Changeset 6269 for branches

Timestamp:

23/11/09 08:54:41 (2 years ago)

Author:

westram

Message:

• merged 6262-6267

Location:

branches/clusters

Files:

• ARBDB/ad_prot.h (modified) (1 diff)
• ARBDB/adstring.c (modified) (1 diff)
• AWTC/AWTC_constructSequence.cxx (deleted)
• AWTC/AWTC_seq_search.cxx (deleted)
• AWTC/Makefile (modified) (2 diffs)
• AWTC/awtc_constructSequence.hxx (deleted)
• AWTC/awtc_seq_search.hxx (deleted)
• EDIT4/ED4_root.cxx (modified) (1 diff)
• EDIT4/Makefile (modified) (1 diff)
• PERL_SCRIPTS/GENOME/GI.pm (modified) (3 diffs)
• PERL_SCRIPTS/GENOME/import_proteomdata.pl (modified) (2 diffs)
• PERL_SCRIPTS/SPECIES/tools.pm (modified) (1 diff)
• SL/FAST_ALIGNER/AWTC_constructSequence.cxx (copied) (copied from trunk/SL/FAST_ALIGNER/AWTC_constructSequence.cxx)
• SL/FAST_ALIGNER/AWTC_seq_search.cxx (copied) (copied from trunk/SL/FAST_ALIGNER/AWTC_seq_search.cxx)
• SL/FAST_ALIGNER/ClustalV.cxx (modified) (7 diffs)
• SL/FAST_ALIGNER/Makefile (modified) (3 diffs)
• SL/FAST_ALIGNER/awtc_constructSequence.hxx (copied) (copied from trunk/SL/FAST_ALIGNER/awtc_constructSequence.hxx)
• SL/FAST_ALIGNER/awtc_seq_search.hxx (copied) (copied from trunk/SL/FAST_ALIGNER/awtc_seq_search.hxx)
• SL/FAST_ALIGNER/fast_aligner.cxx (modified) (8 diffs)
• SOURCE_TOOLS/generate_all_links.sh (modified) (1 diff)
• lib/macros/ARB/SEQ_DATA/dashes2dots_at_sequenceends_of_marked.amc (modified) (1 diff)
• lib/macros/replamb.amc (modified) (1 diff)
• lib/macros/test.amc (modified) (1 diff)
• lib/macros/testwl.amc (modified) (1 diff)
• lib/macros/toggle_color.amc (modified) (1 diff)
• lib/macros/xopen.amc (modified) (1 diff)

branches/clusters/ARBDB/ad_prot.h

@@ -41 +41 @@
 GB_ERROR GB_export_IO_error P_((const char *action, const char *filename));
 GB_ERROR GB_print_error P_((void));
-GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED;
+NOT4PERL GB_ERROR GB_get_error P_((void)) __ATTR__DEPRECATED;
 GB_BOOL GB_have_error P_((void));
 GB_ERROR GB_await_error P_((void));

branches/clusters/ARBDB/adstring.c

@@ -296 +296 @@
 }
 
-GB_ERROR GB_get_error() {
+NOT4PERL GB_ERROR GB_get_error() {
     /* goes to header: __ATTR__DEPRECATED  */
 

branches/clusters/AWTC/Makefile

@@ -29 +29 @@
 # For formatting issues see SOURCE_TOOLS/fix_depends.pl
 
-AWTC_constructSequence.o: awtc_constructSequence.hxx
-AWTC_constructSequence.o: awtc_seq_search.hxx
-AWTC_constructSequence.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
-AWTC_constructSequence.o: $(ARBHOME)/INCLUDE/ad_prot.h
-AWTC_constructSequence.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
-AWTC_constructSequence.o: $(ARBHOME)/INCLUDE/arb_assert.h
-AWTC_constructSequence.o: $(ARBHOME)/INCLUDE/arbdb.h
-AWTC_constructSequence.o: $(ARBHOME)/INCLUDE/arbdb_base.h
-AWTC_constructSequence.o: $(ARBHOME)/INCLUDE/arbdbt.h
-AWTC_constructSequence.o: $(ARBHOME)/INCLUDE/arbtools.h
-AWTC_constructSequence.o: $(ARBHOME)/INCLUDE/attributes.h
-AWTC_constructSequence.o: $(ARBHOME)/INCLUDE/aw_device.hxx
-AWTC_constructSequence.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
-AWTC_constructSequence.o: $(ARBHOME)/INCLUDE/aw_position.hxx
-AWTC_constructSequence.o: $(ARBHOME)/INCLUDE/aw_root.hxx
-AWTC_constructSequence.o: $(ARBHOME)/INCLUDE/aw_window.hxx
-
 AWTC_next_neighbours.o: awtc_next_neighbours.hxx
 AWTC_next_neighbours.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
@@ -65 +48 @@
 AWTC_next_neighbours.o: $(ARBHOME)/INCLUDE/servercntrl.h
 
