gramene-search 2.0.5 → 2.0.7

package/dist/index.js

@@ -11,6 +11,7 @@ var $gXNCa$gramenebinsclient = require("gramene-bins-client");
 var $gXNCa$gramenetreesclient = require("gramene-trees-client");
 var $gXNCa$gramenetaxonomywithgenomes = require("gramene-taxonomy-with-genomes");
 var $gXNCa$reactga4 = require("react-ga4");
+var $gXNCa$moneyclip = require("money-clip");
 var $gXNCa$reactbootstrap = require("react-bootstrap");
 var $gXNCa$reactswitch = require("react-switch");
 var $gXNCa$reacticonsio5 = require("react-icons/io5");
@@ -1456,6 +1457,12 @@ const $24971af0a229e0e3$var$grameneViews = {
                     show: 'off',
                     shouldScroll: false
                 },
+                {
+                    id: 'gsea',
+                    name: 'Gene set enrichment',
+                    show: 'off',
+                    shouldScroll: false
+                },
                 {
                     id: 'userLists',
                     name: 'User Gene Lists',
@@ -1551,7 +1558,9 @@ const $24971af0a229e0e3$var$grameneViews = {
         const resultDependentIds = new Set([
             'taxonomy',
             'list',
-            'export'
+            'export',
+            'exprViz',
+            'gsea'
         ]);
         const autoDisable = numFound === 0 || !hasFilters;
         const hasFirebase = !!(config && config.firebaseConfig);
@@ -1599,6 +1608,16 @@ const $24971af0a229e0e3$var$grameneViews = {
 var $24971af0a229e0e3$export$2e2bcd8739ae039 = $24971af0a229e0e3$var$grameneViews;
 
 
+
+// Dedicated IndexedDB store for the full pathway corpus, persisted
+// indefinitely (default maxAge of `Infinity`). The pathway set is small
+// and stable enough to keep around across sessions, so we bulk-load it
+// once with `?rows=-1` and reuse it instead of issuing per-id requests.
+const $671312b287158a8a$var$pathwayCache = (0, $gXNCa$moneyclip.getConfiguredCache)({
+    version: 1,
+    name: 'gramene_pathways'
+});
+let $671312b287158a8a$var$pathwaysBulkPromise = null;
 const $671312b287158a8a$var$grameneDocs = {
     name: 'grameneDocs',
     getReducer: ()=>{
@@ -1803,26 +1822,37 @@ const $671312b287158a8a$var$grameneDocs = {
                 });
             }
         },
-    doRequestGramenePathways: (ids)=>({ dispatch: dispatch, store: store })=>{
-            const pathways = store.selectGramenePathways();
-            let newIds = ids.filter((id)=>!pathways.hasOwnProperty(id));
-            if (newIds) {
-                dispatch({
-                    type: 'GRAMENE_PATHWAYS_REQUESTED',
-                    payload: newIds
-                });
-                if (newIds.length === 1) newIds.push(0);
-                fetch(`${store.selectGrameneAPI()}/pathways?idList=${newIds.join(',')}`).then((res)=>res.json()).then((res)=>{
-                    let pathways = {};
-                    res.forEach((p)=>{
-                        pathways[p._id] = p;
+    // Signature kept for backward compatibility; the `ids` argument is
+    // ignored. On first call we bulk-load every pathway record from the
+    // dedicated IndexedDB cache (or `${api}/pathways?rows=-1` on miss),
+    // dispatch a single GRAMENE_PATHWAYS_RECEIVED, and short-circuit all
+    // subsequent calls.
+    doRequestGramenePathways: (_ids)=>({ dispatch: dispatch, store: store })=>{
+            if ($671312b287158a8a$var$pathwaysBulkPromise) return $671312b287158a8a$var$pathwaysBulkPromise;
+            $671312b287158a8a$var$pathwaysBulkPromise = $671312b287158a8a$var$pathwayCache.get('all').then((cached)=>{
+                if (cached) {
+                    dispatch({
+                        type: 'GRAMENE_PATHWAYS_RECEIVED',
+                        payload: cached
+                    });
+                    return;
+                }
+                return fetch(`${store.selectGrameneAPI()}/pathways?rows=-1`).then((res)=>res.json()).then((res)=>{
+                    const pathways = {};
+                    (res || []).forEach((p)=>{
+                        if (p && p._id != null) pathways[p._id] = p;
                     });
                     dispatch({
                         type: 'GRAMENE_PATHWAYS_RECEIVED',
                         payload: pathways
                     });
+                    $671312b287158a8a$var$pathwayCache.set('all', pathways).catch((e)=>console.warn('Failed to cache pathways', e));
                 });
-            }
+            }).catch((err)=>{
+                console.error('Failed to load pathways', err);
+                $671312b287158a8a$var$pathwaysBulkPromise = null; // allow retry on next call
+            });
+            return $671312b287158a8a$var$pathwaysBulkPromise;
         },
     doRequestExpressionStudies: (id)=>({ dispatch: dispatch, store: store })=>{
             fetch(`${store.selectGrameneAPI()}/experiments?rows=-1`).then((res)=>res.json()).then((res)=>{
@@ -2076,7 +2106,7 @@ var $0d54502f6cafe273$export$2e2bcd8739ae039 = $0d54502f6cafe273$var$grameneGeno
 
 
 var $65709bd8598fce20$exports = {};
-$65709bd8598fce20$exports = JSON.parse('{"groups":{"core":{"label":"Core identifiers","order":0},"location":{"label":"Genomic location","order":1},"structure":{"label":"Gene structure","order":2},"homology":{"label":"Homology","order":3},"expression":{"label":"Gene expression","order":4},"differential":{"label":"Differential expression","order":5},"hierarchical":{"label":"Hierarchical annotations","order":6},"pathways":{"label":"Pathways","order":7},"GO":{"label":"Gene Ontology","order":7},"PO":{"label":"Plant Ontology","order":8},"lof":{"label":"Loss of function alleles","order":9},"MAKER":{"label":"MAKER transcript metrics","order":10},"xrefs":{"label":"External references","order":11},"other":{"label":"Other","order":99}},"patterns":[{"id":"homology","match":"^homology__(.+)$","group":"homology","multiValued":true,"labelTemplate":"Homology: $1"},{"id":"pathways","match":"^pathways__(.+)$","group":"pathways","multiValued":true,"labelTemplate":"Pathway: $1"},{"id":"maker","match":"^MAKER__(.+)__attr_([a-z])$","group":"MAKER","labelTemplate":"MAKER: $1"},{"id":"xrefs","match":"^(.+)__xrefs$","group":"xrefs","multiValued":true,"labelTemplate":"$1 (xrefs)"},{"id":"expr","match":"^(E[-_][A-Za-z0-9_-]+?)_g(\\\\d+)__expr$","group":"expression","expression":true,"labelTemplate":"$1 \xb7 g$2"},{"id":"diffexpr","match":"^(E[-_][A-Za-z0-9_-]+?)_g(\\\\d+)_g(\\\\d+)_(pval|logfc|l2fc)_attr_([a-z])$","group":"differential","diffExpression":true,"labelTemplate":"$1 \xb7 g$2 vs g$3 \xb7 $4"},{"id":"bins","match":"^(fixed|uniform)_([0-9a-zA-Z]+)__bin$","group":"bins","is_hidden":true,"labelTemplate":"$1 bin ($2)"},{"id":"neighbors","match":".*neighbors_[0-9]+$","group":"neighbors","is_hidden":true,"labelTemplate":"neighbors"},{"id":"vep_merged","match":"^VEP__merged__(NAT|EMS)__attr_ss$","group":"lof","multiValued":true,"labelTemplate":"Merged $1 accessions"},{"id":"vep_detail","match":"^VEP__(.+?)__(homo|het)__(.+?)__(\\\\d+)__attr_ss$","group":"lof","multiValued":true,"labelTemplate":"$1 ($2) $3/$4"},{"id":"generic_attr","match":"^(.+)__attr_([a-z])$","group":"other","labelTemplate":"$1"}],"fields":{"id":{"group":"core","label":"Gene ID","order":1},"name":{"group":"core","label":"Name","order":2},"description":{"group":"core","label":"Description","order":4},"summary":{"group":"core","label":"Summary","order":5},"synonyms":{"group":"core","label":"Synonyms","multiValued":true,"order":3},"biotype":{"group":"core","label":"Biotype","order":6},"taxon_id":{"group":"core","label":"Taxon ID","order":8},"system_name":{"group":"core","label":"System name","order":7},"db_type":{"group":"core","label":"DB type","order":9},"closest_rep_id":{"group":"homology","label":"Closest representative ID","order":1},"closest_rep_name":{"group":"homology","label":"Closest representative name","order":2},"closest_rep_identity":{"group":"homology","label":"Closest representative identity","order":3},"closest_rep_taxon_id":{"group":"homology","label":"Closest representative taxon","order":4},"closest_rep_description":{"group":"homology","label":"Closest representative description","order":5},"model_rep_id":{"group":"homology","label":"Model representative ID","order":6},"model_rep_name":{"group":"homology","label":"Model representative name","order":7},"model_rep_identity":{"group":"homology","label":"Model representative identity","order":8},"model_rep_taxon_id":{"group":"homology","label":"Model representative taxon","order":9},"model_rep_description":{"group":"homology","label":"Model representative description","order":10},"gene_tree":{"group":"homology","label":"Gene tree ID","order":11},"pan_tree":{"group":"homology","label":"Pan-gene tree ID","order":14},"capabilities":{"group":"other","label":"Capabilities","multiValued":true},"map":{"group":"location","label":"Map","order":1},"region":{"group":"location","label":"Region","order":2},"start":{"group":"location","label":"Start","order":3},"end":{"group":"location","label":"End","order":4},"strand":{"group":"location","label":"Strand","order":5},"GO__ancestors":{"group":"hierarchical","label":"GO terms","multiValued":true,"order":1},"PO__ancestors":{"group":"hierarchical","label":"PO terms","multiValued":true,"order":2},"TO__ancestors":{"group":"hierarchical","label":"TO terms","multiValued":true,"order":3},"QTL_TO__ancestors":{"group":"hierarchical","label":"QTL traits (TO)","multiValued":true,"order":7},"domains__ancestors":{"group":"hierarchical","label":"Domains","multiValued":true,"order":4},"taxonomy__ancestors":{"group":"hierarchical","label":"Taxonomy","multiValued":true,"order":6},"supertree_attr_s":{"group":"homology","label":"Supertree","order":13},"gene_tree_root_taxon_id":{"group":"homology","label":"Gene tree root taxon","order":12},"protein__length":{"group":"structure","label":"Protein length"},"transcript__count":{"group":"structure","label":"Transcript count"},"transcript__exons":{"group":"structure","label":"Exon count"},"transcript__length":{"group":"structure","label":"Transcript length"},"expressed_in_gxa_attr_ss":{"group":"expression","label":"Expressed in GXA","multiValued":true},"MAKER__AED__attr_f":{"group":"MAKER","label":"AED","description":"Annotation Edit Distance"},"MAKER__QI1__attr_i":{"group":"MAKER","label":"QI1: Length of the 5\' UTR"},"MAKER__QI2__attr_f":{"group":"MAKER","label":"QI2: Fraction of splice sites confirmed by EST"},"MAKER__QI3__attr_f":{"group":"MAKER","label":"QI3: Fraction of exons overlapping an EST"},"MAKER__QI4__attr_f":{"group":"MAKER","label":"QI4: Fraction of exons overlapping EST or protein"},"MAKER__QI5__attr_f":{"group":"MAKER","label":"QI5: Fraction of splice sites confirmed by SNAP"},"MAKER__QI6__attr_f":{"group":"MAKER","label":"QI6: Fraction of exons overlapping a SNAP"},"MAKER__QI7__attr_i":{"group":"MAKER","label":"QI7: Number of exons in the mRNA"},"MAKER__QI8__attr_i":{"group":"MAKER","label":"QI8: Length of the 3\' UTR"},"MAKER__QI9__attr_i":{"group":"MAKER","label":"QI9: Length of the protein sequence"},"homology__all_orthologs":{"group":"homology","label":"All orthologs","multiValued":true,"order":15},"homology__ortholog_one2one":{"group":"homology","label":"1:1 orthologs","multiValued":true,"order":16},"homology__ortholog_one2many":{"group":"homology","label":"1:many orthologs","multiValued":true,"order":17},"homology__ortholog_many2many":{"group":"homology","label":"Many:many orthologs","multiValued":true,"order":18},"homology__syntenic_ortholog_one2one":{"group":"homology","label":"Syntenic 1:1 orthologs","multiValued":true,"order":19},"homology__within_species_paralog":{"group":"homology","label":"Within-species paralogs","multiValued":true,"order":20},"pathways__ancestors":{"group":"hierarchical","label":"Pathways","multiValued":true,"order":5},"canonical_transcript__attr_s":{"group":"structure","label":"Canonical transcript ID"}},"hidden":["_version_","_terms","score","gene_idx","gene_idx_multi","species_idx","compara_idx","compara_idx_multi","_id","annotations","bins","gene_structure","homology","location","xrefs","domain_roots","familyRoot__ancestors","taxonomy__ancestors","capabilities","saved_search"]}');
+$65709bd8598fce20$exports = JSON.parse('{"groups":{"core":{"label":"Core identifiers","order":0},"location":{"label":"Genomic location","order":1},"structure":{"label":"Gene structure","order":2},"homology":{"label":"Homology","order":3},"expression":{"label":"Gene expression","order":4},"differential":{"label":"Differential expression","order":5},"hierarchical":{"label":"Hierarchical annotations","order":6},"pathways":{"label":"Pathways","order":7},"GO":{"label":"Gene Ontology","order":7},"PO":{"label":"Plant Ontology","order":8},"lof":{"label":"Loss of function alleles","order":9},"MAKER":{"label":"MAKER transcript metrics","order":10},"xrefs":{"label":"External references","order":11},"other":{"label":"Other","order":99}},"patterns":[{"id":"homology","match":"^homology__(.+)$","group":"homology","multiValued":true,"labelTemplate":"Homology: $1"},{"id":"pathways","match":"^pathways__(.+)$","group":"pathways","multiValued":true,"labelTemplate":"Pathway: $1"},{"id":"maker","match":"^MAKER__(.+)__attr_([a-z])$","group":"MAKER","labelTemplate":"MAKER: $1"},{"id":"xrefs","match":"^(.+)__xrefs$","group":"xrefs","multiValued":true,"labelTemplate":"$1 (xrefs)"},{"id":"expr","match":"^(E[-_][A-Za-z0-9_-]+?)_g(\\\\d+)__expr$","group":"expression","expression":true,"labelTemplate":"$1 \xb7 g$2"},{"id":"diffexpr","match":"^(E[-_][A-Za-z0-9_-]+?)_g(\\\\d+)_g(\\\\d+)_(pval|l2fc)_attr_([a-z])$","group":"differential","diffExpression":true,"labelTemplate":"$1 \xb7 g$2 vs g$3 \xb7 $4"},{"id":"bins","match":"^(fixed|uniform)_([0-9a-zA-Z]+)__bin$","group":"bins","is_hidden":true,"labelTemplate":"$1 bin ($2)"},{"id":"neighbors","match":".*neighbors_[0-9]+$","group":"neighbors","is_hidden":true,"labelTemplate":"neighbors"},{"id":"vep_merged","match":"^VEP__merged__(NAT|EMS)__attr_ss$","group":"lof","multiValued":true,"labelTemplate":"Merged $1 accessions"},{"id":"vep_detail","match":"^VEP__(.+?)__(homo|het)__(.+?)__(\\\\d+)__attr_ss$","group":"lof","multiValued":true,"labelTemplate":"$1 ($2) $3/$4"},{"id":"generic_attr","match":"^(.+)__attr_([a-z])$","group":"other","labelTemplate":"$1"}],"fields":{"id":{"group":"core","label":"Gene ID","order":1},"name":{"group":"core","label":"Name","order":2},"description":{"group":"core","label":"Description","order":4},"summary":{"group":"core","label":"Summary","order":5},"synonyms":{"group":"core","label":"Synonyms","multiValued":true,"order":3},"biotype":{"group":"core","label":"Biotype","order":6},"taxon_id":{"group":"core","label":"Taxon ID","order":8},"system_name":{"group":"core","label":"System name","order":7},"db_type":{"group":"core","label":"DB type","order":9},"closest_rep_id":{"group":"homology","label":"Closest representative ID","order":1},"closest_rep_name":{"group":"homology","label":"Closest representative name","order":2},"closest_rep_identity":{"group":"homology","label":"Closest representative identity","order":3},"closest_rep_taxon_id":{"group":"homology","label":"Closest representative taxon","order":4},"closest_rep_description":{"group":"homology","label":"Closest representative description","order":5},"model_rep_id":{"group":"homology","label":"Model representative ID","order":6},"model_rep_name":{"group":"homology","label":"Model representative name","order":7},"model_rep_identity":{"group":"homology","label":"Model representative identity","order":8},"model_rep_taxon_id":{"group":"homology","label":"Model representative taxon","order":9},"model_rep_description":{"group":"homology","label":"Model representative description","order":10},"gene_tree":{"group":"homology","label":"Gene tree ID","order":11},"pan_tree":{"group":"homology","label":"Pan-gene tree ID","order":14},"capabilities":{"group":"other","label":"Capabilities","multiValued":true},"map":{"group":"location","label":"Map","order":1},"region":{"group":"location","label":"Region","order":2},"start":{"group":"location","label":"Start","order":3},"end":{"group":"location","label":"End","order":4},"strand":{"group":"location","label":"Strand","order":5},"GO__ancestors":{"group":"hierarchical","label":"GO terms","multiValued":true,"order":1},"PO__ancestors":{"group":"hierarchical","label":"PO terms","multiValued":true,"order":2},"TO__ancestors":{"group":"hierarchical","label":"TO terms","multiValued":true,"order":3},"QTL_TO__ancestors":{"group":"hierarchical","label":"QTL traits (TO)","multiValued":true,"order":7},"domains__ancestors":{"group":"hierarchical","label":"Domains","multiValued":true,"order":4},"taxonomy__ancestors":{"group":"hierarchical","label":"Taxonomy","multiValued":true,"order":6},"supertree_attr_s":{"group":"homology","label":"Supertree","order":13},"gene_tree_root_taxon_id":{"group":"homology","label":"Gene tree root taxon","order":12},"protein__length":{"group":"structure","label":"Protein length"},"transcript__count":{"group":"structure","label":"Transcript count"},"transcript__exons":{"group":"structure","label":"Exon count"},"transcript__length":{"group":"structure","label":"Transcript length"},"expressed_in_gxa_attr_ss":{"group":"expression","label":"Expressed in GXA","multiValued":true},"MAKER__AED__attr_f":{"group":"MAKER","label":"AED","description":"Annotation Edit Distance"},"MAKER__QI1__attr_i":{"group":"MAKER","label":"QI1: Length of the 5\' UTR"},"MAKER__QI2__attr_f":{"group":"MAKER","label":"QI2: Fraction of splice sites confirmed by EST"},"MAKER__QI3__attr_f":{"group":"MAKER","label":"QI3: Fraction of exons overlapping an EST"},"MAKER__QI4__attr_f":{"group":"MAKER","label":"QI4: Fraction of exons overlapping EST or protein"},"MAKER__QI5__attr_f":{"group":"MAKER","label":"QI5: Fraction of splice sites confirmed by SNAP"},"MAKER__QI6__attr_f":{"group":"MAKER","label":"QI6: Fraction of exons overlapping a SNAP"},"MAKER__QI7__attr_i":{"group":"MAKER","label":"QI7: Number of exons in the mRNA"},"MAKER__QI8__attr_i":{"group":"MAKER","label":"QI8: Length of the 3\' UTR"},"MAKER__QI9__attr_i":{"group":"MAKER","label":"QI9: Length of the protein sequence"},"homology__all_orthologs":{"group":"homology","label":"All orthologs","multiValued":true,"order":15},"homology__ortholog_one2one":{"group":"homology","label":"1:1 orthologs","multiValued":true,"order":16},"homology__ortholog_one2many":{"group":"homology","label":"1:many orthologs","multiValued":true,"order":17},"homology__ortholog_many2many":{"group":"homology","label":"Many:many orthologs","multiValued":true,"order":18},"homology__syntenic_ortholog_one2one":{"group":"homology","label":"Syntenic 1:1 orthologs","multiValued":true,"order":19},"homology__within_species_paralog":{"group":"homology","label":"Within-species paralogs","multiValued":true,"order":20},"pathways__ancestors":{"group":"hierarchical","label":"Pathways","multiValued":true,"order":5},"canonical_transcript__attr_s":{"group":"structure","label":"Canonical transcript ID"}},"hidden":["_version_","_terms","score","gene_idx","gene_idx_multi","species_idx","compara_idx","compara_idx_multi","_id","annotations","bins","gene_structure","homology","location","xrefs","domain_roots","familyRoot__ancestors","taxonomy__ancestors","capabilities","saved_search"]}');
 
 
 const $49d5cbca2ec74b2f$export$428c2f647a2a7545 = {
@@ -2379,14 +2409,13 @@ function $0f839422d0d8c772$var$buildSpeciesNameIndex(grameneMaps) {
 function $0f839422d0d8c772$var$fieldExperimentId(name) {
     let m = name.match(/^(\w+?)_g\d+__expr$/);
     if (m) return m[1].replace(/_/g, '-');
-    m = name.match(/^(\w+?)_g\d+_g\d+_(pval|logfc|l2fc)_attr_[a-z]$/);
+    m = name.match(/^(\w+?)_g\d+_g\d+_(pval|l2fc)_attr_[a-z]$/);
     if (m) return m[1].replace(/_/g, '-');
     return null;
 }
 const $0f839422d0d8c772$var$STAT_RANK = {
     l2fc: 0,
-    logfc: 1,
-    pval: 2
+    pval: 1
 };
 function $0f839422d0d8c772$var$collapseDiffExprInSubgroups(subgroups, fieldsOut, collator) {
     for (const taxGroup of subgroups)for (const expGroup of taxGroup.subgroups || []){
@@ -2423,7 +2452,7 @@ function $0f839422d0d8c772$var$collapseDiffExprInSubgroups(subgroups, fieldsOut,
             });
             const rep = names[0];
             const repEntry = fieldsOut[rep];
-            const label = (repEntry.label || rep).replace(/\s+\((?:pval|logfc|l2fc)\)/, '');
+            const label = (repEntry.label || rep).replace(/\s+\((?:pval|l2fc)\)/, '');
             fieldsOut[rep] = {
                 ...repEntry,
                 label: label,
@@ -2726,15 +2755,12 @@ $0f839422d0d8c772$var$grameneFieldCatalog.selectFieldCatalog = (0, $gXNCa$reduxb
     const present = new Set(fieldNames);
     // Build a synthetic doc from the discovered field names; values carry the
     // right JS type so inferType picks the correct multiValued/type (arrays
-    // for multi-valued fields, scalars otherwise). Derive pval/logfc
-    // companions from every l2fc field.
