Changeset 8287

Timestamp:

09/12/11 10:03:56 (6 months ago)

Author:

westram

Message:

• sync from trunk (unity/suse12.1)

Location:

branches/e4fix

Files:

• !BRANCH_STATE (modified) (2 diffs)
• AISC_MKPTPS/mkptypes.cxx (modified) (3 diffs)
• ARBDB/ad_prot.h (modified) (9 diffs)
• ARBDB/ad_t_prot.h (modified) (2 diffs)
• ARBDB/gb_prot.h (modified) (6 diffs)
• GL/glAW/GLwDrawA.c (modified) (1 diff)
• Makefile (modified) (1 diff)
• NTREE/AP_consensus.cxx (modified) (1 diff)
• NTREE/NT_cb.cxx (modified) (1 diff)
• NTREE/nt_cb.hxx (modified) (1 diff)
• NTREE/nt_internal.h (modified) (2 diffs)
• PROBE/pt_prototypes.h (modified) (2 diffs)
• WINDOW/AW_modal.cxx (modified) (1 diff)
• WINDOW/AW_nawar.cxx (modified) (1 diff)
• WINDOW/AW_window.cxx (modified) (17 diffs)
• WINDOW/aw_nawar.hxx (modified) (1 diff)
• WINDOW/aw_window.hxx (modified) (4 diffs)
• WINDOW/aw_window_Xm.hxx (modified) (2 diffs)
• arb_INSTALL.txt (modified) (2 diffs)

branches/e4fix/!BRANCH_STATE

@@ -8 +8 @@
 
                 8220 -> 8223
-                8205 8212 8216 8217 8225 8233 8234 8240 8241 8242 8243 8244 8245 8246 8247 8248 8249 8250 8251 8252 8253 8254 8255 8256 8257 8258 8259 8260 8261 8262 8263 8264 8265 8266 8267 8268 8269 8270 8271 8272 8273 -> 8274  
+                8205 8212 8216 8217 8225 8233 8234 8240 8241 8242 8243 8244 8245 8246 8247 8248 8249 8250 8251 8252 8253 8254 8255 8256 8257 8258 8259 8260 8261 8262 8263 8264 8265 8266 8267 8268 8269 8270 8271 8272 8273 -> 8274
+                8278 8279 8280 8283 8284 8285 -> 8287
 
     skipped patches (depends, already there, ...)
@@ -16 +17 @@
         --- current try above
 
-
-    not reviewed: 8275:HEAD
+    not reviewed: 8288:HEAD
 
 BRANCH->TRUNK

branches/e4fix/AISC_MKPTPS/mkptypes.cxx

@@ -1480 +1480 @@
 }
 
+static int string_comparator(const void *v0, const void *v1) {
+    return strcmp(*(const char **)v0, *(const char **)v1);
+}
+
 int ARB_main(int argc, const char *argv[]) {
     FILE *f;
@@ -1652 +1656 @@
     }
     else {
+        const char *filename[1000];
+        int         fcount = 0;
 
         while (argc > 0 && *argv) {
+            filename[fcount++] = *argv;
+            argc--; argv++;
+        }
+
+        qsort(&filename, fcount, sizeof(filename[0]), string_comparator);
+
+        for (int i = 0; i<fcount; ++i) {
             DEBUG_PRINT("trying new file '");
-            DEBUG_PRINT(*argv);
+            DEBUG_PRINT(filename[i]);
             DEBUG_PRINT("'\n");
 
-            if (!(f = fopen(*argv, "r"))) {
-                perror(*argv);
+            if (!(f = fopen(filename[i], "r"))) {
+                perror(filename[i]);
                 exit(EXIT_FAILURE);
             }
@@ -1667 +1680 @@
             newline_seen = 1;
             glastc       = ' ';
-            getdecl(f, *argv);
-            argc--; argv++;
+            getdecl(f, filename[i]);
             fclose(f);
 

branches/e4fix/ARBDB/ad_prot.h

@@ -13 +13 @@
 #endif
 
+
+/* adExperiment.cxx */
+GBDATA *EXP_get_experiment_data(GBDATA *gb_species);
+GBDATA *EXP_find_experiment_rel_exp_data(GBDATA *gb_experiment_data, const char *name);
+GBDATA *EXP_find_experiment(GBDATA *gb_species, const char *name);
+GBDATA *EXP_expect_experiment(GBDATA *gb_species, const char *name);
+GBDATA *EXP_first_experiment_rel_exp_data(GBDATA *gb_experiment_data);
+GBDATA *EXP_next_experiment(GBDATA *gb_experiment);
+GBDATA *EXP_find_or_create_experiment_rel_exp_data(GBDATA *gb_experiment_data, const char *name);
+
+/* adGene.cxx */
+bool GEN_is_genome_db(GBDATA *gb_main, int default_value);
+GBDATA *GEN_findOrCreate_gene_data(GBDATA *gb_species);
+GBDATA *GEN_find_gene_data(GBDATA *gb_species);
+GBDATA *GEN_expect_gene_data(GBDATA *gb_species);
+GBDATA *GEN_find_gene_rel_gene_data(GBDATA *gb_gene_data, const char *name);
+GBDATA *GEN_find_gene(GBDATA *gb_species, const char *name);
+GBDATA *GEN_create_nonexisting_gene_rel_gene_data(GBDATA *gb_gene_data, const char *name);
+GBDATA *GEN_create_nonexisting_gene(GBDATA *gb_species, const char *name);
+GBDATA *GEN_find_or_create_gene_rel_gene_data(GBDATA *gb_gene_data, const char *name);
+GBDATA *GEN_find_or_create_gene(GBDATA *gb_species, const char *name);
+GBDATA *GEN_first_gene(GBDATA *gb_species);
+GBDATA *GEN_first_gene_rel_gene_data(GBDATA *gb_gene_data);
+GBDATA *GEN_next_gene(GBDATA *gb_gene);
+GBDATA *GEN_first_marked_gene(GBDATA *gb_species);
+GBDATA *GEN_next_marked_gene(GBDATA *gb_gene);
+GEN_position *GEN_new_position(int parts, bool joinable);
+void GEN_use_uncertainties(GEN_position *pos);
+void GEN_free_position(GEN_position *pos);
+GEN_position *GEN_read_position(GBDATA *gb_gene);
+GB_ERROR GEN_write_position(GBDATA *gb_gene, const GEN_position *pos);
+void GEN_sortAndMergeLocationParts(GEN_position *location);
+const char *GEN_origin_organism(GBDATA *gb_pseudo);
+const char *GEN_origin_gene(GBDATA *gb_pseudo);
+bool GEN_is_pseudo_gene_species(GBDATA *gb_species);
+GB_ERROR GEN_organism_not_found(GBDATA *gb_pseudo);
+GBDATA *GEN_read_pseudo_species_from_hash(GB_HASH *pseudo_hash, const char *organism_name, const char *gene_name);
+void GEN_add_pseudo_species_to_hash(GBDATA *gb_pseudo, GB_HASH *pseudo_hash);
+GB_HASH *GEN_create_pseudo_species_hash(GBDATA *gb_main, int additionalSize);
+GBDATA *GEN_find_pseudo_species(GBDATA *gb_main, const char *organism_name, const char *gene_name, GB_HASH *pseudo_hash);
+GBDATA *GEN_find_origin_organism(GBDATA *gb_pseudo, GB_HASH *organism_hash);
+GBDATA *GEN_find_origin_gene(GBDATA *gb_pseudo, GB_HASH *organism_hash);
+GBDATA *GEN_first_pseudo_species(GBDATA *gb_main);
+GBDATA *GEN_first_pseudo_species_rel_species_data(GBDATA *gb_species_data);
+GBDATA *GEN_next_pseudo_species(GBDATA *gb_species);
+GBDATA *GEN_first_marked_pseudo_species(GBDATA *gb_main);
+GBDATA *GEN_next_marked_pseudo_species(GBDATA *gb_species);
+bool GEN_is_organism(GBDATA *gb_species);
+GBDATA *GEN_find_organism(GBDATA *gb_main, const char *name);
+GBDATA *GEN_first_organism(GBDATA *gb_main);
+GBDATA *GEN_next_organism(GBDATA *gb_organism);
+long GEN_get_organism_count(GBDATA *gb_main);
+GBDATA *GEN_first_marked_organism(GBDATA *gb_main);
+GBDATA *GEN_next_marked_organism(GBDATA *gb_organism);
+char *GEN_global_gene_identifier(GBDATA *gb_gene, GBDATA *gb_organism);
 
 /* adTest.cxx */
@@ -38 +93 @@
 GB_ERROR GB_save_quick(GBDATA *gb, const char *refpath);
 void GB_disable_path(GBDATA *gbd, const char *path);
+
+/* adcache.cxx */
+char *GB_set_cache_size(GBDATA *gbd, size_t size);
 
 /* adcomm.cxx */
@@ -50 +108 @@
 GB_ERROR GB_install_pid(int mode);
 const char *GB_date_string(void);
+
+/* adcompr.cxx */
+bool GB_is_dictionary_compressed(GBDATA *gbd);
+
+/* adfile.cxx */
+GB_CSTR GB_getcwd(void);
+char *GB_find_all_files(const char *dir, const char *mask, bool filename_only);
+char *GB_find_latest_file(const char *dir, const char *mask);
+const char *GB_existing_file(const char *file, bool warn_when_not_found);
+char *GB_lib_file(bool warn_when_not_found, const char *libprefix, const char *filename);
+char *GB_property_file(bool warn_when_not_found, const char *filename);
+void GBS_read_dir(StrArray &names, const char *dir, const char *mask);
+bool GB_test_textfile_difflines(const char *file1, const char *file2, int expected_difflines, int special_mode);
+size_t GB_test_mem_equal(const unsigned char *buf1, const unsigned char *buf2, size_t common);
+bool GB_test_files_equal(const char *file1, const char *file2);
+void GBT_transform_names(StrArray &dest, const StrArray &source, char *transform (const char *, void *), void *client_data);
 
 /* adhash.cxx */
@@ -81 +155 @@
 void GBS_free_numhash(GB_NUMHASH *hs);
 
-/* adcache.cxx */
-char *GB_set_cache_size(GBDATA *gbd, size_t size);
-
 /* adhashtools.cxx */
 void GBT_add_item_to_hash(GBDATA *gb_item, GB_HASH *item_hash);
@@ -92 +163 @@
 GB_HASH *GBT_create_organism_hash(GBDATA *gb_main);
 
+/* adindex.cxx */
+GB_ERROR GB_create_index(GBDATA *gbd, const char *key, GB_CASE case_sens, long estimated_size) __ATTR__USERESULT;
+NOT4PERL void GB_dump_indices(GBDATA *gbd);
+GB_ERROR GB_request_undo_type(GBDATA *gb_main, GB_UNDO_TYPE type) __ATTR__USERESULT_TODO;
+GB_UNDO_TYPE GB_get_requested_undo_type(GBDATA *gb_main);
+GB_ERROR GB_undo(GBDATA *gb_main, GB_UNDO_TYPE type) __ATTR__USERESULT;
+char *GB_undo_info(GBDATA *gb_main, GB_UNDO_TYPE type);
+GB_ERROR GB_set_undo_mem(GBDATA *gbd, long memsize);
+
 /* adlang1.cxx */
 NOT4PERL void GB_set_export_sequence_hook(gb_export_sequence_cb escb);
@@ -105 +185 @@
 NOT4PERL void *GB_recalloc(void *ptr, unsigned int oelem, unsigned int nelem, unsigned int elsize);
 void GB_memerr(void);
+
+/* admap.cxx */
+bool GB_supports_mapfile(void);
 
