gramene-search 2.5.3 → 2.7.0

package/dist/index.js

@@ -7417,6 +7417,460 @@ const $5c2c79352d3d7b81$export$b2e089eb3692b073 = (props)=>/*#__PURE__*/ (0, $gX
     });
 
 
+// Host-defined tbrowse zone for the Homology gene tree, redesigned to compare
+// expression across a gene family. Three parts, aligned to the tree leaves:
+//   1. a gene × organ heatmap of ordinal expression levels (expr_organ_level),
+//      with markers on each gene's tissue-specific / -enhanced organs;
+//   2. a Max TPM column (expr_max_tpm), log-scaled magnitude;
+//   3. a Stress column of ↑activated / ↓repressed condition chips
+//      (expr_activated_by / expr_repressed_by).
+// Data is threaded in via hostData.exprAttrs (built by buildExprData from the
+// tree-scoped /search response), mirroring how the neighborhood / genome zones
+// receive their async data. Color/legend conventions follow exprViz/HeatmapPlot.
+
+
+
+// Canonical anatomical ordering (vegetative → reproductive → seed). Organs not
+// listed here are appended alphabetically so nothing is ever dropped.
+const $cd8bc494277e92a4$var$ORGAN_ORDER = [
+    'root',
+    'shoot',
+    'stem',
+    'leaf',
+    'meristem',
+    'vasculature',
+    'tuber',
+    'cotyledon',
+    'inflorescence',
+    'flower',
+    'anther_pollen',
+    'fruit',
+    'pericarp',
+    'seed',
+    'endosperm',
+    'embryo'
+];
+// Short column-header codes; unknown organs fall back to their first 3 letters.
+const $cd8bc494277e92a4$var$ORGAN_ABBR = {
+    root: 'rt',
+    shoot: 'sht',
+    stem: 'stm',
+    leaf: 'lf',
+    meristem: 'mer',
+    vasculature: 'vas',
+    tuber: 'tbr',
+    cotyledon: 'cot',
+    inflorescence: 'inf',
+    flower: 'flw',
+    anther_pollen: 'ant',
+    fruit: 'frt',
+    pericarp: 'per',
+    seed: 'sd',
+    endosperm: 'end',
+    embryo: 'emb'
+};
+const $cd8bc494277e92a4$var$abbr = (o)=>$cd8bc494277e92a4$var$ORGAN_ABBR[o] || o.slice(0, 3);
+// Ordinal expression level → color. not_expressed gets a distinct pale tint (it
+// IS a measurement); an organ a species doesn't report stays transparent (= not
+// assayed). Ramp matches HeatmapPlot's pale→dark blue.
+const $cd8bc494277e92a4$var$LEVEL_ORDER = [
+    'not_expressed',
+    'low',
+    'medium',
+    'high',
+    'very_high'
+];
+const $cd8bc494277e92a4$var$LEVEL_COLOR = {
+    not_expressed: '#eef2f6',
+    low: '#cfe0ee',
+    medium: '#8fbbdc',
+    high: '#3f86c2',
+    very_high: '#0a3d72'
+};
+const $cd8bc494277e92a4$var$LEVEL_LABEL = {
+    not_expressed: 'not expressed',
+    low: 'low',
+    medium: 'medium',
+    high: 'high',
+    very_high: 'very high'
+};
+// Stress chips: activated (induced) = warm, repressed = cool.
