Changeset 6358 for branches/stable_5.0

Timestamp:

19/01/10 14:11:52 (2 years ago)

Author:

westram

Message:

• backport [6353], [6354] and [6357]

Location:

branches/stable_5.0

Files:

• EDIT4/ED4_cursor.cxx (modified) (5 diffs)
• EDIT4/ED4_main.cxx (modified) (2 diffs)
• EDIT4/ED4_no_class.cxx (modified) (1 diff)
• EDIT4/ED4_root.cxx (modified) (2 diffs)
• EDIT4/EDB_root_bact.cxx (modified) (3 diffs)
• EDIT4/ed4_class.hxx (modified) (1 diff)
• EDIT4/ed4_defs.hxx (modified) (1 diff)
• NTREE/NT_edconf.cxx (modified) (3 diffs)

branches/stable_5.0/EDIT4/ED4_cursor.cxx

@@ -592 +592 @@
 }
 
+void ED4_init_notFoundMessage() {
+    not_found_counter = 0;
+    not_found_message = GBS_stropen(10000);
+    // GBS_strcat(not_found_message,"Species not found: ");
+}
+void ED4_finish_and_show_notFoundMessage() {
+    if (not_found_counter != 0) {
+        GBS_strcat(not_found_message, GBS_global_string("(skipped display of %zu more species)\n", not_found_counter-MAX_SHOWN_MISSING_SPECIES));
+        char *out_message = GBS_strclose(not_found_message);
+        aw_message(out_message);
+        aw_message(GBS_global_string("Couldn't load %zu species:", not_found_counter));
+        free(out_message);
+    }
+    else {
+        GBS_strforget(not_found_message);
+    }
+    not_found_message = 0;
+}
+
 void ED4_get_and_jump_to_species(GB_CSTR species_name)
 {
@@ -608 +627 @@
         ED4_index                  lot                 = 0;
 
-        all_found         = 0;
-        not_found_message = GBS_stropen(1000);
-        GBS_strcat(not_found_message,"Species not found: ");
+        ED4_init_notFoundMessage();
 
         sprintf(string, "-L%s", species_name);
@@ -618 +635 @@
         loaded = 1;
 
-        {
-            char *out_message = GBS_strclose(not_found_message);
-            not_found_message = 0;
-            if (all_found != 0) aw_message(out_message);
-            free(out_message);
-        }
+        ED4_finish_and_show_notFoundMessage();
 
         {
@@ -699 +711 @@
         aw_status("Loading species...");
 
-        all_found         = 0;
-        not_found_message = GBS_stropen(1000);
-        GBS_strcat(not_found_message,"Species not found: ");
+        ED4_init_notFoundMessage();
 
         while (gb_species) {
@@ -755 +765 @@
         aw_message(GBS_global_string("Loaded %i of %i marked species.", inserted, marked));
 
-        {
-            char *out_message = GBS_strclose(not_found_message);
-            not_found_message = 0;
-            if (all_found != 0) aw_message(out_message);
-            free(out_message);
-        }
-
+        ED4_finish_and_show_notFoundMessage();
+        
         if (inserted) {
             /* new AAseqTerminals should be created if it is in ProtView mode */

branches/stable_5.0/EDIT4/ED4_main.cxx

@@ -52 +52 @@
 
 long           ED4_counter = 0;
-long           all_found;       // nr of species which haven't been found
-long           species_read;    // nr of species read; important during loading
+size_t         not_found_counter;                   // nr of species which haven't been found
 GBS_strstruct *not_found_message;
-long           max_seq_terminal_length; // global maximum of sequence terminal length
-ED4_EDITMODI   awar_edit_modus;
-long           awar_edit_direction;
-bool           move_cursor;     // only needed for editing in consensus
-bool           DRAW;
-bool           last_window_reached; // needed for refreshing all windows (if TRUE refresh/...-flags will be cleared)
+
+long         max_seq_terminal_length;               // global maximum of sequence terminal length
+ED4_EDITMODI awar_edit_modus;
+long         awar_edit_direction;
+bool         move_cursor;                           // only needed for editing in consensus
+bool         DRAW;
+bool         last_window_reached;                   // needed for refreshing all windows (if TRUE refresh/...-flags will be cleared)
 
 size_t status_count_total;                          // used for consensus progress bar
@@ -69 +69 @@
 void ED4_config_change_cb(AW_root *)
 {
-
     // @@@ FIXME: ok to be empty ? check!
 }

branches/stable_5.0/EDIT4/ED4_no_class.cxx

@@ -1316 +1316 @@
     ED4_calc_terminal_extentions();
 
-    all_found = 0;
-    species_read = 0;
     max_seq_terminal_length = 0;
-    not_found_message = GBS_stropen(1000);
-    GBS_strcat(not_found_message,"Some species not found:\n");
+    
+    ED4_init_notFoundMessage();
 
 

branches/stable_5.0/EDIT4/ED4_root.cxx

@@ -732 +732 @@
     aw_root->add_timed_callback(2000,ED4_timer,(AW_CL)0,(AW_CL)0);
 
-    char *out_message = GBS_strclose(not_found_message);
-    not_found_message = 0;
-    if (all_found != 0) aw_message(out_message);
-    free(out_message);
+    ED4_finish_and_show_notFoundMessage();
 
     return ( ED4_R_OK );
@@ -1969 +1966 @@
     DRAW                    = 1;
     move_cursor             = 0;
-    all_found               = 0;
-    species_read            = 0;
     max_seq_terminal_length = 0;
 
