#include <awt.hxx>
 #include <awt_filter.hxx>
 #include <awt_sel_boxes.hxx>
+
+#include <aw_window.hxx>
 #include <aw_awars.hxx>
 #include <aw_msg.hxx>
+#include <aw_root.hxx>
+
 #include <arb_progress.h>
-#include <aw_root.hxx>
 #include <arbdbt.h>
 
@@ -122 +124 @@
 
         // Load and use Sequence-Filter
-        AP_filter *filter = awt_get_filter(aw_root, (adfiltercbstruct*)res_from_awt_create_select_filter);
+        AP_filter *filter = awt_get_filter((adfiltercbstruct*)res_from_awt_create_select_filter);
 
         /*

trunk/SL/AW_NAME/AW_names_admin.cxx

@@ -11 +11 @@
 #include "AW_rename.hxx"
 
-#include <awt.hxx>
+#include <aw_window.hxx>
 #include <aw_advice.hxx>
 #include <aw_edit.hxx>

trunk/SL/AW_NAME/Makefile

@@ -60 +60 @@
 AW_names_admin.o: $(ARBHOME)/INCLUDE/aw_root.hxx
 AW_names_admin.o: $(ARBHOME)/INCLUDE/aw_window.hxx
-AW_names_admin.o: $(ARBHOME)/INCLUDE/awt.hxx
 AW_names_admin.o: $(ARBHOME)/INCLUDE/cb.h
 AW_names_admin.o: $(ARBHOME)/INCLUDE/dupstr.h

trunk/SL/DB_SCANNER/Makefile

@@ -1 +1 @@
 # INCLUDE und GLOBALS MAIN CC cflags werden von aussen uebergeben
 
-.SUFFIXES: .o .c .cxx .depend
+.SUFFIXES: .o .cxx .depend
 
-C_OBJECTS = 
-CPP_OBJECTS = db_scanner.o 
-OBJECTS=$(C_OBJECTS) $(CPP_OBJECTS)
+OBJECTS=$(subst .cxx,.o,$(wildcard *.cxx))
 
 $(MAIN): $(OBJECTS)
@@ -12 +10 @@
 .cxx.o:
         $(CPP) $(cflags) -c $< $(CPPINCLUDES) $(POST_COMPILE)
-
-.c.o:
-        $(ACC) $(cflags) -c $< $(AINCLUDES) $(POST_COMPILE)
 
 clean:
@@ -61 +56 @@
 db_scanner.o: $(ARBHOME)/INCLUDE/aw_select.hxx
 db_scanner.o: $(ARBHOME)/INCLUDE/aw_window.hxx
-db_scanner.o: $(ARBHOME)/INCLUDE/awt.hxx
 db_scanner.o: $(ARBHOME)/INCLUDE/cb.h
 db_scanner.o: $(ARBHOME)/INCLUDE/dupstr.h
+db_scanner.o: $(ARBHOME)/INCLUDE/items.h
 db_scanner.o: $(ARBHOME)/INCLUDE/smartptr.h
 db_scanner.o: $(ARBHOME)/INCLUDE/test_global.h

trunk/SL/DB_SCANNER/db_scanner.cxx

@@ -10 +10 @@
 
 #include <db_scanner.hxx>
+#include <items.h>
 
 #include <AW_rename.hxx>
-
-#include <awt.hxx>
 
 #include <aw_awars.hxx>
@@ -560 +559 @@
 /*!********** Unmap edit field if 'key_data' has been changed (maybe entries deleted)
  *********/
-static void scanner_changed_cb2(GBDATA *dummy, db_scanner_data *cbs, GB_CB_TYPE gbtype)
-{
+static void scanner_changed_cb2(GBDATA *dummy, db_scanner_data *cbs, GB_CB_TYPE gbtype) {
     cbs->aws->get_root()->awar(cbs->awarname_current_item)->write_pointer(NULL);
     // unmap edit field
@@ -567 +565 @@
 }
 