+const $cd8bc494277e92a4$var$STRESS = {
+    up: {
+        bg: '#fdecea',
+        fg: '#c0392b'
+    },
+    down: {
+        bg: '#eaf2fb',
+        fg: '#2e6fae'
+    }
+};
+const $cd8bc494277e92a4$var$MARKER = '#d35400'; // specific-to dot / enhanced-in outline
+const $cd8bc494277e92a4$var$ORGAN_CELL_W = 16;
+const $cd8bc494277e92a4$var$MAXTPM_W = 46;
+const $cd8bc494277e92a4$var$STRESS_MIN = 120;
+function $cd8bc494277e92a4$export$965a6b1d7408d496(docs, tree) {
+    const nodeOf = {};
+    const nodeGene = {}; // leaf nodeId -> gene id, for every leaf (hover readout)
+    if (tree && tree.nodes) Object.values(tree.nodes).forEach((n)=>{
+        if (n.isLeaf && n.geneId) {
+            nodeOf[n.geneId] = n.id;
+            nodeGene[n.id] = n.geneId;
+        }
+    });
+    const organSet = new Set();
+    const byNode = {};
+    let tpmMin = Infinity;
+    let tpmMax = -Infinity;
+    (docs || []).forEach((d)=>{
+        if (!d || !d.id) return;
+        const nodeId = nodeOf[d.id];
+        if (!nodeId) return;
+        const organLevels = {};
+        (d.expr_organ_level__attr_ss || []).forEach((t)=>{
+            const i = t.lastIndexOf(':');
+            if (i < 0) return;
+            const organ = t.slice(0, i);
+            organLevels[organ] = t.slice(i + 1);
+            organSet.add(organ);
+        });
+        const maxTpm = Number.isFinite(+d.expr_max_tpm__attr_f) ? +d.expr_max_tpm__attr_f : null;
+        if (maxTpm !== null) {
+            if (maxTpm < tpmMin) tpmMin = maxTpm;
+            if (maxTpm > tpmMax) tpmMax = maxTpm;
+        }
+        byNode[nodeId] = {
+            cls: d.expr_class__attr_ss || [],
+            organLevels: organLevels,
+            specificTo: new Set(d.expr_specific_to__attr_ss || []),
+            enhancedIn: new Set(d.expr_enhanced_in__attr_ss || []),
+            maxTpm: maxTpm,
+            activatedBy: d.expr_activated_by__attr_ss || [],
+            repressedBy: d.expr_repressed_by__attr_ss || []
+        };
+    });
+    const known = $cd8bc494277e92a4$var$ORGAN_ORDER.filter((o)=>organSet.has(o));
+    const unknown = [
+        ...organSet
+    ].filter((o)=>!$cd8bc494277e92a4$var$ORGAN_ORDER.includes(o)).sort();
+    return {
+        organs: [
+            ...known,
+            ...unknown
+        ],
+        byNode: byNode,
+        nodeGene: nodeGene,
+        maxTpm: {
+            min: tpmMin === Infinity ? 0 : tpmMin,
+            max: tpmMax === -Infinity ? 0 : tpmMax
+        }
+    };
+}
+// Shared row-highlight background, matching the other zones so hovering any zone
+// lights up the same row across all of them.
+function $cd8bc494277e92a4$var$rowHighlight(isSelected, isExactHover, isInHoveredSubtree) {
+    if (isSelected) return 'var(--tbrowse-row-select-bg)';
+    if (isExactHover) return 'var(--tbrowse-row-hover-bg)';
+    if (isInHoveredSubtree) return 'var(--tbrowse-row-subtree-bg)';
+    return 'transparent';
+}
+// Log-scaled fraction of v within [min,max], for the Max TPM heat background.
+function $cd8bc494277e92a4$var$tpmFraction(v, range) {
+    if (!Number.isFinite(v)) return null;
+    const lo = Math.log10((range.min || 0) + 1);
+    const hi = Math.log10((range.max || 0) + 1);
+    if (hi <= lo) return 0.5;
+    return Math.max(0, Math.min(1, (Math.log10(v + 1) - lo) / (hi - lo)));
+}
+function $cd8bc494277e92a4$var$fmtTpm(v) {
+    if (!Number.isFinite(v)) return '';
+    return v >= 10 ? String(Math.round(v)) : String(Math.round(v * 10) / 10);
+}
+function $cd8bc494277e92a4$var$fmtClass(cls) {
+    return cls && cls.length ? cls.map((c)=>c.replace(/_/g, ' ')).join(', ') : null;
+}
+const $cd8bc494277e92a4$var$gridBorder = '1px solid var(--tbrowse-grid-line, rgba(0,0,0,0.06))';
+const $cd8bc494277e92a4$var$stressWidth = (width, organCount)=>Math.max($cd8bc494277e92a4$var$STRESS_MIN, width - organCount * $cd8bc494277e92a4$var$ORGAN_CELL_W - $cd8bc494277e92a4$var$MAXTPM_W);
+const $cd8bc494277e92a4$var$ExprHeader = ({ zoneState: zoneState, setZoneState: setZoneState, width: width, data: data, hoveredNodeId: hoveredNodeId })=>{
+    const ea = data.hostData && data.hostData.exprAttrs || {};
+    const organs = ea.organs || [];
+    const gid = hoveredNodeId && ea.nodeGene && ea.nodeGene[hoveredNodeId];
+    const gene = hoveredNodeId && ea.byNode && ea.byNode[hoveredNodeId];
+    const clsText = gene && $cd8bc494277e92a4$var$fmtClass(gene.cls);
+    return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+        style: {
+            height: '100%',
+            display: 'flex',
+            flexDirection: 'column',
+            justifyContent: 'flex-end',
+            overflow: 'hidden'
+        },
+        children: [
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+                style: {
+                    display: 'flex',
+                    alignItems: 'center',
+                    gap: 8,
+                    padding: '0 4px',
+                    fontSize: 12
+                },
+                children: [
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$tbrowse.EditableZoneName), {
+                        defaultName: "Expression",
+                        customName: zoneState?.name,
+                        onChange: (next)=>setZoneState((s)=>({
+                                    ...s ?? {},