 /* admatch.cxx */
@@ -130 +213 @@
 /* adperl.cxx */
 GB_ERROR GBC_await_error(void);
+
+/* adquery.cxx */
+const char *GB_get_GBDATA_path(GBDATA *gbd);
+GBDATA *GB_find_sub_by_quark(GBDATA *father, GBQUARK key_quark, GBDATA *after, size_t skip_over);
+NOT4PERL GBDATA *GB_find_subcontent_by_quark(GBDATA *father, GBQUARK key_quark, GB_TYPES type, const char *val, GB_CASE case_sens, GBDATA *after, size_t skip_over);
+GBDATA *GB_find(GBDATA *gbd, const char *key, GB_SEARCH_TYPE gbs);
+GBDATA *GB_find_string(GBDATA *gbd, const char *key, const char *str, GB_CASE case_sens, GB_SEARCH_TYPE gbs);
+NOT4PERL GBDATA *GB_find_int(GBDATA *gbd, const char *key, long val, GB_SEARCH_TYPE gbs);
+GBDATA *GB_child(GBDATA *father);
+GBDATA *GB_nextChild(GBDATA *child);
+GBDATA *GB_entry(GBDATA *father, const char *key);
+GBDATA *GB_nextEntry(GBDATA *entry);
+GBDATA *GB_followingEntry(GBDATA *entry, size_t skip_over);
+GBDATA *GB_brother(GBDATA *entry, const char *key);
+char *GB_first_non_key_char(const char *str);
+GBDATA *GB_search(GBDATA *gbd, const char *fieldpath, GB_TYPES create);
+GBDATA *GB_searchOrCreate_string(GBDATA *gb_container, const char *fieldpath, const char *default_value);
+GBDATA *GB_searchOrCreate_int(GBDATA *gb_container, const char *fieldpath, long default_value);
+GBDATA *GB_searchOrCreate_float(GBDATA *gb_container, const char *fieldpath, double default_value);
+GBDATA *GB_search_last_son(GBDATA *gbd);
+long GB_number_of_marked_subentries(GBDATA *gbd);
+GBDATA *GB_first_marked(GBDATA *gbd, const char *keystring);
+GBDATA *GB_following_marked(GBDATA *gbd, const char *keystring, size_t skip_over);
+GBDATA *GB_next_marked(GBDATA *gbd, const char *keystring);
+char *GB_command_interpreter(GBDATA *gb_main, const char *str, const char *commands, GBDATA *gbd, const char *default_tree_name);
+
+/* adsocket.cxx */
+void GB_usleep(long usec);
+char *GB_read_fp(FILE *in);
+char *GB_read_file(const char *path);
+char *GB_map_FILE(FILE *in, int writeable);
+char *GB_map_file(const char *path, int writeable);
+GB_ULONG GB_time_of_day(void);
+long GB_last_saved_clock(GBDATA *gb_main);
+GB_ULONG GB_last_saved_time(GBDATA *gb_main);
+GB_ERROR GB_textprint(const char *path) __ATTR__USERESULT;
+GB_ERROR GB_xterm(void) __ATTR__USERESULT;
+GB_ERROR GB_xcmd(const char *cmd, bool background, bool wait_only_if_error) __ATTR__USERESULT_TODO;
+char *GB_executable(GB_CSTR exe_name);
+char *GB_find_executable(GB_CSTR description_of_executable, ...) __ATTR__SENTINEL;
+void GB_setenv(const char *var, const char *value);
+GB_CSTR GB_getenvARB_XTERM(void);
+GB_CSTR GB_getenvARB_XCMD(void);
+GB_CSTR GB_getenvUSER(void);
+GB_CSTR GB_getenvHOME(void);
+GB_CSTR GB_getenvARBHOME(void);
+GB_CSTR GB_getenvARBMACRO(void);
+GB_CSTR GB_getenvARBMACROHOME(void);
+GB_CSTR GB_getenvARBCONFIG(void);
+GB_CSTR GB_getenvPATH(void);
+GB_CSTR GB_getenvARB_GS(void);
+GB_CSTR GB_getenvARB_PDFVIEW(void);
+GB_CSTR GB_getenvARB_TEXTEDIT(void);
+GB_CSTR GB_getenvDOCPATH(void);
+GB_CSTR GB_getenvHTMLDOCPATH(void);
+NOT4PERL gb_getenv_hook GB_install_getenv_hook(gb_getenv_hook hook);
+GB_CSTR GB_getenv(const char *env);
+bool GB_host_is_local(const char *hostname);
+GB_ULONG GB_get_physical_memory(void);
+GB_CSTR GB_append_suffix(const char *name, const char *suffix);
+GB_CSTR GB_canonical_path(const char *anypath);
+GB_CSTR GB_concat_path(GB_CSTR anypath_left, GB_CSTR anypath_right);
+GB_CSTR GB_concat_full_path(const char *anypath_left, const char *anypath_right);
+GB_CSTR GB_unfold_path(const char *pwd_envar, const char *path);
+GB_CSTR GB_path_in_ARBHOME(const char *relative_path);
+GB_CSTR GB_path_in_ARBLIB(const char *relative_path);
+GB_CSTR GB_path_in_arbprop(const char *relative_path);
+GB_CSTR GB_path_in_ARBHOME(const char *relative_path_left, const char *anypath_right);
+GB_CSTR GB_path_in_ARBLIB(const char *relative_path_left, const char *anypath_right);
+FILE *GB_fopen_tempfile(const char *filename, const char *fmode, char **res_fullname);
+char *GB_create_tempfile(const char *name);
+char *GB_unique_filename(const char *name_prefix, const char *suffix);
+void GB_remove_on_exit(const char *filename);
+void GB_split_full_path(const char *fullpath, char **res_dir, char **res_fullname, char **res_name_only, char **res_suffix);
 
 /* adstring.cxx */
@@ -158 +315 @@
 char *GBS_trim(const char *str);
 char *GBS_log_dated_action_to(const char *comment, const char *action);
-
-/* adfile.cxx */
-GB_CSTR GB_getcwd(void);
-char *GB_find_all_files(const char *dir, const char *mask, bool filename_only);
-char *GB_find_latest_file(const char *dir, const char *mask);
-const char *GB_existing_file(const char *file, bool warn_when_not_found);
-char *GB_lib_file(bool warn_when_not_found, const char *libprefix, const char *filename);
-char *GB_property_file(bool warn_when_not_found, const char *filename);
-void GBS_read_dir(StrArray &names, const char *dir, const char *mask);
-bool GB_test_textfile_difflines(const char *file1, const char *file2, int expected_difflines, int special_mode);
-size_t GB_test_mem_equal(const unsigned char *buf1, const unsigned char *buf2, size_t common);
-bool GB_test_files_equal(const char *file1, const char *file2);
-void GBT_transform_names(StrArray &dest, const StrArray &source, char *transform (const char *, void *), void *client_data);
 
 /* adsystem.cxx */
@@ -326 +470 @@
 long GB_number_of_subentries(GBDATA *gbd);
 
-/* adExperiment.cxx */
-GBDATA *EXP_get_experiment_data(GBDATA *gb_species);
-GBDATA *EXP_find_experiment_rel_exp_data(GBDATA *gb_experiment_data, const char *name);
-GBDATA *EXP_find_experiment(GBDATA *gb_species, const char *name);
-GBDATA *EXP_expect_experiment(GBDATA *gb_species, const char *name);
-GBDATA *EXP_first_experiment_rel_exp_data(GBDATA *gb_experiment_data);
-GBDATA *EXP_next_experiment(GBDATA *gb_experiment);
-GBDATA *EXP_find_or_create_experiment_rel_exp_data(GBDATA *gb_experiment_data, const char *name);
-
-/* adGene.cxx */
-bool GEN_is_genome_db(GBDATA *gb_main, int default_value);
-GBDATA *GEN_findOrCreate_gene_data(GBDATA *gb_species);
-GBDATA *GEN_find_gene_data(GBDATA *gb_species);
-GBDATA *GEN_expect_gene_data(GBDATA *gb_species);
-GBDATA *GEN_find_gene_rel_gene_data(GBDATA *gb_gene_data, const char *name);
-GBDATA *GEN_find_gene(GBDATA *gb_species, const char *name);
-GBDATA *GEN_create_nonexisting_gene_rel_gene_data(GBDATA *gb_gene_data, const char *name);
-GBDATA *GEN_create_nonexisting_gene(GBDATA *gb_species, const char *name);
-GBDATA *GEN_find_or_create_gene_rel_gene_data(GBDATA *gb_gene_data, const char *name);
-GBDATA *GEN_find_or_create_gene(GBDATA *gb_species, const char *name);
-GBDATA *GEN_first_gene(GBDATA *gb_species);
-GBDATA *GEN_first_gene_rel_gene_data(GBDATA *gb_gene_data);
-GBDATA *GEN_next_gene(GBDATA *gb_gene);
-GBDATA *GEN_first_marked_gene(GBDATA *gb_species);
-GBDATA *GEN_next_marked_gene(GBDATA *gb_gene);
-GEN_position *GEN_new_position(int parts, bool joinable);
-void GEN_use_uncertainties(GEN_position *pos);
-void GEN_free_position(GEN_position *pos);
-GEN_position *GEN_read_position(GBDATA *gb_gene);
-GB_ERROR GEN_write_position(GBDATA *gb_gene, const GEN_position *pos);
-void GEN_sortAndMergeLocationParts(GEN_position *location);
-const char *GEN_origin_organism(GBDATA *gb_pseudo);
-const char *GEN_origin_gene(GBDATA *gb_pseudo);
-bool GEN_is_pseudo_gene_species(GBDATA *gb_species);
-GB_ERROR GEN_organism_not_found(GBDATA *gb_pseudo);
-GBDATA *GEN_read_pseudo_species_from_hash(GB_HASH *pseudo_hash, const char *organism_name, const char *gene_name);
-void GEN_add_pseudo_species_to_hash(GBDATA *gb_pseudo, GB_HASH *pseudo_hash);
-GB_HASH *GEN_create_pseudo_species_hash(GBDATA *gb_main, int additionalSize);
-GBDATA *GEN_find_pseudo_species(GBDATA *gb_main, const char *organism_name, const char *gene_name, GB_HASH *pseudo_hash);
-GBDATA *GEN_find_origin_organism(GBDATA *gb_pseudo, GB_HASH *organism_hash);
-GBDATA *GEN_find_origin_gene(GBDATA *gb_pseudo, GB_HASH *organism_hash);
-GBDATA *GEN_first_pseudo_species(GBDATA *gb_main);
-GBDATA *GEN_first_pseudo_species_rel_species_data(GBDATA *gb_species_data);
-GBDATA *GEN_next_pseudo_species(GBDATA *gb_species);
-GBDATA *GEN_first_marked_pseudo_species(GBDATA *gb_main);
-GBDATA *GEN_next_marked_pseudo_species(GBDATA *gb_species);
-bool GEN_is_organism(GBDATA *gb_species);
-GBDATA *GEN_find_organism(GBDATA *gb_main, const char *name);
-GBDATA *GEN_first_organism(GBDATA *gb_main);
-GBDATA *GEN_next_organism(GBDATA *gb_organism);
-long GEN_get_organism_count(GBDATA *gb_main);
-GBDATA *GEN_first_marked_organism(GBDATA *gb_main);
-GBDATA *GEN_next_marked_organism(GBDATA *gb_organism);
-char *GEN_global_gene_identifier(GBDATA *gb_gene, GBDATA *gb_organism);
-
-/* adcompr.cxx */
-bool GB_is_dictionary_compressed(GBDATA *gbd);
-
-/* adindex.cxx */
-GB_ERROR GB_create_index(GBDATA *gbd, const char *key, GB_CASE case_sens, long estimated_size) __ATTR__USERESULT;
-NOT4PERL void GB_dump_indices(GBDATA *gbd);
-GB_ERROR GB_request_undo_type(GBDATA *gb_main, GB_UNDO_TYPE type) __ATTR__USERESULT_TODO;
-GB_UNDO_TYPE GB_get_requested_undo_type(GBDATA *gb_main);
-GB_ERROR GB_undo(GBDATA *gb_main, GB_UNDO_TYPE type) __ATTR__USERESULT;
-char *GB_undo_info(GBDATA *gb_main, GB_UNDO_TYPE type);
-GB_ERROR GB_set_undo_mem(GBDATA *gbd, long memsize);
-
-/* admap.cxx */
-bool GB_supports_mapfile(void);
-
-/* adquery.cxx */
-const char *GB_get_GBDATA_path(GBDATA *gbd);
-GBDATA *GB_find_sub_by_quark(GBDATA *father, GBQUARK key_quark, GBDATA *after, size_t skip_over);
-NOT4PERL GBDATA *GB_find_subcontent_by_quark(GBDATA *father, GBQUARK key_quark, GB_TYPES type, const char *val, GB_CASE case_sens, GBDATA *after, size_t skip_over);
-GBDATA *GB_find(GBDATA *gbd, const char *key, GB_SEARCH_TYPE gbs);
-GBDATA *GB_find_string(GBDATA *gbd, const char *key, const char *str, GB_CASE case_sens, GB_SEARCH_TYPE gbs);
-NOT4PERL GBDATA *GB_find_int(GBDATA *gbd, const char *key, long val, GB_SEARCH_TYPE gbs);
-GBDATA *GB_child(GBDATA *father);
-GBDATA *GB_nextChild(GBDATA *child);
-GBDATA *GB_entry(GBDATA *father, const char *key);
-GBDATA *GB_nextEntry(GBDATA *entry);
-GBDATA *GB_followingEntry(GBDATA *entry, size_t skip_over);
-GBDATA *GB_brother(GBDATA *entry, const char *key);
-char *GB_first_non_key_char(const char *str);
-GBDATA *GB_search(GBDATA *gbd, const char *fieldpath, GB_TYPES create);
-GBDATA *GB_searchOrCreate_string(GBDATA *gb_container, const char *fieldpath, const char *default_value);
-GBDATA *GB_searchOrCreate_int(GBDATA *gb_container, const char *fieldpath, long default_value);
-GBDATA *GB_searchOrCreate_float(GBDATA *gb_container, const char *fieldpath, double default_value);
-GBDATA *GB_search_last_son(GBDATA *gbd);
-long GB_number_of_marked_subentries(GBDATA *gbd);
-GBDATA *GB_first_marked(GBDATA *gbd, const char *keystring);
-GBDATA *GB_following_marked(GBDATA *gbd, const char *keystring, size_t skip_over);
-GBDATA *GB_next_marked(GBDATA *gbd, const char *keystring);
-char *GB_command_interpreter(GBDATA *gb_main, const char *str, const char *commands, GBDATA *gbd, const char *default_tree_name);
-
-/* adsocket.cxx */
-void GB_usleep(long usec);
-char *GB_read_fp(FILE *in);
-char *GB_read_file(const char *path);
-char *GB_map_FILE(FILE *in, int writeable);
-char *GB_map_file(const char *path, int writeable);
-GB_ULONG GB_time_of_day(void);
-long GB_last_saved_clock(GBDATA *gb_main);
-GB_ULONG GB_last_saved_time(GBDATA *gb_main);
-GB_ERROR GB_textprint(const char *path) __ATTR__USERESULT;
-GB_ERROR GB_xterm(void) __ATTR__USERESULT;
-GB_ERROR GB_xcmd(const char *cmd, bool background, bool wait_only_if_error) __ATTR__USERESULT_TODO;
-char *GB_executable(GB_CSTR exe_name);
-char *GB_find_executable(GB_CSTR description_of_executable, ...) __ATTR__SENTINEL;
-void GB_setenv(const char *var, const char *value);
-GB_CSTR GB_getenvARB_XTERM(void);
-GB_CSTR GB_getenvARB_XCMD(void);
-GB_CSTR GB_getenvUSER(void);
-GB_CSTR GB_getenvHOME(void);
-GB_CSTR GB_getenvARBHOME(void);
-GB_CSTR GB_getenvARBMACRO(void);
-GB_CSTR GB_getenvARBMACROHOME(void);
-GB_CSTR GB_getenvARBCONFIG(void);
-GB_CSTR GB_getenvPATH(void);
-GB_CSTR GB_getenvARB_GS(void);
-GB_CSTR GB_getenvARB_PDFVIEW(void);
-GB_CSTR GB_getenvARB_TEXTEDIT(void);
-GB_CSTR GB_getenvDOCPATH(void);
-GB_CSTR GB_getenvHTMLDOCPATH(void);
-NOT4PERL gb_getenv_hook GB_install_getenv_hook(gb_getenv_hook hook);
-GB_CSTR GB_getenv(const char *env);
-bool GB_host_is_local(const char *hostname);
-GB_ULONG GB_get_physical_memory(void);
-GB_CSTR GB_append_suffix(const char *name, const char *suffix);
-GB_CSTR GB_canonical_path(const char *anypath);
-GB_CSTR GB_concat_path(GB_CSTR anypath_left, GB_CSTR anypath_right);
-GB_CSTR GB_concat_full_path(const char *anypath_left, const char *anypath_right);
-GB_CSTR GB_unfold_path(const char *pwd_envar, const char *path);
-GB_CSTR GB_path_in_ARBHOME(const char *relative_path);
-GB_CSTR GB_path_in_ARBLIB(const char *relative_path);
-GB_CSTR GB_path_in_arbprop(const char *relative_path);
-GB_CSTR GB_path_in_ARBHOME(const char *relative_path_left, const char *anypath_right);
-GB_CSTR GB_path_in_ARBLIB(const char *relative_path_left, const char *anypath_right);
-FILE *GB_fopen_tempfile(const char *filename, const char *fmode, char **res_fullname);
-char *GB_create_tempfile(const char *name);
-char *GB_unique_filename(const char *name_prefix, const char *suffix);
-void GB_remove_on_exit(const char *filename);
-void GB_split_full_path(const char *fullpath, char **res_dir, char **res_fullname, char **res_name_only, char **res_suffix);
-
 #else
 #error ad_prot.h included twice

