Gene track improvements

backend-server/egs-data/egs/v16/common/track-style.eard

@@ -2,69 +2,80 @@ export procedure track_styles() {
   style!("""
 
   dots/ {
-    system: tracking-window;
-    depth: 56;
+    system: tracking-window; # x-scrollable, bp position units, y-attached to viewport
+    depth: 56; # z-index (-128..128)
   }
 
   tracks/ {
     padding-top: 16;
-    priority: 1;
+    priority: 1; # vertical stacking order (of sibling containers)
     depth: 0;
   }
 
   tracks/flagtop/ {
     min-height: 32;
     priority: 0;
-    system: tracking;
+    system: tracking; # x-scrollable, position in bp
   }
 
   tracks/track/ {
-    min-height: 100;
+    padding-top: 10;
     priority: 1;
   }
 
-  tracks/track/*/ {
-    padding-top: 8;
-    padding-bottom: 8;
+  tracks/track/*/ { # track root container
+    min-height: 80;
     height-adjust: tracking;
   }
 
-  tracks/track/*/title/ {
-    system: content;
-    type: overlay;
+  tracks/track/*/title/ { # track name container
+    system: content; # stays on screen, position 0..1
+    type: overlay; # draws over other track elements
     indent: left;
     padding-top: 2;
     padding-bottom: 10;
-    priority: -1000;
+    priority: -1000; # top of stack
   }
 
   tracks/track/*/main/ {
     type: overlay;
     priority: 0;
   }
 
-  tracks/track/*/main/letter/ {
+  tracks/track/*/main/letter/ { # track category container
     system: content;
     bump-height: none;
-    indent: datum(pad-left);
+    indent: datum(pad-left); # a variable (defined in framing.eard)
     depth: 60;
   }
 
-  tracks/track/*/title/letter/ {
-    system: content;
-    indent: datum(pad-left);
-    depth: 60;
-  }
+  #tracks/track/*/title/letter/ { # not used
+  #  system: content;
+  #  indent: datum(pad-left);
+  #  depth: 60;
+  #}
 
-  tracks/track/*/main/main/ {
+  tracks/track/*/main/main/ { # track foreground content
     system: tracking;
-    priority: 1000;
+    type: overlay;
+    priority: 1000; # draw at the bottom (of sibling containers)
+  }
+
+  tracks/track/*/main/main/*/ {
+    type: overlay;
   }
 
   tracks/track/*/main/background/ {
     system: content;
   }
 
+  tracks/track/gc/main/main/ {
+    padding-top: -7;
+  }
+  tracks/track/gc/main/background/ {
+    padding-top: -7;
+  }
+
   """);
 }
 
@@ -74,5 +85,9 @@ export procedure set_track_style(track_id, path_suffix, style_names, style_value
 }
 
 export procedure new_track_style(track_id, display_order) {
-  set_track_style(track_id, "", ["priority", "report"], [display_order, push_str("track;switch-id=", track_id)]);
+  set_track_style(
+    track_id, "", 
+    ["priority", "report"], 
+    [display_order, push_str("track;switch-id=", track_id)]
+  );
 }

backend-server/egs-data/egs/v16/gene/focus-gene.eard

@@ -17,10 +17,6 @@ style!("""
         type: bumper;
     }
 
-    **/main/main/*/ {
-        type: overlay;
-    }
-
     **/main/main/*/blocks/ {
         depth: 4;
     }
@@ -77,7 +73,7 @@ gene.leaf_index = repeat(4,len(gene.start));
 let paint = paint_solid(colour!("#229afc"));
 rectangle(coord(gene.start,[0,...],[-0.5,...]),coord(gene.end,[5,...],[0.5,...]),paint,[leaf.main,...]);
 
-let pen = pen("'IBM Plex Mono', sans-serif",10,[colour!("#6f8190"),...],[colour!("transparent"),...]);
+let pen = pen("'IBM Plex Mono', sans-serif",11,[colour!("#1b2c39"),...],[colour!("transparent"),...]);
 running_text(coord(gene.start,[8,...],[0,...]),coord(gene.end,[8,...],[0,...]),pen,gene.name,[leaf.text,...]);
 