+                                    name: next
+                                }))
+                    }),
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
+                        style: {
+                            display: 'flex',
+                            alignItems: 'center',
+                            gap: 1,
+                            fontSize: 9,
+                            opacity: 0.85
+                        },
+                        title: "expression level",
+                        children: $cd8bc494277e92a4$var$LEVEL_ORDER.map((lv)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
+                                title: $cd8bc494277e92a4$var$LEVEL_LABEL[lv],
+                                style: {
+                                    width: 10,
+                                    height: 10,
+                                    background: $cd8bc494277e92a4$var$LEVEL_COLOR[lv],
+                                    border: $cd8bc494277e92a4$var$gridBorder,
+                                    display: 'inline-block'
+                                }
+                            }, lv))
+                    })
+                ]
+            }),
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
+                title: gid ? clsText ? `${gid} \xb7 ${clsText}` : gid : 'hover a node to see its gene and expression class',
+                style: {
+                    padding: '0 4px 2px',
+                    fontSize: 11,
+                    overflow: 'hidden',
+                    whiteSpace: 'nowrap',
+                    textOverflow: 'ellipsis'
+                },
+                children: gid ? /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactjsxruntime.Fragment), {
+                    children: [
+                        /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("b", {
+                            children: gid
+                        }),
+                        clsText ? /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
+                            style: {
+                                opacity: 0.7
+                            },
+                            children: ` \xb7 ${clsText}`
+                        }) : null
+                    ]
+                }) : /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
+                    style: {
+                        opacity: 0.5
+                    },
+                    children: "hover a node\u2026"
+                })
+            }),
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+                style: {
+                    display: 'flex',
+                    width: width
+                },
+                children: [
+                    organs.map((o)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
+                            title: o.replace(/_/g, ' '),
+                            style: {
+                                width: $cd8bc494277e92a4$var$ORGAN_CELL_W,
+                                fontSize: 8,
+                                textAlign: 'center',
+                                overflow: 'hidden',
+                                whiteSpace: 'nowrap',
+                                borderRight: $cd8bc494277e92a4$var$gridBorder,
+                                opacity: 0.8
+                            },
+                            children: $cd8bc494277e92a4$var$abbr(o)
+                        }, o)),
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
+                        style: {
+                            width: $cd8bc494277e92a4$var$MAXTPM_W,
+                            fontSize: 9,
+                            fontWeight: 600,
+                            textAlign: 'right',
+                            paddingRight: 4,
+                            opacity: 0.8
+                        },
+                        children: "TPM"
+                    }),
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
+                        style: {
+                            width: $cd8bc494277e92a4$var$stressWidth(width, organs.length),
+                            fontSize: 9,
+                            fontWeight: 600,
+                            paddingLeft: 4,
+                            opacity: 0.8
+                        },
+                        children: "Stress"
+                    })
+                ]
+            })
+        ]
+    });
+};
+const $cd8bc494277e92a4$var$OrganCell = ({ organ: organ, gene: gene })=>{
+    const level = gene && gene.organLevels[organ];
+    const specific = !!(gene && gene.specificTo.has(organ));
+    const enhanced = !!(gene && gene.enhancedIn.has(organ));
+    const title = level ? `${organ.replace(/_/g, ' ')}: ${$cd8bc494277e92a4$var$LEVEL_LABEL[level] || level}${specific ? " \xb7 specific" : enhanced ? " \xb7 enhanced" : ''}` : `${organ.replace(/_/g, ' ')}: not assayed`;
+    const style = {
+        position: 'relative',
+        width: $cd8bc494277e92a4$var$ORGAN_CELL_W,
+        height: '100%',
+        boxSizing: 'border-box',
+        background: level ? $cd8bc494277e92a4$var$LEVEL_COLOR[level] || 'transparent' : 'transparent',
+        borderRight: $cd8bc494277e92a4$var$gridBorder
+    };
+    // enhanced-in: thin outline; specific-to (stronger): corner dot.