branches/e4fix/ARBDB/ad_t_prot.h

@@ -29 +29 @@
 NOT4PERL GB_ERROR GBT_determine_T_or_U(GB_alignment_type alignment_type, char *T_or_U, const char *supposed_target);
 NOT4PERL void GBT_reverseComplementNucSequence(char *seq, long length, char T_or_U);
+
+/* adali.cxx */
+int GBT_count_alignments(GBDATA *gb_main);
+GB_ERROR GBT_check_data(GBDATA *Main, const char *alignment_name);
+void GBT_get_alignment_names(ConstStrArray &names, GBDATA *gbd);
+GB_ERROR GBT_check_alignment_name(const char *alignment_name);
+GBDATA *GBT_create_alignment(GBDATA *gbd, const char *name, long len, long aligned, long security, const char *type);
+NOT4PERL GB_ERROR GBT_check_alignment(GBDATA *gb_main, GBDATA *preset_alignment, GB_HASH *species_name_hash);
+GB_ERROR GBT_rename_alignment(GBDATA *gbMain, const char *source, const char *dest, int copy, int dele);
+NOT4PERL GBDATA *GBT_add_data(GBDATA *species, const char *ali_name, const char *key, GB_TYPES type) __ATTR__DEPRECATED_TODO("better use GBT_create_sequence_data()");
+NOT4PERL GBDATA *GBT_create_sequence_data(GBDATA *species, const char *ali_name, const char *key, GB_TYPES type, int security_write);
+GB_ERROR GBT_write_sequence(GBDATA *gb_data, const char *ali_name, long ali_len, const char *sequence);
+GBDATA *GBT_gen_accession_number(GBDATA *gb_species, const char *ali_name);
+int GBT_is_partial(GBDATA *gb_species, int default_value, int define_if_undef);
+GBDATA *GBT_read_sequence(GBDATA *gb_species, const char *aliname);
+char *GBT_get_default_alignment(GBDATA *gb_main);
+GB_ERROR GBT_set_default_alignment(GBDATA *gb_main, const char *alignment_name);
+GBDATA *GBT_get_alignment(GBDATA *gb_main, const char *aliname);
+long GBT_get_alignment_len(GBDATA *gb_main, const char *aliname);
+GB_ERROR GBT_set_alignment_len(GBDATA *gb_main, const char *aliname, long new_len);
+int GBT_get_alignment_aligned(GBDATA *gb_main, const char *aliname);
+char *GBT_get_alignment_type_string(GBDATA *gb_main, const char *aliname);
+GB_alignment_type GBT_get_alignment_type(GBDATA *gb_main, const char *aliname);
+bool GBT_is_alignment_protein(GBDATA *gb_main, const char *alignment_name);
+NOT4PERL char *GBT_read_gene_sequence_and_length(GBDATA *gb_gene, bool use_revComplement, char partSeparator, size_t *gene_length);
+char *GBT_read_gene_sequence(GBDATA *gb_gene, bool use_revComplement, char partSeparator);
 
 /* adcolumns.cxx */
@@ -162 +188 @@
 char *GBT_existing_tree(GBDATA *gb_main, const char *tree_name);
 
-/* adali.cxx */
-int GBT_count_alignments(GBDATA *gb_main);
-GB_ERROR GBT_check_data(GBDATA *Main, const char *alignment_name);
-void GBT_get_alignment_names(ConstStrArray &names, GBDATA *gbd);
-GB_ERROR GBT_check_alignment_name(const char *alignment_name);
-GBDATA *GBT_create_alignment(GBDATA *gbd, const char *name, long len, long aligned, long security, const char *type);
-NOT4PERL GB_ERROR GBT_check_alignment(GBDATA *gb_main, GBDATA *preset_alignment, GB_HASH *species_name_hash);
-GB_ERROR GBT_rename_alignment(GBDATA *gbMain, const char *source, const char *dest, int copy, int dele);
-NOT4PERL GBDATA *GBT_add_data(GBDATA *species, const char *ali_name, const char *key, GB_TYPES type) __ATTR__DEPRECATED_TODO("better use GBT_create_sequence_data()");
-NOT4PERL GBDATA *GBT_create_sequence_data(GBDATA *species, const char *ali_name, const char *key, GB_TYPES type, int security_write);
-GB_ERROR GBT_write_sequence(GBDATA *gb_data, const char *ali_name, long ali_len, const char *sequence);
-GBDATA *GBT_gen_accession_number(GBDATA *gb_species, const char *ali_name);
-int GBT_is_partial(GBDATA *gb_species, int default_value, int define_if_undef);
-GBDATA *GBT_read_sequence(GBDATA *gb_species, const char *aliname);
-char *GBT_get_default_alignment(GBDATA *gb_main);
-GB_ERROR GBT_set_default_alignment(GBDATA *gb_main, const char *alignment_name);
-GBDATA *GBT_get_alignment(GBDATA *gb_main, const char *aliname);
-long GBT_get_alignment_len(GBDATA *gb_main, const char *aliname);
-GB_ERROR GBT_set_alignment_len(GBDATA *gb_main, const char *aliname, long new_len);
-int GBT_get_alignment_aligned(GBDATA *gb_main, const char *aliname);
-char *GBT_get_alignment_type_string(GBDATA *gb_main, const char *aliname);
-GB_alignment_type GBT_get_alignment_type(GBDATA *gb_main, const char *aliname);
-bool GBT_is_alignment_protein(GBDATA *gb_main, const char *alignment_name);
-NOT4PERL char *GBT_read_gene_sequence_and_length(GBDATA *gb_gene, bool use_revComplement, char partSeparator, size_t *gene_length);
-char *GBT_read_gene_sequence(GBDATA *gb_gene, bool use_revComplement, char partSeparator);
-
 #else
 #error ad_t_prot.h included twice

branches/e4fix/ARBDB/gb_prot.h

@@ -13 +13 @@
 #endif
 
-
-/* ad_load.cxx */
-GB_ERROR gb_read_ascii(const char *path, GBCONTAINER *gbd);
-long gb_read_bin_rek(FILE *in, GBCONTAINER *gbd, long nitems, long version, long reversed);
-long gb_recover_corrupt_file(GBCONTAINER *gbd, FILE *in, GB_ERROR recovery_reason);
-long gb_read_bin_rek_V2(FILE *in, GBCONTAINER *gbd, long nitems, long version, long reversed, long deep);
-GBDATA *gb_search_system_folder_rek(GBDATA *gbd);
-void gb_search_system_folder(GBDATA *gb_main);
-long gb_read_bin(FILE *in, GBCONTAINER *gbd, int diff_file_allowed);
-GB_MAIN_IDX gb_make_main_idx(GB_MAIN_TYPE *Main);
-void gb_release_main_idx(GB_MAIN_TYPE *Main);
-GB_ERROR gb_login_remote(GB_MAIN_TYPE *Main, const char *path, const char *opent);
-
-/* ad_save_load.cxx */
-char *gb_findExtension(char *path);
-GB_CSTR gb_oldQuicksaveName(GB_CSTR path, int nr);
-GB_CSTR gb_quicksaveName(GB_CSTR path, int nr);
-GB_CSTR gb_mapfile_name(GB_CSTR path);
-GB_CSTR gb_overwriteName(GB_CSTR path);
-GB_CSTR gb_reffile_name(GB_CSTR path);
-GB_ERROR gb_delete_reference(const char *master);
-GB_ERROR gb_create_reference(const char *master);
-GB_ERROR gb_add_reference(const char *master, const char *changes);
-GB_ERROR gb_remove_all_but_main(GB_MAIN_TYPE *Main, const char *path);
-long gb_ascii_2_bin(const char *source, GBDATA *gbd);
-GB_BUFFER gb_bin_2_ascii(GBDATA *gbd);
-long gb_read_in_long(FILE *in, long reversed);
-long gb_read_number(FILE *in);
-void gb_put_number(long i, FILE *out);
-long gb_read_bin_error(FILE *in, GBDATA *gbd, const char *text);
-long gb_write_out_long(long data, FILE *out);
-int gb_is_writeable(gb_header_list *header, GBDATA *gbd, long version, long diff_save);
-int gb_write_bin_sub_containers(FILE *out, GBCONTAINER *gbc, long version, long diff_save, int is_root);
-long gb_write_bin_rek(FILE *out, GBDATA *gbd, long version, long diff_save, long index_of_master_file);
-int gb_write_bin(FILE *out, GBDATA *gbd, long version);
-char *gb_full_path(const char *path);
-GB_ERROR gb_check_saveable(GBDATA *gbd, const char *path, const char *flags);
-
-/* adcomm.cxx */
-GB_ERROR gbcm_unfold_client(GBCONTAINER *gbd, long deep, long index_pos) __ATTR__USERESULT;
-GB_ERROR gbcmc_begin_sendupdate(GBDATA *gbd);
-GB_ERROR gbcmc_end_sendupdate(GBDATA *gbd);
-GB_ERROR gbcmc_sendupdate_create(GBDATA *gbd);
-GB_ERROR gbcmc_sendupdate_delete(GBDATA *gbd);
-GB_ERROR gbcmc_sendupdate_update(GBDATA *gbd, int send_headera);
-GB_ERROR gbcmc_begin_transaction(GBDATA *gbd);
-GB_ERROR gbcmc_init_transaction(GBCONTAINER *gbd);
-GB_ERROR gbcmc_commit_transaction(GBDATA *gbd);
-GB_ERROR gbcmc_abort_transaction(GBDATA *gbd);
-GB_ERROR gbcms_add_to_delete_list(GBDATA *gbd);
-long gbcmc_key_alloc(GBDATA *gbd, const char *key);
-GB_ERROR gbcmc_send_undo_commands(GBDATA *gbd, enum gb_undo_commands command) __ATTR__USERESULT;
-char *gbcmc_send_undo_info_commands(GBDATA *gbd, enum gb_undo_commands command);
-GB_ERROR gbcm_login(GBCONTAINER *gb_main, const char *loginname);
-GBCM_ServerResult gbcmc_close(gbcmc_comm *link);
-GB_ERROR gbcm_logout(GB_MAIN_TYPE *Main, const char *loginname);
-
-/* adhash.cxx */
-size_t gbs_get_a_prime(size_t above_or_equal_this);
-
-/* adcache.cxx */
-void gb_init_cache(GB_MAIN_TYPE *Main);
-void gb_destroy_cache(GB_MAIN_TYPE *Main);
-char *gb_read_cache(GBDATA *gbd);
-void gb_free_cache(GB_MAIN_TYPE *Main, GBDATA *gbd);
-char *gb_alloc_cache_index(GBDATA *gbd, size_t size);
-void gb_flush_cache(GBDATA *gbd);
-
-/* adlang1.cxx */
-void gbl_install_standard_commands(GBDATA *gb_main);
-
-/* admalloc.cxx */
-void gbm_flush_mem(void);
-void gbm_init_mem(void);
-void gbm_debug_mem(void);
-
-/* adoptimize.cxx */
-GB_ERROR gb_convert_V2_to_V3(GBDATA *gb_main);
-char *gb_uncompress_by_dictionary(GBDATA *gbd, GB_CSTR s_source, long size, long *new_size);
-char *gb_compress_by_dictionary(GB_DICTIONARY *dict, GB_CSTR s_source, long size, long *msize, int last_flag, int search_backward, int search_forward);
-GB_ERROR gb_create_dictionaries(GB_MAIN_TYPE *Main, long maxmem);
-
-/* adstring.cxx */
-void gbs_uppercase(char *str);
-void gbs_memcopy(char *dest, const char *source, long len);
-char *gbs_add_path(char *path, char *name);
-
-/* adfile.cxx */
-GB_ERROR gb_scan_directory(char *basename, gb_scandir *sd) __ATTR__USERESULT_TODO;
-
-/* adsystem.cxx */
-GB_ERROR gb_load_dictionary_data(GBDATA *gb_main, const char *key, char **dict_data, long *size);
-GB_DICTIONARY *gb_create_dict(GBDATA *gb_dict);
-void gb_system_key_changed_cb(GBDATA *gbd, int *cl, GB_CB_TYPE type);
-void gb_system_master_changed_cb(GBDATA *gbd, int *cl, GB_CB_TYPE type);
-void gb_load_single_key_data(GBDATA *gb_main, GBQUARK q);
-GB_ERROR gb_save_dictionary_data(GBDATA *gb_main, const char *key, const char *dict, int size);
-GB_ERROR gb_load_key_data_and_dictionaries(GBDATA *gb_main) __ATTR__USERESULT;
-
-/* arbdb.cxx */
-GBDATA *gb_remembered_db(void);
-GB_ERROR gb_unfold(GBCONTAINER *gbd, long deep, int index_pos);
-void gb_close_unclosed_DBs(void);
-int gb_read_nr(GBDATA *gbd);
-GB_ERROR gb_write_compressed_pntr(GBDATA *gbd, const char *s, long memsize, long stored_size);
-int gb_get_compression_mask(GB_MAIN_TYPE *Main, GBQUARK key, int gb_type);
-GB_ERROR gb_security_error(GBDATA *gbd) __ATTR__USERESULT;
-GB_CSTR gb_read_key_pntr(GBDATA *gbd);
-GBQUARK gb_key_2_existing_quark(GB_MAIN_TYPE *Main, const char *key);
-GBQUARK gb_key_2_quark(GB_MAIN_TYPE *Main, const char *key);
-GBDATA *gb_create(GBDATA *father, const char *key, GB_TYPES type);
-GBDATA *gb_create_container(GBDATA *father, const char *key);
-void gb_rename(GBCONTAINER *gbc, const char *new_key);
-GB_ERROR gb_delete_force(GBDATA *source);
-GB_ERROR gb_set_compression(GBDATA *source);
-GB_ERROR gb_init_transaction(GBCONTAINER *gbd);
-void gb_add_changed_callback_list(GBDATA *gbd, gb_transaction_save *old, GB_CB_TYPE gbtype, GB_CB func, int *clientdata);
-void gb_add_delete_callback_list(GBDATA *gbd, gb_transaction_save *old, GB_CB func, int *clientdata);
-GB_ERROR gb_do_callback_list(GB_MAIN_TYPE *Main);
-GB_MAIN_TYPE *gb_get_main_during_cb(void);
-GB_CSTR gb_read_pntr_ts(GBDATA *gbd, gb_transaction_save *ts);
-int gb_info(GBDATA *gbd, int deep);
 
