gramene-search 2.20.0 → 2.20.2

package/dist/index.js

@@ -2643,10 +2643,25 @@ function $0f839422d0d8c772$var$buildExperimentTitleIndex(expressionStudies) {
     }
     return index;
 }
+// Label for each species group, used by the expression and differential-expression
+// field pickers.
+//
+// A group can hold many genomes — sorghum_v11 has 120 under 4558 — so which one
+// supplies the label matters. This took the first it encountered, and since
+// grameneMaps is keyed by taxon_id, Object.values walks integer-like keys in
+// ascending numeric order: 4558001 (Sb verticilliflorum 353, a wild relative) beat
+// the anchor 4558006 (Sb bicolor BTx623 v3). Searching msd2 then returned a BTx623
+// gene while the picker was labelled with a different genome entirely. Every other
+// group here holds exactly one genome, which is why only sorghum showed it.
+//
+// Prefer the group's anchor, falling back to first-seen for releases that carry no
+// anchor flags at all (gramene main today).
 function $0f839422d0d8c772$var$buildSpeciesNameIndex(grameneMaps) {
     const idx = {};
     if (!grameneMaps) return idx;
-    for (const m of Object.values(grameneMaps))if (m && m.anchor_taxon_id && !idx[m.anchor_taxon_id]) idx[m.anchor_taxon_id] = m.display_name || String(m.anchor_taxon_id);
+    const genomes = Object.values(grameneMaps);
+    for (const m of genomes)if (m && m.anchor_taxon_id && m.is_anchor) idx[m.anchor_taxon_id] = m.display_name || String(m.anchor_taxon_id);
+    for (const m of genomes)if (m && m.anchor_taxon_id && !idx[m.anchor_taxon_id]) idx[m.anchor_taxon_id] = m.display_name || String(m.anchor_taxon_id);
     return idx;
 }
 function $0f839422d0d8c772$var$fieldExperimentId(name) {
@@ -4911,7 +4926,6 @@ const $4b8473139e48e77e$export$c6dbe9be8c8b382e = {
         fg: '#c0392b'
     }
 };
-const $4b8473139e48e77e$export$39a35029fe99c21 = '#d35400'; // specific-to dot / enhanced-in outline
 function $4b8473139e48e77e$export$8ca7625ba2054603(tokens) {
     const out = {};
     (tokens || []).forEach((t)=>{
@@ -8195,7 +8209,7 @@ const $5c2c79352d3d7b81$export$b2e089eb3692b073 = (props)=>/*#__PURE__*/ (0, $gX
 // Host-defined tbrowse zone for the Homology gene tree, redesigned to compare
 // expression across a gene family. Three parts, aligned to the tree leaves:
 //   1. a gene × organ heatmap of ordinal expression levels (expr_organ_level),
-//      with markers on each gene's tissue-specific / -enhanced organs;
+//      tissue-specific / -enhanced organs are noted in cell tooltips;
 //   2. a Max TPM column (expr_max_tpm), log-scaled magnitude;
 //   3. a Stress column of ↑activated / ↓repressed condition chips
 //      (expr_activated_by / expr_repressed_by).
@@ -8387,29 +8401,17 @@ const $cd8bc494277e92a4$var$OrganCell = ({ organ: organ, gene: gene })=>{
     const enhanced = !!(gene && gene.enhancedIn.has(organ));
     const title = level ? `${(0, $4b8473139e48e77e$export$50c1f966fd3af83e)(organ)}: ${(0, $4b8473139e48e77e$export$433053e2c141d410)[level] || level}${specific ? " \xb7 specific" : enhanced ? " \xb7 enhanced" : ''}` : `${(0, $4b8473139e48e77e$export$50c1f966fd3af83e)(organ)}: not assayed`;
     const style = {
-        position: 'relative',
         width: $cd8bc494277e92a4$var$ORGAN_CELL_W,
         height: '100%',
         boxSizing: 'border-box',
         background: level ? (0, $4b8473139e48e77e$export$b352e11f7a2ac9c5)[level] || 'transparent' : 'transparent',
         borderRight: $cd8bc494277e92a4$var$gridBorder
     };
-    // enhanced-in: thin outline; specific-to (stronger): corner dot.
-    if (enhanced && !specific) style.boxShadow = `inset 0 0 0 1px ${0, $4b8473139e48e77e$export$39a35029fe99c21}`;
+    // Tissue-specific / -enhanced organs are reported in the cell's tooltip rather
+    // than with a marker, so the grid reads purely as expression level.
     return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
         title: title,
-        style: style,
-        children: specific && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
-            style: {
-                position: 'absolute',
-                top: 1,
-                right: 1,
-                width: 4,
-                height: 4,
-                borderRadius: '50%',
-                background: (0, $4b8473139e48e77e$export$39a35029fe99c21)
-            }
-        })
+        style: style
     });
 };
 const $cd8bc494277e92a4$var$StressCell = ({ gene: gene, width: width })=>{
@@ -18076,14 +18078,11 @@ const $8f8e530286a37ce9$var$AttrTableViewCmp = (props)=>{
                             return `${(0, $4b8473139e48e77e$export$50c1f966fd3af83e)(o)}: ${(0, $4b8473139e48e77e$export$433053e2c141d410)[lvl] || lvl}${sp}`;
                         },
                         comparator: (a, b)=>((0, $4b8473139e48e77e$export$a61929d6d484c6d4)[a] ?? -1) - ((0, $4b8473139e48e77e$export$a61929d6d484c6d4)[b] ?? -1),
-                        cellStyle: (p)=>{
-                            const style = {
+                        // Specific / enhanced are reported in the tooltip above rather than
+                        // with an outline, so the grid reads purely as expression level.
+                        cellStyle: (p)=>({
                                 background: p.value ? (0, $4b8473139e48e77e$export$b352e11f7a2ac9c5)[p.value] || 'transparent' : 'transparent'
-                            };
-                            if (p.data && p.data._specific.has(o)) style.boxShadow = `inset 0 0 0 2px ${0, $4b8473139e48e77e$export$39a35029fe99c21}`;
-                            else if (p.data && p.data._enhanced.has(o)) style.boxShadow = `inset 0 0 0 1px ${0, $4b8473139e48e77e$export$39a35029fe99c21}`;
-                            return style;
-                        }
+                            })
                     });
                 });
                 return;