+    if (enhanced && !specific) style.boxShadow = `inset 0 0 0 1px ${$cd8bc494277e92a4$var$MARKER}`;
+    return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
+        title: title,
+        style: style,
+        children: specific && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
+            style: {
+                position: 'absolute',
+                top: 1,
+                right: 1,
+                width: 4,
+                height: 4,
+                borderRadius: '50%',
+                background: $cd8bc494277e92a4$var$MARKER
+            }
+        })
+    });
+};
+const $cd8bc494277e92a4$var$StressCell = ({ gene: gene, width: width })=>{
+    const up = gene && gene.activatedBy || [];
+    const down = gene && gene.repressedBy || [];
+    const title = [
+        up.length ? `\u{2191} ${up.join(', ')}` : '',
+        down.length ? `\u{2193} ${down.join(', ')}` : ''
+    ].filter(Boolean).join('   ');
+    const chip = (c, dir, key)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
+            style: {
+                fontSize: 9,
+                lineHeight: '14px',
+                padding: '0 3px',
+                borderRadius: 2,
+                whiteSpace: 'nowrap',
+                background: $cd8bc494277e92a4$var$STRESS[dir].bg,
+                color: $cd8bc494277e92a4$var$STRESS[dir].fg
+            },
+            children: (dir === 'up' ? "\u2191" : "\u2193") + c
+        }, key);
+    return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+        title: title,
+        style: {
+            width: width,
+            display: 'flex',
+            flexWrap: 'nowrap',
+            gap: 2,
+            overflow: 'hidden',
+            alignItems: 'center',
+            paddingLeft: 4,
+            boxSizing: 'border-box'
+        },
+        children: [
+            up.map((c, i)=>chip(c, 'up', `u${i}`)),
+            down.map((c, i)=>chip(c, 'down', `d${i}`))
+        ]
+    });
+};
+const $cd8bc494277e92a4$var$ExprBody = ({ visibleRows: visibleRows, rowRange: rowRange, width: width, data: data, hoveredNodeId: hoveredNodeId, hoveredSubtreeIds: hoveredSubtreeIds, selectedNodeId: selectedNodeId, onHoverNode: onHoverNode, onSelectNode: onSelectNode })=>{
+    const ea = data.hostData && data.hostData.exprAttrs || {};
+    const organs = ea.organs || [];
+    const byNode = ea.byNode || {};
+    const tpmRange = ea.maxTpm || {
+        min: 0,
+        max: 0
+    };
+    const sW = $cd8bc494277e92a4$var$stressWidth(width, organs.length);
+    const totalHeight = visibleRows.length ? visibleRows[visibleRows.length - 1].y + visibleRows[visibleRows.length - 1].height : 0;
+    const rows = visibleRows.slice(rowRange.startIndex, rowRange.endIndex);
+    return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
+        style: {
+            position: 'relative',
+            width: width,
+            height: totalHeight,
+            overflow: 'hidden'
+        },
+        children: rows.map((r)=>{
+            const gene = byNode[r.nodeId];
+            const background = $cd8bc494277e92a4$var$rowHighlight(selectedNodeId === r.nodeId, hoveredNodeId === r.nodeId, !!(hoveredSubtreeIds && hoveredSubtreeIds.has(r.nodeId)));
+            const tpmFrac = gene ? $cd8bc494277e92a4$var$tpmFraction(gene.maxTpm, tpmRange) : null;
+            return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+                onMouseEnter: ()=>onHoverNode(r.nodeId),
+                onMouseLeave: ()=>onHoverNode(null),
+                onClick: ()=>onSelectNode(r.nodeId),
+                style: {
+                    position: 'absolute',
+                    top: r.y,
+                    height: r.height,