 /* ad_core.cxx */
@@ -172 +50 @@
 GB_ERROR gb_commit_transaction_local_rek(GBDATA *gbd, long mode, int *pson_created);
 
+/* ad_load.cxx */
+GB_ERROR gb_read_ascii(const char *path, GBCONTAINER *gbd);
+long gb_read_bin_rek(FILE *in, GBCONTAINER *gbd, long nitems, long version, long reversed);
+long gb_recover_corrupt_file(GBCONTAINER *gbd, FILE *in, GB_ERROR recovery_reason);
+long gb_read_bin_rek_V2(FILE *in, GBCONTAINER *gbd, long nitems, long version, long reversed, long deep);
+GBDATA *gb_search_system_folder_rek(GBDATA *gbd);
+void gb_search_system_folder(GBDATA *gb_main);
+long gb_read_bin(FILE *in, GBCONTAINER *gbd, int diff_file_allowed);
+GB_MAIN_IDX gb_make_main_idx(GB_MAIN_TYPE *Main);
+void gb_release_main_idx(GB_MAIN_TYPE *Main);
+GB_ERROR gb_login_remote(GB_MAIN_TYPE *Main, const char *path, const char *opent);
+
+/* ad_save_load.cxx */
+char *gb_findExtension(char *path);
+GB_CSTR gb_oldQuicksaveName(GB_CSTR path, int nr);
+GB_CSTR gb_quicksaveName(GB_CSTR path, int nr);
+GB_CSTR gb_mapfile_name(GB_CSTR path);
+GB_CSTR gb_overwriteName(GB_CSTR path);
+GB_CSTR gb_reffile_name(GB_CSTR path);
+GB_ERROR gb_delete_reference(const char *master);
+GB_ERROR gb_create_reference(const char *master);
+GB_ERROR gb_add_reference(const char *master, const char *changes);
+GB_ERROR gb_remove_all_but_main(GB_MAIN_TYPE *Main, const char *path);
+long gb_ascii_2_bin(const char *source, GBDATA *gbd);
+GB_BUFFER gb_bin_2_ascii(GBDATA *gbd);
+long gb_read_in_long(FILE *in, long reversed);
+long gb_read_number(FILE *in);
+void gb_put_number(long i, FILE *out);
+long gb_read_bin_error(FILE *in, GBDATA *gbd, const char *text);
+long gb_write_out_long(long data, FILE *out);
+int gb_is_writeable(gb_header_list *header, GBDATA *gbd, long version, long diff_save);
+int gb_write_bin_sub_containers(FILE *out, GBCONTAINER *gbc, long version, long diff_save, int is_root);
+long gb_write_bin_rek(FILE *out, GBDATA *gbd, long version, long diff_save, long index_of_master_file);
+int gb_write_bin(FILE *out, GBDATA *gbd, long version);
+char *gb_full_path(const char *path);
+GB_ERROR gb_check_saveable(GBDATA *gbd, const char *path, const char *flags);
+
+/* adcache.cxx */
+void gb_init_cache(GB_MAIN_TYPE *Main);
+void gb_destroy_cache(GB_MAIN_TYPE *Main);
+char *gb_read_cache(GBDATA *gbd);
+void gb_free_cache(GB_MAIN_TYPE *Main, GBDATA *gbd);
+char *gb_alloc_cache_index(GBDATA *gbd, size_t size);
+void gb_flush_cache(GBDATA *gbd);
+
+/* adcomm.cxx */
+GB_ERROR gbcm_unfold_client(GBCONTAINER *gbd, long deep, long index_pos) __ATTR__USERESULT;
+GB_ERROR gbcmc_begin_sendupdate(GBDATA *gbd);
+GB_ERROR gbcmc_end_sendupdate(GBDATA *gbd);
+GB_ERROR gbcmc_sendupdate_create(GBDATA *gbd);
+GB_ERROR gbcmc_sendupdate_delete(GBDATA *gbd);
+GB_ERROR gbcmc_sendupdate_update(GBDATA *gbd, int send_headera);
+GB_ERROR gbcmc_begin_transaction(GBDATA *gbd);
+GB_ERROR gbcmc_init_transaction(GBCONTAINER *gbd);
+GB_ERROR gbcmc_commit_transaction(GBDATA *gbd);
+GB_ERROR gbcmc_abort_transaction(GBDATA *gbd);
+GB_ERROR gbcms_add_to_delete_list(GBDATA *gbd);
+long gbcmc_key_alloc(GBDATA *gbd, const char *key);
+GB_ERROR gbcmc_send_undo_commands(GBDATA *gbd, enum gb_undo_commands command) __ATTR__USERESULT;
+char *gbcmc_send_undo_info_commands(GBDATA *gbd, enum gb_undo_commands command);
+GB_ERROR gbcm_login(GBCONTAINER *gb_main, const char *loginname);
+GBCM_ServerResult gbcmc_close(gbcmc_comm *link);
+GB_ERROR gbcm_logout(GB_MAIN_TYPE *Main, const char *loginname);
+
 /* adcompr.cxx */
 gb_compress_tree *gb_build_uncompress_tree(const unsigned char *data, long short_flag, char **end);
@@ -191 +133 @@
 GB_CBUFFER gb_uncompress_data(GBDATA *gbd, GB_CBUFFER source, long size);
 
+/* adfile.cxx */
+GB_ERROR gb_scan_directory(char *basename, gb_scandir *sd) __ATTR__USERESULT_TODO;
+
+/* adhash.cxx */
+size_t gbs_get_a_prime(size_t above_or_equal_this);
+
 /* adindex.cxx */
 char *gb_index_check_in(GBDATA *gbd);
@@ -204 +152 @@
 void gb_check_in_undo_delete(GB_MAIN_TYPE *Main, GBDATA *gbd, int deep);
 
+/* adlang1.cxx */
+void gbl_install_standard_commands(GBDATA *gb_main);
+
+/* admalloc.cxx */
+void gbm_flush_mem(void);
+void gbm_init_mem(void);
+void gbm_debug_mem(void);
+
 /* admap.cxx */
 GB_ERROR gb_save_mapfile(GB_MAIN_TYPE *Main, GB_CSTR path);
@@ -209 +165 @@
 GBDATA *gb_map_mapfile(const char *path);
 int gb_isMappedMemory(void *mem);
+
+/* adoptimize.cxx */
+GB_ERROR gb_convert_V2_to_V3(GBDATA *gb_main);
+char *gb_uncompress_by_dictionary(GBDATA *gbd, GB_CSTR s_source, long size, long *new_size);
+char *gb_compress_by_dictionary(GB_DICTIONARY *dict, GB_CSTR s_source, long size, long *msize, int last_flag, int search_backward, int search_forward);
+GB_ERROR gb_create_dictionaries(GB_MAIN_TYPE *Main, long maxmem);
 
 /* adquery.cxx */
@@ -236 +198 @@
 long gbcm_read_long(int socket);
 
+/* adstring.cxx */
+void gbs_uppercase(char *str);
+void gbs_memcopy(char *dest, const char *source, long len);
+char *gbs_add_path(char *path, char *name);
+
+/* adsystem.cxx */
+GB_ERROR gb_load_dictionary_data(GBDATA *gb_main, const char *key, char **dict_data, long *size);
+GB_DICTIONARY *gb_create_dict(GBDATA *gb_dict);
+void gb_system_key_changed_cb(GBDATA *gbd, int *cl, GB_CB_TYPE type);
+void gb_system_master_changed_cb(GBDATA *gbd, int *cl, GB_CB_TYPE type);
+void gb_load_single_key_data(GBDATA *gb_main, GBQUARK q);
+GB_ERROR gb_save_dictionary_data(GBDATA *gb_main, const char *key, const char *dict, int size);
+GB_ERROR gb_load_key_data_and_dictionaries(GBDATA *gb_main) __ATTR__USERESULT;
+
+/* arbdb.cxx */
+GBDATA *gb_remembered_db(void);
+GB_ERROR gb_unfold(GBCONTAINER *gbd, long deep, int index_pos);
+void gb_close_unclosed_DBs(void);
+int gb_read_nr(GBDATA *gbd);
+GB_ERROR gb_write_compressed_pntr(GBDATA *gbd, const char *s, long memsize, long stored_size);
+int gb_get_compression_mask(GB_MAIN_TYPE *Main, GBQUARK key, int gb_type);
+GB_ERROR gb_security_error(GBDATA *gbd) __ATTR__USERESULT;
+GB_CSTR gb_read_key_pntr(GBDATA *gbd);
+GBQUARK gb_key_2_existing_quark(GB_MAIN_TYPE *Main, const char *key);
+GBQUARK gb_key_2_quark(GB_MAIN_TYPE *Main, const char *key);
+GBDATA *gb_create(GBDATA *father, const char *key, GB_TYPES type);
+GBDATA *gb_create_container(GBDATA *father, const char *key);
+void gb_rename(GBCONTAINER *gbc, const char *new_key);
+GB_ERROR gb_delete_force(GBDATA *source);
+GB_ERROR gb_set_compression(GBDATA *source);
+GB_ERROR gb_init_transaction(GBCONTAINER *gbd);
+void gb_add_changed_callback_list(GBDATA *gbd, gb_transaction_save *old, GB_CB_TYPE gbtype, GB_CB func, int *clientdata);
+void gb_add_delete_callback_list(GBDATA *gbd, gb_transaction_save *old, GB_CB func, int *clientdata);
+GB_ERROR gb_do_callback_list(GB_MAIN_TYPE *Main);
+GB_MAIN_TYPE *gb_get_main_during_cb(void);
+GB_CSTR gb_read_pntr_ts(GBDATA *gbd, gb_transaction_save *ts);
+int gb_info(GBDATA *gbd, int deep);
+
 #else
 #error gb_prot.h included twice

branches/e4fix/GL/glAW/GLwDrawA.c

@@ -603 +603 @@
     cb.height = glw->core.height;
     XtCallCallbackList((Widget)glw, glw->glwDrawingArea.inputCallback, &cb);
-  }
-
-
-#ifdef __GLX_MOTIF
-
-// Create routine
+}
+
+void GLwDrawingAreaMakeCurrent(Widget w, GLXContext ctx) {
+    // Make context current
+    // ARB note: define it independent from __GLX_MOTIF (undefined on suse12.1) 
+    glXMakeCurrent(XtDisplay(w), XtWindow(w), ctx);
+}
+
+#ifdef __GLX_MOTIF
+
 Widget GLwCreateMDrawingArea(Widget parent, char *name, ArgList arglist, Cardinal argcount) {
-  return XtCreateWidget(name, glwMDrawingAreaWidgetClass, parent, arglist, argcount);
-  }
-
-#endif
-
-
-#ifndef __GLX_MOTIF
-
-// Make context current
-void GLwDrawingAreaMakeCurrent(Widget w, GLXContext ctx) {
-  glXMakeCurrent(XtDisplay(w), XtWindow(w), ctx);
-  }
-
-
-// Swap buffers convenience function
+    // Create routine
+    return XtCreateWidget(name, glwMDrawingAreaWidgetClass, parent, arglist, argcount);
+}
+
+#else
+
 void GLwDrawingAreaSwapBuffers(Widget w) {
-  glXSwapBuffers(XtDisplay(w), XtWindow(w));
-  }
-
-#endif
+    // Swap buffers convenience function
+    glXSwapBuffers(XtDisplay(w), XtWindow(w));
+}
+
+#endif

branches/e4fix/Makefile

@@ -59 +59 @@
         4.4 4.4.1 4.4.3 4.4.5 \
         4.5.2 \
-        4.6.1
+        4.6 4.6.1
 
 ALLOWED_GCC_VERSIONS=$(ALLOWED_GCC_4xx_VERSIONS)

branches/e4fix/NTREE/AP_consensus.cxx

@@ -55 +55 @@
 #include <arbdbt.h>
 #include <arb_strbuf.h>
+
+// AISC_MKPT_PROMOTE:#ifndef AW_BASE_HXX
+// AISC_MKPT_PROMOTE:#include <aw_base.hxx>
+// AISC_MKPT_PROMOTE:#endif
 