-void map_db_scanner(AW_CL arbdb_scanid, GBDATA *gb_pntr, const char *key_path)
-{
+void map_db_scanner(AW_CL arbdb_scanid, GBDATA *gb_pntr, const char *key_path) {
     db_scanner_data *cbs = (db_scanner_data *)arbdb_scanid;
     GB_push_transaction(cbs->gb_main);
@@ -595 +592 @@
     GB_pop_transaction(cbs->gb_main);
 }
+
+GBDATA *get_db_scanner_main(AW_CL arbdb_scanid) {
+    db_scanner_data *cbs = (db_scanner_data *)arbdb_scanid;
+    return cbs->gb_main;
+}
+

trunk/SL/DB_SCANNER/db_scanner.hxx

@@ -64 +64 @@
 void map_db_scanner(AW_CL arbdb_scanid, GBDATA *gb_pntr, const char *key_path);
 
+
+GBDATA *get_db_scanner_main(AW_CL arbdb_scanid);
+
 #else
 #error db_scanner.hxx included twice

trunk/SL/DB_SCANNER/needs_libs

@@ -2 +2 @@
 
 SL/AW_NAME/AW_NAME.a
+SL/ITEMS/ITEMS.a

trunk/SL/GUI_ALIVIEW/AWT_filter.cxx

@@ -1 @@
-#include "awt.hxx"
 #include "awt_filter.hxx"
 #include "awt_sel_boxes.hxx"
-
+#include "ga_local.h"
+
+#include <aw_window.hxx>
 #include <aw_awars.hxx>
 #include <aw_root.hxx>
@@ -203 +204 @@
         int len = strlen(def_name);
 
-        awt_assert(len >= 5);
-        awt_assert(strcmp(def_name+len-5, "/name") == 0); // filter awar has to be "SOMETHING/name"
+        ga_assert(len >= 5);
+        ga_assert(strcmp(def_name+len-5, "/name") == 0); // filter awar has to be "SOMETHING/name"
     }
 #endif                          // DEBUG
@@ -390 +391 @@
 }
 
-AP_filter *awt_get_filter(AW_root *aw_root, adfiltercbstruct *acbs) {
+AP_filter *awt_get_filter(adfiltercbstruct *acbs) {
     AP_filter *filter = NULL;
 
     if (acbs) {
-        awt_assert(aw_root == acbs->awr);               // @@@ if this doesnt fail, remove aw_root from params
-        
         GB_push_transaction(acbs->gb_main);
 
-        char *filter_string = aw_root->awar(acbs->def_filter)->read_string();
+        char *filter_string = acbs->awr->awar(acbs->def_filter)->read_string();
         long  len           = 0;
 
         {
-            char *use = aw_root->awar(acbs->def_alignment)->read_string();
+            char *use = acbs->awr->awar(acbs->def_alignment)->read_string();
 
             len = GBT_get_alignment_len(acbs->gb_main, use);
@@ -410 +409 @@
         if (len != -1) { // have alignment
             filter  = new AP_filter(filter_string, "0", len);
-            int sim = aw_root->awar(acbs->def_simplify)->read_int();
+            int sim = acbs->awr->awar(acbs->def_simplify)->read_int();
             filter->enable_simplify((AWT_FILTER_SIMPLIFY)sim);
             free(filter_string);

trunk/SL/GUI_ALIVIEW/ColumnStat.cxx

@@ -11 +11 @@
 #include "ColumnStat.hxx"
 #include "awt_sel_boxes.hxx"
+#include "ga_local.h"
 
 #include <AP_filter.hxx>
@@ -26 +27 @@
 #define AWAR_COLSTAT_ENABLE_HELIX "/name=/enable_helix"
 
-#define cs_assert(cond) arb_assert(cond)
-
 void ColumnStat::refresh_selection_list() {
     GB_transaction ta(gb_main);
@@ -61 +60 @@
     awar_enable_helix = GBS_string_eval(awar_template, AWAR_COLSTAT_ENABLE_HELIX, 0);
 
-    cs_assert(strcmp(awar_name, awar_alignment) != 0); // awar_template must end with (or contain) "/name"
+    ga_assert(strcmp(awar_name, awar_alignment) != 0); // awar_template must end with (or contain) "/name"
 
     awr->awar_string(awar_name, "NONE");

trunk/SL/GUI_ALIVIEW/GUI_aliview.cxx

@@ -32 +32 @@
 
 AP_filter *WeightedFilter::create_filter() const {
-    return awt_get_filter(adfilter->awr, adfilter);
+    return awt_get_filter(adfilter);
 }
 

trunk/SL/GUI_ALIVIEW/Makefile

@@ -41 +41 @@
 
 AWT_filter.o: awt_filter.hxx
+AWT_filter.o: ga_local.h
 AWT_filter.o: $(ARBHOME)/INCLUDE/ad_prot.h
 AWT_filter.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
@@ -61 +62 @@
 AWT_filter.o: $(ARBHOME)/INCLUDE/aw_root.hxx
 AWT_filter.o: $(ARBHOME)/INCLUDE/aw_window.hxx
-AWT_filter.o: $(ARBHOME)/INCLUDE/awt.hxx
 AWT_filter.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx
 AWT_filter.o: $(ARBHOME)/INCLUDE/cb.h
@@ -69 +69 @@
 