-AWTC_seq_search.o: awtc_seq_search.hxx
-AWTC_seq_search.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
-AWTC_seq_search.o: $(ARBHOME)/INCLUDE/ad_prot.h
-AWTC_seq_search.o: $(ARBHOME)/INCLUDE/arb_assert.h
-AWTC_seq_search.o: $(ARBHOME)/INCLUDE/arbdb.h
-AWTC_seq_search.o: $(ARBHOME)/INCLUDE/arbdb_base.h
-AWTC_seq_search.o: $(ARBHOME)/INCLUDE/arbtools.h
-AWTC_seq_search.o: $(ARBHOME)/INCLUDE/attributes.h
-AWTC_seq_search.o: $(ARBHOME)/INCLUDE/aw_root.hxx
-
 AWTC_submission.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
 AWTC_submission.o: $(ARBHOME)/INCLUDE/ad_prot.h

branches/clusters/EDIT4/ED4_root.cxx

@@ -18 +18 @@
 
 #include <fast_aligner.hxx>
-#include <awtc_constructSequence.hxx>
+// #include <awtc_constructSequence.hxx>
 
 #include <arb_version.h>

branches/clusters/EDIT4/Makefile

@@ -491 +491 @@
 ED4_root.o: $(ARBHOME)/INCLUDE/awt_map_key.hxx
 ED4_root.o: $(ARBHOME)/INCLUDE/awt_seq_colors.hxx
-ED4_root.o: $(ARBHOME)/INCLUDE/awtc_constructSequence.hxx
 ED4_root.o: $(ARBHOME)/INCLUDE/BI_helix.hxx
 ED4_root.o: $(ARBHOME)/INCLUDE/fast_aligner.hxx

branches/clusters/PERL_SCRIPTS/GENOME/GI.pm

@@ -72 +72 @@
       $gb_orf = BIO::create_nonexisting_gene($gb_genome, $orf);
       if (!$gb_orf) {
-        my $reason = ARB::get_error();
+        my $reason = ARB::await_error();
         $error = "cannot create gene '$orf' ($reason)";
       }
@@ -78 +78 @@
         my $gb_locus_tag = ARB::search($gb_orf, "locus_tag", "STRING");
         if (!$gb_locus_tag) {
-          my $reason = ARB::get_error();
+          my $reason = ARB::await_error();
           $error = "cannot create field 'locus_tag' ($reason)";
         }
@@ -106 +106 @@
     $gb_field = ARB::search($gb_container, $field_name, $field_type);
     if (!$gb_field) {
-      my $reason = ARB::get_error();
+      my $reason = ARB::await_error();
       $error = "Can't create '$field_name' ($reason)";
     }

branches/clusters/PERL_SCRIPTS/GENOME/import_proteomdata.pl

@@ -54 +54 @@
 my $gb_gene_data = ARB::search($gb_genome, "gene_data", "CONTAINER");
 if (!$gb_gene_data) {
-  my $reason = ARB::get_error();
+  my $reason = ARB::await_error();
   GI::error("Couldn't find or create container 'gene_data' for organism '$genome_name' ($reason)");
 }
@@ -78 +78 @@
 
     if (!$gb_substrate) {
-      my $reason = ARB::get_error();
+      my $reason = ARB::await_error();
       $error = "Could not create container '$substrate_field' ($reason)";
     }

branches/clusters/PERL_SCRIPTS/SPECIES/tools.pm

@@ -37 +37 @@
 sub expectError($) {
   my ($where) = @_;
-  my $err = ARB::get_error();
+  my $err = ARB::await_error();
 
-  if (not $err) { $err = "Unknown error"; }
   dieOnError($err,$where);
 }

branches/clusters/SL/FAST_ALIGNER/ClustalV.cxx

@@ -384 +384 @@
 
 #if (defined(DISPLAY_DIFF) || defined(MATRIX_DUMP))
-static GB_ERROR p_decode(const unsigned char *naseq, unsigned char *seq, int l) {
+static void p_decode(const unsigned char *naseq, unsigned char *seq, int l) {
     int len = strlen(amino_acid_order);
 