 /* ZMenus */

backend-server/egs-data/egs/v16/gene/gene-common-visual.eard

@@ -3,25 +3,37 @@ export procedure gene_styles() {
         tracks/track/gene-other-rev/ {
             priority: 110;
             report: "track;switch-id=gene-other-rev;has-labels=true";
-            min-height: 92;
+        }
+        tracks/track/gene-other-rev/main/main/ {
+            padding-top: 5;
         }
 
         tracks/track/gene-pc-rev/ {
             priority: 100;
             report: "track;switch-id=gene-pc-rev;has-labels=true";
-            min-height: 92;
+        }
+        tracks/track/gene-pc-rev/main/main/ {
+            padding-top: 5;
         }
 
         tracks/track/gene-other-fwd/ {
             priority: -100;
             report: "track;switch-id=gene-other-fwd;has-labels=true";
-            min-height: 92;
+        }
+        tracks/track/gene-other-fwd/main/main/ {
+            padding-top: 5;
         }
 
         tracks/track/gene-pc-fwd/ {
             priority: -110;
             report: "track;switch-id=gene-pc-fwd;has-labels=true";
-            min-height: 92;
+        }
+        tracks/track/gene-pc-fwd/main/main/ {
+            padding-top: 5;
+        }
+
+        tracks/track/focus/main/main/ {
+            padding-top: 5;
         }
     """);
 }

backend-server/egs-data/egs/v16/gene/gene-overview.eard

@@ -12,14 +12,6 @@ track_styles();
 gene_styles();
 
 style!("""
-    **/main/main/ {
-        type: overlay;
-    }
-
-    **/main/main/*/ {
-        type: overlay;
-    }
-
     **/main/main/*/blocks/ {
         depth: 4;
     }

backend-server/egs-data/egs/v16/gene/gene.eard

@@ -13,21 +13,13 @@ track_styles();
 gene_styles();
 
 style!("""
-    **/main/main/ {
-        type: bumper;
-    }
-
-    **/main/main/*/ {
-        type: overlay;
-    }
-
     **/main/main/*/blocks/ {
         depth: 4;
     }
 
     **/main/main/*/text/ {
         bump-width: none;
-        system: tracking-special;
+        system: tracking-special; # for gene labels (sticks to window edge within gene bounds)
     }
 
     **/main/background/content {
@@ -69,7 +61,7 @@ let gene.text_leaf = set(gene.text_leaf,gene.is_focus,[leaf(""),...]);
 let paint = make_gene_paint(*gene);
 rectangle(coord(gene.start,[0,...],[-0.5,...]),coord(gene.end,[5,...],[0.5,...]),paint,gene.block_leaf);
 
-let pen = pen("'IBM Plex Mono', sans-serif",10,[colour!("#6f8190"),...],[colour!("transparent"),...]);
+let pen = pen("'IBM Plex Mono', sans-serif",15,[colour!("#1b2c39"),...],[colour!("transparent"),...]);
 running_text(coord(gene.start,[8,...],[0,...]),coord(gene.end,[8,...],[0,...]),pen,gene.name,gene.text_leaf);
 
 /* ZMenus */

backend-server/egs-data/egs/v16/gene/transcript.eard

@@ -89,7 +89,7 @@ rectangle(coord(thick_exon.start,y+2,[0,...]),coord(thick_exon.end,y+8,[0,...]),
 
 let text = tr_label_text(*gene,*tr_gene,*tr,last_tr,enabled_gene_labels(),enabled_transcript_labels());
 let y = tr.position_in_gene * 20;
-let pen = pen("'IBM Plex Mono', sans-serif",10,[colour!("#6f81ff"),...],[colour!("transparent"),...]);
+let pen = pen("'IBM Plex Mono', sans-serif",11,[colour!("#1b2c39"),...],[colour!("transparent"),...]);
 running_text(coord(tr_gene.start,y+10,[0,...]),coord(tr_gene.end,y+10,[0,...]),pen,text,leaf_tr.text_leaf);
 
 /* Draw zmenus */

backend-server/egs-data/egs/v16/other/contig.eard

@@ -10,8 +10,6 @@ track_styles();
 
 style!("""
     tracks/track/contig/ {
-        min-height: 50;
-        priority: 0;
         report: "track;switch-id=contig";
     }
 

backend-server/egs-data/egs/v16/regulation/regulation-common.eard

@@ -53,7 +53,6 @@ export procedure get_regulation_track_data(track_name, track_label) {
 export procedure regulation_track_styles() {
 style!("""
     tracks/track/regulation/ {
-        min-height: 80;
         priority: 300;
         report: "track;switch-id=regulation";
     }

backend-server/egs-data/egs/v16/repeat/repeat-summary.eard

@@ -10,7 +10,6 @@ let track_id = setting_string("track_id", []);
 let track_display_order = setting_string("display_order", []);
 track_styles();
 new_track_style(track_id, track_display_order);
-set_track_style(track_id, "", ["min-height"], ["40"]);
 
 // Draw track furniture
 let track_name = setting_string("track_name", []);