 ColumnStat.o: ColumnStat.hxx
+ColumnStat.o: ga_local.h
 ColumnStat.o: $(ARBHOME)/INCLUDE/ad_prot.h
 ColumnStat.o: $(ARBHOME)/INCLUDE/ad_t_prot.h

trunk/SL/GUI_ALIVIEW/awt_filter.hxx

@@ -53 +53 @@
 AW_window *awt_create_select_filter_win(AW_root *aw_root, AW_CL cd_adfiltercbstruct);
 
-AP_filter *awt_get_filter(AW_root *aw_root, adfiltercbstruct *acbs);
+AP_filter *awt_get_filter(adfiltercbstruct *acbs);
 void awt_destroy_filter(AP_filter *filter);
 

trunk/SL/Makefile

@@ -6 +6 @@
         AW_HELIX/AW_HELIX.dummy  \
         AW_NAME/AW_NAME.dummy  \
+        DB_QUERY/DB_QUERY.dummy  \
         DB_SCANNER/DB_SCANNER.dummy  \
+        DB_UI/DB_UI.dummy  \
         SEQIO/SEQIO.dummy  \
         FAST_ALIGNER/FAST_ALIGNER.dummy  \
@@ -13 +15 @@
         GUI_ALIVIEW/GUI_ALIVIEW.dummy  \
         HELIX/HELIX.dummy  \
+        ITEMS/ITEMS.dummy  \
         MATRIX/MATRIX.dummy  \
+        NDS/NDS.dummy  \
         NEIGHBOURJOIN/NEIGHBOURJOIN.dummy  \
         PRONUC/PRONUC.dummy  \

trunk/SL/TREEDISP/Makefile

@@ -70 +70 @@
 irstree_display.o: $(ARBHOME)/INCLUDE/aw_window.hxx
 irstree_display.o: $(ARBHOME)/INCLUDE/awt_canvas.hxx
-irstree_display.o: $(ARBHOME)/INCLUDE/awt_nds.hxx
 irstree_display.o: $(ARBHOME)/INCLUDE/cb.h
 irstree_display.o: $(ARBHOME)/INCLUDE/downcast.h
 irstree_display.o: $(ARBHOME)/INCLUDE/dupstr.h
+irstree_display.o: $(ARBHOME)/INCLUDE/nds.h
 irstree_display.o: $(ARBHOME)/INCLUDE/smartptr.h
 irstree_display.o: $(ARBHOME)/INCLUDE/test_global.h
@@ -106 +106 @@
 TreeCallbacks.o: $(ARBHOME)/INCLUDE/aw_root.hxx
 TreeCallbacks.o: $(ARBHOME)/INCLUDE/aw_window.hxx
-TreeCallbacks.o: $(ARBHOME)/INCLUDE/awt.hxx
 TreeCallbacks.o: $(ARBHOME)/INCLUDE/awt_canvas.hxx
 TreeCallbacks.o: $(ARBHOME)/INCLUDE/cb.h
@@ -145 +144 @@
 TreeDisplay.o: $(ARBHOME)/INCLUDE/aw_root.hxx
 TreeDisplay.o: $(ARBHOME)/INCLUDE/aw_window.hxx
-TreeDisplay.o: $(ARBHOME)/INCLUDE/awt.hxx
 TreeDisplay.o: $(ARBHOME)/INCLUDE/awt_attributes.hxx
 TreeDisplay.o: $(ARBHOME)/INCLUDE/awt_canvas.hxx
-TreeDisplay.o: $(ARBHOME)/INCLUDE/awt_nds.hxx
 TreeDisplay.o: $(ARBHOME)/INCLUDE/cb.h
 TreeDisplay.o: $(ARBHOME)/INCLUDE/downcast.h
 TreeDisplay.o: $(ARBHOME)/INCLUDE/dupstr.h
+TreeDisplay.o: $(ARBHOME)/INCLUDE/nds.h
 TreeDisplay.o: $(ARBHOME)/INCLUDE/smartptr.h
 TreeDisplay.o: $(ARBHOME)/INCLUDE/test_global.h