@@ -392 +392 @@
         seq[i] = amino_acid_order[naseq[i]];
     }
-
-    return 0;
-}
-
-static GB_ERROR n_decode(const unsigned char *naseq, unsigned char *seq, int l) {
+}
+
+static void n_decode(const unsigned char *naseq, unsigned char *seq, int l) {
     int len = strlen(nucleic_acid_order);
 
@@ -404 +402 @@
         seq[i] = nucleic_acid_order[naseq[i]];
     }
-
-    return 0;
 }
 #endif
@@ -1106 +1102 @@
 }
 
-static GB_ERROR p_encode(const unsigned char *seq, unsigned char *naseq, int l) /* code seq as ints .. use -2 for gap */ {
+static void p_encode(const unsigned char *seq, unsigned char *naseq, int l) /* code seq as ints .. use -2 for gap */ {
     bool warned = false;
 
@@ -1130 +1126 @@
         naseq[i] = c;
     }
-
-    return 0;
-}
-
-static GB_ERROR n_encode(const unsigned char *seq,unsigned char *naseq,int l)
+}
+
+static void n_encode(const unsigned char *seq,unsigned char *naseq,int l)
 {                                       /* code seq as ints .. use -2 for gap */
     int i;
@@ -1156 +1150 @@
         naseq[i] = c;
     }
-
-    return 0;
 }
 
@@ -1212 +1204 @@
 
         {
-            GB_ERROR (*encode)(const unsigned char*,unsigned char*,int) = dnaflag ? n_encode : p_encode;
-
-            error = encode((const unsigned char*)(seq1-1), seq_array[1], length1);
-            if (!error) {
-                seqlen_array[1] = length1;
-                error = encode((const unsigned char*)(seq2-1), seq_array[2], length2);
-                if (!error) {
-                    seqlen_array[2] = length2;
-
-                    do_align(/* gap_open,*/ score, max(length1,length2));
-                    int alignedLength = add_ggaps(max_seq_length);
-
-                    *resultPtr1   = result[1]+1;
-                    *resultPtr2   = result[2]+1;
-                    *resLengthPtr = alignedLength;
-                }
-            }
+            void (*encode)(const unsigned char*,unsigned char*,int) = dnaflag ? n_encode : p_encode;
+
+            encode((const unsigned char*)(seq1-1), seq_array[1], length1);
+            seqlen_array[1] = length1;
+            encode((const unsigned char*)(seq2-1), seq_array[2], length2);
+            seqlen_array[2] = length2;
+
+            do_align(/* gap_open,*/ score, max(length1,length2));
+            int alignedLength = add_ggaps(max_seq_length);
+
+            *resultPtr1   = result[1]+1;
+            *resultPtr2   = result[2]+1;
+            *resLengthPtr = alignedLength;
         }
     }