+    // for multi-valued fields, scalars otherwise). Derive the pval companion
+    // from every l2fc field.
     const doc = {};
     for (const name of present){
         doc[name] = $0f839422d0d8c772$var$synthesizedValue(name);
-        if (/_l2fc_attr_f$/.test(name)) {
-            doc[name.replace('_l2fc_', '_pval_')] = 0;
-            doc[name.replace('_l2fc_', '_logfc_')] = 0;
-        }
+        if (/_l2fc_attr_f$/.test(name)) doc[name.replace('_l2fc_', '_pval_')] = 0;
     }
     const catalog = $0f839422d0d8c772$var$buildCatalog([
         doc
@@ -2749,7 +2775,7 @@ var $0f839422d0d8c772$export$2e2bcd8739ae039 = $0f839422d0d8c772$var$grameneFiel
 
 
 const $6d28e8e62a4d602f$var$EXPR_FIELD_RE = /^(E[-_][A-Za-z0-9_-]+?)_g(\d+)__expr$/;
-const $6d28e8e62a4d602f$var$DIFFEXPR_FIELD_RE = /^(E[-_][A-Za-z0-9_-]+?)_g(\d+)_g(\d+)_(pval|logfc|l2fc)_attr_([a-z])$/;
+const $6d28e8e62a4d602f$var$DIFFEXPR_FIELD_RE = /^(E[-_][A-Za-z0-9_-]+?)_g(\d+)_g(\d+)_(pval|l2fc)_attr_([a-z])$/;
 const $6d28e8e62a4d602f$export$adbe84e3322ddf23 = [
     'experiment',
     'experiment_name',
@@ -2874,7 +2900,7 @@ function $6d28e8e62a4d602f$export$ba4cd509d0763838(doc, diffExpressionFields, ex
             byContrast.set(key, entry);
         }
         if (parsed.stat === 'pval') entry.pval = val;
-        else entry.l2fc = val; // l2fc or logfc
+        else entry.l2fc = val;
     }
     const maxPval = cutoffs && cutoffs.diffMaxPval;
     const maxPvalActive = maxPval !== null && maxPval !== undefined && maxPval !== '' && Number.isFinite(+maxPval);
@@ -3769,13 +3795,21 @@ const $1508f5a42be6e7b5$var$exporter = {
 var $1508f5a42be6e7b5$export$2e2bcd8739ae039 = $1508f5a42be6e7b5$var$exporter;
 
 
+
 const $c921a0d2b34aadb6$var$ONT_KEYS = [
     'GO',
     'PO',
     'TO',
     'domains'
 ];
-const $c921a0d2b34aadb6$var$BATCH_SIZE = 200;
+// Dedicated IndexedDB store for ontology records. The full term set per
+// ontology is stable enough to keep around indefinitely (default maxAge of
+// `Infinity`), and we don't want it to share the short TTL of the app-wide
+// cache configured in demo.js.
+const $c921a0d2b34aadb6$var$cache = (0, $gXNCa$moneyclip.getConfiguredCache)({
+    version: 1,
+    name: 'gramene_ontologies'
+});
 const $c921a0d2b34aadb6$var$inflight = {};
 const $c921a0d2b34aadb6$var$ontologies = {
     name: 'ontologies',
@@ -3784,95 +3818,64 @@ const $c921a0d2b34aadb6$var$ontologies = {
             GO: {},
             PO: {},
             TO: {},
-            domains: {}
+            domains: {},
+            loaded: {}
         };
         return (state = initialState, { type: type, payload: payload })=>{
             switch(type){
-                case 'ONTOLOGY_RECORDS_REQUESTED':
-                    {
-                        const { key: key, ids: ids } = payload;
-                        const bucket = {
-                            ...state[key]
-                        };
-                        for (const id of ids)if (!bucket.hasOwnProperty(id)) bucket[id] = null;
-                        return {
-                            ...state,
-                            [key]: bucket
-                        };
-                    }
-                case 'ONTOLOGY_RECORDS_RECEIVED':
-                    {
-                        const { key: key, records: records } = payload;
-                        return {
-                            ...state,
-                            [key]: {
-                                ...state[key],
-                                ...records
-                            }
-                        };
-                    }
+                case 'ONTOLOGY_BULK_LOADED':
+                    return {
+                        ...state,
+                        [payload.key]: payload.records,
+                        loaded: {
+                            ...state.loaded,
+                            [payload.key]: true
+                        }
+                    };
                 default:
                     return state;
             }
         };
     },
-    doEnsureOntologyRecords: (key, ids)=>({ dispatch: dispatch, store: store })=>{
+    // Signature kept for backward compatibility — the `ids` argument is
+    // ignored. On first call per ontology key we load the full term set
+    // (cache hit if available, otherwise `${api}/${key}?rows=-1`) and
+    // dispatch a single bulk load. Subsequent calls are no-ops.
+    doEnsureOntologyRecords: (key, _ids)=>({ dispatch: dispatch, store: store })=>{
             if (!$c921a0d2b34aadb6$var$ONT_KEYS.includes(key)) return Promise.resolve();
-            if (!Array.isArray(ids) || ids.length === 0) return Promise.resolve();
-            const existing = store.selectOntologies()[key] || {};
-            const missing = [];
-            for (const id of ids){
-                if (id == null) continue;
-                const idNum = +id;
-                if (!existing.hasOwnProperty(idNum) && !($c921a0d2b34aadb6$var$inflight[key] && $c921a0d2b34aadb6$var$inflight[key].has(idNum))) missing.push(idNum);
-            }
-            if (missing.length === 0) return Promise.resolve();
-            if (!$c921a0d2b34aadb6$var$inflight[key]) $c921a0d2b34aadb6$var$inflight[key] = new Set();
-            for (const id of missing)$c921a0d2b34aadb6$var$inflight[key].add(id);
-            dispatch({
-                type: 'ONTOLOGY_RECORDS_REQUESTED',
-                payload: {
-                    key: key,
-                    ids: missing
-                }
-            });
-            const api = store.selectGrameneAPI();
-            const batches = [];
-            for(let i = 0; i < missing.length; i += $c921a0d2b34aadb6$var$BATCH_SIZE)batches.push(missing.slice(i, i + $c921a0d2b34aadb6$var$BATCH_SIZE));
-            const fetchBatch = (batch)=>{
-                const idList = batch.length === 1 ? `${batch[0]},0` : batch.join(',');
-                return fetch(`${api}/${key}?idList=${idList}&rows=${batch.length + 1}`).then((r)=>r.json()).then((docs)=>{
-                    const records = {};
-                    for (const d of docs || [])if (d && d._id != null) records[d._id] = d;
-                    for (const id of batch)if (!records.hasOwnProperty(id)) records[id] = {
-                        _id: id,
-                        missing: true
-                    };
+            const state = store.selectOntologies();
+            if (state.loaded && state.loaded[key]) return Promise.resolve();
+            if ($c921a0d2b34aadb6$var$inflight[key]) return $c921a0d2b34aadb6$var$inflight[key];
+            $c921a0d2b34aadb6$var$inflight[key] = $c921a0d2b34aadb6$var$cache.get(key).then((cached)=>{
+                if (cached) {
                     dispatch({
-                        type: 'ONTOLOGY_RECORDS_RECEIVED',
+                        type: 'ONTOLOGY_BULK_LOADED',
                         payload: {
                             key: key,
-                            records: records
+                            records: cached
                         }
                     });
-                }).catch(()=>{
+                    return;
+                }
+                const api = store.selectGrameneAPI();
+                return fetch(`${api}/${key}?rows=-1`).then((r)=>r.json()).then((docs)=>{
                     const records = {};
-                    for (const id of batch)records[id] = {
-                        _id: id,
-                        missing: true
-                    };
+                    for (const d of docs || [])if (d && d._id != null) records[d._id] = d;
                     dispatch({
-                        type: 'ONTOLOGY_RECORDS_RECEIVED',
+                        type: 'ONTOLOGY_BULK_LOADED',
                         payload: {
                             key: key,
                             records: records
                         }
                     });
-                }).finally(()=>{
-                    for (const id of batch)$c921a0d2b34aadb6$var$inflight[key].delete(id);
+                    $c921a0d2b34aadb6$var$cache.set(key, records).catch((e)=>console.warn('Failed to cache ontology', key, e));
                 });
-            };
-            return Promise.all(batches.map(fetchBatch));
+            }).catch((err)=>{
+                console.error(`Failed to load ontology ${key}`, err);
+            }).finally(()=>{
+                delete $c921a0d2b34aadb6$var$inflight[key];
+            });
+            return $c921a0d2b34aadb6$var$inflight[key];
         },
     selectOntologies: (state)=>state.ontologies
 };
@@ -4447,232 +4450,910 @@ const $4f15cd8a7d970b18$var$exprViz = {
 var $4f15cd8a7d970b18$export$2e2bcd8739ae039 = $4f15cd8a7d970b18$var$exprViz;
 
 
-var $5df6c55c1bef3469$export$2e2bcd8739ae039 = [
-    ...(0, $9d9aeaf9299e61a1$export$2e2bcd8739ae039),
-    (0, $671312b287158a8a$export$2e2bcd8739ae039),
-    (0, $af4441dd29af05df$export$2e2bcd8739ae039),
-    (0, $24971af0a229e0e3$export$2e2bcd8739ae039),
-    (0, $0d54502f6cafe273$export$2e2bcd8739ae039),
-    (0, $0f839422d0d8c772$export$2e2bcd8739ae039),
-    (0, $1508f5a42be6e7b5$export$2e2bcd8739ae039),
-    (0, $c921a0d2b34aadb6$export$2e2bcd8739ae039),
-    (0, $4f15cd8a7d970b18$export$2e2bcd8739ae039)
-];
-
-
-
 
-
-const $2fec4872fbf7ebd2$var$Gene = ({ gene: gene })=>{
-    return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
-        className: "row",
-        children: gene.id
-    });
-};
-const $2fec4872fbf7ebd2$var$Genes = (results, rows, doChangeQuantity)=>{
-    if (results && results.numFound > 0) {
-        const moreButton = results.numFound > rows ? /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("button", {
-            onClick: (e)=>doChangeQuantity('Genes', 20),
-            children: "more"
-        }) : '';
-        const fewerButton = rows > 20 ? /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("button", {
-            onClick: (e)=>doChangeQuantity('Genes', -20),
-            children: "fewer"
-        }) : '';
-        const docsToShow = results.response.docs.slice(0, rows);
-        return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
-            id: "Genes",
-            className: "container mb40 anchor",
-            children: [
-                /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
-                    className: "fancy-title mb40",
-                    children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("h4", {
-                        children: "Genes"
-                    })
-                }),
-                docsToShow.map((doc, idx)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($2fec4872fbf7ebd2$var$Gene, {
-                        gene: doc
-                    }, idx)),
-                fewerButton,
-                moreButton
-            ]
-        });
+// Gene Set Enrichment Analysis bundle.
+//
+// For each species tab we run:
+//   foreground: q=<filters>&fq=taxon_id:<tid>&rows=0 + facet on six __ancestors fields
+//   background: q=taxon_id:<tid>&rows=0           + same facets (cached forever per tid)
+//
+// Per-ontology denominators (n_ont, N_ont) come from the root term's facet
+// count, since every annotated gene carries the root in __ancestors. Roots
+// are identified once ontology records are loaded by picking the ancestor
+// (or self) with the highest background facet count — this works for
+// multi-rooted GO (BP/MF/CC) and for the rice-rooted pathway tree.
+//
+// Enrichment uses the upper-tail Fisher exact (hypergeometric); p-values
+// are corrected per ontology with Benjamini–Hochberg. The "most-specific"
+// collapse is applied AFTER BH so a parent term that's significant on its
+// own is preserved even when none of its children clear the cutoff.
