Changeset 6668 for trunk

Timestamp:

26/05/10 19:01:23 (21 months ago)

Author:

westram

Message:

• moved match visualization ("GUCACGGCU-=NN=====g=-CAGCAGCCC") from match_string() (aisc:MATCH_STRING) to get_match_overlay()
• removed redundant calculation of wmis/wmismatches (MATCHLIST_WMISMATCHES)
• added rpc hook for get_match_overlay() to PT.aisc (MATCHLIST_OVERLAY)
• removed rpc hook for unused variable is_member (MATCHLIST_IS_MEMBER)

(thx to elmar)

Location:

trunk

Files:

• PROBE/PT_match.cxx (modified) (10 diffs)
• PROBE_COM/PT.aisc (modified) (2 diffs)

trunk/PROBE/PT_match.cxx

@@ -354 +354 @@
     if (list_len <= 1) return;
     my_list = (PT_probematch **)calloc(sizeof(void *), list_len);
-    for (i=0, match = locs->pm;
-         match;
-         i++, match=match->next)
-    {
+    for (i=0, match = locs->pm; match; i++, match=match->next) {
         my_list[i] = match;
     }
@@ -364 +361 @@
         aisc_unlink((struct_dllheader_ext*)my_list[i]);
         aisc_link(&locs->ppm, my_list[i]);
+    //        printf("%i\t%i\t%s\n",my_list[i]->name,my_list[i]->b_pos,virt_name(my_list[i]));
     }
     free(my_list);
@@ -434 +432 @@
     locs->matches_truncated = 0;
 
-#if defined(DEBUG)
+#if defined(DEBUG) && 0
     PT_pdc *pdc = locs->pdc;
-    printf("Current bond values:\n");
-    for (int y = 0; y<4; y++) {
-        for (int x = 0; x<4; x++) {
-            printf("%5.2f", pdc->bond[y*4+x].val);
-        }
-        printf("\n");
+    if (pdc) {
+        printf("Current bond values:\n");
+        for (int y = 0; y<4; y++) {
+            for (int x = 0; x<4; x++) {
+                printf("%5.2f", pdc->bond[y*4+x].val);
+            }
+            printf("\n");
+        }
     }
 #endif // DEBUG
@@ -587 +587 @@
 inline void cat_dashed_right(GBS_strstruct *memfile, const char *text, int width) { cat_internal(memfile, strlen(text), text, width, '-', false); }
 
-static const char *get_match_info_formatted(PT_probematch  *ml, const format_props& format)
+extern "C" char *get_match_overlay(PT_probematch *ml)
 {
-    int    pr_pos, al_pos;
     int    pr_len = strlen(ml->sequence);
-    double wmis   = 0.0;
-    double h;
-    int    a, b;
 
     PT_local *locs = (PT_local *)ml->mh.parent->parent;
@@ -600 +596 @@
     char *ref    = (char *)calloc(sizeof(char), 21+pr_len);
     memset(ref, '.', 10);
-    for (pr_pos  = 8, al_pos = ml->rpos-1;
+    for (int pr_pos  = 8, al_pos = ml->rpos-1;
          pr_pos >= 0 && al_pos >= 0;
          pr_pos--, al_pos--)
@@ -611 +607 @@
     pt_build_pos_to_weight((PT_MATCH_TYPE)locs->sort_by, ml->sequence);
 
-    for (pr_pos = 0, al_pos = ml->rpos;
+    for (int pr_pos = 0, al_pos = ml->rpos;
          pr_pos < pr_len && al_pos < psg.data[ml->name].size;
          pr_pos++, al_pos++)
     {
-        if ((a=ml->sequence[pr_pos]) == (b=psg.data[ml->name].data[al_pos])) {
+        int a = ml->sequence[pr_pos];
+        int b = psg.data[ml->name].data[al_pos];
+        if (a == b) {
             ref[pr_pos+10] = '=';
         }
@@ -621 +619 @@
             ref[pr_pos+10] = b;
             if (pdc && a >= PT_A && a <= PT_T && b >= PT_A && b<=PT_T) {
-                h = ptnd_check_split(pdc, ml->sequence, pr_pos, b);
-                if (h<0.0) {
-                    h = -h;
-                }
-                else {
+                double h = ptnd_check_split(pdc, ml->sequence, pr_pos, b);
+                if (h>=0.0) {
                     ref[pr_pos+10] = " nacgu"[b];
                 }
-                wmis += psg.pos_to_weight[pr_pos] * h;
-            }
-        }
-
-    }
-
-    for (pr_pos = 0, al_pos = ml->rpos+pr_len;
+            }
+        }
+
+    }
+
+    for (int pr_pos = 0, al_pos = ml->rpos+pr_len;
          pr_pos < 9 && al_pos < psg.data[ml->name].size;
          pr_pos++, al_pos++)
@@ -643 +637 @@
     PT_base_2_string(ref, 0);
 
+    return ref;
+}
+
+static const char *get_match_info_formatted(PT_probematch  *ml, const format_props& format) {
     GBS_strstruct *memfile = GBS_stropen(256);
     GBS_strcat(memfile, "  ");
@@ -653 +651 @@
         cat_spaced_right(memfile, GBS_global_string("%i", ml->N_mismatches), format.N_mis_width());
     }
-    cat_spaced_right(memfile, GBS_global_string("%.1f", wmis), format.wmis_width());
+    cat_spaced_right(memfile, GBS_global_string("%.1f", ml->wmismatches), format.wmis_width());
     cat_spaced_right(memfile, GBS_global_string("%i", ml->b_pos), format.pos_width);
     if (format.show_gpos) {
@@ -663 +661 @@
     cat_spaced_left(memfile, GBS_global_string("%i", ml->reversed), format.rev_width());
 
+    char *ref = get_match_overlay(ml);
     GBS_strcat(memfile, ref);
-
     free(ref);
 

trunk/PROBE_COM/PT.aisc

@@ -172 +172 @@
     double,     wmismatches,    t,    r,    ,       WMISMATCHES,    16,     ,      (~number of weighted mismatches~);
     int,        N_mismatches,   t,    r,    ,       N_MISMATCHES,   17,     ,      (~number of 'N' mismatches~);
-    int,        is_member,      t,    r,    ,       IS_MEMBER,      18,     ,      (~member of group~);
+#    int,        is_member,      t,    r,    ,       IS_MEMBER,      18,     ,      (~member of group~);
     double,     dt,             t,    r,    ,       DT,             19,     ,      (~the dt of a probe~);
     char,       sequence,       l,    r,    ,       SEQUENCE,       22,     ,      (~path of probe~);
@@ -178 +178 @@
 #    aisc_string,get_match_hinfo,%,    r,    ,       INFO_HEADER,    26,     ,      (~the combined info text of _one_ probe match (header)~);
 #    aisc_string,get_match_info, %,    r,    ,       INFO,           27,     ,      (~the combined info text of _one_ probe match~);
+    aisc_string,get_match_overlay,%,  r,    ,       OVERLAY,        28,     ,      (~ascii visualization of match~);
 };