trunk/SL/TREEDISP/TreeCallbacks.cxx

@@ -15 +15 @@
 #include <aw_msg.hxx>
 #include <aw_root.hxx>
-#include <awt.hxx>
 
 #include <cctype>
@@ -89 +88 @@
     }
 
-    awt_assert(strlen(text) < AWAR_FOOTER_MAX_LEN); // text too long!
+    td_assert(strlen(text) < AWAR_FOOTER_MAX_LEN); // text too long!
 
     ntw->awr->awar(AWAR_FOOTER)->write_string(text);
@@ -124 +123 @@
 static int nt_sequence_is_partial(GBDATA *gb_species, void *cd_partial) {
     long wanted  = (long)cd_partial;
-    awt_assert(wanted == 0 || wanted == 1);
+    td_assert(wanted == 0 || wanted == 1);
     int partial = GBT_is_partial(gb_species, 1-wanted, 0);
 
@@ -169 +168 @@
         }
         default:
-            awt_assert(0); // illegal mode
+            td_assert(0); // illegal mode
             break;
     }
@@ -203 +202 @@
         }
         default:
-            awt_assert(0); // illegal mode
+            td_assert(0); // illegal mode
             break;
     }
@@ -235 +234 @@
                 break;
             default:
-                awt_assert(0); // illegal mode
+                td_assert(0); // illegal mode
                 break;
         }
@@ -278 +277 @@
 
     int color_group = mark_mode>>4;
-    awt_assert(mark_mode&(4|8)); // either 4 or 8 has to be set
+    td_assert(mark_mode&(4|8)); // either 4 or 8 has to be set
     bool mark_matching = (mark_mode&4) == 4;
     mark_mode    = mark_mode&3;
@@ -290 +289 @@
                 case 1: GB_write_flag(gb_species, 1); break;
                 case 2: GB_write_flag(gb_species, !GB_read_flag(gb_species)); break;
-                default: awt_assert(0); break;
+                default: td_assert(0); break;
             }
         }
@@ -314 +313 @@
         case 1: label_base = "all_mark_color"; break;
         case 2: label_base = "all_invert_mark_color"; break;
-        default: awt_assert(0); break;
+        default: td_assert(0); break;
     }
 
@@ -401 +400 @@
 static void nt_insert_mark_topics(AW_window_menu_modes *awm, AW_active mask, AWT_canvas *ntw, int affect, const char *attrib)
 {
-    awt_assert(affect == (affect&MARK_MODE_UPPER_BITS)); // only bits 2 .. 4 are allowed
+    td_assert(affect == (affect&MARK_MODE_UPPER_BITS)); // only bits 2 .. 4 are allowed
 
     nt_insert_mark_topic(awm, mask, attrib, "mark_all",            "Mark all %sSpecies%s",                    "M", "sp_mrk_all.hlp",    (AW_CB)NT_mark_all_cb,     (AW_CL)ntw, (AW_CL)(1+affect));
@@ -493 +492 @@
 #define MAXENTRY (AW_COLOR_GROUP_NAME_LEN+10)
 
-    awt_assert(ntree_canvas != 0);
+    td_assert(ntree_canvas != 0);
 
     awm->insert_sub_menu("Group all except Color ...", "C");
@@ -755 +754 @@
                 break;
             }
-            default: awt_assert(0); break;
+            default: td_assert(0); break;
         }
     }
@@ -797 +796 @@
             }
             else {
-                awt_assert(zombies);
+                td_assert(zombies);
                 msg = GBS_global_string("%i zombie%s", zombies, plural(zombies));
             }
@@ -813 +812 @@
 void NT_recompute_cb(AW_window *, AWT_canvas *ntw, AW_CL cl2) {
     AWT_graphic_tree *gt = dynamic_cast<AWT_graphic_tree*>(ntw->tree_disp);
-    awt_assert(gt);
+    td_assert(gt);
 
     gt->get_root_node()->compute_tree(ntw->gb_main);

trunk/SL/TREEDISP/TreeDisplay.cxx

@@ -11 +11 @@
 #include "TreeDisplay.hxx"
 