+const $0736cb5a41609896$var$ONTOLOGIES = [
+    {
+        key: 'GO',
+        field: 'GO__ancestors',
+        label: 'Gene Ontology',
+        bucket: 'GO'
+    },
+    {
+        key: 'PO',
+        field: 'PO__ancestors',
+        label: 'Plant Ontology',
+        bucket: 'PO'
+    },
+    {
+        key: 'TO',
+        field: 'TO__ancestors',
+        label: 'Trait Ontology',
+        bucket: 'TO'
+    },
+    {
+        key: 'QTL_TO',
+        field: 'QTL_TO__ancestors',
+        label: 'QTL Traits (TO)',
+        bucket: 'TO'
+    },
+    {
+        key: 'domains',
+        field: 'domains__ancestors',
+        label: 'InterPro Domains',
+        bucket: 'domains'
+    },
+    {
+        key: 'pathways',
+        field: 'pathways__ancestors',
+        label: 'Pathways',
+        bucket: null
     }
-};
-const $2fec4872fbf7ebd2$var$Pathway = ({ pathway: pathway })=>{
-    return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
-        className: "row",
-        children: pathway.name
-    });
-};
-const $2fec4872fbf7ebd2$var$Pathways = (results)=>{
-    if (results && results.numFound > 0) return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
-        id: "Pathways",
-        className: "container mb40 anchor",
-        children: [
-            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
-                className: "fancy-title",
-                children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("h4", {
-                    children: "Pathways"
-                })
-            }),
-            results.pathways.map((doc, idx)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($2fec4872fbf7ebd2$var$Pathway, {
-                    pathway: doc
-                }, idx))
-        ]
-    });
-};
-const $2fec4872fbf7ebd2$var$Domain = ({ domain: domain })=>{
-    return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
-        className: "row",
-        children: domain.id
-    });
-};
-const $2fec4872fbf7ebd2$var$Domains = (results)=>{
-    if (results && results.numFound > 0) return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
-        id: "Domains",
-        className: "container mb40 anchor",
-        children: [
-            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
-                className: "fancy-title mb40",
-                children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("h4", {
-                    children: "Domains"
-                })
-            }),
-            results.domains.map((doc, idx)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($2fec4872fbf7ebd2$var$Domain, {
-                    domain: doc
-                }, idx))
-        ]
-    });
-};
-const $2fec4872fbf7ebd2$var$Taxon = ({ taxon: taxon })=>{
-    return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
-        className: "row",
-        children: taxon.id
-    });
-};
-const $2fec4872fbf7ebd2$var$Species = (results)=>{
-    if (results && results.numFound > 0) return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
-        id: "Species",
-        className: "container mb40 anchor",
-        children: [
-            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
-                className: "fancy-title mb40",
-                children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("h4", {
-                    children: "Species"
-                })
-            }),
-            results.taxonomy.map((doc, idx)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($2fec4872fbf7ebd2$var$Taxon, {
-                    taxon: doc
-                }, idx))
-        ]
-    });
-};
-const $2fec4872fbf7ebd2$var$ResultList = ({ grameneGenes: grameneGenes, grameneDomains: grameneDomains, gramenePathways: gramenePathways, grameneTaxonomy: grameneTaxonomy, searchUI: searchUI, searchUpdated: searchUpdated, doChangeQuantity: doChangeQuantity })=>{
-    if (searchUI.Gramene) return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
-        id: "gramene",
-        className: "row",
-        children: [
-            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
-                className: "fancy-title pt50",
-                children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("h3", {
-                    children: "Gramene search results"
-                })
-            }),
-            searchUI.Genes && $2fec4872fbf7ebd2$var$Genes(grameneGenes, searchUI.rows.Genes, doChangeQuantity),
-            searchUI.Domains && $2fec4872fbf7ebd2$var$Domains(grameneDomains),
-            searchUI.Pathways && $2fec4872fbf7ebd2$var$Pathways(gramenePathways),
-            searchUI.Species && $2fec4872fbf7ebd2$var$Species(grameneTaxonomy)
-        ]
-    });
-    else return null;
-};
-var $2fec4872fbf7ebd2$export$2e2bcd8739ae039 = (0, $gXNCa$reduxbundlerreact.connect)('selectGrameneGenes', 'selectGrameneDomains', 'selectGramenePathways', 'selectGrameneTaxonomy', 'selectSearchUI', 'selectSearchUpdated', 'doChangeQuantity', $2fec4872fbf7ebd2$var$ResultList);
-
-
-
-
-
-const $27617dbc24e7faf0$var$getStatus = (cat, results, isChecked, toggle)=>{
-    const tally = results ? results.numFound : /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("img", {
-        src: "/static/images/dna_spinner.svg"
-    });
-    return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("li", {
-        className: "category-leaf",
-        children: [
-            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("input", {
-                type: "checkbox",
-                checked: isChecked,
-                onChange: (e)=>toggle(cat)
-            }),
-            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("a", {
-                "data-scroll": true,
-                href: `#${cat}`,
-                className: "nav-link active",
-                children: [
-                    cat,
-                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
-                        style: {
-                            float: "right"
+];
+const $0736cb5a41609896$var$FACET_PARAMS = $0736cb5a41609896$var$ONTOLOGIES.map((o)=>`facet.field=${encodeURIComponent(`{!facet.limit=10000 facet.mincount=1 key=${o.key}}${o.field}`)}`).join('&');
+const $0736cb5a41609896$var$fgPending = {};
+const $0736cb5a41609896$var$bgPending = {};
+function $0736cb5a41609896$var$fgSig(q, taxon) {
+    return `${q}|${taxon}`;
+}
+function $0736cb5a41609896$var$bgSig(taxon) {
+    return `bg|${taxon}`;
+}
+function $0736cb5a41609896$var$parseFacets(json) {
+    const out = {};
+    const ff = json && json.facet_counts && json.facet_counts.facet_fields || {};
+    for (const o of $0736cb5a41609896$var$ONTOLOGIES){
+        const arr = ff[o.key] || [];
+        const map = {};
+        for(let i = 0; i < arr.length; i += 2)map[+arr[i]] = +arr[i + 1];
+        out[o.key] = map;
+    }
+    return out;
+}
+const $0736cb5a41609896$var$gsea = {
+    name: 'gsea',
+    // Background facet counts depend only on the species — they're invariant
+    // across filter changes and across sessions, so we persist whenever a bg
+    // fetch completes. Foreground state piggybacks on the same write but is
+    // self-invalidated by the signature check in the reactor.
+    persistActions: [
+        'GSEA_BG_SUCCEEDED'
+    ],
+    getReducer: ()=>{
+        const initialState = {
+            activeTaxon: null,
+            byTaxon: {},
+            ui: {
+                pAdjCutoff: 0.05,
+                minK: 2,
+                mostSpecific: true,
+                ontology: 'all',
+                search: ''
+            }
+        };
+        function ensureTaxon(state, tid) {
+            if (state.byTaxon[tid]) return state;
+            return {
+                ...state,
+                byTaxon: {
+                    ...state.byTaxon,
+                    [tid]: {
+                        fg: {
+                            status: 'idle',
+                            signature: null,
+                            requestId: 0,
+                            terms: null,
+                            numFound: 0,
+                            error: null
                         },
-                        children: tally
-                    })
-                ]
-            })
-        ]
-    });
-};
-const $27617dbc24e7faf0$var$ResultSummary = ({ grameneGenes: grameneGenes, gramenePathways: gramenePathways, grameneDomains: grameneDomains, grameneTaxonomy: grameneTaxonomy, searchUI: searchUI, searchUpdated: searchUpdated, doToggleCategory: doToggleCategory })=>{
-    const status = grameneGenes ? grameneGenes.numFound : /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("img", {
-        src: "/static/images/dna_spinner.svg"
-    });
-    if (searchUI.Gramene) return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("li", {
-        className: "active category-expanded",
-        children: [
-            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("a", {
-                onClick: (e)=>doToggleCategory('Gramene'),
-                children: [
-                    "Gramene Search",
-                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
-                        style: {
-                            float: "right"
-                        },
-                        children: status
-                    })
-                ]
+                        bg: {
+                            status: 'idle',
+                            signature: null,
+                            requestId: 0,
+                            terms: null,
+                            numFound: 0,
+                            error: null
+                        }
+                    }
+                }
+            };
+        }
+        return (state = initialState, { type: type, payload: payload })=>{
+            switch(type){
+                case 'GSEA_ACTIVE_TAXON_SET':
+                    return {
+                        ...ensureTaxon(state, payload),
+                        activeTaxon: payload
+                    };
+                case 'GSEA_UI_SET':
+                    return {
+                        ...state,
+                        ui: {
+                            ...state.ui,
+                            ...payload || {}
+                        }
+                    };
+                case 'GSEA_FG_STARTED':
+                    {
+                        const next = ensureTaxon(state, payload.taxon);
+                        const t = next.byTaxon[payload.taxon];
+                        return {
+                            ...next,
+                            byTaxon: {
+                                ...next.byTaxon,
+                                [payload.taxon]: {
+                                    ...t,
+                                    fg: {
+                                        status: 'loading',
+                                        signature: payload.signature,
+                                        requestId: payload.requestId,
+                                        terms: t.fg.terms,
+                                        numFound: t.fg.numFound,
+                                        error: null
+                                    }
+                                }
+                            }
+                        };
+                    }
+                case 'GSEA_FG_SUCCEEDED':
+                    {
+                        const t = state.byTaxon[payload.taxon];
+                        if (!t || payload.requestId !== t.fg.requestId) return state;
+                        return {
+                            ...state,
+                            byTaxon: {
+                                ...state.byTaxon,
+                                [payload.taxon]: {
+                                    ...t,
+                                    fg: {
+                                        ...t.fg,
+                                        status: 'ready',
+                                        terms: payload.terms,
+                                        numFound: payload.numFound
+                                    }
+                                }
+                            }
+                        };
+                    }
+                case 'GSEA_FG_FAILED':
+                    {
+                        const t = state.byTaxon[payload.taxon];
+                        if (!t || payload.requestId !== t.fg.requestId) return state;
+                        return {
+                            ...state,
+                            byTaxon: {
+                                ...state.byTaxon,
+                                [payload.taxon]: {
+                                    ...t,
+                                    fg: {
+                                        ...t.fg,
+                                        status: 'error',
+                                        error: payload.error
+                                    }
+                                }
+                            }
+                        };
+                    }
+                case 'GSEA_BG_STARTED':
+                    {
+                        const next = ensureTaxon(state, payload.taxon);
+                        const t = next.byTaxon[payload.taxon];
+                        return {
+                            ...next,
+                            byTaxon: {
+                                ...next.byTaxon,
+                                [payload.taxon]: {
+                                    ...t,
+                                    bg: {
+                                        status: 'loading',
+                                        signature: payload.signature,
+                                        requestId: payload.requestId,
+                                        terms: t.bg.terms,
+                                        numFound: t.bg.numFound,
+                                        error: null
+                                    }
+                                }
+                            }
+                        };
+                    }
+                case 'GSEA_BG_SUCCEEDED':
+                    {
+                        const t = state.byTaxon[payload.taxon];
+                        if (!t || payload.requestId !== t.bg.requestId) return state;
+                        return {
+                            ...state,
+                            byTaxon: {
+                                ...state.byTaxon,
+                                [payload.taxon]: {
+                                    ...t,
+                                    bg: {
+                                        ...t.bg,
+                                        status: 'ready',
+                                        terms: payload.terms,
+                                        numFound: payload.numFound
+                                    }
+                                }
+                            }
+                        };
+                    }
+                case 'GSEA_BG_FAILED':
+                    {
+                        const t = state.byTaxon[payload.taxon];
+                        if (!t || payload.requestId !== t.bg.requestId) return state;
+                        return {
+                            ...state,
+                            byTaxon: {
+                                ...state.byTaxon,
+                                [payload.taxon]: {
+                                    ...t,
+                                    bg: {
+                                        ...t.bg,
+                                        status: 'error',
+                                        error: payload.error
+                                    }
+                                }
+                            }
+                        };
+                    }
+                case 'GRAMENE_SEARCH_CLEARED':
+                    {
+                        // Filters changed — invalidate foreground but keep background
+                        // (it depends only on taxon).
+                        const newByTaxon = {};
+                        for (const tid of Object.keys(state.byTaxon)){
+                            const t = state.byTaxon[tid];
+                            newByTaxon[tid] = {
+                                ...t,
+                                fg: {
+                                    status: 'idle',
+                                    signature: null,
+                                    requestId: 0,
+                                    terms: null,
+                                    numFound: 0,
+                                    error: null
+                                }
+                            };
+                        }
+                        return {
+                            ...state,
+                            byTaxon: newByTaxon
+                        };
+                    }
+                default:
+                    return state;
+            }
+        };
+    },
+    doSetGseaActiveTaxon: (tid)=>({ dispatch: dispatch })=>dispatch({
+                type: 'GSEA_ACTIVE_TAXON_SET',
+                payload: tid
             }),
-            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("ul", {
-                className: "list-unstyled",
-                children: [
-                    $27617dbc24e7faf0$var$getStatus('Genes', grameneGenes, searchUI.Genes, doToggleCategory),
-                    $27617dbc24e7faf0$var$getStatus('Domains', grameneDomains, searchUI.Domains, doToggleCategory),
-                    $27617dbc24e7faf0$var$getStatus('Pathways', gramenePathways, searchUI.Pathways, doToggleCategory),
-                    $27617dbc24e7faf0$var$getStatus('Species', grameneTaxonomy, searchUI.Species, doToggleCategory)
-                ]
-            })
-        ]
-    });
-    else return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("li", {
-        className: "active category-collapsed",
-        children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("a", {
-            onClick: (e)=>doToggleCategory('Gramene'),
-            children: [
-                "Gramene Search",
-                /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
-                    style: {
-                        float: "right"
-                    },
-                    children: status
-                })
+    doSetGseaUI: (patch)=>({ dispatch: dispatch })=>dispatch({
+                type: 'GSEA_UI_SET',
+                payload: patch
+            }),
+    doFetchGseaForeground: (taxon)=>({ dispatch: dispatch, store: store })=>{
+            const q = store.selectGrameneFiltersQueryString();
+            const signature = $0736cb5a41609896$var$fgSig(q, taxon);
+            const state = store.selectGsea();
+            const t = state.byTaxon[taxon];
+            if (t && t.fg.signature === signature && (t.fg.status === 'loading' || t.fg.status === 'ready')) return;
+            const requestId = $0736cb5a41609896$var$fgPending[taxon] = ($0736cb5a41609896$var$fgPending[taxon] || 0) + 1;
+            dispatch({
+                type: 'GSEA_FG_STARTED',
+                payload: {
+                    taxon: taxon,
+                    signature: signature,
+                    requestId: requestId
+                }
+            });
+            const api = store.selectGrameneAPI();
+            const url = `${api}/search?q=${q}&fq=taxon_id:${taxon}&rows=0&facet=true&${$0736cb5a41609896$var$FACET_PARAMS}`;
+            fetch(url).then((r)=>r.json()).then((json)=>{
+                if (requestId !== $0736cb5a41609896$var$fgPending[taxon]) return;
+                const terms = $0736cb5a41609896$var$parseFacets(json);
+                const numFound = json && json.response && json.response.numFound || 0;
+                dispatch({
+                    type: 'GSEA_FG_SUCCEEDED',
+                    payload: {
+                        taxon: taxon,
+                        requestId: requestId,
+                        terms: terms,
+                        numFound: numFound
+                    }
+                });
+                store.doEnsureGseaTermRecords(taxon);
+            }).catch((err)=>{
+                if (requestId !== $0736cb5a41609896$var$fgPending[taxon]) return;
+                dispatch({
+                    type: 'GSEA_FG_FAILED',
+                    payload: {
+                        taxon: taxon,
+                        requestId: requestId,
+                        error: String(err)
+                    }
+                });
+            });
+        },
+    doFetchGseaBackground: (taxon)=>({ dispatch: dispatch, store: store })=>{
+            const signature = $0736cb5a41609896$var$bgSig(taxon);
+            const state = store.selectGsea();
+            const t = state.byTaxon[taxon];
+            if (t && t.bg.signature === signature && (t.bg.status === 'loading' || t.bg.status === 'ready')) return;
+            const requestId = $0736cb5a41609896$var$bgPending[taxon] = ($0736cb5a41609896$var$bgPending[taxon] || 0) + 1;
+            dispatch({
+                type: 'GSEA_BG_STARTED',
+                payload: {
+                    taxon: taxon,
+                    signature: signature,
+                    requestId: requestId
+                }
+            });
+            const api = store.selectGrameneAPI();
+            const url = `${api}/search?q=taxon_id:${taxon}&rows=0&facet=true&${$0736cb5a41609896$var$FACET_PARAMS}`;
+            fetch(url).then((r)=>r.json()).then((json)=>{
+                if (requestId !== $0736cb5a41609896$var$bgPending[taxon]) return;
+                const terms = $0736cb5a41609896$var$parseFacets(json);
+                const numFound = json && json.response && json.response.numFound || 0;
+                dispatch({
+                    type: 'GSEA_BG_SUCCEEDED',
+                    payload: {
+                        taxon: taxon,
+                        requestId: requestId,
+                        terms: terms,
+                        numFound: numFound
+                    }
+                });
+                store.doEnsureGseaTermRecords(taxon);
+            }).catch((err)=>{
+                if (requestId !== $0736cb5a41609896$var$bgPending[taxon]) return;
+                dispatch({
+                    type: 'GSEA_BG_FAILED',
+                    payload: {
+                        taxon: taxon,
+                        requestId: requestId,
+                        error: String(err)
+                    }
+                });
+            });
+        },
+    doEnsureGseaTermRecords: (taxon)=>({ store: store })=>{
+            const state = store.selectGsea();
+            if (!state.byTaxon[taxon]) return;
+            // The ontologies and pathways bundles bulk-load + persist on first
+            // request; we just need to nudge each one once.
+            const buckets = new Set();
+            for (const o of $0736cb5a41609896$var$ONTOLOGIES)if (o.bucket) buckets.add(o.bucket);
+            for (const k of buckets)store.doEnsureOntologyRecords(k);
+            if (store.doRequestGramenePathways) store.doRequestGramenePathways();
+        },
+    reactGseaFetch: (0, $gXNCa$reduxbundler.createSelector)('selectGsea', 'selectGrameneFiltersStatus', 'selectGrameneFiltersQueryString', 'selectGrameneViewsOn', (gs, fStatus, q, viewsOn)=>{
+        if (!viewsOn || !viewsOn.has('gsea')) return;
+        if (fStatus === 'init') return;
+        const tid = gs.activeTaxon;
+        if (!tid) return;
+        const t = gs.byTaxon[tid];
+        if (!t) return;
+        const sig = $0736cb5a41609896$var$fgSig(q, tid);
+        // A 'loading' status from a rehydrated state with no live request is
+        // treated as idle — otherwise we'd deadlock waiting on a fetch that
+        // ended when the previous tab closed.
+        const fgInFlight = t.fg.status === 'loading' && ($0736cb5a41609896$var$fgPending[tid] || 0) === t.fg.requestId && t.fg.requestId > 0;
+        if (t.fg.signature !== sig && !fgInFlight) return {
+            actionCreator: 'doFetchGseaForeground',
+            args: [
+                tid
             ]
-        })
-    });
+        };
+        const bgInFlight = t.bg.status === 'loading' && ($0736cb5a41609896$var$bgPending[tid] || 0) === t.bg.requestId && t.bg.requestId > 0;
+        if (t.bg.status !== 'ready' && !bgInFlight) return {
+            actionCreator: 'doFetchGseaBackground',
+            args: [
+                tid
+            ]
+        };
+    }),
+    selectGsea: (state)=>state.gsea,
+    selectGseaUI: (state)=>state.gsea.ui,
+    selectGseaOntologyDefs: ()=>$0736cb5a41609896$var$ONTOLOGIES,
+    selectGseaResults: (0, $gXNCa$reduxbundler.createSelector)('selectGsea', 'selectOntologies', 'selectGramenePathways', (gs, ontoBuckets, pathwayDocs)=>{
+        const tid = gs.activeTaxon;
+        if (!tid) return null;
+        const t = gs.byTaxon[tid];
+        if (!t || !t.fg.terms || !t.bg.terms) return null;
+        const ui = gs.ui;
+        const out = {};
+        for (const o of $0736cb5a41609896$var$ONTOLOGIES){
+            const fg = t.fg.terms[o.key] || {};
+            const bg = t.bg.terms[o.key] || {};
+            const recs = o.key === 'pathways' ? pathwayDocs || {} : ontoBuckets && ontoBuckets[o.bucket] || {};
+            // Forest-fallback denominators: when a term is itself a forest root
+            // (no parents in `recs` — common for InterPro), root finding returns
+            // the term and we'd get fold=1 by construction. Use the maximum
+            // counts across the ontology as a proxy for "annotated in this
+            // ontology" instead. For ontologies with a true synthetic root,
+            // these maxima equal the root counts and the answer is unchanged.