 #define AWAR_MAX_FREQ   "tmp/CON_MAX_FREQ/"

branches/e4fix/NTREE/NT_cb.cxx

@@ -27 +27 @@
 // AISC_MKPT_PROMOTE:#include <aw_base.hxx>
 // AISC_MKPT_PROMOTE:#endif
-// AISC_MKPT_PROMOTE:
-// AISC_MKPT_PROMOTE:class AW_window;
 // AISC_MKPT_PROMOTE:class AWT_canvas;
 

branches/e4fix/NTREE/nt_cb.hxx

@@ -20 +20 @@
 #include <aw_base.hxx>
 #endif
-
-class AW_window;
 class AWT_canvas;
 

branches/e4fix/NTREE/nt_internal.h

@@ -12 +12 @@
 
 
-/* NT_cb.cxx */
+/* AP_consensus.cxx */
 
-#ifndef ARBDB_BASE_H
-#include <arbdb_base.h>
-#endif
 #ifndef AW_BASE_HXX
 #include <aw_base.hxx>
 #endif
 
-class AW_window;
-class AWT_canvas;
-
-void NT_delete_mark_all_cb(void *, AWT_canvas *ntw);
-AW_window *NT_open_select_tree_window(AW_root *awr, char *awar_tree);
-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 cl_command, AW_CL cl_auto_help_file);
-void NT_system_in_xterm_cb(AW_window *aww, AW_CL cl_command, AW_CL cl_auto_help_file);
-
-/* AP_consensus.cxx */
 AW_window *AP_open_con_expert_window(AW_root *aw_root);
 AW_window *AP_open_consensus_window(AW_root *aw_root);
@@ -43 +29 @@
 AW_window *AP_open_cprofile_window(AW_root *aw_root);
 
+/* AP_pos_var_pars.cxx */
+void AP_calc_pos_var_pars(AW_window *aww);
+AW_window *AP_open_pos_var_pars_window(AW_root *root);
+
 /* ColumnStat_2_gnuplot.cxx */
 AW_window *NT_create_colstat_2_gnuplot_window(AW_root *root);
 
-/* AP_pos_var_pars.cxx */
-void AP_calc_pos_var_pars(AW_window *aww);
-AW_window *AP_open_pos_var_pars_window(AW_root *root);
+/* NT_cb.cxx */
+
+#ifndef ARBDB_BASE_H
+#include <arbdb_base.h>
+#endif
+#ifndef AW_BASE_HXX
+#include <aw_base.hxx>
+#endif
+class AWT_canvas;
+
+void NT_delete_mark_all_cb(void *, AWT_canvas *ntw);
+AW_window *NT_open_select_tree_window(AW_root *awr, char *awar_tree);
+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 cl_command, AW_CL cl_auto_help_file);
+void NT_system_in_xterm_cb(AW_window *aww, AW_CL cl_command, AW_CL cl_auto_help_file);
 
 /* NT_concatenate.cxx */

branches/e4fix/PROBE/pt_prototypes.h

@@ -19 +19 @@
 ARB_ERROR enter_stage_1_build_tree(PT_main *, char *tname) __ATTR__USERESULT;
 ARB_ERROR enter_stage_3_load_tree(PT_main *, const char *tname) __ATTR__USERESULT;
+
+/* PT_debug.cxx */
+void PT_dump_tree_statistics(void);
+void PT_dump_POS_TREE_recursive(POS_TREE *IF_DEBUG (pt), const char *IF_DEBUG (prefix));
+void PT_dump_POS_TREE(POS_TREE *IF_DEBUG (node));
 
 /* PT_etc.cxx */
@@ -109 +114 @@
 ARB_ERROR PTD_read_leafs_from_disk(const char *fname, POS_TREE **pnode) __ATTR__USERESULT;
 
-/* PT_debug.cxx */
-void PT_dump_tree_statistics(void);
-void PT_dump_POS_TREE_recursive(POS_TREE *IF_DEBUG (pt), const char *IF_DEBUG (prefix));
-void PT_dump_POS_TREE(POS_TREE *IF_DEBUG (node));
-
 /* probe_tree.h */
 template <typename T >int PT_forwhole_chain(POS_TREE *node, T func);

branches/e4fix/WINDOW/AW_modal.cxx

@@ -26 +26 @@
 #define AWAR_QUESTION "tmp/question"
 
-#define AW_MESSAGE_LISTEN_DELAY 500 // look in ms whether a father died
+#define AW_MESSAGE_LISTEN_DELAY 100 // look in ms whether a father died
 
 int aw_message_cb_result;

branches/e4fix/WINDOW/AW_nawar.cxx

@@ -619 +619 @@
         error = GB_push_transaction(gb_main);
         if (!error) {
-            aw_update_awar_window_geometry(this);
+            aw_update_all_window_geometry_awars(this);
             error = GB_pop_transaction(gb_main);
             if (!error) error = GB_save_in_arbprop(gb_main, filename, "a");

branches/e4fix/WINDOW/AW_window.cxx

@@ -601 +601 @@
 #define aw_awar_name_height(aww) aw_size_awar_name((aww), "height")
 
-static void aw_calculate_WM_offsets(AW_window *aww) {
-    if (p_aww(aww)->WM_top_offset == AW_FIX_POS_ON_EXPOSE) {        // very bad hack continued
-        // get last position stored in properties
-        AW_root *root  = aww->get_root();
-        int      oposx = root->awar(aw_awar_name_posx(aww))->read_int();
-        int      oposy = root->awar(aw_awar_name_posy(aww))->read_int();
-
-        // get current window position
-        short            posy, posx;
-        AW_window_Motif *motif = p_aww(aww);
-        XtVaGetValues(motif->shell,  XmNx, &posx, XmNy, &posy, NULL);
-
+void AW_window::create_user_geometry_awars(int posx, int posy, int width, int height) {
+    get_root()->awar_int(aw_awar_name_posx(this), posx);
+    get_root()->awar_int(aw_awar_name_posy(this), posy);
+    get_root()->awar_int(aw_awar_name_width(this), width);
+    get_root()->awar_int(aw_awar_name_height(this), height);
+}
+
+
+void AW_window::store_size_in_awars(int width, int height) {
+    get_root()->awar(aw_awar_name_width(this))->write_int(width);
+    get_root()->awar(aw_awar_name_height(this))->write_int(height);
+}
+
+void AW_window::get_size_from_awars(int& width, int& height) {
+    width  = get_root()->awar(aw_awar_name_width(this))->read_int();
+    height = get_root()->awar(aw_awar_name_height(this))->read_int();
+}
+
+void AW_window::store_pos_in_awars(int posx, int posy) {
+    get_root()->awar(aw_awar_name_posx(this))->write_int(posx);
+    get_root()->awar(aw_awar_name_posy(this))->write_int(posy);
+}
+
+void AW_window::get_pos_from_awars(int& posx, int& posy) {
+    posx = get_root()->awar(aw_awar_name_posx(this))->read_int();
+    posy = get_root()->awar(aw_awar_name_posy(this))->read_int();
+}
+
+#undef aw_awar_name_posx
+#undef aw_awar_name_posy
+#undef aw_awar_name_width
+#undef aw_awar_name_height
+
+static void aw_onExpose_calc_WM_offsets(AW_window *aww);
+static void aw_calc_WM_offsets_delayed(AW_root *, AW_CL cl_aww, AW_CL) { aw_onExpose_calc_WM_offsets((AW_window*)cl_aww); }
+
+static void aw_onExpose_calc_WM_offsets(AW_window *aww) {
+    AW_window_Motif *motif = p_aww(aww);
+
+    int posx,  posy;  aww->get_window_content_pos(posx, posy);
+
+    bool knows_window_position = posx != 0 || posy != 0;
+
+    if (!knows_window_position) { // oops - motif has no idea where the window has been placed
+        // assume positions stored in awars are correct and use them.
+        // This works around problems with unclickable GUI-elements when running on 'Unity'
+
+        int oposx, oposy; aww->get_pos_from_awars(oposx, oposy);
+        aww->set_window_frame_pos(oposx, oposy);
+
+        if (!motif->knows_WM_offset()) {
+            aww->get_root()->add_timed_callback(100, aw_calc_WM_offsets_delayed, (AW_CL)aww, 0);
+        }
+    }
+    else if (!motif->knows_WM_offset()) {
+        int oposx, oposy; aww->get_pos_from_awars(oposx, oposy);
         // calculate offset
         motif->WM_top_offset  = posy-oposy;
         motif->WM_left_offset = posx-oposx;
-
-#if defined(DEBUG) && 0
-        printf("aw_calculate_WM_offsets: WM_left_offset=%i WM_top_offset=%i\n", motif->WM_left_offset, motif->WM_top_offset);
-#endif // DEBUG
-    }
-
-#if defined(DEBUG) && 0
-    {
-        short posx, posy;
-        AW_window_Motif *motif = p_aww(aww);
-        XtVaGetValues(motif->shell,  XmNx, &posx, XmNy, &posy, NULL);
-        printf("[expose] Position reported by motif: %i/%i\n", posx, posy);
-    }
-#endif // DEBUG
+    }
 }
 
@@ -952 +983 @@
 }
 
-void AW_window::set_window_pos(int x, int y) {
+void AW_window::set_window_frame_pos(int x, int y) {
+    // this will set the position of the frame around the client-area (see also WM_top_offset ..)
     XtVaSetValues(p_w->shell, XmNx, (int)x, XmNy, (int)y, NULL);
 }
-void AW_window::get_window_pos(int& xpos, int& ypos) {
+void AW_window::get_window_content_pos(int& xpos, int& ypos) {
+    // this will report the position of the client-area (see also WM_top_offset ..)
     unsigned short x, y;
     XtVaGetValues(p_w->shell, XmNx, &x, XmNy, &y, NULL);
@@ -1682 +1715 @@
 }
 
-static long aw_loop_get_window_geometry(const char *, long val, void *) {
-    AW_window *aww = (AW_window *)val;
-    short posx, posy;
-
-    AW_root *root = aww->get_root();
+void aw_update_window_geometry_awars(AW_window *aww) {
+    AW_window_Motif *motif = p_aww(aww);
+
+    short          posx, posy;
     unsigned short width, height, borderwidth;
-
-    XtVaGetValues(p_aww(aww)->shell,                // bad hack
+    XtVaGetValues(motif->shell, // bad hack
                   XmNborderWidth, &borderwidth,
                   XmNwidth, &width,
@@ -1697 +1728 @@
                   NULL);
 
-    if (p_aww(aww)->WM_top_offset != AW_FIX_POS_ON_EXPOSE) {
-        posy -= p_aww(aww)->WM_top_offset;
-    }
-    posx -= p_aww(aww)->WM_left_offset;
-
-    if (posx<0) posx = 0;
-    if (posy<0) posy = 0;
-
-    root->awar(aw_awar_name_width (aww))->write_int(width);
-    root->awar(aw_awar_name_height(aww))->write_int(height);
-    root->awar(aw_awar_name_posx (aww))->write_int(posx);
-    root->awar(aw_awar_name_posy (aww))->write_int(posy);
-
+    if (motif->knows_WM_offset()) {
+        posy -= motif->WM_top_offset;
+        posx -= motif->WM_left_offset;
+
+        if (posx<0) posx = 0;
+        if (posy<0) posy = 0;
+
+        aww->store_pos_in_awars(posx, posy);
+    }
+#if defined(DEBUG)
+    else {
+        fprintf(stderr, " WM_offsets unknown. Did not update awars!\n");
+    }
+#endif
+    aww->store_size_in_awars(width, height);
+}
+
+static long aw_loop_get_window_geometry(const char *, long val, void *) {
+    aw_update_window_geometry_awars((AW_window *)val);
     return val;
 }
 
-void aw_update_awar_window_geometry(AW_root *awr) {
+void aw_update_all_window_geometry_awars(AW_root *awr) {
     GBS_hash_do_loop(awr->hash_for_windows, aw_loop_get_window_geometry, NULL);
 }
@@ -1787 +1824 @@
         bool has_user_geometry = false;
 
-        const char *temp = aw_awar_name_width(aww);
-        root->awar_int(temp, width);
+        aww->create_user_geometry_awars(posx, posy, width, height);
+
+        int user_width, user_height; aww->get_size_from_awars(user_width, user_height);
+        int user_posx,  user_posy;   aww->get_pos_from_awars(user_posx,  user_posy);
+
         if (allow_resize) {
-            int found_width = (int)root->awar(temp)->read_int();
-            if (width != found_width) {
-                has_user_geometry = true;
-                width = found_width;
-            }
-        }
-
-        temp = aw_awar_name_height(aww);
-        root->awar_int(temp, height);
-        if (allow_resize) {
-            int found_height = (int)root->awar(temp)->read_int();
-            if (height != found_height) {
-                has_user_geometry = true;
-                height = found_height;
-            }
-        }
-
-        temp = aw_awar_name_posx(aww);
-        root->awar_int(temp, posx)->set_minmax(0, 4000);
+            if (width != user_width) { width = user_width; has_user_geometry = true; }
+            if (height != user_height) { height = user_height; has_user_geometry = true; }
+        }
+
         // @@@ FIXME:  maximum should be set to current screen size minus some offset
         // to ensure that windows do not appear outside screen
-        // same for posy below!
-
-        int found_posx = (int)root->awar(temp)->read_int();
-        if (posx != found_posx) {
-            has_user_geometry = true;
-            posx = found_posx;
-        }
-
-        temp = aw_awar_name_posy(aww);
-        root->awar_int(temp, posy)->set_minmax(0, 3000);
-        int found_posy = (int)root->awar(temp)->read_int();
-        if (posy != found_posy) {
-            has_user_geometry = true;
-            posy = found_posy;
-        }
+        if (posx != user_posx) { posx = user_posx; has_user_geometry = true; }
+        if (posy != user_posy) { posy = user_posy; has_user_geometry = true; }
 
         if (has_user_geometry) {
@@ -1860 +1872 @@
         GBK_terminatef("Failed to load icon pixmap for window '%s'\n", aww->window_defaults_name);
     }
-
-#if defined(DEBUG) && 0
-    printf("aw_create_shell: pos=%i/%i size=%i%i\n", posx, posy, width, height);
-#endif // DEBUG
 
     int focusPolicy = root->focus_follows_mouse ? XmPOINTER : XmEXPLICIT;
@@ -1953 +1961 @@
     }
     XtRealizeWidget(p_aww(aww)->shell);
-    p_aww(aww)->WM_top_offset = AW_FIX_POS_ON_EXPOSE;
-}
-
-void AW_window_menu_modes::init(AW_root *root_in, const char *wid, const char *windowname, int  width, int height) {
+    p_aww(aww)->WM_top_offset = AW_CALC_OFFSET_ON_EXPOSE;
+}
+
+void AW_window_menu_modes::init(AW_root *root_in, const char *wid, const char *windowname, int  width, int height) { 
     Widget      main_window;
     Widget      help_popup;
@@ -1979 +1987 @@
 
     main_window = XtVaCreateManagedWidget("mainWindow1",
-            xmMainWindowWidgetClass, p_w->shell,
-            NULL);
+                                          xmMainWindowWidgetClass, p_w->shell,
+                                          NULL);
 
     p_w->menu_bar[0] = XtVaCreateManagedWidget("menu1", xmRowColumnWidgetClass,
-            main_window,
-            XmNrowColumnType, XmMENU_BAR,
-            NULL);
+                                               main_window,
+                                               XmNrowColumnType, XmMENU_BAR,
+                                               NULL);
 