-#include <awt.hxx>
-#include <awt_nds.hxx>
+#include <nds.h>
 #include <aw_preset.hxx>
 #include <aw_awars.hxx>
@@ -115 +114 @@
                 case 1: GB_write_flag(at->gb_node, 1); break;
                 case 2: GB_write_flag(at->gb_node, !GB_read_flag(at->gb_node)); break;
-                default: awt_assert(0);
+                default: td_assert(0);
             }
         }
@@ -146 +145 @@
                     case 1: GB_write_flag(at->gb_node, 1); break;
                     case 2: GB_write_flag(at->gb_node, !oldMark); break;
-                    default: awt_assert(0);
+                    default: td_assert(0);
                 }
             }
@@ -430 +429 @@
 
     resort_tree(lmode, at->get_leftson());
-    awt_assert(leafname);
+    td_assert(leafname);
     const char *leftleafname = leafname;
 
     resort_tree(rmode, at->get_rightson());
-    awt_assert(leafname);
+    td_assert(leafname);
     const char *rightleafname = leafname;
 
-    awt_assert(leftleafname && rightleafname);
+    td_assert(leftleafname && rightleafname);
 
     if (leftleafname && rightleafname) {
@@ -583 +582 @@
             break;
         default:
-            awt_assert(0);
+            td_assert(0);
     }
 
@@ -749 +748 @@
             }
             else {
-                awt_assert(0);
+                td_assert(0);
             }
 
@@ -850 +849 @@
                         while (root_node->father) root_node = root_node->get_father(); // search father
 
-                        awt_assert(root_node);
+                        td_assert(root_node);
 
                         AWT_graphic_tree_group_state state;
@@ -1706 +1705 @@
     tree_static = new AP_tree_root(aliview, tree_prototype, seq_prototype, insert_delete_cbs);
 
-    awt_assert(!insert_delete_cbs || link_to_database); // inserting delete callbacks w/o linking to DB has no effect!
+    td_assert(!insert_delete_cbs || link_to_database); // inserting delete callbacks w/o linking to DB has no effect!
     link_to_database = link_to_database_;
 }
@@ -1879 +1878 @@
 
     if (show) {
-        awt_assert(text != 0);
+        td_assert(text != 0);
         device->text(AWT_GC_BRANCH_REMARK, text, pos, alignment, filteri);
     }
@@ -2283 +2282 @@
         case AP_LIST_NDS:
             // rulers not allowed in these display modes
-            awt_assert(0);
+            td_assert(0);
             tree_awar = 0;
             break;
@@ -2399 +2398 @@
     size_t get_part_count() const { return part_count; }
     const Column& get_column(size_t p) const {
-        awt_assert(p<part_count);
+        td_assert(p<part_count);
         return column[p];
     }
@@ -2489 +2488 @@
     }
 
-    awt_assert(species_count <= displayed_rows);
+    td_assert(species_count <= displayed_rows);
 
     // calculate column offsets and detect column alignment
@@ -2709 +2708 @@
 class fake_AW_GC : public AW_GC {
     virtual void wm_set_foreground_color(AW_rgb /*col*/) {  }
-    virtual void wm_set_function(AW_function /*mode*/) { awt_assert(0); }
+    virtual void wm_set_function(AW_function /*mode*/) { td_assert(0); }
     virtual void wm_set_lineattributes(short /*lwidth*/, AW_linestyle /*lstyle*/) {}
     virtual void wm_set_font(AW_font /*font_nr*/, int size, int */*found_size*/) {
@@ -2720 +2719 @@
     fake_AW_GC(AW_common *common_) : AW_GC(common_) {}
     virtual int get_available_fontsizes(AW_font /*font_nr*/, int */*available_sizes*/) const {
-        awt_assert(0);
+        td_assert(0);
         return 0;
     }
@@ -2785 +2784 @@
         Rectangle drawn = size_device.get_size_information();
 
-        awt_assert(drawn.surface() >= 0.0);
+        td_assert(drawn.surface() >= 0.0);
 
         double zoomx = SCREENSIZE/drawn.width();

trunk/SL/TREEDISP/TreeDisplay.hxx

@@ -18 +18 @@
 #include <awt_canvas.hxx>
 #endif
+
+#define td_assert(cond) arb_assert(cond)
 