+            let maxFg = 0, maxBg = 0;
+            for (const idStr of Object.keys(bg)){
+                const v = bg[idStr];
+                if (v > maxBg) maxBg = v;
+            }
+            for (const idStr of Object.keys(fg)){
+                const v = fg[idStr];
+                if (v > maxFg) maxFg = v;
+            }
+            const rootCache = {};
+            const rootOf = (id)=>{
+                if (rootCache.hasOwnProperty(id)) return rootCache[id];
+                const r = $0736cb5a41609896$var$findRoot(o.key, id, recs, bg);
+                rootCache[id] = r;
+                return r;
+            };
+            const rows = [];
+            for (const idStr of Object.keys(fg)){
+                const id = +idStr;
+                const k = fg[id];
+                const K = bg[id] || 0;
+                if (K < k) continue; // bg should always be >= fg
+                if (k < ui.minK) continue;
+                const termRec = recs && recs[id];
+                if (termRec && (termRec.is_obsolete || termRec.obsolete)) continue;
+                const root = rootOf(id);
+                // If the "root" is the term itself, the term is a forest root in
+                // this ontology — fall back to ontology-wide maxima.
+                const fellBack = +root === id;
+                const n = fellBack ? maxFg : root != null && fg[root] ? fg[root] : k;
+                const N = fellBack ? maxBg : root != null && bg[root] ? bg[root] : K;
+                if (n <= 0 || N <= 0) continue;
+                if (k > n || K > N) continue;
+                const fold = k / n / (K / N);
+                const p = $0736cb5a41609896$var$fisherUpperTail(k, n, K, N);
+                rows.push({
+                    ontology: o.key,
+                    ontology_label: o.label,
+                    term_id: id,
+                    field: o.field,
+                    k: k,
+                    n: n,
+                    K: K,
+                    N: N,
+                    fold: fold,
+                    p: p,
+                    pAdj: 1,
+                    root: root,
+                    denomFallback: fellBack
+                });
+            }
+            // GO is split into its three top-level namespaces (BP / MF / CC)
+            // and each is tested as its own ontology — both BH correction and
+            // most-specific collapse run within a namespace. We only split once
+            // ontology records have arrived and root finding has produced
+            // canonical roots; otherwise we'd see a swarm of singleton groups
+            // during the brief loading window between bg landing and records
+            // being fetched.
+            if (o.key === 'GO' && Object.keys(recs).length > 0) {
+                const byRoot = {};
+                for (const r of rows){
+                    const k = String(r.root);
+                    if (!byRoot[k]) byRoot[k] = [];
+                    byRoot[k].push(r);
+                }
+                const rootKeys = Object.keys(byRoot).sort((a, b)=>{
+                    const na = $0736cb5a41609896$var$goRootName(recs[+a]) || a;
+                    const nb = $0736cb5a41609896$var$goRootName(recs[+b]) || b;
+                    return na.localeCompare(nb);
+                });
+                for (const rootKey of rootKeys){
+                    const rootRec = recs[+rootKey];
+                    const rootName = $0736cb5a41609896$var$goRootName(rootRec);
+                    const sectionKey = `GO:${rootKey}`;
+                    const sectionLabel = rootName ? `GO: ${$0736cb5a41609896$var$titleCase(rootName)}` : `GO: ${rootKey}`;
+                    out[sectionKey] = $0736cb5a41609896$var$finalizeBlock(byRoot[rootKey], o.key, o.field, recs, ui, sectionKey, sectionLabel);
+                }
+            } else out[o.key] = $0736cb5a41609896$var$finalizeBlock(rows, o.key, o.field, recs, ui, o.key, o.label);
+        }
+        return out;
+    })
 };
-var $27617dbc24e7faf0$export$2e2bcd8739ae039 = (0, $gXNCa$reduxbundlerreact.connect)('selectGrameneGenes', 'selectGramenePathways', 'selectGrameneDomains', 'selectGrameneTaxonomy', 'selectSearchUI', 'selectSearchUpdated', 'doToggleCategory', $27617dbc24e7faf0$var$ResultSummary);
-
-
-
-
+function $0736cb5a41609896$var$goRootName(rec) {
+    if (!rec) return '';
+    return rec.name || rec.display_name || rec.namespace || '';
+}
+function $0736cb5a41609896$var$titleCase(s) {
+    return String(s).split('_').map((w)=>w ? w[0].toUpperCase() + w.slice(1) : '').join(' ');
+}
+// BH correction + most-specific collapse + metadata + final sort, returning
+// the block descriptor consumed by the view layer.
+function $0736cb5a41609896$var$finalizeBlock(rows, ontKey, ontField, recs, ui, sectionKey, sectionLabel) {
+    rows.sort((a, b)=>a.p - b.p);
+    const m = rows.length;
+    let prev = 1;
+    for(let i = m - 1; i >= 0; i--){
+        const adj = Math.min(prev, rows[i].p * m / (i + 1));
+        rows[i].pAdj = adj;
+        prev = adj;
+    }
+    const passing = rows.filter((r)=>r.pAdj <= ui.pAdjCutoff);
+    let display = passing;
+    if (ui.mostSpecific) display = $0736cb5a41609896$var$collapseToMostSpecific(ontKey, passing, recs);
+    for (const r of display){
+        const rec = recs && recs[r.term_id];
+        if (rec) {
+            r.term_name = rec.name || rec.display_name || '';
+            r.term_namespace = rec.namespace || rec.type || '';
+            r.term_display_id = rec.id != null ? String(rec.id) : String(r.term_id);
+        } else {
+            r.term_name = '';
+            r.term_namespace = '';
+            r.term_display_id = String(r.term_id);
+        }
+    }
+    display.sort((a, b)=>a.pAdj - b.pAdj || b.fold - a.fold);
+    return {
+        ontology: sectionKey,
+        label: sectionLabel,
+        field: ontField,
+        tested: rows.length,
+        passing: passing.length,
+        rows: display
+    };
+}
+// ---------- math helpers ----------
+const $0736cb5a41609896$var$LF_CACHE = [
+    0,
+    0
+];
+function $0736cb5a41609896$var$logFactorial(n) {
+    if (n < $0736cb5a41609896$var$LF_CACHE.length) return $0736cb5a41609896$var$LF_CACHE[n];
+    let lf = $0736cb5a41609896$var$LF_CACHE[$0736cb5a41609896$var$LF_CACHE.length - 1];
+    for(let i = $0736cb5a41609896$var$LF_CACHE.length; i <= n; i++){
+        lf += Math.log(i);
+        $0736cb5a41609896$var$LF_CACHE.push(lf);
+    }
+    return $0736cb5a41609896$var$LF_CACHE[n];
+}
+function $0736cb5a41609896$var$logChoose(n, k) {
+    if (k < 0 || k > n) return -Infinity;
+    return $0736cb5a41609896$var$logFactorial(n) - $0736cb5a41609896$var$logFactorial(k) - $0736cb5a41609896$var$logFactorial(n - k);
+}
+function $0736cb5a41609896$var$logHypergeom(x, n, K, N) {
+    return $0736cb5a41609896$var$logChoose(K, x) + $0736cb5a41609896$var$logChoose(N - K, n - x) - $0736cb5a41609896$var$logChoose(N, n);
+}
+function $0736cb5a41609896$var$logSumExp(a, b) {
+    if (a === -Infinity) return b;
+    if (b === -Infinity) return a;
+    const m = Math.max(a, b);
+    return m + Math.log(Math.exp(a - m) + Math.exp(b - m));
+}
+function $0736cb5a41609896$var$fisherUpperTail(k, n, K, N) {
+    const upper = Math.min(n, K);
+    let logP = -Infinity;
+    for(let x = k; x <= upper; x++)logP = $0736cb5a41609896$var$logSumExp(logP, $0736cb5a41609896$var$logHypergeom(x, n, K, N));
+    const p = Math.exp(logP);
+    if (!isFinite(p)) return 1;
+    return Math.min(1, Math.max(0, p));
+}
+// ---------- ontology graph helpers ----------
+// Pick the "root" for a term as the ancestor (or self) with the highest
+// background facet count. The true root has every annotated gene under it,
+// so this selects BP/MF/CC for GO terms automatically and the rice root
+// for pathways without needing per-ontology hardcoded ids.
+function $0736cb5a41609896$var$findRoot(ontKey, id, recs, bgCounts) {
+    const rec = recs && recs[id];
+    const candidates = new Set([
+        +id
+    ]);
+    if (rec) {
+        if (ontKey === 'pathways') for (const k of Object.keys(rec)){
+            if (k.startsWith('ancestors_') && Array.isArray(rec[k])) for (const a of rec[k])candidates.add(+a);
+        }
+        else if (Array.isArray(rec.ancestors)) for (const a of rec.ancestors)candidates.add(+a);
+        else if (Array.isArray(rec.is_a)) {
+            const stack = rec.is_a.slice();
+            while(stack.length){
+                const cur = +stack.pop();
+                if (candidates.has(cur)) continue;
+                candidates.add(cur);
+                const r = recs[cur];
+                if (r && Array.isArray(r.is_a)) for (const p of r.is_a)stack.push(p);
+            }
+        }
+    }
+    let best = +id;
+    let bestCount = bgCounts[+id] || 0;
+    for (const c of candidates){
+        const cnt = bgCounts[c] || 0;
+        if (cnt > bestCount) {
+            bestCount = cnt;
+            best = c;
+        }
+    }
+    return best;
+}
+function $0736cb5a41609896$var$ancestorsOf(ontKey, id, recs) {
+    const out = new Set();
+    const rec = recs && recs[id];
+    if (!rec) return out;
+    if (ontKey === 'pathways') {
+        for (const k of Object.keys(rec))if (k.startsWith('ancestors_') && Array.isArray(rec[k])) {
+            for (const a of rec[k])if (+a !== +id) out.add(+a);
+        }
+        return out;
+    }
+    if (Array.isArray(rec.ancestors)) {
+        for (const a of rec.ancestors)if (+a !== +id) out.add(+a);
+        return out;
+    }
+    if (Array.isArray(rec.is_a)) {
+        const stack = rec.is_a.slice();
+        while(stack.length){
+            const cur = +stack.pop();
+            if (out.has(cur)) continue;
+            out.add(cur);
+            const r = recs[cur];
+            if (r && Array.isArray(r.is_a)) for (const p of r.is_a)stack.push(p);
+        }
+    }
+    return out;
+}
+// Drop any term that is an ancestor of another term in the same passing set.
+// Applied AFTER BH so a parent term can survive when none of its children
+// pass the p_adj cutoff.
+function $0736cb5a41609896$var$collapseToMostSpecific(ontKey, rows, recs) {
+    if (!rows || rows.length <= 1) return rows;
+    const inSet = new Set(rows.map((r)=>+r.term_id));
+    const covered = new Set();
+    for (const r of rows){
+        const ancs = $0736cb5a41609896$var$ancestorsOf(ontKey, +r.term_id, recs);
+        for (const a of ancs)if (inSet.has(a)) covered.add(a);
+    }
+    return rows.filter((r)=>!covered.has(+r.term_id));
+}
+var $0736cb5a41609896$export$2e2bcd8739ae039 = $0736cb5a41609896$var$gsea;
+
+
+var $5df6c55c1bef3469$export$2e2bcd8739ae039 = [
+    ...(0, $9d9aeaf9299e61a1$export$2e2bcd8739ae039),
+    (0, $671312b287158a8a$export$2e2bcd8739ae039),
+    (0, $af4441dd29af05df$export$2e2bcd8739ae039),
+    (0, $24971af0a229e0e3$export$2e2bcd8739ae039),
+    (0, $0d54502f6cafe273$export$2e2bcd8739ae039),
+    (0, $0f839422d0d8c772$export$2e2bcd8739ae039),
+    (0, $1508f5a42be6e7b5$export$2e2bcd8739ae039),
+    (0, $c921a0d2b34aadb6$export$2e2bcd8739ae039),
+    (0, $4f15cd8a7d970b18$export$2e2bcd8739ae039),
+    (0, $0736cb5a41609896$export$2e2bcd8739ae039)
+];
+
+
+
+
+
+const $2fec4872fbf7ebd2$var$Gene = ({ gene: gene })=>{
+    return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
+        className: "row",
+        children: gene.id
+    });
+};
+const $2fec4872fbf7ebd2$var$Genes = (results, rows, doChangeQuantity)=>{
+    if (results && results.numFound > 0) {
+        const moreButton = results.numFound > rows ? /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("button", {
+            onClick: (e)=>doChangeQuantity('Genes', 20),
+            children: "more"
+        }) : '';
+        const fewerButton = rows > 20 ? /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("button", {
+            onClick: (e)=>doChangeQuantity('Genes', -20),
+            children: "fewer"
+        }) : '';
+        const docsToShow = results.response.docs.slice(0, rows);
+        return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+            id: "Genes",
+            className: "container mb40 anchor",
+            children: [
+                /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
+                    className: "fancy-title mb40",
+                    children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("h4", {
+                        children: "Genes"
+                    })
+                }),
+                docsToShow.map((doc, idx)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($2fec4872fbf7ebd2$var$Gene, {
+                        gene: doc
+                    }, idx)),
+                fewerButton,
+                moreButton
+            ]
+        });
+    }
+};
+const $2fec4872fbf7ebd2$var$Pathway = ({ pathway: pathway })=>{
+    return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
+        className: "row",
+        children: pathway.name
+    });
+};
+const $2fec4872fbf7ebd2$var$Pathways = (results)=>{
+    if (results && results.numFound > 0) return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+        id: "Pathways",
+        className: "container mb40 anchor",
+        children: [
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
+                className: "fancy-title",
+                children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("h4", {
+                    children: "Pathways"
+                })
+            }),
+            results.pathways.map((doc, idx)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($2fec4872fbf7ebd2$var$Pathway, {
+                    pathway: doc
+                }, idx))
+        ]
+    });
+};
+const $2fec4872fbf7ebd2$var$Domain = ({ domain: domain })=>{
+    return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
+        className: "row",
+        children: domain.id
+    });
+};
+const $2fec4872fbf7ebd2$var$Domains = (results)=>{
+    if (results && results.numFound > 0) return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+        id: "Domains",
+        className: "container mb40 anchor",
+        children: [
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
+                className: "fancy-title mb40",
+                children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("h4", {
+                    children: "Domains"
+                })
+            }),
+            results.domains.map((doc, idx)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($2fec4872fbf7ebd2$var$Domain, {
+                    domain: doc
+                }, idx))
+        ]
+    });
+};
+const $2fec4872fbf7ebd2$var$Taxon = ({ taxon: taxon })=>{
+    return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
+        className: "row",
+        children: taxon.id
+    });
+};
+const $2fec4872fbf7ebd2$var$Species = (results)=>{
+    if (results && results.numFound > 0) return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+        id: "Species",
+        className: "container mb40 anchor",
+        children: [
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
+                className: "fancy-title mb40",
+                children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("h4", {
+                    children: "Species"
+                })
+            }),
+            results.taxonomy.map((doc, idx)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($2fec4872fbf7ebd2$var$Taxon, {
+                    taxon: doc
+                }, idx))
+        ]
+    });
+};
+const $2fec4872fbf7ebd2$var$ResultList = ({ grameneGenes: grameneGenes, grameneDomains: grameneDomains, gramenePathways: gramenePathways, grameneTaxonomy: grameneTaxonomy, searchUI: searchUI, searchUpdated: searchUpdated, doChangeQuantity: doChangeQuantity })=>{
+    if (searchUI.Gramene) return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+        id: "gramene",
+        className: "row",
+        children: [
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
+                className: "fancy-title pt50",
+                children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("h3", {
+                    children: "Gramene search results"
+                })
+            }),
+            searchUI.Genes && $2fec4872fbf7ebd2$var$Genes(grameneGenes, searchUI.rows.Genes, doChangeQuantity),
+            searchUI.Domains && $2fec4872fbf7ebd2$var$Domains(grameneDomains),
+            searchUI.Pathways && $2fec4872fbf7ebd2$var$Pathways(gramenePathways),
+            searchUI.Species && $2fec4872fbf7ebd2$var$Species(grameneTaxonomy)
+        ]
+    });
+    else return null;
+};
+var $2fec4872fbf7ebd2$export$2e2bcd8739ae039 = (0, $gXNCa$reduxbundlerreact.connect)('selectGrameneGenes', 'selectGrameneDomains', 'selectGramenePathways', 'selectGrameneTaxonomy', 'selectSearchUI', 'selectSearchUpdated', 'doChangeQuantity', $2fec4872fbf7ebd2$var$ResultList);
+
+
+
+
+
+const $27617dbc24e7faf0$var$getStatus = (cat, results, isChecked, toggle)=>{
+    const tally = results ? results.numFound : /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("img", {
+        src: "/static/images/dna_spinner.svg"
+    });
+    return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("li", {
+        className: "category-leaf",
+        children: [
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("input", {
+                type: "checkbox",
+                checked: isChecked,
+                onChange: (e)=>toggle(cat)
+            }),
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("a", {
+                "data-scroll": true,
+                href: `#${cat}`,
+                className: "nav-link active",
+                children: [
+                    cat,
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
+                        style: {
+                            float: "right"
+                        },
+                        children: tally
+                    })
+                ]
+            })
+        ]
+    });
+};
+const $27617dbc24e7faf0$var$ResultSummary = ({ grameneGenes: grameneGenes, gramenePathways: gramenePathways, grameneDomains: grameneDomains, grameneTaxonomy: grameneTaxonomy, searchUI: searchUI, searchUpdated: searchUpdated, doToggleCategory: doToggleCategory })=>{
+    const status = grameneGenes ? grameneGenes.numFound : /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("img", {
+        src: "/static/images/dna_spinner.svg"
+    });
+    if (searchUI.Gramene) return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("li", {
+        className: "active category-expanded",
+        children: [
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("a", {
+                onClick: (e)=>doToggleCategory('Gramene'),
+                children: [
+                    "Gramene Search",
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
+                        style: {
+                            float: "right"
+                        },
+                        children: status
+                    })
+                ]
+            }),
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("ul", {
+                className: "list-unstyled",
+                children: [
+                    $27617dbc24e7faf0$var$getStatus('Genes', grameneGenes, searchUI.Genes, doToggleCategory),
+                    $27617dbc24e7faf0$var$getStatus('Domains', grameneDomains, searchUI.Domains, doToggleCategory),
+                    $27617dbc24e7faf0$var$getStatus('Pathways', gramenePathways, searchUI.Pathways, doToggleCategory),
+                    $27617dbc24e7faf0$var$getStatus('Species', grameneTaxonomy, searchUI.Species, doToggleCategory)
+                ]
+            })
+        ]
+    });
+    else return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("li", {
+        className: "active category-collapsed",
+        children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("a", {
+            onClick: (e)=>doToggleCategory('Gramene'),
+            children: [
+                "Gramene Search",
+                /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
+                    style: {
+                        float: "right"
+                    },
+                    children: status
+                })
+            ]
+        })
+    });
+};
+var $27617dbc24e7faf0$export$2e2bcd8739ae039 = (0, $gXNCa$reduxbundlerreact.connect)('selectGrameneGenes', 'selectGramenePathways', 'selectGrameneDomains', 'selectGrameneTaxonomy', 'selectSearchUI', 'selectSearchUpdated', 'doToggleCategory', $27617dbc24e7faf0$var$ResultSummary);
+
+
+
+
 
 
 
@@ -7920,6 +8601,36 @@ const $b36244140732570a$var$examples = [
             ]
         }
     },
+    {
+        subsite: {
+            maize: 1,
+            sorghum: 1,
+            grapevine: 1,
+            rice: 1,
+            main: 1
+        },
+        text: "Which genes are curated in the scientific literature?",
+        filters: {
+            status: 'init',
+            rows: 20,
+            operation: 'AND',
+            negate: false,
+            leftIdx: 0,
+            rightIdx: 3,
+            children: [
+                {
+                    fq_field: 'capabilities',
+                    fq_value: 'pubs',
+                    name: 'publication',
+                    category: 'Curated',
+                    leftIdx: 1,
+                    rightIdx: 2,
+                    negate: false,
+                    marked: false
+                }
+            ]
+        }
+    },
     {
         subsite: {
             grapevine: 1
@@ -11390,12 +12101,22 @@ const $4ab64e76c1caef59$var$baseColDefs = [
         suppressMovable: true
     }
 ];
+// Hoisted so the reference is stable across renders. ag-grid otherwise sees a
+// "new" defaultColDef on every parent re-render (e.g. when hovering a row
+// triggers setHoveredId in the parent) and re-applies column state, which
+// snaps any user-resized columns back to their original widths.