     // create shell for help-cascade
     help_popup = XtVaCreatePopupShell("menu_shell", xmMenuShellWidgetClass,
-            p_w->menu_bar[0],
-            XmNwidth, 1,
-            XmNheight, 1,
-            XmNallowShellResize, true,
-            XmNoverrideRedirect, true,
-            NULL);
+                                      p_w->menu_bar[0],
+                                      XmNwidth, 1,
+                                      XmNheight, 1,
+                                      XmNallowShellResize, true,
+                                      XmNoverrideRedirect, true,
+                                      NULL);
 
     // create row column in Pull-Down shell
     p_w->help_pull_down = XtVaCreateWidget("menu_row_column",
-            xmRowColumnWidgetClass, help_popup,
-            XmNrowColumnType, XmMENU_PULLDOWN,
-            NULL);
+                                           xmRowColumnWidgetClass, help_popup,
+                                           XmNrowColumnType, XmMENU_PULLDOWN,
+                                           NULL);
 
     // create HELP-label in menu bar
     help_label = XtVaCreateManagedWidget("menu1_top_b1",
-            xmCascadeButtonWidgetClass, p_w->menu_bar[0],
-            RES_CONVERT(XmNlabelString, help_button),
-                                          RES_CONVERT(XmNmnemonic, help_mnemonic),
-                                          XmNsubMenuId, p_w->help_pull_down, NULL);
+                                         xmCascadeButtonWidgetClass, p_w->menu_bar[0],
+                                         RES_CONVERT(XmNlabelString, help_button),
+                                         RES_CONVERT(XmNmnemonic, help_mnemonic),
+                                         XmNsubMenuId, p_w->help_pull_down, NULL);
     XtVaSetValues(p_w->menu_bar[0], XmNmenuHelpWidget, help_label, NULL);
     root->make_sensitive(help_label, AWM_ALL);
 
     form1 = XtVaCreateManagedWidget("form1",
-    xmFormWidgetClass,
-    main_window,
-    // XmNwidth, width,
-    // XmNheight, height,
-    XmNresizePolicy, XmRESIZE_NONE,
-    // XmNx, 0,
-    // XmNy, 0,
-    NULL);
+                                    xmFormWidgetClass,
+                                    main_window,
+                                    // XmNwidth, width,
+                                    // XmNheight, height,
+                                    XmNresizePolicy, XmRESIZE_NONE,
+                                    // XmNx, 0,
+                                    // XmNy, 0,
+                                    NULL);
 
     p_w->mode_area = XtVaCreateManagedWidget("mode area",
-    xmDrawingAreaWidgetClass,
-    form1,
-    XmNresizePolicy, XmRESIZE_NONE,
-    XmNwidth, 38,
-    XmNheight, height,
-    XmNx, 0,
-    XmNy, 0,
-    XmNleftOffset, 0,
-    XmNtopOffset, 0,
-    XmNbottomAttachment, XmATTACH_FORM,
-    XmNleftAttachment, XmATTACH_POSITION,
-    XmNtopAttachment, XmATTACH_POSITION,
-    XmNmarginHeight, 2,
-    XmNmarginWidth, 1,
-    NULL);
+                                             xmDrawingAreaWidgetClass,
+                                             form1,
+                                             XmNresizePolicy, XmRESIZE_NONE,
+                                             XmNwidth, 38,
+                                             XmNheight, height,
+                                             XmNx, 0,
+                                             XmNy, 0,
+                                             XmNleftOffset, 0,
+                                             XmNtopOffset, 0,
+                                             XmNbottomAttachment, XmATTACH_FORM,
+                                             XmNleftAttachment, XmATTACH_POSITION,
+                                             XmNtopAttachment, XmATTACH_POSITION,
+                                             XmNmarginHeight, 2,
+                                             XmNmarginWidth, 1,
+                                             NULL);
 
     separator = XtVaCreateManagedWidget("separator",
-    xmSeparatorWidgetClass,
-    form1,
-    XmNx, 37,
-    XmNshadowThickness, 4,
-    XmNorientation, XmVERTICAL,
-    XmNbottomAttachment, XmATTACH_FORM,
-    XmNtopAttachment, XmATTACH_FORM,
-    XmNleftAttachment, XmATTACH_NONE,
-    XmNleftWidget, NULL,
-    XmNrightAttachment, XmATTACH_NONE,
-    XmNleftOffset, 70,
-    XmNleftPosition, 0,
-    NULL);
+                                        xmSeparatorWidgetClass,
+                                        form1,
+                                        XmNx, 37,
+                                        XmNshadowThickness, 4,
+                                        XmNorientation, XmVERTICAL,
+                                        XmNbottomAttachment, XmATTACH_FORM,
+                                        XmNtopAttachment, XmATTACH_FORM,
+                                        XmNleftAttachment, XmATTACH_NONE,
+                                        XmNleftWidget, NULL,
+                                        XmNrightAttachment, XmATTACH_NONE,
+                                        XmNleftOffset, 70,
+                                        XmNleftPosition, 0,
+                                        NULL);
 
     form2 = XtVaCreateManagedWidget("form2",
-    xmFormWidgetClass,
-    form1,
-    XmNwidth, width,
-    XmNheight, height,
-    XmNtopOffset, 0,
-    XmNbottomOffset, 0,
-    XmNleftOffset, 0,
-    XmNrightOffset, 0,
-    XmNrightAttachment, XmATTACH_FORM,
-    XmNbottomAttachment, XmATTACH_FORM,
-    XmNleftAttachment, XmATTACH_WIDGET,
-    XmNleftWidget, separator,
-    XmNtopAttachment, XmATTACH_POSITION,
-    XmNresizePolicy, XmRESIZE_NONE,
-    XmNx, 0,
-    XmNy, 0,
-    NULL);
+                                    xmFormWidgetClass,
+                                    form1,
+                                    XmNwidth, width,
+                                    XmNheight, height,
+                                    XmNtopOffset, 0,
+                                    XmNbottomOffset, 0,
+                                    XmNleftOffset, 0,
+                                    XmNrightOffset, 0,
+                                    XmNrightAttachment, XmATTACH_FORM,
+                                    XmNbottomAttachment, XmATTACH_FORM,
+                                    XmNleftAttachment, XmATTACH_WIDGET,
+                                    XmNleftWidget, separator,
+                                    XmNtopAttachment, XmATTACH_POSITION,
+                                    XmNresizePolicy, XmRESIZE_NONE,
+                                    XmNx, 0,
+                                    XmNy, 0,
+                                    NULL);
     p_w->areas[AW_INFO_AREA] =
-    new AW_area_management(root, form2, XtVaCreateManagedWidget("info_area",
-            xmDrawingAreaWidgetClass,
-            form2,
-            XmNheight, 0,
-            XmNbottomAttachment, XmATTACH_NONE,
-            XmNtopAttachment, XmATTACH_FORM,
-            XmNleftAttachment, XmATTACH_FORM,
-            XmNrightAttachment, XmATTACH_FORM,
-            XmNmarginHeight, 2,
-            XmNmarginWidth, 2,
-            NULL));
+        new AW_area_management(root, form2, XtVaCreateManagedWidget("info_area",
+                                                                    xmDrawingAreaWidgetClass,
+                                                                    form2,
+                                                                    XmNheight, 0,
+                                                                    XmNbottomAttachment, XmATTACH_NONE,
+                                                                    XmNtopAttachment, XmATTACH_FORM,
+                                                                    XmNleftAttachment, XmATTACH_FORM,
+                                                                    XmNrightAttachment, XmATTACH_FORM,
+                                                                    XmNmarginHeight, 2,
+                                                                    XmNmarginWidth, 2,
+                                                                    NULL));
 
     p_w->areas[AW_BOTTOM_AREA] =
-    new AW_area_management(root, form2, XtVaCreateManagedWidget("bottom_area",
-            xmDrawingAreaWidgetClass,
-            form2,
-            XmNheight, 0,
-            XmNbottomAttachment, XmATTACH_FORM,
-            XmNtopAttachment, XmATTACH_NONE,
-            XmNleftAttachment, XmATTACH_FORM,
-            XmNrightAttachment, XmATTACH_FORM,
-            NULL));
+        new AW_area_management(root, form2, XtVaCreateManagedWidget("bottom_area",
+                                                                    xmDrawingAreaWidgetClass,
+                                                                    form2,
+                                                                    XmNheight, 0,
+                                                                    XmNbottomAttachment, XmATTACH_FORM,
+                                                                    XmNtopAttachment, XmATTACH_NONE,
+                                                                    XmNleftAttachment, XmATTACH_FORM,
+                                                                    XmNrightAttachment, XmATTACH_FORM,
+                                                                    NULL));
 
     p_w->scroll_bar_horizontal = XtVaCreateManagedWidget("scroll_bar_horizontal",
-    xmScrollBarWidgetClass,
-    form2,
-    XmNheight, 15,
-    XmNminimum, 0,
-    XmNmaximum, AW_SCROLL_MAX,
-    XmNincrement, 10,
-    XmNsliderSize, AW_SCROLL_MAX,
-    XmNrightAttachment, XmATTACH_FORM,
-    XmNbottomAttachment, XmATTACH_FORM,
-    XmNbottomOffset, 0,
-    XmNleftAttachment, XmATTACH_FORM,
-    XmNtopAttachment, XmATTACH_NONE,
-    XmNorientation, XmHORIZONTAL,
-    XmNrightOffset, 18,
-    NULL);
+                                                         xmScrollBarWidgetClass,
+                                                         form2,
+                                                         XmNheight, 15,
+                                                         XmNminimum, 0,
+                                                         XmNmaximum, AW_SCROLL_MAX,
+                                                         XmNincrement, 10,
+                                                         XmNsliderSize, AW_SCROLL_MAX,
+                                                         XmNrightAttachment, XmATTACH_FORM,
+                                                         XmNbottomAttachment, XmATTACH_FORM,
+                                                         XmNbottomOffset, 0,
+                                                         XmNleftAttachment, XmATTACH_FORM,
+                                                         XmNtopAttachment, XmATTACH_NONE,
+                                                         XmNorientation, XmHORIZONTAL,
+                                                         XmNrightOffset, 18,
+                                                         NULL);
 
     p_w->scroll_bar_vertical = XtVaCreateManagedWidget("scroll_bar_vertical",
-    xmScrollBarWidgetClass,
-    form2,
-    XmNwidth, 15,
-    XmNminimum, 0,
-    XmNmaximum, AW_SCROLL_MAX,
-    XmNincrement, 10,
-    XmNsliderSize, AW_SCROLL_MAX,
-    XmNrightAttachment, XmATTACH_FORM,
-    XmNbottomAttachment, XmATTACH_WIDGET,
-    XmNbottomWidget, p_w->scroll_bar_horizontal,
-    XmNbottomOffset, 3,
-    XmNleftOffset, 3,
-    XmNrightOffset, 3,
-    XmNleftAttachment, XmATTACH_NONE,
-    XmNtopAttachment, XmATTACH_WIDGET,
-    XmNtopWidget, INFO_WIDGET,
-    NULL);
+                                                       xmScrollBarWidgetClass,
+                                                       form2,
+                                                       XmNwidth, 15,
+                                                       XmNminimum, 0,
+                                                       XmNmaximum, AW_SCROLL_MAX,
+                                                       XmNincrement, 10,
+                                                       XmNsliderSize, AW_SCROLL_MAX,
+                                                       XmNrightAttachment, XmATTACH_FORM,
+                                                       XmNbottomAttachment, XmATTACH_WIDGET,
+                                                       XmNbottomWidget, p_w->scroll_bar_horizontal,
+                                                       XmNbottomOffset, 3,
+                                                       XmNleftOffset, 3,
+                                                       XmNrightOffset, 3,
+                                                       XmNleftAttachment, XmATTACH_NONE,
+                                                       XmNtopAttachment, XmATTACH_WIDGET,
+                                                       XmNtopWidget, INFO_WIDGET,
+                                                       NULL);
 
     p_w->frame = XtVaCreateManagedWidget("draw_area",
-    xmFrameWidgetClass,
-    form2,
-    XmNshadowType, XmSHADOW_IN,
-    XmNshadowThickness, 2,
-    XmNleftOffset, 3,
-    XmNtopOffset, 3,
-    XmNbottomOffset, 3,
-    XmNrightOffset, 3,
-    XmNbottomAttachment, XmATTACH_WIDGET,
-    XmNbottomWidget, p_w->scroll_bar_horizontal,
-    XmNtopAttachment, XmATTACH_FORM,
-    XmNtopOffset, 0,
-    XmNleftAttachment, XmATTACH_FORM,
-    XmNrightAttachment, XmATTACH_WIDGET,
-    XmNrightWidget, p_w->scroll_bar_vertical,
-    NULL);
+                                         xmFrameWidgetClass,
+                                         form2,
+                                         XmNshadowType, XmSHADOW_IN,
+                                         XmNshadowThickness, 2,
+                                         XmNleftOffset, 3,
+                                         XmNtopOffset, 3,
+                                         XmNbottomOffset, 3,
+                                         XmNrightOffset, 3,
+                                         XmNbottomAttachment, XmATTACH_WIDGET,
+                                         XmNbottomWidget, p_w->scroll_bar_horizontal,
+                                         XmNtopAttachment, XmATTACH_FORM,
+                                         XmNtopOffset, 0,
+                                         XmNleftAttachment, XmATTACH_FORM,
+                                         XmNrightAttachment, XmATTACH_WIDGET,
+                                         XmNrightWidget, p_w->scroll_bar_vertical,
+                                         NULL);
 
     p_w->areas[AW_MIDDLE_AREA] =
-    new AW_area_management(root, p_w->frame, XtVaCreateManagedWidget("draw area",
-            xmDrawingAreaWidgetClass,
-            p_w->frame,
-            XmNmarginHeight, 0,
-            XmNmarginWidth, 0,
-            NULL));
+        new AW_area_management(root, p_w->frame, XtVaCreateManagedWidget("draw area",
+                                                                         xmDrawingAreaWidgetClass,
+                                                                         p_w->frame,
+                                                                         XmNmarginHeight, 0,
+                                                                         XmNmarginWidth, 0,
+                                                                         NULL));
 