 #define AWAR_DTREE_BASELINEWIDTH   "awt/dtree/baselinewidth"

trunk/SL/TREEDISP/irstree_display.cxx

@@ -11 +11 @@
 #include "TreeDisplay.hxx"
 
-#include <awt_nds.hxx>
+#include <nds.h>
 #include <aw_awars.hxx>
 

trunk/SL/TREEDISP/needs_libs

@@ -2 +2 @@
 
 SL/AP_TREE/AP_TREE.a
+SL/NDS/NDS.a

trunk/SL/TREE_WRITE/Makefile

@@ -51 +51 @@
 TreeWrite.o: $(ARBHOME)/INCLUDE/attributes.h
 TreeWrite.o: $(ARBHOME)/INCLUDE/aw_base.hxx
-TreeWrite.o: $(ARBHOME)/INCLUDE/awt_nds.hxx
 TreeWrite.o: $(ARBHOME)/INCLUDE/dupstr.h
+TreeWrite.o: $(ARBHOME)/INCLUDE/nds.h
 TreeWrite.o: $(ARBHOME)/INCLUDE/smartptr.h
 TreeWrite.o: $(ARBHOME)/INCLUDE/test_global.h

trunk/SL/TREE_WRITE/TreeWrite.h

@@ -15 +15 @@
 #include <arbdb_base.h>
 #endif
-#ifndef AWT_NDS_HXX
-#include <awt_nds.hxx>
+#ifndef NDS_H
+#include <nds.h>
 #endif
 

trunk/SOURCE_TOOLS/generate_all_links.sh

@@ -216 +216 @@
 symlink_file ../AWT/awt_hotkeys.hxx INCLUDE/awt_hotkeys.hxx &&
 symlink_file ../AWT/awt_input_mask.hxx INCLUDE/awt_input_mask.hxx &&
-symlink_file ../AWT/awt_item_sel_list.hxx INCLUDE/awt_item_sel_list.hxx &&
 symlink_file ../AWT/awt_macro.hxx INCLUDE/awt_macro.hxx &&
 symlink_file ../AWT/awt_map_key.hxx INCLUDE/awt_map_key.hxx &&
-symlink_file ../AWT/awt_nds.hxx INCLUDE/awt_nds.hxx &&
 symlink_file ../AWT/awt_sel_boxes.hxx INCLUDE/awt_sel_boxes.hxx &&
 symlink_file ../AWT/awt_seq_colors.hxx INCLUDE/awt_seq_colors.hxx &&
 symlink_file ../AWT/awt_www.hxx INCLUDE/awt_www.hxx &&
 symlink_file ../AWT/awtlocal.hxx INCLUDE/awtlocal.hxx &&
-symlink_file ../AWT/refentries.h INCLUDE/refentries.h &&
 symlink_file ../AWTC/awtc_next_neighbours.hxx INCLUDE/awtc_next_neighbours.hxx &&
 symlink_file ../AWTC/awtc_submission.hxx INCLUDE/awtc_submission.hxx &&
@@ -263 +260 @@
 symlink_file ../SL/AW_NAME/AW_rename.hxx INCLUDE/AW_rename.hxx &&
 symlink_file ../SL/DB_SCANNER/db_scanner.hxx INCLUDE/db_scanner.hxx &&
+symlink_file ../SL/DB_QUERY/db_query.h INCLUDE/db_query.h &&
+symlink_file ../SL/DB_UI/dbui.h INCLUDE/dbui.h &&
 symlink_file ../SL/SEQIO/seqio.hxx INCLUDE/seqio.hxx &&
 symlink_file ../SL/FAST_ALIGNER/fast_aligner.hxx INCLUDE/fast_aligner.hxx &&
@@ -272 +271 @@
 symlink_file ../SL/HELIX/BI_helix.hxx INCLUDE/BI_helix.hxx &&
 symlink_file ../SL/HELIX/BI_basepos.hxx INCLUDE/BI_basepos.hxx &&
+symlink_file ../SL/ITEMS/items.h INCLUDE/items.h &&
+symlink_file ../SL/ITEMS/item_sel_list.h INCLUDE/item_sel_list.h &&
 symlink_file ../SL/MATRIX/AP_matrix.hxx INCLUDE/AP_matrix.hxx &&
+symlink_file ../SL/NDS/nds.h INCLUDE/nds.h &&
 symlink_file ../SL/NEIGHBOURJOIN/neighbourjoin.hxx INCLUDE/neighbourjoin.hxx &&
 symlink_file ../SL/PRONUC/AP_codon_table.hxx INCLUDE/AP_codon_table.hxx &&
 symlink_file ../SL/PRONUC/AP_pro_a_nucs.hxx INCLUDE/AP_pro_a_nucs.hxx &&
 symlink_file ../SL/PRONUC/iupac.h INCLUDE/iupac.h &&
+symlink_file ../SL/REFENTRIES/refentries.h INCLUDE/refentries.h &&
 symlink_file ../SL/REGEXPR/RegExpr.hxx INCLUDE/RegExpr.hxx &&
 symlink_file ../SL/SEQUENCE/AP_seq_dna.hxx INCLUDE/AP_seq_dna.hxx &&