+                    left: 0,
+                    width: width,
+                    display: 'flex',
+                    boxSizing: 'border-box',
+                    background: background,
+                    cursor: 'pointer',
+                    opacity: r.opacity ?? 1
+                },
+                children: [
+                    organs.map((o)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($cd8bc494277e92a4$var$OrganCell, {
+                            organ: o,
+                            gene: gene
+                        }, o)),
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
+                        title: gene && Number.isFinite(gene.maxTpm) ? `max TPM: ${gene.maxTpm}` : '',
+                        style: {
+                            width: $cd8bc494277e92a4$var$MAXTPM_W,
+                            height: '100%',
+                            boxSizing: 'border-box',
+                            borderRight: $cd8bc494277e92a4$var$gridBorder,
+                            display: 'flex',
+                            alignItems: 'center',
+                            justifyContent: 'flex-end',
+                            paddingRight: 4,
+                            fontSize: 9,
+                            fontVariantNumeric: 'tabular-nums',
+                            color: 'var(--tbrowse-text)',
+                            background: tpmFrac === null ? 'transparent' : `rgba(33, 102, 172, ${(0.1 + 0.65 * tpmFrac).toFixed(3)})`
+                        },
+                        children: gene ? $cd8bc494277e92a4$var$fmtTpm(gene.maxTpm) : ''
+                    }),
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($cd8bc494277e92a4$var$StressCell, {
+                        gene: gene,
+                        width: sW
+                    })
+                ]
+            }, r.nodeId);
+        })
+    });
+};
+const $cd8bc494277e92a4$export$44e8c3b1eee47e9e = {
+    id: 'expression',
+    displayName: 'Expression',
+    Header: $cd8bc494277e92a4$var$ExprHeader,
+    Body: $cd8bc494277e92a4$var$ExprBody,
+    defaultWidth: 70,
+    minWidth: 280,
+    defaultZoneState: {},
+    // Stay hidden until its async data lands; tbrowse's auto-enable effect flips
+    // it on once isAvailable() turns true (same lifecycle as neighborhood/genome).
+    isAvailable: (data)=>Boolean(data.hostData && data.hostData.exprAttrs && data.hostData.exprAttrs.organs && data.hostData.exprAttrs.organs.length),
+    defaultVisible: false
+};
+
+
 
 const $047461923b1badda$export$54387eca9e368edc = (config)=>{
     if (!config) return null;
@@ -7480,7 +7934,10 @@ class $64fad37f770d2bfe$var$Homology extends (0, ($parcel$interopDefault($gXNCa$
             neighborhoodStatus: undefined,
             geneStructures: null,
             geneStructuresTreeId: null,
-            geneStructuresStatus: undefined
+            geneStructuresStatus: undefined,
+            exprAttrs: null,
+            exprAttrsTreeId: null,
+            exprAttrsStatus: undefined
         };
         if (!props.geneDocs.hasOwnProperty(props.searchResult.id)) props.requestGene(props.searchResult.id);
         this.taxonomy = (0, ($parcel$interopDefault($gXNCa$gramenetreesclientsrctaxonomy))).tree(Object.values(props.grameneTaxonomy));
@@ -7501,11 +7958,19 @@ class $64fad37f770d2bfe$var$Homology extends (0, ($parcel$interopDefault($gXNCa$
     isGenomeZoneEnabled() {
         return !!(this.props.configuration && this.props.configuration.enable_tbrowse_genome_zone);
     }
+    // The expression-attributes zone is opt-in per site via
+    // `enable_tbrowse_expression_zone` (defaults to false) — the expr_*__attr_*
+    // fields are sorghum-specific.