     XmMainWindowSetAreas(main_window, p_w->menu_bar[0], (Widget) NULL, (Widget) NULL, (Widget) NULL, form1);
@@ -2166 +2174 @@
 }
 
-void AW_window_menu::init(AW_root *root_in, const char *wid, const char *windowname, int width, int height) {
+void AW_window_menu::init(AW_root *root_in, const char *wid, const char *windowname, int width, int height) { 
     Widget      main_window;
     Widget      help_popup;
@@ -2189 +2197 @@
 
     main_window = XtVaCreateManagedWidget("mainWindow1",
-            xmMainWindowWidgetClass, p_w->shell,
-            NULL);
+                                          xmMainWindowWidgetClass, p_w->shell,
+                                          NULL);
 
     p_w->menu_bar[0] = XtVaCreateManagedWidget("menu1", xmRowColumnWidgetClass,
-            main_window,
-            XmNrowColumnType, XmMENU_BAR,
-            NULL);
+                                               main_window,
+                                               XmNrowColumnType, XmMENU_BAR,
+                                               NULL);
 
     // create shell for help-cascade
     help_popup = XtVaCreatePopupShell("menu_shell", xmMenuShellWidgetClass,
-            p_w->menu_bar[0],
-            XmNwidth, 1,
-            XmNheight, 1,
-            XmNallowShellResize, true,
-            XmNoverrideRedirect, true,
-            NULL);
+                                      p_w->menu_bar[0],
+                                      XmNwidth, 1,
+                                      XmNheight, 1,
+                                      XmNallowShellResize, true,
+                                      XmNoverrideRedirect, true,
+                                      NULL);
 
     // create row column in Pull-Down shell
     p_w->help_pull_down = XtVaCreateWidget("menu_row_column",
-            xmRowColumnWidgetClass, help_popup,
-            XmNrowColumnType, XmMENU_PULLDOWN,
-            NULL);
+                                           xmRowColumnWidgetClass, help_popup,
+                                           XmNrowColumnType, XmMENU_PULLDOWN,
+                                           NULL);
 
     // create HELP-label in menu bar
     help_label = XtVaCreateManagedWidget("menu1_top_b1",
-            xmCascadeButtonWidgetClass, p_w->menu_bar[0],
-            RES_CONVERT(XmNlabelString, help_button),
-                                          RES_CONVERT(XmNmnemonic, help_mnemonic),
-                                          XmNsubMenuId, p_w->help_pull_down, NULL);
+                                         xmCascadeButtonWidgetClass, p_w->menu_bar[0],
+                                         RES_CONVERT(XmNlabelString, help_button),
+                                         RES_CONVERT(XmNmnemonic, help_mnemonic),
+                                         XmNsubMenuId, p_w->help_pull_down, NULL);
     XtVaSetValues(p_w->menu_bar[0], XmNmenuHelpWidget, help_label, NULL);
     root->make_sensitive(help_label, AWM_ALL);
 
     form1 = XtVaCreateManagedWidget("form1",
-    xmFormWidgetClass,
-    main_window,
-    // XmNwidth, width,
-    // XmNheight, height,
-    XmNresizePolicy, XmRESIZE_NONE,
-    // XmNx, 0,
-    // XmNy, 0,
-    NULL);
+                                    xmFormWidgetClass,
+                                    main_window,
+                                    // XmNwidth, width,
+                                    // XmNheight, height,
+                                    XmNresizePolicy, XmRESIZE_NONE,
+                                    // XmNx, 0,
+                                    // XmNy, 0,
+                                    NULL);
 
     p_w->mode_area = XtVaCreateManagedWidget("mode area",
-    xmDrawingAreaWidgetClass,
-    form1,
-    XmNresizePolicy, XmRESIZE_NONE,
-    XmNwidth, 17,
-    XmNheight, height,
-    XmNx, 0,
-    XmNy, 0,
-    XmNleftOffset, 0,
-    XmNtopOffset, 0,
-    XmNbottomAttachment, XmATTACH_FORM,
-    XmNleftAttachment, XmATTACH_POSITION,
-    XmNtopAttachment, XmATTACH_POSITION,
-    XmNmarginHeight, 2,
-    XmNmarginWidth, 1,
-    NULL);
+                                             xmDrawingAreaWidgetClass,
+                                             form1,
+                                             XmNresizePolicy, XmRESIZE_NONE,
+                                             XmNwidth, 17,
+                                             XmNheight, height,
+                                             XmNx, 0,
+                                             XmNy, 0,
+                                             XmNleftOffset, 0,
+                                             XmNtopOffset, 0,
+                                             XmNbottomAttachment, XmATTACH_FORM,
+                                             XmNleftAttachment, XmATTACH_POSITION,
+                                             XmNtopAttachment, XmATTACH_POSITION,
+                                             XmNmarginHeight, 2,
+                                             XmNmarginWidth, 1,
+                                             NULL);
 
     separator = p_w->mode_area;
 
     form2 = XtVaCreateManagedWidget("form2",
-    xmFormWidgetClass,
-    form1,
-    XmNwidth, width,
-    XmNheight, height,
-    XmNtopOffset, 0,
-    XmNbottomOffset, 0,
-    XmNleftOffset, 0,
-    XmNrightOffset, 0,
-    XmNrightAttachment, XmATTACH_FORM,
-    XmNbottomAttachment, XmATTACH_FORM,
-    XmNleftAttachment, XmATTACH_WIDGET,
-    XmNleftWidget, separator,
-    XmNtopAttachment, XmATTACH_POSITION,
-    XmNresizePolicy, XmRESIZE_NONE,
-    XmNx, 0,
-    XmNy, 0,
-    NULL);
+                                    xmFormWidgetClass,
+                                    form1,
+                                    XmNwidth, width,
+                                    XmNheight, height,
+                                    XmNtopOffset, 0,
+                                    XmNbottomOffset, 0,
+                                    XmNleftOffset, 0,
+                                    XmNrightOffset, 0,
+                                    XmNrightAttachment, XmATTACH_FORM,
+                                    XmNbottomAttachment, XmATTACH_FORM,
+                                    XmNleftAttachment, XmATTACH_WIDGET,
+                                    XmNleftWidget, separator,
+                                    XmNtopAttachment, XmATTACH_POSITION,
+                                    XmNresizePolicy, XmRESIZE_NONE,
+                                    XmNx, 0,
+                                    XmNy, 0,
+                                    NULL);
     p_w->areas[AW_INFO_AREA] =
-    new AW_area_management(root, form2, XtVaCreateManagedWidget("info_area",
-            xmDrawingAreaWidgetClass,
-            form2,
-            XmNheight, 0,
-            XmNbottomAttachment, XmATTACH_NONE,
-            XmNtopAttachment, XmATTACH_FORM,
-            XmNleftAttachment, XmATTACH_FORM,
-            XmNrightAttachment, XmATTACH_FORM,
-            XmNmarginHeight, 2,
-            XmNmarginWidth, 2,
-            NULL));
+        new AW_area_management(root, form2, XtVaCreateManagedWidget("info_area",
+                                                                    xmDrawingAreaWidgetClass,
+                                                                    form2,
+                                                                    XmNheight, 0,
+                                                                    XmNbottomAttachment, XmATTACH_NONE,
+                                                                    XmNtopAttachment, XmATTACH_FORM,
+                                                                    XmNleftAttachment, XmATTACH_FORM,
+                                                                    XmNrightAttachment, XmATTACH_FORM,
+                                                                    XmNmarginHeight, 2,
+                                                                    XmNmarginWidth, 2,
+                                                                    NULL));
 
     p_w->areas[AW_BOTTOM_AREA] =
-    new AW_area_management(root, form2, XtVaCreateManagedWidget("bottom_area",
-            xmDrawingAreaWidgetClass,
-            form2,
-            XmNheight, 0,
-            XmNbottomAttachment, XmATTACH_FORM,
-            XmNtopAttachment, XmATTACH_NONE,
-            XmNleftAttachment, XmATTACH_FORM,
-            XmNrightAttachment, XmATTACH_FORM,
-            NULL));
+        new AW_area_management(root, form2, XtVaCreateManagedWidget("bottom_area",
+                                                                    xmDrawingAreaWidgetClass,
+                                                                    form2,
+                                                                    XmNheight, 0,
+                                                                    XmNbottomAttachment, XmATTACH_FORM,
+                                                                    XmNtopAttachment, XmATTACH_NONE,
+                                                                    XmNleftAttachment, XmATTACH_FORM,
+                                                                    XmNrightAttachment, XmATTACH_FORM,
+                                                                    NULL));
 
     p_w->scroll_bar_horizontal = XtVaCreateManagedWidget("scroll_bar_horizontal",
-    xmScrollBarWidgetClass,
-    form2,
-    XmNheight, 15,
-    XmNminimum, 0,
-    XmNmaximum, AW_SCROLL_MAX,
-    XmNincrement, 10,
-    XmNsliderSize, AW_SCROLL_MAX,
-    XmNrightAttachment, XmATTACH_FORM,
-    XmNbottomAttachment, XmATTACH_FORM,
-    XmNbottomOffset, 0,
-    XmNleftAttachment, XmATTACH_FORM,
-    XmNtopAttachment, XmATTACH_NONE,
-    XmNorientation, XmHORIZONTAL,
-    XmNrightOffset, 18,
-    NULL);
+                                                         xmScrollBarWidgetClass,
+                                                         form2,
+                                                         XmNheight, 15,
+                                                         XmNminimum, 0,
+                                                         XmNmaximum, AW_SCROLL_MAX,
+                                                         XmNincrement, 10,
+                                                         XmNsliderSize, AW_SCROLL_MAX,
+                                                         XmNrightAttachment, XmATTACH_FORM,
+                                                         XmNbottomAttachment, XmATTACH_FORM,
+                                                         XmNbottomOffset, 0,
+                                                         XmNleftAttachment, XmATTACH_FORM,
+                                                         XmNtopAttachment, XmATTACH_NONE,
+                                                         XmNorientation, XmHORIZONTAL,
+                                                         XmNrightOffset, 18,
+                                                         NULL);
 
     p_w->scroll_bar_vertical = XtVaCreateManagedWidget("scroll_bar_vertical",
-    xmScrollBarWidgetClass,
-    form2,
-    XmNwidth, 15,
-    XmNminimum, 0,
-    XmNmaximum, AW_SCROLL_MAX,
-    XmNincrement, 10,
-    XmNsliderSize, AW_SCROLL_MAX,
-    XmNrightAttachment, XmATTACH_FORM,
-    XmNbottomAttachment, XmATTACH_WIDGET,
-    XmNbottomWidget, p_w->scroll_bar_horizontal,
-    XmNbottomOffset, 3,
-    XmNleftOffset, 3,
-    XmNrightOffset, 3,
-    XmNleftAttachment, XmATTACH_NONE,
-    XmNtopAttachment, XmATTACH_WIDGET,
-    XmNtopWidget, INFO_WIDGET,
-    NULL);
+                                                       xmScrollBarWidgetClass,
+                                                       form2,
+                                                       XmNwidth, 15,
+                                                       XmNminimum, 0,
+                                                       XmNmaximum, AW_SCROLL_MAX,
+                                                       XmNincrement, 10,
+                                                       XmNsliderSize, AW_SCROLL_MAX,
+                                                       XmNrightAttachment, XmATTACH_FORM,
+                                                       XmNbottomAttachment, XmATTACH_WIDGET,
+                                                       XmNbottomWidget, p_w->scroll_bar_horizontal,
+                                                       XmNbottomOffset, 3,
+                                                       XmNleftOffset, 3,
+                                                       XmNrightOffset, 3,
+                                                       XmNleftAttachment, XmATTACH_NONE,
+                                                       XmNtopAttachment, XmATTACH_WIDGET,
+                                                       XmNtopWidget, INFO_WIDGET,
+                                                       NULL);
 
     p_w->frame = XtVaCreateManagedWidget("draw_area",
-    xmFrameWidgetClass,
-    form2,
-    XmNshadowType, XmSHADOW_IN,
-    XmNshadowThickness, 2,
-    XmNleftOffset, 3,
-    XmNtopOffset, 3,
-    XmNbottomOffset, 3,
-    XmNrightOffset, 3,
-    XmNbottomAttachment, XmATTACH_WIDGET,
-    XmNbottomWidget, p_w->scroll_bar_horizontal,
-    XmNtopAttachment, XmATTACH_FORM,
-    XmNtopOffset, 0,
-    XmNleftAttachment, XmATTACH_FORM,
-    XmNrightAttachment, XmATTACH_WIDGET,
-    XmNrightWidget, p_w->scroll_bar_vertical,
-    NULL);
+                                         xmFrameWidgetClass,
+                                         form2,
+                                         XmNshadowType, XmSHADOW_IN,
+                                         XmNshadowThickness, 2,
+                                         XmNleftOffset, 3,
+                                         XmNtopOffset, 3,
+                                         XmNbottomOffset, 3,
+                                         XmNrightOffset, 3,
+                                         XmNbottomAttachment, XmATTACH_WIDGET,
+                                         XmNbottomWidget, p_w->scroll_bar_horizontal,
+                                         XmNtopAttachment, XmATTACH_FORM,
+                                         XmNtopOffset, 0,
+                                         XmNleftAttachment, XmATTACH_FORM,
+                                         XmNrightAttachment, XmATTACH_WIDGET,
+                                         XmNrightWidget, p_w->scroll_bar_vertical,
+                                         NULL);
 
     p_w->areas[AW_MIDDLE_AREA] =
-    new AW_area_management(root, p_w->frame, XtVaCreateManagedWidget("draw area",
-            xmDrawingAreaWidgetClass,
-            p_w->frame,
-            XmNmarginHeight, 0,
-            XmNmarginWidth, 0,
-            NULL));
+        new AW_area_management(root, p_w->frame, XtVaCreateManagedWidget("draw area",
+                                                                         xmDrawingAreaWidgetClass,
+                                                                         p_w->frame,
+                                                                         XmNmarginHeight, 0,
+                                                                         XmNmarginWidth, 0,
+                                                                         NULL));
 