trunk/STAT/Makefile

@@ -117 +117 @@
 ST_window.o: $(ARBHOME)/INCLUDE/aw_select.hxx
 ST_window.o: $(ARBHOME)/INCLUDE/aw_window.hxx
-ST_window.o: $(ARBHOME)/INCLUDE/awt.hxx
 ST_window.o: $(ARBHOME)/INCLUDE/awt_filter.hxx
-ST_window.o: $(ARBHOME)/INCLUDE/awt_item_sel_list.hxx
 ST_window.o: $(ARBHOME)/INCLUDE/cb.h
 ST_window.o: $(ARBHOME)/INCLUDE/ColumnStat.hxx
 ST_window.o: $(ARBHOME)/INCLUDE/dupstr.h
 ST_window.o: $(ARBHOME)/INCLUDE/gui_aliview.hxx
+ST_window.o: $(ARBHOME)/INCLUDE/item_sel_list.h
+ST_window.o: $(ARBHOME)/INCLUDE/items.h
 ST_window.o: $(ARBHOME)/INCLUDE/smartptr.h
 ST_window.o: $(ARBHOME)/INCLUDE/test_global.h

trunk/STAT/ST_window.cxx

@@ -18 +18 @@
 #include <aw_root.hxx>
 #include <aw_msg.hxx>
-#include <awt.hxx>
-#include <awt_item_sel_list.hxx>
+#include <item_sel_list.h>
 #include <awt_filter.hxx>
 

trunk/TOOLS/Makefile

@@ -170 +170 @@
 arb_export_tree.o: $(ARBHOME)/INCLUDE/attributes.h
 arb_export_tree.o: $(ARBHOME)/INCLUDE/aw_base.hxx
-arb_export_tree.o: $(ARBHOME)/INCLUDE/awt_nds.hxx
 arb_export_tree.o: $(ARBHOME)/INCLUDE/dupstr.h
+arb_export_tree.o: $(ARBHOME)/INCLUDE/nds.h
 arb_export_tree.o: $(ARBHOME)/INCLUDE/smartptr.h
 arb_export_tree.o: $(ARBHOME)/INCLUDE/test_global.h

trunk/WETC/WETC_main.cxx

@@ -10 +10 @@
 
 #include <awt.hxx>
+#include <aw_window.hxx>
 #include <aw_root.hxx>
 #include <arbdb.h>

trunk/WINDOW/AW_edit.cxx

@@ -135 +135 @@
 }
 
-
+void AW_system(AW_window *aww, GBDATA *gb_main, const char *command, const char *auto_help_file) {
+    if (auto_help_file) AW_POPUP_HELP(aww, (AW_CL)auto_help_file);
+    if (GBCMC_system(gb_main, command) != 0) {
+        const char *error = GBS_global_string("Failed to execute '%s'\n(Reason: %s)", command, GB_await_error());
+        aw_message(error);
+    }
+}

trunk/WINDOW/aw_detach.hxx

@@ -13 +13 @@
 #define AW_DETACH_HXX
 
+#ifndef AW_AWAR_HXX
+#include "aw_awar.hxx"
+#endif
 #ifndef AW_ROOT_HXX
 #include "aw_root.hxx"

trunk/WINDOW/aw_root.hxx

@@ -186 +186 @@
 inline AW_default get_AW_ROOT_DEFAULT() { return AW_root::SINGLETON->check_properties(NULL); }
 
+void AW_system(AW_window *aww, GBDATA *gb_main, const char *command, const char *auto_help_file);
 
 #else