+const $4ab64e76c1caef59$var$DEFAULT_COL_DEF = {
+    resizable: true,
+    sortable: true,
+    filter: false,
+    suppressMenu: true
+};
 function $4ab64e76c1caef59$var$arraysEqual(a, b) {
     if (a.length !== b.length) return false;
     for(let i = 0; i < a.length; i++)if (a[i] !== b[i]) return false;
     return true;
 }
-function $4ab64e76c1caef59$var$buildFieldInfo(fields, studies, expressionSamples) {
+function $4ab64e76c1caef59$export$7b242440eb2c300d(fields, studies, expressionSamples) {
     const info = {};
     if (!fields || !studies || !expressionSamples) return info;
     const wanted = new Set(fields);
@@ -11684,7 +12405,7 @@ function $4ab64e76c1caef59$var$buildColumnDefs(fields, fieldInfo, expanded, togg
     ];
 }
 const $4ab64e76c1caef59$var$ExprTable = ({ rows: rows, fields: fields, onReorder: onReorder, studies: studies, expressionSamples: expressionSamples, onHoverRow: onHoverRow })=>{
-    const fieldInfo = (0, $gXNCa$react.useMemo)(()=>$4ab64e76c1caef59$var$buildFieldInfo(fields, studies, expressionSamples), [
+    const fieldInfo = (0, $gXNCa$react.useMemo)(()=>$4ab64e76c1caef59$export$7b242440eb2c300d(fields, studies, expressionSamples), [
         fields,
         studies,
         expressionSamples
@@ -11730,12 +12451,7 @@ const $4ab64e76c1caef59$var$ExprTable = ({ rows: rows, fields: fields, onReorder
         children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$aggridreact.AgGridReact), {
             rowData: rows,
             columnDefs: columnDefs,
-            defaultColDef: {
-                resizable: true,
-                sortable: true,
-                filter: false,
-                suppressMenu: true
-            },
+            defaultColDef: $4ab64e76c1caef59$var$DEFAULT_COL_DEF,
             animateRows: false,
             suppressFieldDotNotation: true,
             suppressDragLeaveHidesColumns: true,
@@ -12071,564 +12787,1384 @@ const $caf32827df861c4e$var$ParallelCoordsPlot = ({ rows: rows, fields: fields,
         const target = paths.filter(function() {
             return this.getAttribute('data-id') === String(hoveredId);
         });
-        target.classed('exprviz-pc-line-hover', true).raise();
-    }, [
-        hoveredId,
-        rows,
-        fields,
-        scale
-    ]);
-    if (!fields || fields.length === 0) return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
-        className: "exprviz-plot-empty",
-        children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("em", {
-            children: "Select fields to plot."
-        })
+        target.classed('exprviz-pc-line-hover', true).raise();
+    }, [
+        hoveredId,
+        rows,
+        fields,
+        scale
+    ]);
+    if (!fields || fields.length === 0) return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
+        className: "exprviz-plot-empty",
+        children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("em", {
+            children: "Select fields to plot."
+        })
+    });
+    return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+        ref: containerRef,
+        className: "exprviz-pc-container",
+        children: [
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("svg", {
+                ref: svgRef,
+                width: "100%",
+                height: "100%",
+                preserveAspectRatio: "none"
+            }),
+            tooltip && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($caf32827df861c4e$var$AxisTooltip, {
+                x: tooltip.x,
+                y: tooltip.y,
+                info: tooltip.info
+            })
+        ]
+    });
+};
+// Position-fixed so it can escape the plot pane's clipping. Offset slightly
+// from the cursor and clamped to the viewport so it never spills off-screen.
+const $caf32827df861c4e$var$AxisTooltip = ({ x: x, y: y, info: info })=>{
+    const ref = (0, $gXNCa$react.useRef)(null);
+    const [pos, setPos] = (0, $gXNCa$react.useState)({
+        left: x + 12,
+        top: y + 12
+    });
+    (0, $gXNCa$react.useEffect)(()=>{
+        const el = ref.current;
+        if (!el) return;
+        const w = el.offsetWidth;
+        const h = el.offsetHeight;
+        const vw = window.innerWidth;
+        const vh = window.innerHeight;
+        let left = x + 12;
+        let top = y + 12;
+        if (left + w > vw - 4) left = Math.max(4, x - 12 - w);
+        if (top + h > vh - 4) top = Math.max(4, y - 12 - h);
+        setPos({
+            left: left,
+            top: top
+        });
+    }, [
+        x,
+        y,
+        info
+    ]);
+    const { studyTitle: studyTitle, group: group, factors: factors, characteristics: characteristics } = info;
+    return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+        ref: ref,
+        className: "exprviz-pc-tooltip",
+        style: pos,
+        children: [
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+                children: [
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
+                        className: "exprviz-pc-tip-key",
+                        children: "Study:"
+                    }),
+                    " ",
+                    studyTitle,
+                    group ? ` (${group})` : ''
+                ]
+            }),
+            factors.length > 0 && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactjsxruntime.Fragment), {
+                children: [
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
+                        className: "exprviz-pc-tip-section",
+                        children: "Factors"
+                    }),
+                    factors.map((p, i)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+                            className: "exprviz-pc-tip-row",
+                            children: [
+                                /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("span", {
+                                    className: "exprviz-pc-tip-key",
+                                    children: [
+                                        p.name,
+                                        ":"
+                                    ]
+                                }),
+                                " ",
+                                p.value
+                            ]
+                        }, `f-${i}`))
+                ]
+            }),
+            characteristics.length > 0 && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactjsxruntime.Fragment), {
+                children: [
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
+                        className: "exprviz-pc-tip-section",
+                        children: "Characteristics"
+                    }),
+                    characteristics.map((p, i)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+                            className: "exprviz-pc-tip-row",
+                            children: [
+                                /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("span", {
+                                    className: "exprviz-pc-tip-key",
+                                    children: [
+                                        p.name,
+                                        ":"
+                                    ]
+                                }),
+                                " ",
+                                p.value
+                            ]
+                        }, `c-${i}`))
+                ]
+            })
+        ]
+    });
+};
+var $caf32827df861c4e$export$2e2bcd8739ae039 = $caf32827df861c4e$var$ParallelCoordsPlot;
+
+
+
+function $1fd2507769d5bd00$var$speciesTaxonId(tid) {
+    const n = +tid;
+    return n > 1000000 ? Math.floor(n / 1000) : n;
+}
+function $1fd2507769d5bd00$var$genomeName(grameneMaps, tid) {
+    if (!grameneMaps) return tid;
+    const direct = grameneMaps[tid];
+    if (direct && direct.display_name) return direct.display_name;
+    const sp = grameneMaps[$1fd2507769d5bd00$var$speciesTaxonId(tid)];
+    if (sp && sp.display_name) return sp.display_name;
+    return tid;
+}
+const $1fd2507769d5bd00$var$ExprVizViewCmp = (props)=>{
+    const { exprVizPivot: pivot, exprViz: exprViz, exprVizActiveTaxon: activeTaxon, grameneMaps: grameneMaps, expressionStudies: expressionStudies, expressionSamples: expressionSamples, doSetExprVizActiveTaxon: doSetExprVizActiveTaxon, doToggleExprVizFieldsModal: doToggleExprVizFieldsModal, doFetchExprVizData: doFetchExprVizData } = props;
+    const studiesFor = (tid)=>{
+        if (!expressionStudies) return [];
+        return expressionStudies[tid] || expressionStudies[$1fd2507769d5bd00$var$speciesTaxonId(tid)] || [];
+    };
+    const taxa = (0, $gXNCa$react.useMemo)(()=>{
+        const ids = Object.keys(pivot.data || {});
+        if (!grameneMaps) return ids;
+        return ids.sort((a, b)=>{
+            const ma = grameneMaps[a] || grameneMaps[$1fd2507769d5bd00$var$speciesTaxonId(a)];
+            const mb = grameneMaps[b] || grameneMaps[$1fd2507769d5bd00$var$speciesTaxonId(b)];
+            return (ma && ma.left_index || 0) - (mb && mb.left_index || 0);
+        });
+    }, [
+        pivot.data,
+        grameneMaps
+    ]);
+    (0, $gXNCa$react.useEffect)(()=>{
+        if (taxa.length === 0) return;
+        if (!activeTaxon || !taxa.includes(String(activeTaxon))) doSetExprVizActiveTaxon(taxa[0]);
+    }, [
+        taxa,
+        activeTaxon,
+        doSetExprVizActiveTaxon
+    ]);
+    if (pivot.status === 'loading') return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
+        className: "exprviz-view",
+        children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("em", {
+            children: "Loading studies\u2026"
+        })
+    });
+    if (pivot.status === 'error') return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
+        className: "exprviz-view",
+        children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("em", {
+            children: [
+                "Error: ",
+                pivot.error
+            ]
+        })
+    });
+    if (taxa.length === 0) return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
+        className: "exprviz-view",
+        children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("em", {
+            children: "No expression studies for current results."
+        })
+    });
+    return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+        className: "exprviz-view",
+        children: [
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Tabs), {
+                activeKey: activeTaxon || taxa[0],
+                onSelect: (k)=>doSetExprVizActiveTaxon(k),
+                className: "exprviz-tabs",
+                children: taxa.map((tid)=>{
+                    const studies = studiesFor(tid);
+                    const taxName = $1fd2507769d5bd00$var$genomeName(grameneMaps, tid);
+                    const geneCount = pivot.data[tid] || 0;
+                    return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Tab), {
+                        eventKey: tid,
+                        title: `${taxName} (${studies.length} studies \xb7 ${geneCount} genes)`,
+                        children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($1fd2507769d5bd00$var$TaxonPanel, {
+                            taxon: tid,
+                            studies: studies,
+                            expressionSamples: expressionSamples,
+                            tabState: exprViz.byTaxon[tid],
+                            onOpenFields: ()=>doToggleExprVizFieldsModal(tid, true),
+                            onLoad: ()=>doFetchExprVizData(tid),
+                            onReorder: (next)=>props.doReorderExprVizFields(tid, next),
+                            onAddRangeQuery: props.doAddGrameneRangeQuery
+                        })
+                    }, tid);
+                })
+            }),
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $4d0c2e01f58b53b1$export$2e2bcd8739ae039), {})
+        ]
+    });
+};
+// Compact axis labels for the parallel-coords plot. The raw Solr field name
+// (e.g. "E_CURD_148_g5__expr") is uninformative; we prefer the assay's
+// factor labels, falling back to "organism part" then to the group id.
+// `full` is exposed via an SVG <title> so the user can hover to see study,
+// group, and every factor/characteristic.
+const $1fd2507769d5bd00$var$AXIS_LABEL_MAX = 22;
+function $1fd2507769d5bd00$var$truncateLabel(s, n) {
+    if (!s) return '';
+    return s.length > n ? s.slice(0, n - 1) + "\u2026" : s;
+}
+function $1fd2507769d5bd00$var$compactAssayLabel(assay, group) {
+    if (!assay) return group || '';
+    const factorVals = (assay.factor || []).map((f)=>f && f.label).filter(Boolean);
+    if (factorVals.length) return factorVals.join('; ');
+    const chars = assay.characteristic || [];
+    const organ = chars.find((c)=>c && c.type === 'organism part');
+    if (organ && organ.label) return organ.label;
+    const firstChar = chars.find((c)=>c && c.label);
+    if (firstChar) return firstChar.label;
+    return group || '';
+}
+function $1fd2507769d5bd00$var$assayPairs(list) {
+    return (list || []).filter((x)=>x && x.label).map((x)=>({
+            name: x.type || '',
+            value: x.label
+        }));
+}
+function $1fd2507769d5bd00$var$buildAxisLabels(fields, studies, expressionSamples) {
+    const labels = {};
+    if (!fields) return labels;
+    const studyById = {};
+    (studies || []).forEach((s)=>{
+        if (s && s._id) studyById[s._id] = s;
+    });
+    const findAssay = (studyId, group)=>{
+        const arr = expressionSamples && expressionSamples[studyId];
+        return arr ? arr.find((a)=>a.group === group) : null;
+    };
+    for (const f of fields){
+        const m = f.match(/^(.+?)_g(\d+)__expr$/);
+        if (!m) {
+            labels[f] = {
+                short: $1fd2507769d5bd00$var$truncateLabel(f.replace(/__expr$/, ''), $1fd2507769d5bd00$var$AXIS_LABEL_MAX),
+                structured: {
+                    studyTitle: f,
+                    group: '',
+                    factors: [],
+                    characteristics: []
+                }
+            };
+            continue;
+        }
+        const expId = m[1].replace(/_/g, '-');
+        const group = 'g' + m[2];
+        const assay = findAssay(expId, group);
+        const study = studyById[expId];
+        const studyName = study && study.description || expId;
+        labels[f] = {
+            short: $1fd2507769d5bd00$var$truncateLabel($1fd2507769d5bd00$var$compactAssayLabel(assay, group), $1fd2507769d5bd00$var$AXIS_LABEL_MAX),
+            structured: {
+                studyTitle: studyName,
+                group: group,
+                factors: $1fd2507769d5bd00$var$assayPairs(assay && assay.factor),
+                characteristics: $1fd2507769d5bd00$var$assayPairs(assay && assay.characteristic)
+            }
+        };
+    }
+    return labels;
+}
+function $1fd2507769d5bd00$var$rowMatchesSelections(row, selections) {
+    for (const f of Object.keys(selections)){
+        const v = row[f];
+        if (v == null || Array.isArray(v)) return false;
+        const n = +v;
+        if (!Number.isFinite(n)) return false;
+        const [lo, hi] = selections[f];
+        if (n < lo || n > hi) return false;
+    }
+    return true;
+}
+function $1fd2507769d5bd00$var$fmt(n) {
+    if (!Number.isFinite(n)) return String(n);
+    const a = Math.abs(n);
+    if (a !== 0 && (a < 0.001 || a >= 1e6)) return n.toExponential(3);
+    return Number(n.toFixed(4)).toString();
+}
+function $1fd2507769d5bd00$var$tsvCell(v) {
+    if (v == null) return '';
+    if (Array.isArray(v)) return v.join(',');
+    const s = typeof v === 'object' ? JSON.stringify(v) : String(v);
+    return s.replace(/[\t\r\n]+/g, ' ');
+}
+// Mirror the on-screen table header in the TSV: one row per metadata level
+// the table is showing (Study, then one row per distinct factor type, then
+// one row per distinct characteristic type), followed by the leaf header
+// (Gene ID / Name / per-sample group). The first two columns are repurposed
+// to carry the row category and the row's specific name, matching the
+// pinned-column labels in ExprTable.
+function $1fd2507769d5bd00$var$downloadTsv(filename, rows, fields, studies, expressionSamples) {
+    const cols = [
+        'id',
+        'name',
+        ...fields
+    ];
+    const fieldInfo = (0, $4ab64e76c1caef59$export$7b242440eb2c300d)(fields, studies, expressionSamples);
+    const factorTypes = new Set();
+    const charTypes = new Set();
+    for (const f of fields){
+        const info = fieldInfo[f];
+        if (!info) continue;
+        Object.keys(info.factors || {}).forEach((t)=>factorTypes.add(t));
+        Object.keys(info.characteristics || {}).forEach((t)=>charTypes.add(t));
+    }
+    const factorTypeList = Array.from(factorTypes).sort();
+    const charTypeList = Array.from(charTypes).sort();
+    const metaRow = (cat, label, getValue)=>{
+        const cells = [
+            cat,
+            label
+        ];
+        for (const f of fields)cells.push($1fd2507769d5bd00$var$tsvCell(getValue(fieldInfo[f] || {})));
+        return cells.join('\t');
+    };
+    const lines = [];
+    lines.push(metaRow('Study', 'Title', (info)=>info.studyDescription || ''));
+    for (const t of factorTypeList)lines.push(metaRow('Factor', t, (info)=>info.factors && info.factors[t] || ''));
+    for (const t of charTypeList)lines.push(metaRow('Characteristic', t, (info)=>info.characteristics && info.characteristics[t] || ''));
+    // Leaf header — column ids for the data rows.
+    lines.push([
+        'Gene ID',
+        'Name',
+        ...fields.map((f)=>{
+            const info = fieldInfo[f];
+            return info && info.group || f.replace(/__expr$/, '');
+        })
+    ].join('\t'));
+    for (const r of rows)lines.push(cols.map((c)=>$1fd2507769d5bd00$var$tsvCell(r[c])).join('\t'));
+    const blob = new Blob([
+        lines.join('\n') + '\n'
+    ], {
+        type: 'text/tab-separated-values'
+    });
+    const url = URL.createObjectURL(blob);
+    const a = document.createElement('a');
+    a.href = url;
+    a.download = filename;
+    document.body.appendChild(a);
+    a.click();
+    document.body.removeChild(a);
+    URL.revokeObjectURL(url);
+}
+const $1fd2507769d5bd00$var$TaxonPanel = ({ taxon: taxon, studies: studies, expressionSamples: expressionSamples, tabState: tabState, onOpenFields: onOpenFields, onLoad: onLoad, onReorder: onReorder, onAddRangeQuery: onAddRangeQuery })=>{
+    const selected = tabState && tabState.selectedFields || [];
+    const rows = tabState && tabState.rows || [];
+    const fetchInfo = tabState && tabState.fetch || {
+        status: 'idle',
+        total: 0
+    };
+    const [scale, setScale] = (0, $gXNCa$react.useState)('linear');
+    const [selections, setSelections] = (0, $gXNCa$react.useState)({});
+    const [clearVersion, setClearVersion] = (0, $gXNCa$react.useState)(0);
+    const [hoveredId, setHoveredId] = (0, $gXNCa$react.useState)(null);
+    const [plotHeight, setPlotHeight] = (0, $gXNCa$react.useState)(320);
+    const resizeStateRef = (0, $gXNCa$react.useRef)(null);
+    // Drag the horizontal separator between the plot and the table to retune
+    // their relative sizes. Bounded so neither pane disappears entirely.