+    isExpressionZoneEnabled() {
+        return !!(this.props.configuration && this.props.configuration.enable_tbrowse_expression_zone);
+    }
     getTbrowseZones() {
-        return this.isGenomeZoneEnabled() ? [
-            ...$64fad37f770d2bfe$var$TBROWSE_BASE_ZONES,
-            $64fad37f770d2bfe$var$genomeZone
-        ] : $64fad37f770d2bfe$var$TBROWSE_BASE_ZONES;
+        const zones = [
+            ...$64fad37f770d2bfe$var$TBROWSE_BASE_ZONES
+        ];
+        if (this.isGenomeZoneEnabled()) zones.push($64fad37f770d2bfe$var$genomeZone);
+        if (this.isExpressionZoneEnabled()) zones.push((0, $cd8bc494277e92a4$export$44e8c3b1eee47e9e));
+        return zones;
     }
     getHeight() {
         const h = this.getHomologySlice().height;
@@ -7529,6 +7994,42 @@ class $64fad37f770d2bfe$var$Homology extends (0, ($parcel$interopDefault($gXNCa$
             tbrowse: viewState
         });
     }
+    // When the user has limited the search to a subset of genomes
+    // (grameneGenomes.active), prune the gene tree to genes from those genomes
+    // — mirroring the taxon_id filter api.js applies to the search itself, and
+    // the genomesOfInterest TreeVis already honours. Returns the ids of the
+    // highest nodes whose entire subtree lies outside the active set (maximal
+    // excluded clades), rather than individual leaves: tbrowse then sheds one
+    // stub per clade instead of one per leaf, and its single-marker count is
+    // meaningful. The gene of interest is always kept so the tree never
+    // collapses to nothing. Empty active set means "no limit" → full tree.
+    getGenomePrunedIds() {
+        const active = this.props.grameneGenomes && this.props.grameneGenomes.active || {};
+        const activeIds = Object.keys(active);
+        if (activeIds.length === 0) return [];
+        if (!this._tbrowseData) return [];
+        const activeSet = new Set(activeIds.map(String));
+        const keepGeneId = this.gene && this.gene._id;
+        const nodes = this._tbrowseData.tree.nodes;
+        const children = {};
+        Object.values(nodes).forEach((n)=>{
+            if (n.parentId != null) (children[n.parentId] = children[n.parentId] || []).push(n.id);
+        });
+        // hasKept(node): does the subtree contain a leaf we must keep (its taxon
+        // is active, or it's the gene of interest)? Memoised post-order walk.
+        const memo = {};
+        const hasKept = (id)=>{
+            if (id in memo) return memo[id];
+            const n = nodes[id];
+            const v = n.isLeaf ? n.taxonomyId != null && activeSet.has(String(n.taxonomyId)) || n.geneId === keepGeneId : (children[id] || []).some(hasKept);
+            memo[id] = v;
+            return v;
+        };
+        // A node is a maximal excluded clade when it keeps nothing but its parent
+        // does (or it's the root) — i.e. the highest fully-excluded node on its
+        // path. The root always keeps the gene of interest, so it is never pruned.
+        return Object.values(nodes).filter((n)=>!hasKept(n.id) && (n.parentId == null || hasKept(n.parentId))).map((n)=>n.id);
+    }
     // Seed the bundle with a pivot-computed initial tbrowse view state once the
     // tree data is available and the user is actually looking at the tbrowse
     // viewer. Called from lifecycle (not render) to avoid dispatching mid-render.
@@ -7605,6 +8106,8 @@ class $64fad37f770d2bfe$var$Homology extends (0, ($parcel$interopDefault($gXNCa$
         this.fetchNeighborhood(treeId);
         // Only pay for gene-structure data when the genome zone is actually enabled.
         if (this.isGenomeZoneEnabled()) this.fetchGeneStructures(treeId, this._tbrowseData.tree);
+        // Same for the per-gene expression attributes zone.
+        if (this.isExpressionZoneEnabled()) this.fetchExprAttrs(treeId, this._tbrowseData.tree);
     }
     fetchNeighborhood(treeId) {
         if (this._neighborhoodFetchedFor === treeId) return;
@@ -7683,6 +8186,49 @@ class $64fad37f770d2bfe$var$Homology extends (0, ($parcel$interopDefault($gXNCa$
             this._geneStructuresFetchedFor = null;
         });
     }
+    // Fetch the expression attributes (expr_*__attr_*) for this tree's genes in a
+    // single query: scope by gene_tree and the `expression_attributes` capability
+    // so only genes that actually have the data come back (rows high enough to
+    // cover the whole tree). Uses /search (not /genes, whose trimmed docs omit the
+    // attr fields) with an fl glob so the columns are discovered from the data
+    // rather than hard-coded. `tree` is still needed to map gene ids to leaf node
+    // ids (see buildExprByNode).