branches/clusters/SL/FAST_ALIGNER/Makefile

@@ -36 +36 @@
 # For formatting issues see SOURCE_TOOLS/fix_depends.pl
 
+AWTC_constructSequence.o: awtc_constructSequence.hxx
+AWTC_constructSequence.o: awtc_seq_search.hxx
+AWTC_constructSequence.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
+AWTC_constructSequence.o: $(ARBHOME)/INCLUDE/ad_prot.h
+AWTC_constructSequence.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
+AWTC_constructSequence.o: $(ARBHOME)/INCLUDE/arb_assert.h
+AWTC_constructSequence.o: $(ARBHOME)/INCLUDE/arbdb.h
+AWTC_constructSequence.o: $(ARBHOME)/INCLUDE/arbdb_base.h
+AWTC_constructSequence.o: $(ARBHOME)/INCLUDE/arbdbt.h
+AWTC_constructSequence.o: $(ARBHOME)/INCLUDE/arbtools.h
+AWTC_constructSequence.o: $(ARBHOME)/INCLUDE/attributes.h
+AWTC_constructSequence.o: $(ARBHOME)/INCLUDE/aw_device.hxx
+AWTC_constructSequence.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
+AWTC_constructSequence.o: $(ARBHOME)/INCLUDE/aw_position.hxx
+AWTC_constructSequence.o: $(ARBHOME)/INCLUDE/aw_root.hxx
+AWTC_constructSequence.o: $(ARBHOME)/INCLUDE/aw_window.hxx
+
+AWTC_seq_search.o: awtc_seq_search.hxx
+AWTC_seq_search.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
+AWTC_seq_search.o: $(ARBHOME)/INCLUDE/ad_prot.h
+AWTC_seq_search.o: $(ARBHOME)/INCLUDE/arb_assert.h
+AWTC_seq_search.o: $(ARBHOME)/INCLUDE/arbdb.h
+AWTC_seq_search.o: $(ARBHOME)/INCLUDE/arbdb_base.h
+AWTC_seq_search.o: $(ARBHOME)/INCLUDE/arbtools.h
+AWTC_seq_search.o: $(ARBHOME)/INCLUDE/attributes.h
+AWTC_seq_search.o: $(ARBHOME)/INCLUDE/aw_root.hxx
+
+ClustalV.o: awtc_seq_search.hxx
 ClustalV.o: ClustalV.hxx
 ClustalV.o: $(ARBHOME)/INCLUDE/ad_k_prot.h
@@ -45 +73 @@
 ClustalV.o: $(ARBHOME)/INCLUDE/attributes.h
 ClustalV.o: $(ARBHOME)/INCLUDE/aw_root.hxx
-ClustalV.o: $(ARBHOME)/INCLUDE/awtc_seq_search.hxx
 
+fast_aligner.o: awtc_seq_search.hxx
 fast_aligner.o: ClustalV.hxx
 fast_aligner.o: fast_aligner.hxx
@@ -67 +95 @@
 fast_aligner.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx
 fast_aligner.o: $(ARBHOME)/INCLUDE/awtc_next_neighbours.hxx
-fast_aligner.o: $(ARBHOME)/INCLUDE/awtc_seq_search.hxx
 fast_aligner.o: $(ARBHOME)/INCLUDE/island_hopping.h

branches/clusters/SL/FAST_ALIGNER/fast_aligner.cxx

@@ -132 +132 @@
 // --------------------------------------------------------------------------------
 
-static inline GB_ERROR species_not_found(GB_CSTR species_name) {
-    return GB_export_errorf("No species '%s' found!", species_name);
-}
-
-static GB_ERROR reverseComplement(GBDATA *gb_species, GB_CSTR ali, int max_protection) {
+ATTRIBUTED(__ATTR__USERESULT, 
+           static inline GB_ERROR species_not_found(GB_CSTR species_name))
+{
+    return GBS_global_string("No species '%s' found!", species_name);
+}
+
+ATTRIBUTED(__ATTR__USERESULT, 
+           static GB_ERROR reverseComplement(GBDATA *gb_species, GB_CSTR ali, int max_protection))
+{
     GBDATA *gbd = GBT_read_sequence(gb_species, ali);
     GB_ERROR error = 0;
 
     if (!gbd) {
-        error = GB_export_errorf("No 'data' found for species '%s'", GBT_read_name(gb_species));
+        error = GBS_global_string("No 'data' found for species '%s'", GBT_read_name(gb_species));
     }
     else {
@@ -159 +163 @@
         }
         else { // protection error
-            error = GB_export_errorf("Cannot reverse-complement species '%s' because of protection level", GBT_read_name(gb_species));
+            error = GBS_global_string("Cannot reverse-complement species '%s' because of protection level", GBT_read_name(gb_species));
         }
 
@@ -1129 +1133 @@
     }
     else {
-        error = GB_export_errorf("No 'data' found for species '%s'", GBT_read_name(gb_species));
+        error = GBS_global_string("No 'data' found for species '%s'", GBT_read_name(gb_species));
         if (dataPtr) *dataPtr = NULL; // (user must not care to free data if we fail)
     }
@@ -1139 +1143 @@
 }
 
-static GB_ERROR writeStringToAlignment(GBDATA *gb_species, GB_CSTR alignment, GB_CSTR data_name, GB_CSTR str, bool temporary) {
+ATTRIBUTED(__ATTR__USERESULT, 
+           static GB_ERROR writeStringToAlignment(GBDATA *gb_species, GB_CSTR alignment, GB_CSTR data_name, GB_CSTR str, bool temporary))
+{
     GBDATA   *gb_ali  = GB_search(gb_species, alignment, GB_DB);
     GB_ERROR  error   = NULL;
@@ -1150 +1156 @@
     }
     else {
-        error = GB_export_errorf("Cannot create entry '%s' for '%s'", data_name, GBT_read_name(gb_species));
+        error = GBS_global_string("Cannot create entry '%s' for '%s'", data_name, GBT_read_name(gb_species));
     }
 