+    const startResize = (e)=>{
+        e.preventDefault();
+        resizeStateRef.current = {
+            startY: e.clientY,
+            startHeight: plotHeight
+        };
+        const onMove = (ev)=>{
+            const s = resizeStateRef.current;
+            if (!s) return;
+            const next = Math.max(120, Math.min(1200, s.startHeight + (ev.clientY - s.startY)));
+            setPlotHeight(next);
+        };
+        const onUp = ()=>{
+            resizeStateRef.current = null;
+            document.removeEventListener('mousemove', onMove);
+            document.removeEventListener('mouseup', onUp);
+            document.body.style.cursor = '';
+            document.body.style.userSelect = '';
+        };
+        document.body.style.cursor = 'row-resize';
+        document.body.style.userSelect = 'none';
+        document.addEventListener('mousemove', onMove);
+        document.addEventListener('mouseup', onUp);
+    };
+    const hasBrush = Object.keys(selections).length > 0;
+    const filteredRows = (0, $gXNCa$react.useMemo)(()=>{
+        if (!hasBrush) return rows;
+        return rows.filter((r)=>$1fd2507769d5bd00$var$rowMatchesSelections(r, selections));
+    }, [
+        rows,
+        selections,
+        hasBrush
+    ]);
+    // Drop fields with no numeric data in the loaded rows so empty axes/columns
+    // don't clutter the visualization. Selected-but-empty fields stay in the
+    // underlying selection so a future load can repopulate them.
+    const visibleFields = (0, $gXNCa$react.useMemo)(()=>{
+        if (rows.length === 0 || selected.length === 0) return selected;
+        return selected.filter((f)=>rows.some((r)=>{
+                const v = r[f];
+                return v != null && !Array.isArray(v) && Number.isFinite(+v);
+            }));
+    }, [
+        rows,
+        selected
+    ]);
+    const handleReorder = onReorder ? (newVisibleOrder)=>{
+        const visibleSet = new Set(newVisibleOrder);
+        const hidden = selected.filter((f)=>!visibleSet.has(f));
+        onReorder([
+            ...newVisibleOrder,
+            ...hidden
+        ]);
+    } : undefined;
+    const axisLabels = (0, $gXNCa$react.useMemo)(()=>$1fd2507769d5bd00$var$buildAxisLabels(visibleFields, studies, expressionSamples), [
+        visibleFields,
+        studies,
+        expressionSamples
+    ]);
+    (0, $gXNCa$react.useEffect)(()=>{
+        if (rows.length === 0 && hasBrush) {
+            setSelections({});
+            setClearVersion((v)=>v + 1);
+        }
+    }, [
+        rows.length,
+        hasBrush
+    ]);
+    return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+        className: "exprviz-tab-panel",
+        children: [
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+                className: "exprviz-toolbar",
+                children: [
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactbootstrap.Button), {
+                        size: "sm",
+                        onClick: onOpenFields,
+                        children: [
+                            "Select fields (",
+                            selected.length,
+                            " selected, ",
+                            studies.length,
+                            " studies)"
+                        ]
+                    }),
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Button), {
+                        size: "sm",
+                        variant: "primary",
+                        disabled: selected.length === 0 || fetchInfo.status === 'loading',
+                        onClick: onLoad,
+                        children: fetchInfo.status === 'loading' ? "Loading\u2026" : 'Load data'
+                    }),
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactbootstrap.ToggleButtonGroup), {
+                        type: "radio",
+                        name: `exprviz-scale-${taxon}`,
+                        size: "sm",
+                        value: scale,
+                        onChange: setScale,
+                        children: [
+                            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.ToggleButton), {
+                                id: `exprviz-scale-${taxon}-lin`,
+                                value: "linear",
+                                variant: "outline-secondary",
+                                children: "Linear"
+                            }),
+                            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.ToggleButton), {
+                                id: `exprviz-scale-${taxon}-log`,
+                                value: "log",
+                                variant: "outline-secondary",
+                                children: "Log"
+                            })
+                        ]
+                    }),
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Button), {
+                        size: "sm",
+                        variant: "outline-secondary",
+                        disabled: !hasBrush,
+                        onClick: ()=>{
+                            setClearVersion((v)=>v + 1);
+                            setSelections({});
+                        },
+                        children: "Clear brushes"
+                    }),
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Button), {
+                        size: "sm",
+                        variant: "outline-secondary",
+                        disabled: filteredRows.length === 0 || visibleFields.length === 0,
+                        onClick: ()=>$1fd2507769d5bd00$var$downloadTsv(`expression_${taxon}.tsv`, filteredRows, visibleFields, studies, expressionSamples),
+                        title: "Download the visible rows and columns as tab-delimited text",
+                        children: "Download TSV"
+                    }),
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Button), {
+                        size: "sm",
+                        variant: "success",
+                        disabled: !hasBrush || !onAddRangeQuery,
+                        onClick: ()=>{
+                            const terms = Object.keys(selections).map((field)=>{
+                                const [lo, hi] = selections[field];
+                                return {
+                                    category: 'Expression',
+                                    name: `${field}: ${$1fd2507769d5bd00$var$fmt(lo)}\u{2013}${$1fd2507769d5bd00$var$fmt(hi)}`,
+                                    fq_field: field,
+                                    fq_value: `[${lo} TO ${hi}]`
+                                };
+                            });
+                            onAddRangeQuery(terms);
+                        },
+                        title: "Add brush ranges as an AND-conjunction filter on the search",
+                        children: "Apply as filter"
+                    }),
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("span", {
+                        className: "exprviz-status",
+                        children: [
+                            hasBrush ? `${filteredRows.length} of ${rows.length}` : rows.length,
+                            fetchInfo.total ? ` / ${fetchInfo.total}` : '',
+                            " genes",
+                            hasBrush ? ' (brushed)' : ' loaded'
+                        ]
+                    })
+                ]
+            }),
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+                className: "exprviz-body",
+                children: [
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
+                        className: "exprviz-plot",
+                        style: {
+                            height: plotHeight
+                        },
+                        children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $caf32827df861c4e$export$2e2bcd8739ae039), {
+                            rows: rows,
+                            fields: visibleFields,
+                            scale: scale,
+                            onBrushChange: setSelections,
+                            onReorder: handleReorder,
+                            clearVersion: clearVersion,
+                            hoveredId: hoveredId,
+                            axisLabels: axisLabels
+                        })
+                    }),
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
+                        className: "exprviz-resizer",
+                        role: "separator",
+                        "aria-orientation": "horizontal",
+                        "aria-label": "Resize plot",
+                        onMouseDown: startResize,
+                        title: "Drag to resize"
+                    }),
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
+                        className: "exprviz-table",
+                        children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $4ab64e76c1caef59$export$2e2bcd8739ae039), {
+                            rows: filteredRows,
+                            fields: visibleFields,
+                            onReorder: handleReorder,
+                            studies: studies,
+                            expressionSamples: expressionSamples,
+                            onHoverRow: setHoveredId
+                        })
+                    })
+                ]
+            })
+        ]
+    });
+};
+var $1fd2507769d5bd00$export$2e2bcd8739ae039 = (0, $gXNCa$reduxbundlerreact.connect)('selectExprViz', 'selectExprVizPivot', 'selectExprVizActiveTaxon', 'selectGrameneMaps', 'selectExpressionStudies', 'selectExpressionSamples', 'doSetExprVizActiveTaxon', 'doToggleExprVizFieldsModal', 'doFetchExprVizData', 'doReorderExprVizFields', 'doAddGrameneRangeQuery', $1fd2507769d5bd00$var$ExprVizViewCmp);
+
+
+
+
+
+
+
+
+function $f511198465122338$var$speciesTaxonId(tid) {
+    const n = +tid;
+    return n > 1000000 ? Math.floor(n / 1000) : n;
+}
+function $f511198465122338$var$genomeName(grameneMaps, tid) {
+    if (!grameneMaps) return String(tid);
+    const direct = grameneMaps[tid];
+    if (direct && direct.display_name) return direct.display_name;
+    const sp = grameneMaps[$f511198465122338$var$speciesTaxonId(tid)];
+    if (sp && sp.display_name) return sp.display_name;
+    return String(tid);
+}
+function $f511198465122338$var$fmtP(p) {
+    if (p == null) return '';
+    if (p === 0) return '0';
+    if (p < 1e-4) return p.toExponential(2);
+    return p.toPrecision(3);
+}
+function $f511198465122338$var$fmtFold(f) {
+    if (!isFinite(f)) return '';
+    if (f >= 100) return f.toFixed(0);
+    return f.toFixed(2);
+}
+// ---------- species tree helpers ----------
+function $f511198465122338$var$findRoots(tax) {
+    return Object.values(tax).filter((n)=>!n.is_a || n.is_a.length === 0 || !n.is_a.some((p)=>tax[p]));
+}
+// Place each facet tid onto a taxonomy node id (fall back to species level
+// when the exact subspecies tid isn't in grameneTaxonomy).
+function $f511198465122338$var$placeTaxa(taxonomy, taxa) {
+    const placement = {};
+    const byPlace = {};
+    for (const { tid: tid, count: count } of taxa){
+        const place = taxonomy[tid] ? +tid : $f511198465122338$var$speciesTaxonId(tid);
+        placement[tid] = place;
+        if (!byPlace[place]) byPlace[place] = [];
+        byPlace[place].push({
+            tid: tid,
+            count: count
+        });
+    }
+    return {
+        placement: placement,
+        byPlace: byPlace
+    };
+}
+// Set of taxonomy node ids on the path from any placed leaf back to its root.
+function $f511198465122338$var$relevantNodeIds(taxonomy, byPlace) {
+    const out = new Set();
+    for (const placeId of Object.keys(byPlace)){
+        let cur = taxonomy[placeId];
+        const seen = new Set();
+        while(cur && !seen.has(+cur._id)){
+            seen.add(+cur._id);
+            out.add(+cur._id);
+            const pid = cur.is_a && cur.is_a[0];
+            cur = pid ? taxonomy[pid] : null;
+        }
+    }
+    return out;
+}
+function $f511198465122338$var$relevantChildren(node, taxonomy, relevant) {
+    return (node.children || []).map((cid)=>taxonomy[cid]).filter((c)=>c && relevant.has(+c._id));
+}
+// Walk down through single-relevant-child internal nodes to a branch / leaf.
+function $f511198465122338$var$compressChain(node, taxonomy, relevant, byPlace) {
+    const chain = [
+        node
+    ];
+    let cur = node;
+    while(true){
+        if (byPlace[cur._id]) break; // node itself is a placed leaf
+        const kids = $f511198465122338$var$relevantChildren(cur, taxonomy, relevant);
+        if (kids.length !== 1) break;
+        cur = kids[0];
+        chain.push(cur);
+    }
+    return {
+        chain: chain,
+        terminal: cur
+    };
+}
+const $f511198465122338$var$CHAIN_DISPLAY_MAX = 3;
+function $f511198465122338$var$renderChain(chain) {
+    const nameOf = (n)=>n.short_name || n.name || String(n._id);
+    if (chain.length <= $f511198465122338$var$CHAIN_DISPLAY_MAX) return chain.map((n, i)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, ($parcel$interopDefault($gXNCa$react))).Fragment, {
+            children: [
+                i > 0 && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
+                    className: "tax-sep",
+                    children: " \u203A "
+                }),
+                nameOf(n)
+            ]
+        }, n._id));
+    const first = chain[0];
+    const last = chain[chain.length - 1];
+    const middle = chain.slice(1, -1);
+    const fullTitle = chain.map(nameOf).join(" \u203A ");
+    return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactjsxruntime.Fragment), {
+        children: [
+            nameOf(first),
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
+                className: "tax-sep",
+                children: " \u203A "
+            }),
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("span", {
+                className: "tax-ellipsis",
+                title: fullTitle,
+                children: [
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
+                        className: "tax-ellipsis-short",
+                        children: "\u2026"
+                    }),
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
+                        className: "tax-ellipsis-full",
+                        children: middle.map((n)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, ($parcel$interopDefault($gXNCa$react))).Fragment, {
+                                children: [
+                                    nameOf(n),
+                                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
+                                        className: "tax-sep",
+                                        children: " \u203A "
+                                    })
+                                ]
+                            }, n._id))
+                    })
+                ]
+            }),
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
+                className: "tax-sep",
+                children: " \u203A "
+            }),
+            nameOf(last)
+        ]
     });
+}
+function $f511198465122338$var$dedupAdjacent(chain) {
+    const out = [];
+    for (const n of chain)if (out.length && out[out.length - 1].name === n.name) out[out.length - 1] = n;
+    else out.push(n);
+    return out;
+}
+const $f511198465122338$var$SpeciesTreeNode = ({ node: node, depth: depth, taxonomy: taxonomy, relevant: relevant, byPlace: byPlace, grameneMaps: grameneMaps, expanded: expanded, onToggleExpand: onToggleExpand, activeTaxon: activeTaxon, onSelect: onSelect })=>{
+    const { chain: rawChain, terminal: terminal } = $f511198465122338$var$compressChain(node, taxonomy, relevant, byPlace);
+    const chain = $f511198465122338$var$dedupAdjacent(rawChain);
+    const placed = byPlace[terminal._id] || [];
+    const kids = $f511198465122338$var$relevantChildren(terminal, taxonomy, relevant);
+    const hasKids = kids.length > 0;
+    const isOpen = expanded.has(+terminal._id);
     return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
-        ref: containerRef,
-        className: "exprviz-pc-container",
+        className: "tax-node gsea-tree-node",
         children: [
-            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("svg", {
-                ref: svgRef,
-                width: "100%",
-                height: "100%",
-                preserveAspectRatio: "none"
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+                className: "tax-row",
+                style: {
+                    paddingLeft: depth * 7
+                },
+                children: [
+                    hasKids ? /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
+                        className: "tax-chevron",
+                        onClick: ()=>onToggleExpand(+terminal._id),
+                        children: isOpen ? /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reacticonsbs.BsChevronDown), {}) : /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reacticonsbs.BsChevronRight), {})
+                    }) : /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
+                        className: "tax-chevron-spacer"
+                    }),
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
+                        className: hasKids ? 'tax-label tax-label-internal' : 'tax-label',
+                        children: $f511198465122338$var$renderChain(chain)
+                    })
+                ]
             }),
-            tooltip && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($caf32827df861c4e$var$AxisTooltip, {
-                x: tooltip.x,
-                y: tooltip.y,
-                info: tooltip.info
+            placed.map(({ tid: tid, count: count })=>{
+                const isActive = String(activeTaxon) === String(tid);
+                return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+                    className: 'gsea-tree-leaf' + (isActive ? ' gsea-tree-leaf-active' : ''),
+                    style: {
+                        paddingLeft: (depth + 1) * 7 + 18
+                    },
+                    onClick: ()=>onSelect(tid),
+                    children: [
+                        /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("input", {
+                            type: "radio",
+                            readOnly: true,
+                            checked: isActive,
+                            onChange: ()=>onSelect(tid)
+                        }),
+                        /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
+                            className: "gsea-tree-leaf-name",
+                            children: $f511198465122338$var$genomeName(grameneMaps, tid)
+                        }),
+                        /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
+                            className: "gsea-tree-leaf-count",
+                            children: count.toLocaleString()
+                        })
+                    ]
+                }, tid);
+            }),
+            hasKids && isOpen && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
+                className: "tax-children",
+                children: kids.map((c)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($f511198465122338$var$SpeciesTreeNode, {
+                        node: c,
+                        depth: depth + 1,
+                        taxonomy: taxonomy,
+                        relevant: relevant,
+                        byPlace: byPlace,
+                        grameneMaps: grameneMaps,
+                        expanded: expanded,
+                        onToggleExpand: onToggleExpand,
+                        activeTaxon: activeTaxon,
+                        onSelect: onSelect
+                    }, c._id))
             })
         ]
     });
 };
-// Position-fixed so it can escape the plot pane's clipping. Offset slightly
-// from the cursor and clamped to the viewport so it never spills off-screen.
-const $caf32827df861c4e$var$AxisTooltip = ({ x: x, y: y, info: info })=>{
-    const ref = (0, $gXNCa$react.useRef)(null);
-    const [pos, setPos] = (0, $gXNCa$react.useState)({
-        left: x + 12,
-        top: y + 12
-    });
+const $f511198465122338$var$SpeciesTree = ({ taxonomy: taxonomy, grameneMaps: grameneMaps, taxa: taxa, activeTaxon: activeTaxon, onSelect: onSelect })=>{
+    const { placement: placement, byPlace: byPlace } = (0, $gXNCa$react.useMemo)(()=>$f511198465122338$var$placeTaxa(taxonomy, taxa), [
+        taxonomy,
+        taxa
+    ]);
+    const relevant = (0, $gXNCa$react.useMemo)(()=>$f511198465122338$var$relevantNodeIds(taxonomy, byPlace), [
+        taxonomy,
+        byPlace
+    ]);
+    const roots = (0, $gXNCa$react.useMemo)(()=>$f511198465122338$var$findRoots(taxonomy).filter((r)=>relevant.has(+r._id)), [
+        taxonomy,
+        relevant
+    ]);
+    // Default: every relevant internal node expanded so the user sees the
+    // full pruned tree on first paint.
+    const [expanded, setExpanded] = (0, $gXNCa$react.useState)(()=>new Set(relevant));
     (0, $gXNCa$react.useEffect)(()=>{
-        const el = ref.current;
-        if (!el) return;
-        const w = el.offsetWidth;
-        const h = el.offsetHeight;
-        const vw = window.innerWidth;
-        const vh = window.innerHeight;
-        let left = x + 12;
-        let top = y + 12;
-        if (left + w > vw - 4) left = Math.max(4, x - 12 - w);
-        if (top + h > vh - 4) top = Math.max(4, y - 12 - h);
-        setPos({
-            left: left,
-            top: top
-        });
+        setExpanded(new Set(relevant));
     }, [
-        x,
-        y,
-        info
+        relevant
     ]);
-    const { studyTitle: studyTitle, group: group, factors: factors, characteristics: characteristics } = info;
-    return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
-        ref: ref,
-        className: "exprviz-pc-tooltip",
-        style: pos,
+    const handleToggle = (id)=>{
+        setExpanded((prev)=>{
+            const next = new Set(prev);
+            next.has(id) ? next.delete(id) : next.add(id);
+            return next;
+        });
+    };
+    // Skip the root spine: if a root has only one relevant child and isn't
+    // itself a placed leaf, render from its child instead.