+    fetchExprAttrs(treeId, tree) {
+        if (this._exprAttrsFetchedFor === treeId) return;
+        this._exprAttrsFetchedFor = treeId;
+        this.setState({
+            exprAttrsStatus: 'loading'
+        });
+        const api = this.props.grameneAPI;
+        const url = new URL(`${api}/search`);
+        url.searchParams.set('q', '*:*');
+        url.searchParams.append('fq', `gene_tree:${treeId}`);
+        url.searchParams.append('fq', 'capabilities:expression_attributes');
+        url.searchParams.set('fl', 'id,expr_*__attr_*');
+        url.searchParams.set('rows', '10000');
+        fetch(url.toString(), {
+            headers: {
+                Accept: 'application/json'
+            }
+        }).then((res)=>{
+            if (!res.ok) throw new Error(`HTTP ${res.status}`);
+            return res.json();
+        }).then((json)=>{
+            if (this._exprAttrsFetchedFor !== treeId) return;
+            const docs = json && json.response && Array.isArray(json.response.docs) ? json.response.docs : [];
+            this.setState({
+                exprAttrs: (0, $cd8bc494277e92a4$export$965a6b1d7408d496)(docs, tree),
+                exprAttrsTreeId: treeId,
+                exprAttrsStatus: 'ready'
+            });
+        }).catch((err)=>{
+            console.warn('tbrowse expression-attrs fetch failed:', err);
+            if (this._exprAttrsFetchedFor === treeId) this.setState({
+                exprAttrsStatus: 'error'
+            });
+            this._exprAttrsFetchedFor = null;
+        });
+    }
     startResize(e) {
         e.preventDefault();
         const startY = e.clientY;
@@ -7746,18 +8292,36 @@ class $64fad37f770d2bfe$var$Homology extends (0, ($parcel$interopDefault($gXNCa$
         }
         const neighborhood = this.state.neighborhoodTreeId === treeId ? this.state.neighborhood : undefined;
         const geneStructures = this.state.geneStructuresTreeId === treeId ? this.state.geneStructures : undefined;
+        const exprAttrs = this.state.exprAttrsTreeId === treeId ? this.state.exprAttrs : undefined;
         // Per-zone status for the TBrowse toolbar — pulses while a fetch
         // is in flight, turns red on failure. Tracked per-tree so a
         // tree-change resets any stale 'ready'/'error' from the prior gene.
         const zoneStatus = {
             neighborhood: this.state.neighborhoodTreeId === treeId ? this.state.neighborhoodStatus : this.state.neighborhoodStatus === 'loading' ? 'loading' : undefined,
-            genome: this.state.geneStructuresTreeId === treeId ? this.state.geneStructuresStatus : this.state.geneStructuresStatus === 'loading' ? 'loading' : undefined
+            genome: this.state.geneStructuresTreeId === treeId ? this.state.geneStructuresStatus : this.state.geneStructuresStatus === 'loading' ? 'loading' : undefined,
+            expression: this.state.exprAttrsTreeId === treeId ? this.state.exprAttrsStatus : this.state.exprAttrsStatus === 'loading' ? 'loading' : undefined
         };
         // Bundle-driven (controlled) view state. If we're rendering tbrowse before
         // componentDidMount/Update has seeded the bundle slice, skip this turn and
         // let the re-render with the seeded state do the work.
         const tbrowseVS = this.getHomologySlice().tbrowse;
         if (!tbrowseVS) return null;
+        // Layer the genome-limit prune set on top of the user's own prunes for the
+        // controlled view state, but persist only the user's prunes (strip the
+        // genome-derived ones in onViewStateChange) so the bundle stays free of
+        // filter-derived state and re-applies cleanly when the filter changes.