     XmMainWindowSetAreas(main_window, p_w->menu_bar[0], (Widget) NULL,
-    (Widget) NULL, (Widget) NULL, form1);
+                         (Widget) NULL, (Widget) NULL, form1);
 
     aw_realize_widget(this);
@@ -2399 +2407 @@
 }
 
-void AW_window_simple_menu::init(AW_root *root_in, const char *wid, const char *windowname) {
+void AW_window_simple_menu::init(AW_root *root_in, const char *wid, const char *windowname) { 
     root = root_in; // for macro
 
@@ -2420 +2428 @@
 
     main_window = XtVaCreateManagedWidget("mainWindow1",
-            xmMainWindowWidgetClass, p_w->shell,
-            NULL);
+                                          xmMainWindowWidgetClass, p_w->shell,
+                                          NULL);
 
     p_w->menu_bar[0] = XtVaCreateManagedWidget("menu1", xmRowColumnWidgetClass,
-            main_window,
-            XmNrowColumnType, XmMENU_BAR,
-            NULL);
+                                               main_window,
+                                               XmNrowColumnType, XmMENU_BAR,
+                                               NULL);
 
     // create shell for help-cascade
     help_popup = XtVaCreatePopupShell("menu_shell", xmMenuShellWidgetClass,
-            p_w->menu_bar[0],
-            XmNwidth, 1,
-            XmNheight, 1,
-            XmNallowShellResize, true,
-            XmNoverrideRedirect, true,
-            NULL);
+                                      p_w->menu_bar[0],
+                                      XmNwidth, 1,
+                                      XmNheight, 1,
+                                      XmNallowShellResize, true,
+                                      XmNoverrideRedirect, true,
+                                      NULL);
 
     // create row column in Pull-Down shell
     p_w->help_pull_down = XtVaCreateWidget("menu_row_column",
-            xmRowColumnWidgetClass, help_popup,
-            XmNrowColumnType, XmMENU_PULLDOWN,
-            NULL);
+                                           xmRowColumnWidgetClass, help_popup,
+                                           XmNrowColumnType, XmMENU_PULLDOWN,
+                                           NULL);
 
     // create HELP-label in menu bar
     help_label = XtVaCreateManagedWidget("menu1_top_b1",
-            xmCascadeButtonWidgetClass, p_w->menu_bar[0],
-            RES_CONVERT(XmNlabelString, help_button),
-                                          RES_CONVERT(XmNmnemonic, help_mnemonic),
-                                          XmNsubMenuId, p_w->help_pull_down, NULL);
+                                         xmCascadeButtonWidgetClass, p_w->menu_bar[0],
+                                         RES_CONVERT(XmNlabelString, help_button),
+                                         RES_CONVERT(XmNmnemonic, help_mnemonic),
+                                         XmNsubMenuId, p_w->help_pull_down, NULL);
     XtVaSetValues(p_w->menu_bar[0], XmNmenuHelpWidget, help_label, NULL);
     root->make_sensitive(help_label, AWM_ALL);
 
     form1 = XtVaCreateManagedWidget("form1",
-    xmFormWidgetClass,
-    main_window,
-    XmNtopOffset, 10,
-    XmNresizePolicy, XmRESIZE_NONE,
-    NULL);
+                                    xmFormWidgetClass,
+                                    main_window,
+                                    XmNtopOffset, 10,
+                                    XmNresizePolicy, XmRESIZE_NONE,
+                                    NULL);
 
     p_w->areas[AW_INFO_AREA] =
-    new AW_area_management(root, form1, XtVaCreateManagedWidget("info_area",
-            xmDrawingAreaWidgetClass,
-            form1,
-            XmNbottomAttachment, XmATTACH_FORM,
-            XmNtopAttachment, XmATTACH_FORM,
-            XmNleftAttachment, XmATTACH_FORM,
-            XmNrightAttachment, XmATTACH_FORM,
-            XmNmarginHeight, 2,
-            XmNmarginWidth, 2,
-            NULL));
+        new AW_area_management(root, form1, XtVaCreateManagedWidget("info_area",
+                                                                    xmDrawingAreaWidgetClass,
+                                                                    form1,
+                                                                    XmNbottomAttachment, XmATTACH_FORM,
+                                                                    XmNtopAttachment, XmATTACH_FORM,
+                                                                    XmNleftAttachment, XmATTACH_FORM,
+                                                                    XmNrightAttachment, XmATTACH_FORM,
+                                                                    XmNmarginHeight, 2,
+                                                                    XmNmarginWidth, 2,
+                                                                    NULL));
 
     aw_realize_widget(this);
@@ -3127 +3135 @@
         else {
             aw_assert(recalc_size_at_show == AW_RESIZE_USER);
-            // check whether user size is too small and increase to minimum (aka default)
-            int default_width, default_height;
-            get_window_size(default_width, default_height);
-            AW_root *tmp_root = get_root();
-            int user_width = tmp_root->awar(aw_awar_name_width(this))->read_int();
-            int user_height = tmp_root->awar(aw_awar_name_height(this))->read_int();
-
-            if (user_width<default_width) user_width = default_width;
-            if (user_height<default_height) user_height = default_height;
+            // check whether user size is too small and increase to minimum window size
+
+            int min_width, min_height;   get_window_size(min_width, min_height);
+            int user_width, user_height; get_size_from_awars(user_width, user_height);
+
+            if (user_width <min_width)  user_width  = min_width;
+            if (user_height<min_height) user_height = min_height;
 
             set_window_size(user_width, user_height);
@@ -3142 +3148 @@
     }
 
-    if (recalc_pos_at_show != AW_KEEP_POS) {
+    {
         int  posx, posy;
         bool setPos = false;
@@ -3153 +3159 @@
                 int mx, my; if (!get_mouse_pos(mx, my)) goto FALLBACK_CENTER;
                 int width, height; get_window_size(width, height);
-                int wx, wy; get_window_pos(wx, wy);
-
-                int wx2 = wx+width-1;
-                int wy2 = wy+height-1;
-
-                if (mx<wx || mx>wx2 || my<wy || my>wy2) { // mouse is outside window
+                int wx, wy; get_window_content_pos(wx, wy);
+
+                if (wx || wy) {
+                    if (p_w->knows_WM_offset()) {
+                        wx -= p_w->WM_left_offset;
+                        wy -= p_w->WM_top_offset;
+
+                        width  += p_w->WM_left_offset;
+                        height += p_w->WM_top_offset;
+                    }
+
+                    int wx2 = wx+width-1;
+                    int wy2 = wy+height-1;
+
+                    if (mx<wx) { setPos = true; wx = mx; } else if (mx>wx2) { setPos = true; wx = mx-width+1; }
+                    if (my<wy) { setPos = true; wy = my; } else if (my>wy2) { setPos = true; wy = my-height+1; }
+
+                    posx = wx;
+                    posy = wy;
+                }
+                else {
                     setPos = true;
-                    posx   = mx-width/2; // center window on mouse position
+                    posx   = mx-width/2;
                     posy   = my-height/2;
                 }
+
+                if (posx<0) posx = 0;
+                if (posy<0) posy = 0;
+
                 break;
             }
             case AW_REPOS_TO_CENTER: {
-            FALLBACK_CENTER :
+                  FALLBACK_CENTER :
                 int width, height; get_window_size(width, height);
                 int swidth, sheight; get_screen_size(swidth, sheight);
@@ -3177 +3202 @@
 
             case AW_KEEP_POS:
-                aw_assert(0);
                 break;
         }
 
-        if (setPos) {
-            int currx, curry;
-            get_window_pos(currx, curry);
-            if (currx != posx || curry != posy) {
-#if defined(DEBUG) && 0
-                printf("force position at show_internal: %i/%i\n", posx, posy);
-#endif // DEBUG
-                set_window_pos(posx, posy);
-            }
-        }
+        if (setPos) store_pos_in_awars(posx, posy);
+        else get_pos_from_awars(posx, posy);
+
+        set_window_frame_pos(posx, posy); // always set pos
     }
 
     XtPopup(p_w->shell, grab);
-    if (p_w->WM_top_offset == AW_FIX_POS_ON_EXPOSE) {              // very bad hack
-        set_expose_callback(AW_INFO_AREA, (AW_CB)aw_calculate_WM_offsets, 0, 0);
+    if (!expose_callback_added) {
+        set_expose_callback(AW_INFO_AREA, (AW_CB)aw_onExpose_calc_WM_offsets, 0, 0); // @@@ should be removed after it was called once
+        expose_callback_added = true;
     }
 }
@@ -3211 +3230 @@
 void AW_window::hide() {
     if (window_is_shown) {
+        aw_update_window_geometry_awars(this);
         if (hide_cb) hide_cb(this);
         get_root()->window_hide();

branches/e4fix/WINDOW/aw_nawar.hxx

@@ -92 +92 @@
 };
 
-void aw_update_awar_window_geometry(AW_root *awr);
+void aw_update_window_geometry_awars(AW_window *aww); // one window
+void aw_update_all_window_geometry_awars(AW_root *awr); // all windows
 
 #else

branches/e4fix/WINDOW/aw_window.hxx

@@ -198 +198 @@
 enum AW_PosRecalc {
     AW_KEEP_POS            = 0,                     // do not change position on show
-    AW_REPOS_TO_CENTER     = 1,                     // center the window on show
+    AW_REPOS_TO_CENTER     = 1,                     // center the window on show (unused atm)
     AW_REPOS_TO_MOUSE      = 2,                     // move the window under the current mouse position
     AW_REPOS_TO_MOUSE_ONCE = 3,                     // like AW_REPOS_TO_MOUSE, but only done once!
@@ -210 +210 @@
     aw_hide_cb         hide_cb;
 
+    bool expose_callback_added;
+    
     void all_menus_created() const;
     void create_toggle(const char *var_name, aw_toggle_data *tdata);
@@ -390 +392 @@
 
 
+    void create_user_geometry_awars(int posx, int posy, int width, int height);
+    
     // ************** Control window size  *********
     void set_window_size(int width, int height);
@@ -395 +399 @@
     void window_fit();                              // Recalculate the size of a window with buttons
 
+    void store_size_in_awars(int width, int height);
+    void get_size_from_awars(int& width, int& height);
+
 
     // ************** Control window position  *********
-    void set_window_pos(int width, int height);
-    void get_window_pos(int& xpos, int& ypos);
-
+    void set_window_frame_pos(int xpos, int ypos);
+    void get_window_content_pos(int& xpos, int& ypos);
+
+    void store_pos_in_awars(int xpos, int ypos);
+    void get_pos_from_awars(int& xpos, int& ypos);
+    
+    
     // *****************
 

branches/e4fix/WINDOW/aw_window_Xm.hxx

@@ -272 +272 @@
 
 const int AW_NUMBER_OF_F_KEYS = 20;
-#define AW_FIX_POS_ON_EXPOSE -12345
+#define AW_CALC_OFFSET_ON_EXPOSE -12345
 
 class AW_window_Motif : virtual Noncopyable {
@@ -301 +301 @@
 
     AW_area_management *areas[AW_MAX_AREA];
-    int                 WM_top_offset; // WM top area
-    int                 WM_left_offset;
+
+    int WM_top_offset;                 // correction between position set and position reported ( = size of window frame - in most cases!)
+    int WM_left_offset;
+
+    bool knows_WM_offset() const { return WM_top_offset != AW_CALC_OFFSET_ON_EXPOSE; }
 
     AW_window_Motif();

branches/e4fix/arb_INSTALL.txt

@@ -114 +114 @@
 --------------------------------------------------
 
-- expat, xmllint, sablotron 0.82-1.0 [needed for target 'help' only]
+- expat, xmllint, xsltproc [needed for target 'help' only]
 - openmotif, openmotif-devel
 - xaw???
 - libtiff-devel
-- java 1.3.1 or above [needed for arb_probe_library only]
 - lynx
 
@@ -128 +127 @@
 - mesaglw-devel (opensuse)
 - libpng
-- libglew                 
+- libglew
+- glew-devel (opensuse)
 - freeglut
 - freeglut-devel