+    const topLevel = [];
+    for (const r of roots){
+        const { terminal: terminal } = $f511198465122338$var$compressChain(r, taxonomy, relevant, byPlace);
+        if (byPlace[terminal._id]) topLevel.push(r);
+        else {
+            const kids = $f511198465122338$var$relevantChildren(terminal, taxonomy, relevant);
+            kids.forEach((k)=>topLevel.push(k));
+        }
+    }
+    return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
+        className: "gsea-tree",
+        children: topLevel.map((n)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($f511198465122338$var$SpeciesTreeNode, {
+                node: n,
+                depth: 0,
+                taxonomy: taxonomy,
+                relevant: relevant,
+                byPlace: byPlace,
+                grameneMaps: grameneMaps,
+                expanded: expanded,
+                onToggleExpand: handleToggle,
+                activeTaxon: activeTaxon,
+                onSelect: onSelect
+            }, n._id))
+    });
+};
+// ---------- enrichment panel ----------
+const $f511198465122338$var$ControlsBar = ({ ui: ui, onChange: onChange })=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+        className: "gsea-controls",
         children: [
-            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactbootstrap.Form).Group, {
+                className: "gsea-control",
                 children: [
-                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
-                        className: "exprviz-pc-tip-key",
-                        children: "Study:"
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Form).Label, {
+                        children: "p_adj \u2264"
                     }),
-                    " ",
-                    studyTitle,
-                    group ? ` (${group})` : ''
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Form).Control, {
+                        type: "number",
+                        step: "0.01",
+                        min: "0",
+                        max: "1",
+                        value: ui.pAdjCutoff,
+                        onChange: (e)=>onChange({
+                                pAdjCutoff: +e.target.value
+                            })
+                    })
                 ]
             }),
-            factors.length > 0 && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactjsxruntime.Fragment), {
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactbootstrap.Form).Group, {
+                className: "gsea-control",
                 children: [
-                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
-                        className: "exprviz-pc-tip-section",
-                        children: "Factors"
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Form).Label, {
+                        children: "min k"
                     }),
-                    factors.map((p, i)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
-                            className: "exprviz-pc-tip-row",
-                            children: [
-                                /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("span", {
-                                    className: "exprviz-pc-tip-key",
-                                    children: [
-                                        p.name,
-                                        ":"
-                                    ]
-                                }),
-                                " ",
-                                p.value
-                            ]
-                        }, `f-${i}`))
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Form).Control, {
+                        type: "number",
+                        step: "1",
+                        min: "1",
+                        value: ui.minK,
+                        onChange: (e)=>onChange({
+                                minK: Math.max(1, +e.target.value)
+                            })
+                    })
                 ]
             }),
-            characteristics.length > 0 && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactjsxruntime.Fragment), {
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Form).Check, {
+                className: "gsea-control",
+                type: "switch",
+                id: "gsea-most-specific",
+                label: "Most-specific only",
+                checked: !!ui.mostSpecific,
+                onChange: (e)=>onChange({
+                        mostSpecific: e.target.checked
+                    })
+            }),
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactbootstrap.Form).Group, {
+                className: "gsea-control gsea-control-grow",
                 children: [
-                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
-                        className: "exprviz-pc-tip-section",
-                        children: "Characteristics"
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Form).Label, {
+                        children: "Filter terms"
                     }),
-                    characteristics.map((p, i)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
-                            className: "exprviz-pc-tip-row",
-                            children: [
-                                /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("span", {
-                                    className: "exprviz-pc-tip-key",
-                                    children: [
-                                        p.name,
-                                        ":"
-                                    ]
-                                }),
-                                " ",
-                                p.value
-                            ]
-                        }, `c-${i}`))
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Form).Control, {
+                        type: "text",
+                        placeholder: "term id or name\u2026",
+                        value: ui.search || '',
+                        onChange: (e)=>onChange({
+                                search: e.target.value
+                            })
+                    })
+                ]
+            })
+        ]
+    });
+const $f511198465122338$var$TermRow = ({ row: row, showType: showType, onAddFilter: onAddFilter })=>{
+    const handleClick = ()=>onAddFilter && onAddFilter(row);
+    return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("tr", {
+        onClick: handleClick,
+        title: "Click to add as a filter",
+        children: [
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("td", {
+                className: "gsea-term-id",
+                children: row.term_display_id
+            }),
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("td", {
+                className: "gsea-term-name",
+                children: row.term_name || /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("em", {
+                    children: "(loading\u2026)"
+                })
+            }),
+            showType && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("td", {
+                className: "gsea-term-type",
+                children: row.term_namespace || ''
+            }),
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("td", {
+                className: "gsea-num",
+                children: [
+                    row.k,
+                    " / ",
+                    row.n
+                ]
+            }),
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("td", {
+                className: "gsea-num",
+                children: [
+                    row.K,
+                    " / ",
+                    row.N
                 ]
+            }),
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("td", {
+                className: "gsea-num",
+                children: $f511198465122338$var$fmtFold(row.fold)
+            }),
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("td", {
+                className: "gsea-num",
+                children: $f511198465122338$var$fmtP(row.p)
+            }),
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("td", {
+                className: "gsea-num",
+                children: $f511198465122338$var$fmtP(row.pAdj)
             })
         ]
     });
 };
-var $caf32827df861c4e$export$2e2bcd8739ae039 = $caf32827df861c4e$var$ParallelCoordsPlot;
-
-
-
-function $1fd2507769d5bd00$var$speciesTaxonId(tid) {
-    const n = +tid;
-    return n > 1000000 ? Math.floor(n / 1000) : n;
-}
-function $1fd2507769d5bd00$var$genomeName(grameneMaps, tid) {
-    if (!grameneMaps) return tid;
-    const direct = grameneMaps[tid];
-    if (direct && direct.display_name) return direct.display_name;
-    const sp = grameneMaps[$1fd2507769d5bd00$var$speciesTaxonId(tid)];
-    if (sp && sp.display_name) return sp.display_name;
-    return tid;
-}
-const $1fd2507769d5bd00$var$ExprVizViewCmp = (props)=>{
-    const { exprVizPivot: pivot, exprViz: exprViz, exprVizActiveTaxon: activeTaxon, grameneMaps: grameneMaps, expressionStudies: expressionStudies, expressionSamples: expressionSamples, doSetExprVizActiveTaxon: doSetExprVizActiveTaxon, doToggleExprVizFieldsModal: doToggleExprVizFieldsModal, doFetchExprVizData: doFetchExprVizData } = props;
-    const studiesFor = (tid)=>{
-        if (!expressionStudies) return [];
-        return expressionStudies[tid] || expressionStudies[$1fd2507769d5bd00$var$speciesTaxonId(tid)] || [];
-    };
-    const taxa = (0, $gXNCa$react.useMemo)(()=>{
-        const ids = Object.keys(pivot.data || {});
-        if (!grameneMaps) return ids;
-        return ids.sort((a, b)=>{
-            const ma = grameneMaps[a] || grameneMaps[$1fd2507769d5bd00$var$speciesTaxonId(a)];
-            const mb = grameneMaps[b] || grameneMaps[$1fd2507769d5bd00$var$speciesTaxonId(b)];
-            return (ma && ma.left_index || 0) - (mb && mb.left_index || 0);
-        });
+// InterPro entry types and pathway types are useful per-row context
+// (e.g. Domain vs Family vs Repeat for InterPro), and aren't reflected in
+// the section title the way GO namespaces are. Show a Type column for
+// those two ontologies only.
+const $f511198465122338$var$ONTS_WITH_TYPE_COLUMN = new Set([
+    'domains',
+    'pathways'
+]);
+const $f511198465122338$var$SORT_ACCESSORS = {
+    term: (r)=>r.term_display_id || '',
+    name: (r)=>(r.term_name || '').toLowerCase(),
+    type: (r)=>(r.term_namespace || '').toLowerCase(),
+    k: (r)=>r.k,
+    K: (r)=>r.K,
+    fold: (r)=>r.fold,
+    p: (r)=>r.p,
+    pAdj: (r)=>r.pAdj
+};
+// Defaults chosen so a single click does what the user usually wants:
+// numeric "more interesting" columns (k, K, fold) descend; p-values and
+// text columns ascend.
+const $f511198465122338$var$SORT_DEFAULT_DIR = {
+    term: 'asc',
+    name: 'asc',
+    type: 'asc',
+    k: 'desc',
+    K: 'desc',
+    fold: 'desc',
+    p: 'asc',
+    pAdj: 'asc'
+};
+const $f511198465122338$var$SortableTh = ({ label: label, sortKey: sortKey, activeKey: activeKey, activeDir: activeDir, onSort: onSort, numeric: numeric })=>{
+    const active = activeKey === sortKey;
+    const arrow = active ? activeDir === 'asc' ? " \u25B2" : " \u25BC" : '';
+    const cls = 'gsea-sort-th' + (active ? ' gsea-sort-th-active' : '') + (numeric ? ' gsea-num' : '');
+    return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("th", {
+        className: cls,
+        onClick: ()=>onSort(sortKey),
+        children: [
+            label,
+            arrow
+        ]
+    });
+};
+const $f511198465122338$var$OntologySection = ({ block: block, search: search, onAddFilter: onAddFilter })=>{
+    const filtered = (0, $gXNCa$react.useMemo)(()=>{
+        if (!search) return block.rows;
+        const needle = search.toLowerCase();
+        return block.rows.filter((r)=>r.term_display_id && r.term_display_id.toLowerCase().includes(needle) || r.term_name && r.term_name.toLowerCase().includes(needle));
     }, [
-        pivot.data,
-        grameneMaps
+        block.rows,
+        search
     ]);
-    (0, $gXNCa$react.useEffect)(()=>{
-        if (taxa.length === 0) return;
-        if (!activeTaxon || !taxa.includes(String(activeTaxon))) doSetExprVizActiveTaxon(taxa[0]);
+    const showType = $f511198465122338$var$ONTS_WITH_TYPE_COLUMN.has(block.ontology);
+    const [sortKey, setSortKey] = (0, $gXNCa$react.useState)('pAdj');
+    const [sortDir, setSortDir] = (0, $gXNCa$react.useState)('asc');
+    const handleSort = (key)=>{
+        if (key === sortKey) setSortDir((d)=>d === 'asc' ? 'desc' : 'asc');
+        else {
+            setSortKey(key);
+            setSortDir($f511198465122338$var$SORT_DEFAULT_DIR[key] || 'asc');
+        }
+    };
+    const sorted = (0, $gXNCa$react.useMemo)(()=>{
+        const accessor = $f511198465122338$var$SORT_ACCESSORS[sortKey];
+        if (!accessor) return filtered;
+        const sign = sortDir === 'desc' ? -1 : 1;
+        const arr = filtered.slice();
+        arr.sort((a, b)=>{
+            const va = accessor(a);
+            const vb = accessor(b);
+            if (typeof va === 'number' && typeof vb === 'number') {
+                if (va === vb) return 0;
+                return (va - vb) * sign;
+            }
+            return String(va).localeCompare(String(vb)) * sign;
+        });
+        return arr;
     }, [
-        taxa,
-        activeTaxon,
-        doSetExprVizActiveTaxon
+        filtered,
+        sortKey,
+        sortDir
     ]);
-    if (pivot.status === 'loading') return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
-        className: "exprviz-view",
+    return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactbootstrap.Accordion).Item, {
+        eventKey: block.ontology,
+        children: [
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactbootstrap.Accordion).Header, {
+                children: [
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
+                        className: "gsea-ont-title",
+                        children: block.label
+                    }),
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactbootstrap.Badge), {
+                        bg: "secondary",
+                        className: "gsea-ont-badge",
+                        children: [
+                            block.passing,
+                            " significant / ",
+                            block.tested,
+                            " tested"
+                        ]
+                    })
+                ]
+            }),
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Accordion).Body, {
+                children: sorted.length === 0 ? /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("em", {
+                    children: "No terms pass the current cutoffs."
+                }) : /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("table", {
+                    className: "gsea-table",
+                    children: [
+                        /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("thead", {
+                            children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("tr", {
+                                children: [
+                                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($f511198465122338$var$SortableTh, {
+                                        label: "Term",
+                                        sortKey: "term",
+                                        activeKey: sortKey,
+                                        activeDir: sortDir,
+                                        onSort: handleSort
+                                    }),
+                                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($f511198465122338$var$SortableTh, {
+                                        label: "Name",
+                                        sortKey: "name",
+                                        activeKey: sortKey,
+                                        activeDir: sortDir,
+                                        onSort: handleSort
+                                    }),
+                                    showType && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($f511198465122338$var$SortableTh, {
+                                        label: "Type",
+                                        sortKey: "type",
+                                        activeKey: sortKey,
+                                        activeDir: sortDir,
+                                        onSort: handleSort
+                                    }),
+                                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($f511198465122338$var$SortableTh, {
+                                        label: "k / n",
+                                        sortKey: "k",
+                                        activeKey: sortKey,
+                                        activeDir: sortDir,
+                                        onSort: handleSort,
+                                        numeric: true
+                                    }),
+                                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($f511198465122338$var$SortableTh, {
+                                        label: "K / N",
+                                        sortKey: "K",
+                                        activeKey: sortKey,
+                                        activeDir: sortDir,
+                                        onSort: handleSort,
+                                        numeric: true
+                                    }),
+                                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($f511198465122338$var$SortableTh, {
+                                        label: "Fold",
+                                        sortKey: "fold",
+                                        activeKey: sortKey,
+                                        activeDir: sortDir,
+                                        onSort: handleSort,
+                                        numeric: true
+                                    }),
+                                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($f511198465122338$var$SortableTh, {
+                                        label: "p",
+                                        sortKey: "p",
+                                        activeKey: sortKey,
+                                        activeDir: sortDir,
+                                        onSort: handleSort,
+                                        numeric: true
+                                    }),
+                                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($f511198465122338$var$SortableTh, {
+                                        label: "p_adj",
+                                        sortKey: "pAdj",
+                                        activeKey: sortKey,
+                                        activeDir: sortDir,
+                                        onSort: handleSort,
+                                        numeric: true
+                                    })
+                                ]
+                            })
+                        }),
+                        /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("tbody", {
+                            children: sorted.map((r)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($f511198465122338$var$TermRow, {
+                                    row: r,
+                                    showType: showType,
+                                    onAddFilter: onAddFilter
+                                }, `${r.ontology}:${r.term_id}`))
+                        })
+                    ]
+                })
+            })
+        ]
+    });
+};
+const $f511198465122338$var$TaxonPanel = ({ taxon: taxon, gsea: gsea, results: results, ui: ui, onUiChange: onUiChange, onAddFilter: onAddFilter })=>{
+    if (!taxon) return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
+        className: "gsea-panel",
         children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("em", {
-            children: "Loading studies\u2026"
+            children: "Select a species on the left."
         })
     });
-    if (pivot.status === 'error') return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
-        className: "exprviz-view",
-        children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("em", {
-            children: [
-                "Error: ",
-                pivot.error
-            ]
+    const t = gsea.byTaxon[taxon];
+    if (!t) return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
+        className: "gsea-panel",
+        children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("em", {
+            children: "Initializing\u2026"
         })
     });
-    if (taxa.length === 0) return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
-        className: "exprviz-view",
+    if (t.fg.status === 'loading' || t.bg.status === 'loading' || t.fg.status === 'idle' || t.bg.status === 'idle') return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
+        className: "gsea-panel gsea-loading",
         children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("em", {
-            children: "No expression studies for current results."
+            children: "Loading enrichment\u2026"
         })
     });
-    return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
-        className: "exprviz-view",
-        children: [
-            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Tabs), {
-                activeKey: activeTaxon || taxa[0],
-                onSelect: (k)=>doSetExprVizActiveTaxon(k),
-                className: "exprviz-tabs",
-                children: taxa.map((tid)=>{
-                    const studies = studiesFor(tid);
-                    const taxName = $1fd2507769d5bd00$var$genomeName(grameneMaps, tid);
-                    const geneCount = pivot.data[tid] || 0;
-                    return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Tab), {
-                        eventKey: tid,
-                        title: `${taxName} (${studies.length} studies \xb7 ${geneCount} genes)`,
-                        children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($1fd2507769d5bd00$var$TaxonPanel, {
-                            taxon: tid,
-                            studies: studies,
-                            expressionSamples: expressionSamples,
-                            tabState: exprViz.byTaxon[tid],
-                            onOpenFields: ()=>doToggleExprVizFieldsModal(tid, true),
-                            onLoad: ()=>doFetchExprVizData(tid),
-                            onReorder: (next)=>props.doReorderExprVizFields(tid, next),
-                            onAddRangeQuery: props.doAddGrameneRangeQuery
-                        })
-                    }, tid);
-                })
-            }),
-            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $4d0c2e01f58b53b1$export$2e2bcd8739ae039), {})
-        ]
-    });
-};
-// Compact axis labels for the parallel-coords plot. The raw Solr field name
-// (e.g. "E_CURD_148_g5__expr") is uninformative; we prefer the assay's
-// factor labels, falling back to "organism part" then to the group id.
-// `full` is exposed via an SVG <title> so the user can hover to see study,
-// group, and every factor/characteristic.