+        const genomePrunedIds = this.getGenomePrunedIds();
+        const effectiveVS = genomePrunedIds.length ? {
+            ...tbrowseVS,
+            prunedNodeIds: (0, ($parcel$interopDefault($gXNCa$lodash))).union(tbrowseVS.prunedNodeIds || [], genomePrunedIds)
+        } : tbrowseVS;
+        const onViewStateChange = genomePrunedIds.length ? (next)=>{
+            const genomeSet = new Set(genomePrunedIds);
+            this.setTbrowseViewState({
+                ...next,
+                prunedNodeIds: (next.prunedNodeIds || []).filter((id)=>!genomeSet.has(id))
+            });
+        } : (next)=>this.setTbrowseViewState(next);
         return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactjsxruntime.Fragment), {
             children: [
                 /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
@@ -7775,10 +8339,13 @@ class $64fad37f770d2bfe$var$Homology extends (0, ($parcel$interopDefault($gXNCa$
                         exonJunctions: this._tbrowseData.exonJunctions,
                         neighborhood: neighborhood,
                         geneStructures: geneStructures,
+                        hostData: exprAttrs ? {
+                            exprAttrs: exprAttrs
+                        } : undefined,
                         zones: this.getTbrowseZones(),
                         nodeOfInterest: this.gene._id,
-                        viewState: tbrowseVS,
-                        onViewStateChange: (next)=>this.setTbrowseViewState(next),
+                        viewState: effectiveVS,
+                        onViewStateChange: onViewStateChange,
                         defaultOpenSections: {
                             zones: true,
                             search: true
@@ -8558,18 +9125,20 @@ class $54c74a4689d5a778$var$Pathways extends (0, ($parcel$interopDefault($gXNCa$
         this.props.doRequestGramenePathways(this.pathwayIds);
     }
     makeTaxonSpecific(docs, taxon_id) {
-        let lineageField = 'lineage_' + taxon_id;
-        if (!docs[0].hasOwnProperty(lineageField)) {
-            let tid = Math.floor(taxon_id / 1000);
-            lineageField = 'lineage_' + tid;
-        }
+        // Each pathway doc may carry lineage under lineage_<taxon_id> or
+        // lineage_<floor(taxon_id/1000)>. Resolve per-doc rather than inferring
+        // from docs[0] — when docs is heterogeneous (some species-specific, some
+        // generic), inferring from the first entry leaves the rest with undefined
+        // lineage and crashes getHierarchy.
+        const primaryField = 'lineage_' + taxon_id;
+        const fallbackField = 'lineage_' + Math.floor(taxon_id / 1000);
         return docs.map((doc)=>{
             let tsDoc = (0, ($parcel$interopDefault($gXNCa$lodash))).pick(doc, [
                 '_id',
                 'name',
                 'type'
             ]);
-            tsDoc.lineage = doc[lineageField];
+            tsDoc.lineage = doc[primaryField] || doc[fallbackField];
             return tsDoc;
         });
     }
@@ -8579,6 +9148,7 @@ class $54c74a4689d5a778$var$Pathways extends (0, ($parcel$interopDefault($gXNCa$
         this.pathwayIds.forEach((pwyId)=>{
             if (pathways[pwyId]) {
                 const pwy = pathways[pwyId];
+                if (!pwy.lineage) return; // no lineage for this species — skip
                 pwy.lineage.forEach((line)=>{
                     const parentOffset = line.length - 2;
                     nodes.push({
@@ -8612,8 +9182,13 @@ class $54c74a4689d5a778$var$Pathways extends (0, ($parcel$interopDefault($gXNCa$
             if (node.type === "Pathway") this.loadDiagram(this.stableId(node.id));
             else {
                 const reaction = this.stableId(node.id);
-                const pathway = this.stableId(node.parent.split("/").pop());
-                this.loadDiagram(pathway, reaction);
+                // node.parent is a slash-delimited ancestor path supplied by
+                // react-simple-tree-menu; for a root-level Reaction with no parent
+                // pathway in the tree, fall back to loading the reaction directly
+                // rather than crashing on undefined.split.
+                const parentKey = typeof node.parent === 'string' ? node.parent.split("/").pop() : null;
+                if (parentKey) this.loadDiagram(this.stableId(parentKey), reaction);
+                else this.loadDiagram(reaction);
             }
             this.setState({
                 selectedNode: selectedNode