-    not_found_message = GBS_stropen(1000);
-
-    GBS_strcat(not_found_message,"Some species not found:\n");
+    ED4_init_notFoundMessage();
 
     return ( new_window->aww );

branches/stable_5.0/EDIT4/EDB_root_bact.cxx

@@ -75 +75 @@
     }
 
-
     if (!gb_datamode) { // didn't find this species
         char dummy[150];
-        all_found++;
-        sprintf(dummy,"%ld. %s\n",all_found, str);
-        GBS_strcat(not_found_message,dummy);
+        not_found_counter++;
+        if (not_found_counter <= MAX_SHOWN_MISSING_SPECIES) {
+            sprintf(dummy,"%zu. %s\n", not_found_counter, str);
+            GBS_strcat(not_found_message,dummy);
+        }
         return ED4_R_BREAK;
     }
 
-    // check whether sequence has data in desired alignment
+        // check whether sequence has data in desired alignment
     bool has_alignment = 0 != GB_entry(gb_datamode,ED4_ROOT->alignment_name);
     if (!has_alignment) {
         if (datamode == ED4_D_SPECIES) { // only warn about species w/o data (SAIs are skipped silently)
             char dummy[150];
-            all_found++;
-            sprintf(dummy,"%ld. %s (no data in alignment)\n",all_found, str);
-            GBS_strcat(not_found_message,dummy);
+            not_found_counter++;
+            if (not_found_counter <= MAX_SHOWN_MISSING_SPECIES) {
+                sprintf(dummy,"%zu. %s (no data in alignment)\n", not_found_counter, str);
+                GBS_strcat(not_found_message,dummy);
+            }
         }
         return ED4_R_BREAK;
@@ -138 +141 @@
     local_count_position += max(name_coords, seq_coords);
     name_coords = seq_coords = 0;
-    species_read ++;
 
     if (!(multi_species_manager->flag.hidden)) {
@@ -586 +588 @@
     sequence_terminal->parent->resize_requested_by_child();
 
-    species_read ++;
     (*y) += height_terminal + height_spacer;
 

branches/stable_5.0/EDIT4/ed4_class.hxx

@@ -1966 +1966 @@
 void ED4_selected_SAI_changed_cb     (AW_root *aw_root);
 
+void ED4_init_notFoundMessage();
+void ED4_finish_and_show_notFoundMessage();
+
 extern int  ED4_elements_in_species_container; // # of elements in species container
 void        ED4_undo_redo               (AW_window*, AW_CL undo_type);

branches/stable_5.0/EDIT4/ed4_defs.hxx

@@ -38 +38 @@
 extern int SEQ_TERM_TEXT_YOFFSET;
 
-extern int            MAXSEQUENCECHARACTERLENGTH; // greatest # of characters in a sequence string terminal
-extern int            MAXSPECIESWIDTH;
-extern int            MAXINFOWIDTH;
-extern long           ED4_counter;
-extern long           all_found; // nr of species which haven't been found
-extern long           species_read; // nr of species read; important during loading
-extern GBS_strstruct *not_found_message;
-extern long           max_seq_terminal_length; // global maximum of sequence terminal length
-extern ED4_EDITMODI   awar_edit_modus;
-extern long           awar_edit_direction;
-extern bool           move_cursor; //only needed for editing in consensus
-extern bool           DRAW;
-extern bool           last_window_reached; //only needed for refreshing all windows
+extern int  MAXSEQUENCECHARACTERLENGTH;             // greatest # of characters in a sequence string terminal
+extern int  MAXSPECIESWIDTH;
+extern int  MAXINFOWIDTH;
+extern long ED4_counter;
+
+// use ED4_init_notFoundMessage and ED4_finish_and_show_notFoundMessage to
+// modify the following elements
+#define MAX_SHOWN_MISSING_SPECIES 200U              // limit no of missing species/data printed into not_found_message
+extern size_t         not_found_counter;            // nr of species which haven't been found
+extern GBS_strstruct *not_found_message;            // error message containing (some) missing/unloadable species
+
+extern long         max_seq_terminal_length;        // global maximum of sequence terminal length
+extern ED4_EDITMODI awar_edit_modus;
+extern long         awar_edit_direction;
+extern bool         move_cursor;                    //only needed for editing in consensus
+extern bool         DRAW;
+extern bool         last_window_reached;            //only needed for refreshing all windows
 
 extern size_t status_count_total; // used for consensus progress bar

branches/stable_5.0/NTREE/NT_edconf.cxx

@@ -399 +399 @@
     GBDATA         *gb_configuration = GBT_find_configuration(GLOBAL_gb_main,cn);
     if (!gb_configuration){
-        aw_message(GBS_global_string("Configuration '%s' not found in the database",cn));
+        aw_message(GBS_global_string("Configuration '%s' not found in the database", cn));
     }
     else {
-        GBDATA *gb_middle_area = GB_search(gb_configuration,"middle_area",GB_STRING);
-        char *md = 0;
-        if (gb_middle_area){
+        GBDATA *gb_middle_area  = GB_search(gb_configuration,"middle_area",GB_STRING);
+        char   *md              = 0;
+        size_t  unknown_species = 0;
+
+        if (gb_middle_area) {
             extractType ext_type = extractType(cl_extractType);
 
@@ -455 +457 @@
                         GB_write_flag(gb_species,mark);
                     }
+                    else {
+                        unknown_species++;
+                    }
                 }
             }
@@ -460 +465 @@
             GBS_free_hash(was_marked);
         }
+
+        if (unknown_species>0) {
+            aw_message(GBS_global_string("configuration '%s' contains %zu unknown species", cn, unknown_species));
+        }
+
         free(md);
     }