-const $1fd2507769d5bd00$var$AXIS_LABEL_MAX = 22;
-function $1fd2507769d5bd00$var$truncateLabel(s, n) {
-    if (!s) return '';
-    return s.length > n ? s.slice(0, n - 1) + "\u2026" : s;
-}
-function $1fd2507769d5bd00$var$compactAssayLabel(assay, group) {
-    if (!assay) return group || '';
-    const factorVals = (assay.factor || []).map((f)=>f && f.label).filter(Boolean);
-    if (factorVals.length) return factorVals.join('; ');
-    const chars = assay.characteristic || [];
-    const organ = chars.find((c)=>c && c.type === 'organism part');
-    if (organ && organ.label) return organ.label;
-    const firstChar = chars.find((c)=>c && c.label);
-    if (firstChar) return firstChar.label;
-    return group || '';
-}
-function $1fd2507769d5bd00$var$assayPairs(list) {
-    return (list || []).filter((x)=>x && x.label).map((x)=>({
-            name: x.type || '',
-            value: x.label
-        }));
-}
-function $1fd2507769d5bd00$var$buildAxisLabels(fields, studies, expressionSamples) {
-    const labels = {};
-    if (!fields) return labels;
-    const studyById = {};
-    (studies || []).forEach((s)=>{
-        if (s && s._id) studyById[s._id] = s;
+    if (t.fg.status === 'error') return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
+        className: "gsea-panel",
+        children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("em", {
+            children: [
+                "Foreground error: ",
+                t.fg.error
+            ]
+        })
     });
-    const findAssay = (studyId, group)=>{
-        const arr = expressionSamples && expressionSamples[studyId];
-        return arr ? arr.find((a)=>a.group === group) : null;
-    };
-    for (const f of fields){
-        const m = f.match(/^(.+?)_g(\d+)__expr$/);
-        if (!m) {
-            labels[f] = {
-                short: $1fd2507769d5bd00$var$truncateLabel(f.replace(/__expr$/, ''), $1fd2507769d5bd00$var$AXIS_LABEL_MAX),
-                structured: {
-                    studyTitle: f,
-                    group: '',
-                    factors: [],
-                    characteristics: []
-                }
-            };
-            continue;
-        }
-        const expId = m[1].replace(/_/g, '-');
-        const group = 'g' + m[2];
-        const assay = findAssay(expId, group);
-        const study = studyById[expId];
-        const studyName = study && study.description || expId;
-        labels[f] = {
-            short: $1fd2507769d5bd00$var$truncateLabel($1fd2507769d5bd00$var$compactAssayLabel(assay, group), $1fd2507769d5bd00$var$AXIS_LABEL_MAX),
-            structured: {
-                studyTitle: studyName,
-                group: group,
-                factors: $1fd2507769d5bd00$var$assayPairs(assay && assay.factor),
-                characteristics: $1fd2507769d5bd00$var$assayPairs(assay && assay.characteristic)
-            }
-        };
-    }
-    return labels;
-}
-function $1fd2507769d5bd00$var$rowMatchesSelections(row, selections) {
-    for (const f of Object.keys(selections)){
-        const v = row[f];
-        if (v == null || Array.isArray(v)) return false;
-        const n = +v;
-        if (!Number.isFinite(n)) return false;
-        const [lo, hi] = selections[f];
-        if (n < lo || n > hi) return false;
-    }
-    return true;
-}
-function $1fd2507769d5bd00$var$fmt(n) {
-    if (!Number.isFinite(n)) return String(n);
-    const a = Math.abs(n);
-    if (a !== 0 && (a < 0.001 || a >= 1e6)) return n.toExponential(3);
-    return Number(n.toFixed(4)).toString();
-}
-function $1fd2507769d5bd00$var$tsvCell(v) {
-    if (v == null) return '';
-    if (Array.isArray(v)) return v.join(',');
-    const s = typeof v === 'object' ? JSON.stringify(v) : String(v);
-    return s.replace(/[\t\r\n]+/g, ' ');
-}
-function $1fd2507769d5bd00$var$downloadTsv(filename, rows, fields) {
-    const cols = [
-        'id',
-        'name',
-        ...fields
-    ];
-    const headerLabels = [
-        'id',
-        'name',
-        ...fields.map((f)=>f.replace(/__expr$/, ''))
-    ];
-    const lines = [
-        headerLabels.join('\t')
-    ];
-    for (const r of rows)lines.push(cols.map((c)=>$1fd2507769d5bd00$var$tsvCell(r[c])).join('\t'));
-    const blob = new Blob([
-        lines.join('\n') + '\n'
-    ], {
-        type: 'text/tab-separated-values'
+    if (t.bg.status === 'error') return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
+        className: "gsea-panel",
+        children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("em", {
+            children: [
+                "Background error: ",
+                t.bg.error
+            ]
+        })
     });
-    const url = URL.createObjectURL(blob);
-    const a = document.createElement('a');
-    a.href = url;
-    a.download = filename;
-    document.body.appendChild(a);
-    a.click();
-    document.body.removeChild(a);
-    URL.revokeObjectURL(url);
-}
-const $1fd2507769d5bd00$var$TaxonPanel = ({ taxon: taxon, studies: studies, expressionSamples: expressionSamples, tabState: tabState, onOpenFields: onOpenFields, onLoad: onLoad, onReorder: onReorder, onAddRangeQuery: onAddRangeQuery })=>{
-    const selected = tabState && tabState.selectedFields || [];
-    const rows = tabState && tabState.rows || [];
-    const fetchInfo = tabState && tabState.fetch || {
-        status: 'idle',
-        total: 0
-    };
-    const [scale, setScale] = (0, $gXNCa$react.useState)('linear');
-    const [selections, setSelections] = (0, $gXNCa$react.useState)({});
-    const [clearVersion, setClearVersion] = (0, $gXNCa$react.useState)(0);
-    const [hoveredId, setHoveredId] = (0, $gXNCa$react.useState)(null);
-    const [plotHeight, setPlotHeight] = (0, $gXNCa$react.useState)(320);
-    const resizeStateRef = (0, $gXNCa$react.useRef)(null);
-    // Drag the horizontal separator between the plot and the table to retune
-    // their relative sizes. Bounded so neither pane disappears entirely.
-    const startResize = (e)=>{
+    if (!results) return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
+        className: "gsea-panel",
+        children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("em", {
+            children: "No data."
+        })
+    });
+    const allBlocks = ui.ontology === 'all' ? Object.values(results) : results[ui.ontology] ? [
+        results[ui.ontology]
+    ] : [];
+    // Hide ontologies that aren't used in this species at all.
+    const blocks = allBlocks.filter((b)=>b.tested > 0);
+    return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+        className: "gsea-panel",
+        children: [
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+                className: "gsea-summary",
+                children: [
+                    "Foreground: ",
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("b", {
+                        children: t.fg.numFound.toLocaleString()
+                    }),
+                    " genes \xb7 Background: ",
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("b", {
+                        children: t.bg.numFound.toLocaleString()
+                    }),
+                    " genes"
+                ]
+            }),
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($f511198465122338$var$ControlsBar, {
+                ui: ui,
+                onChange: onUiChange
+            }),
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Accordion), {
+                alwaysOpen: true,
+                defaultActiveKey: blocks.length === 1 ? blocks[0].ontology : undefined,
+                children: blocks.map((b)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($f511198465122338$var$OntologySection, {
+                        block: b,
+                        search: ui.search,
+                        onAddFilter: onAddFilter
+                    }, b.ontology))
+            })
+        ]
+    });
+};
+const $f511198465122338$var$GseaViewCmp = (props)=>{
+    const { grameneSearch: grameneSearch, grameneMaps: grameneMaps, grameneTaxonomy: grameneTaxonomy, gsea: gsea, gseaUI: ui, gseaResults: results, doSetGseaActiveTaxon: doSetGseaActiveTaxon, doSetGseaUI: doSetGseaUI, doFetchGseaForeground: doFetchGseaForeground, doFetchGseaBackground: doFetchGseaBackground, doAcceptGrameneSuggestion: doAcceptGrameneSuggestion } = props;
+    const taxa = (0, $gXNCa$react.useMemo)(()=>{
+        if (!grameneSearch || !grameneSearch.facet_counts) return [];
+        const arr = grameneSearch.facet_counts.facet_fields.taxon_id || [];
+        const ids = [];
+        const counts = {};
+        for(let i = 0; i < arr.length; i += 2){
+            ids.push(arr[i]);
+            counts[arr[i]] = +arr[i + 1];
+        }
+        if (grameneMaps) ids.sort((a, b)=>{
+            const ma = grameneMaps[a] || grameneMaps[$f511198465122338$var$speciesTaxonId(a)];
+            const mb = grameneMaps[b] || grameneMaps[$f511198465122338$var$speciesTaxonId(b)];
+            return (ma && ma.left_index || 0) - (mb && mb.left_index || 0);
+        });
+        return ids.map((tid)=>({
+                tid: tid,
+                count: counts[tid]
+            }));
+    }, [
+        grameneSearch,
+        grameneMaps
+    ]);
+    const activeTaxon = gsea.activeTaxon;
+    const [treeWidth, setTreeWidth] = (0, $gXNCa$react.useState)(280);
+    const beginResize = (e)=>{
         e.preventDefault();
-        resizeStateRef.current = {
-            startY: e.clientY,
-            startHeight: plotHeight
-        };
+        const startX = e.clientX;
+        const startWidth = treeWidth;
         const onMove = (ev)=>{
-            const s = resizeStateRef.current;
-            if (!s) return;
-            const next = Math.max(120, Math.min(1200, s.startHeight + (ev.clientY - s.startY)));
-            setPlotHeight(next);
+            const next = Math.max(150, Math.min(800, startWidth + (ev.clientX - startX)));
+            setTreeWidth(next);
         };
         const onUp = ()=>{
-            resizeStateRef.current = null;
             document.removeEventListener('mousemove', onMove);
             document.removeEventListener('mouseup', onUp);
-            document.body.style.cursor = '';
             document.body.style.userSelect = '';
+            document.body.style.cursor = '';
         };
-        document.body.style.cursor = 'row-resize';
         document.body.style.userSelect = 'none';
+        document.body.style.cursor = 'col-resize';
         document.addEventListener('mousemove', onMove);
         document.addEventListener('mouseup', onUp);
     };
-    const hasBrush = Object.keys(selections).length > 0;
-    const filteredRows = (0, $gXNCa$react.useMemo)(()=>{
-        if (!hasBrush) return rows;
-        return rows.filter((r)=>$1fd2507769d5bd00$var$rowMatchesSelections(r, selections));
-    }, [
-        rows,
-        selections,
-        hasBrush
-    ]);
-    // Drop fields with no numeric data in the loaded rows so empty axes/columns
-    // don't clutter the visualization. Selected-but-empty fields stay in the
-    // underlying selection so a future load can repopulate them.
-    const visibleFields = (0, $gXNCa$react.useMemo)(()=>{
-        if (rows.length === 0 || selected.length === 0) return selected;
-        return selected.filter((f)=>rows.some((r)=>{
-                const v = r[f];
-                return v != null && !Array.isArray(v) && Number.isFinite(+v);
-            }));
+    (0, $gXNCa$react.useEffect)(()=>{
+        if (taxa.length === 0) return;
+        if (!activeTaxon || !taxa.find((t)=>String(t.tid) === String(activeTaxon))) doSetGseaActiveTaxon(taxa[0].tid);
     }, [
-        rows,
-        selected
-    ]);
-    const handleReorder = onReorder ? (newVisibleOrder)=>{
-        const visibleSet = new Set(newVisibleOrder);
-        const hidden = selected.filter((f)=>!visibleSet.has(f));
-        onReorder([
-            ...newVisibleOrder,
-            ...hidden
-        ]);
-    } : undefined;
-    const axisLabels = (0, $gXNCa$react.useMemo)(()=>$1fd2507769d5bd00$var$buildAxisLabels(visibleFields, studies, expressionSamples), [
-        visibleFields,
-        studies,
-        expressionSamples
+        taxa,
+        activeTaxon,
+        doSetGseaActiveTaxon
     ]);
     (0, $gXNCa$react.useEffect)(()=>{
-        if (rows.length === 0 && hasBrush) {
-            setSelections({});
-            setClearVersion((v)=>v + 1);
-        }
+        if (!activeTaxon) return;
+        const t = gsea.byTaxon[activeTaxon];
+        if (!t) return;
+        if (t.fg.status === 'idle') doFetchGseaForeground(activeTaxon);
+        if (t.bg.status === 'idle') doFetchGseaBackground(activeTaxon);
     }, [
-        rows.length,
-        hasBrush
+        activeTaxon,
+        gsea,
+        doFetchGseaForeground,
+        doFetchGseaBackground
     ]);
+    if (taxa.length === 0) return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
+        className: "gsea-view",
+        children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("em", {
+            children: "No species in the current results."
+        })
+    });
+    if (!grameneTaxonomy) return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
+        className: "gsea-view",
+        children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("em", {
+            children: "Loading taxonomy\u2026"
+        })
+    });
+    const handleAddFilter = (row)=>{
+        if (!doAcceptGrameneSuggestion) return;
+        const label = row.term_name ? `${row.term_display_id} ${row.term_name}` : row.term_display_id;
+        doAcceptGrameneSuggestion({
+            fq_field: row.field,
+            fq_value: String(row.term_id),
+            name: label,
+            category: row.ontology_label
+        });
+    };
     return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
-        className: "exprviz-tab-panel",
+        className: "gsea-view gsea-layout",
         children: [
-            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
-                className: "exprviz-toolbar",
-                children: [
-                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactbootstrap.Button), {
-                        size: "sm",
-                        onClick: onOpenFields,
-                        children: [
-                            "Select fields (",
-                            selected.length,
-                            " selected, ",
-                            studies.length,
-                            " studies)"
-                        ]
-                    }),
-                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Button), {
-                        size: "sm",
-                        variant: "primary",
-                        disabled: selected.length === 0 || fetchInfo.status === 'loading',
-                        onClick: onLoad,
-                        children: fetchInfo.status === 'loading' ? "Loading\u2026" : 'Load data'
-                    }),
-                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactbootstrap.ToggleButtonGroup), {
-                        type: "radio",
-                        name: `exprviz-scale-${taxon}`,
-                        size: "sm",
-                        value: scale,
-                        onChange: setScale,
-                        children: [
-                            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.ToggleButton), {
-                                id: `exprviz-scale-${taxon}-lin`,
-                                value: "linear",
-                                variant: "outline-secondary",
-                                children: "Linear"
-                            }),
-                            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.ToggleButton), {
-                                id: `exprviz-scale-${taxon}-log`,
-                                value: "log",
-                                variant: "outline-secondary",
-                                children: "Log"
-                            })
-                        ]
-                    }),
-                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Button), {
-                        size: "sm",
-                        variant: "outline-secondary",
-                        disabled: !hasBrush,
-                        onClick: ()=>{
-                            setClearVersion((v)=>v + 1);
-                            setSelections({});
-                        },
-                        children: "Clear brushes"
-                    }),
-                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Button), {
-                        size: "sm",
-                        variant: "outline-secondary",
-                        disabled: filteredRows.length === 0 || visibleFields.length === 0,
-                        onClick: ()=>$1fd2507769d5bd00$var$downloadTsv(`expression_${taxon}.tsv`, filteredRows, visibleFields),
-                        title: "Download the visible rows and columns as tab-delimited text",
-                        children: "Download TSV"
-                    }),
-                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Button), {
-                        size: "sm",
-                        variant: "success",
-                        disabled: !hasBrush || !onAddRangeQuery,
-                        onClick: ()=>{
-                            const terms = Object.keys(selections).map((field)=>{
-                                const [lo, hi] = selections[field];
-                                return {
-                                    category: 'Expression',
-                                    name: `${field}: ${$1fd2507769d5bd00$var$fmt(lo)}\u{2013}${$1fd2507769d5bd00$var$fmt(hi)}`,
-                                    fq_field: field,
-                                    fq_value: `[${lo} TO ${hi}]`
-                                };
-                            });
-                            onAddRangeQuery(terms);
-                        },
-                        title: "Add brush ranges as an AND-conjunction filter on the search",
-                        children: "Apply as filter"
-                    }),
-                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("span", {
-                        className: "exprviz-status",
-                        children: [
-                            hasBrush ? `${filteredRows.length} of ${rows.length}` : rows.length,
-                            fetchInfo.total ? ` / ${fetchInfo.total}` : '',
-                            " genes",
-                            hasBrush ? ' (brushed)' : ' loaded'
-                        ]
-                    })
-                ]
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
+                className: "gsea-layout-tree",
+                style: {
+                    flex: `0 0 ${treeWidth}px`
+                },
+                children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($f511198465122338$var$SpeciesTree, {
+                    taxonomy: grameneTaxonomy,
+                    grameneMaps: grameneMaps,
+                    taxa: taxa,
+                    activeTaxon: activeTaxon,
+                    onSelect: (tid)=>doSetGseaActiveTaxon(String(tid))
+                })
             }),
-            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
-                className: "exprviz-body",
-                children: [
-                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
-                        className: "exprviz-plot",
-                        style: {
-                            height: plotHeight
-                        },
-                        children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $caf32827df861c4e$export$2e2bcd8739ae039), {
-                            rows: rows,
-                            fields: visibleFields,
-                            scale: scale,
-                            onBrushChange: setSelections,
-                            onReorder: handleReorder,
-                            clearVersion: clearVersion,
-                            hoveredId: hoveredId,
-                            axisLabels: axisLabels
-                        })
-                    }),
-                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
-                        className: "exprviz-resizer",
-                        role: "separator",
-                        "aria-orientation": "horizontal",
-                        "aria-label": "Resize plot",
-                        onMouseDown: startResize,
-                        title: "Drag to resize"
-                    }),
-                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
-                        className: "exprviz-table",
-                        children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $4ab64e76c1caef59$export$2e2bcd8739ae039), {
-                            rows: filteredRows,
-                            fields: visibleFields,
-                            onReorder: handleReorder,
-                            studies: studies,
-                            expressionSamples: expressionSamples,
-                            onHoverRow: setHoveredId
-                        })
-                    })
-                ]
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
+                className: "gsea-splitter",
+                onMouseDown: beginResize,
+                title: "Drag to resize"
+            }),
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
+                className: "gsea-layout-panel",
+                children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($f511198465122338$var$TaxonPanel, {
+                    taxon: activeTaxon ? String(activeTaxon) : null,
+                    gsea: gsea,
+                    results: results,
+                    ui: ui,
+                    onUiChange: doSetGseaUI,
+                    onAddFilter: handleAddFilter
+                })
             })
         ]
     });
 };
-var $1fd2507769d5bd00$export$2e2bcd8739ae039 = (0, $gXNCa$reduxbundlerreact.connect)('selectExprViz', 'selectExprVizPivot', 'selectExprVizActiveTaxon', 'selectGrameneMaps', 'selectExpressionStudies', 'selectExpressionSamples', 'doSetExprVizActiveTaxon', 'doToggleExprVizFieldsModal', 'doFetchExprVizData', 'doReorderExprVizFields', 'doAddGrameneRangeQuery', $1fd2507769d5bd00$var$ExprVizViewCmp);
+var $f511198465122338$export$2e2bcd8739ae039 = (0, $gXNCa$reduxbundlerreact.connect)('selectGrameneSearch', 'selectGrameneMaps', 'selectGrameneTaxonomy', 'selectGsea', 'selectGseaUI', 'selectGseaResults', 'doSetGseaActiveTaxon', 'doSetGseaUI', 'doFetchGseaForeground', 'doFetchGseaBackground', 'doAcceptGrameneSuggestion', $f511198465122338$var$GseaViewCmp);
 
 
 
@@ -12749,6 +14285,7 @@ const $693dd8c7a5607c3a$var$inventory = {
     attribs: (0, $67bf5a43401bffdc$export$2e2bcd8739ae039),
     expression: (0, $261baeb81c4d4d8a$export$2e2bcd8739ae039),
     exprViz: (0, $1fd2507769d5bd00$export$2e2bcd8739ae039),
+    gsea: (0, $f511198465122338$export$2e2bcd8739ae039),
     userLists: (0, $0f50f369018a42ef$export$2e2bcd8739ae039),
     export: (0, $37b3bb0145d266b0$export$2e2bcd8739ae039)
 };