@@ -1498 +1504 @@
             GBDATA *gbd = GBT_read_sequence(gb_toAlign, relSearch.pt_server_alignment); // use a different alignment for next relative search
             if (!gbd) {
-                error = GB_export_errorf("Species '%s' has no data in alignment '%s'", GBT_read_name(gb_toAlign), relSearch.pt_server_alignment);
+                error = GBS_global_string("Species '%s' has no data in alignment '%s'", GBT_read_name(gb_toAlign), relSearch.pt_server_alignment);
             }
             else {
@@ -2207 +2213 @@
 
     if (wasNotAllowedToAlign>0) {
-        const char *mess = GB_export_errorf("%i species were not aligned (because of protection level)", wasNotAllowedToAlign);
+        const char *mess = GBS_global_string("%i species were not aligned (because of protection level)", wasNotAllowedToAlign);
         aw_popup_ok(mess);
     }
@@ -2213 +2219 @@
     if (err_count) {
         if (error) aw_message(error);
-        error = GB_export_errorf("Aligner produced %i error%c", err_count, err_count==1 ? '\0' : 's');
+        error = GBS_global_string("Aligner produced %i error%c", err_count, err_count==1 ? '\0' : 's');
     }
 

branches/clusters/SOURCE_TOOLS/generate_all_links.sh

@@ -175 +175 @@
 symlink ../AWT/awt_www.hxx INCLUDE/awt_www.hxx &&
 symlink ../AWT/awtlocal.hxx INCLUDE/awtlocal.hxx &&
-symlink ../AWTC/awtc_constructSequence.hxx INCLUDE/awtc_constructSequence.hxx &&
+# symlink ../AWTC/awtc_constructSequence.hxx INCLUDE/awtc_constructSequence.hxx &&
 symlink ../AWTC/awtc_next_neighbours.hxx INCLUDE/awtc_next_neighbours.hxx &&
-symlink ../AWTC/awtc_seq_search.hxx INCLUDE/awtc_seq_search.hxx &&
 symlink ../AWTC/awtc_submission.hxx INCLUDE/awtc_submission.hxx &&
 symlink ../AWTI/awti_export.hxx INCLUDE/awti_export.hxx &&

branches/clusters/lib/macros/ARB/SEQ_DATA/dashes2dots_at_sequenceends_of_marked.amc

@@ -5 +5 @@
 $gb_main = ARB::open(":","r");
 if (! $gb_main ) {
-    $error = ARB::get_error();
-    print ("$error\n");
+    $error = ARB::await_error();
+    print ("Error: $error\n");
     exit 0;
 }

branches/clusters/lib/macros/replamb.amc

@@ -5 +5 @@
 $gb_main = ARB::open(":","r");
 if (! $gb_main ) {
-    $error = ARB::get_error();
-    print ("$error\n");
+    $error = ARB::await_error();
+    print ("Error: $error\n");
     exit 0;
 }

branches/clusters/lib/macros/test.amc

@@ -5 +5 @@
 $gb_main = ARB::open(":","r");
 if (! $gb_main ) {
-    $error = ARB::get_error();
-    print ("$error\n");
+    $error = ARB::await_error();
+    print ("Error: $error\n");
     exit 0;
 }

branches/clusters/lib/macros/testwl.amc

@@ -5 +5 @@
 $gb_main = ARB::open(":","r");
 if (! $gb_main ) {
-    $error = ARB::get_error();
-    print ("$error\n");
+    $error = ARB::await_error();
+    print ("Error: $error\n");
     exit 0;
 }

branches/clusters/lib/macros/toggle_color.amc

@@ -5 +5 @@
 $gb_main = ARB::open(":","r");
 if (! $gb_main ) {
-    $error = ARB::get_error();
-    print ("$error\n");
+    $error = ARB::await_error();
+    print ("Error: $error\n");
     exit 0;
 }

branches/clusters/lib/macros/xopen.amc

@@ -5 +5 @@
 $gb_main = ARB::open(":","r");
 if (! $gb_main ) {
-    $error = ARB::get_error();
-    print ("$error\n");
+    $error = ARB::await_error();
+    print ("Error: $error\n");
     exit 0;
 }