gramene-search 2.3.0 → 2.5.0

package/dist/index.js

@@ -7447,12 +7447,13 @@ const $047461923b1badda$export$964d88edb00bbcaa = (suggestion)=>{
 const $64fad37f770d2bfe$var$genomeZone = (0, $gXNCa$tbrowse.createGenomeZone)({
     id: 'genome'
 });
-const $64fad37f770d2bfe$var$TBROWSE_ZONES = [
+// The genome (gene-structure) zone is gated behind the site-config flag
+// `enable_tbrowse_genome_zone` (defaults to false) — see getTbrowseZones().
+const $64fad37f770d2bfe$var$TBROWSE_BASE_ZONES = [
     (0, $gXNCa$tbrowse.treeZone),
     (0, $gXNCa$tbrowse.labelsZone),
     (0, $gXNCa$tbrowse.msaZone),
-    (0, $gXNCa$tbrowse.neighborhoodZone),
-    $64fad37f770d2bfe$var$genomeZone
+    (0, $gXNCa$tbrowse.neighborhoodZone)
 ];
 class $64fad37f770d2bfe$var$Homology extends (0, ($parcel$interopDefault($gXNCa$react))).Component {
     constructor(props){
@@ -7485,7 +7486,18 @@ class $64fad37f770d2bfe$var$Homology extends (0, ($parcel$interopDefault($gXNCa$
         return slice && slice.homology || {};
     }
     getViewer() {
-        return this.getHomologySlice().viewer || 'treevis';
+        return this.getHomologySlice().viewer || 'tbrowse';
+    }
+    // The genome (gene-structure) zone is opt-in per site via
+    // `enable_tbrowse_genome_zone` (defaults to false).
+    isGenomeZoneEnabled() {
+        return !!(this.props.configuration && this.props.configuration.enable_tbrowse_genome_zone);
+    }
+    getTbrowseZones() {
+        return this.isGenomeZoneEnabled() ? [
+            ...$64fad37f770d2bfe$var$TBROWSE_BASE_ZONES,
+            $64fad37f770d2bfe$var$genomeZone
+        ] : $64fad37f770d2bfe$var$TBROWSE_BASE_ZONES;
     }
     getHeight() {
         const h = this.getHomologySlice().height;
@@ -7542,7 +7554,7 @@ class $64fad37f770d2bfe$var$Homology extends (0, ($parcel$interopDefault($gXNCa$
             // logic — zones default to visible unless their definition opts out
             // (e.g. neighborhood and genome opt out so they only appear once
             // their async data lands; tbrowse's Layout auto-flips them on then).
-            zones: $64fad37f770d2bfe$var$TBROWSE_ZONES.map((z)=>({
+            zones: this.getTbrowseZones().map((z)=>({
                     id: z.id,
                     width: z.defaultWidth,
                     visible: z.defaultVisible ?? true
@@ -7583,7 +7595,8 @@ class $64fad37f770d2bfe$var$Homology extends (0, ($parcel$interopDefault($gXNCa$
             ]);
         }
         this.fetchNeighborhood(treeId);
-        this.fetchGeneStructures(treeId, this._tbrowseData.tree);
+        // Only pay for gene-structure data when the genome zone is actually enabled.
+        if (this.isGenomeZoneEnabled()) this.fetchGeneStructures(treeId, this._tbrowseData.tree);
     }
     fetchNeighborhood(treeId) {
         if (this._neighborhoodFetchedFor === treeId) return;
@@ -7754,7 +7767,7 @@ class $64fad37f770d2bfe$var$Homology extends (0, ($parcel$interopDefault($gXNCa$
                         exonJunctions: this._tbrowseData.exonJunctions,
                         neighborhood: neighborhood,
                         geneStructures: geneStructures,
-                        zones: $64fad37f770d2bfe$var$TBROWSE_ZONES,
+                        zones: this.getTbrowseZones(),
                         nodeOfInterest: this.gene._id,
                         viewState: tbrowseVS,
                         onViewStateChange: (next)=>this.setTbrowseViewState(next),
@@ -7791,8 +7804,8 @@ class $64fad37f770d2bfe$var$Homology extends (0, ($parcel$interopDefault($gXNCa$
                 margin: '8px 0'
             },
             children: [
-                btn('treevis', 'TreeVis'),
-                btn('tbrowse', 'TBrowse (beta)')
+                btn('tbrowse', 'TBrowse'),
+                btn('treevis', 'TreeVis')
             ]
         });
     }
@@ -16885,6 +16898,14 @@ var $597fe213417ee6ca$export$2e2bcd8739ae039 = (0, $gXNCa$reduxbundlerreact.conn
 //   data.hostData.bins = { genomesByTaxon: { [taxonId]: genome }, maxScore }
 // where `genome` is a gramene-bins-client genome (fullGenomeSize,
 // _regionsArray, region.bin(i)/binCount()/size/name, bin.results.count).
+//
+// Pan/zoom: a single shared horizontal transform { scale, leftFrac } (fraction
+// space, so it's width-independent and aligns every genome to the same relative
+// window) lives in the ephemeral binsUI store. The header toggles between two
+// interaction modes: 'select' (drag selects a region to count/filter genes,
+// the original gesture) and 'panzoom' (drag pans, wheel zooms toward the
+// cursor). All hit-testing/coordinates are in genome-fraction [0,1] so
+// hovers/selections stay anchored to the genome as you pan and zoom.
 
 
 
@@ -16967,28 +16988,66 @@ function $bfd29d54a0f0e853$var$updateScore(currentScore, baseCount, binScore, bi
     if (typeof currentScore === 'number') return (currentScore * baseCount + binScore * binBasesUsed) / (binBasesUsed + baseCount);
     return binScore;
 }
-// Draw one genome's distribution into [x, x+width) at vertical [y, y+height).
-// Ported from drawGenome() in gramene-search-vis, collapsed to a single row.
-function $bfd29d54a0f0e853$var$drawGenomeRow(ctx, genome, x, y, width, height, maxScore) {
+const $bfd29d54a0f0e853$var$clamp = (v, lo, hi)=>Math.max(lo, Math.min(hi, v));
+const $bfd29d54a0f0e853$var$MAX_SCALE = 1000; // zoom far enough to isolate a single bin
+// Locate the region/bin cursor at a target base offset, so a zoomed draw can
+// start partway into the genome without iterating skipped pixels. Returns null
+// past the end of the genome.
+function $bfd29d54a0f0e853$var$seekCursor(regions, targetBase) {
+    let acc = 0;
+    for(let regionIdx = 0; regionIdx < regions.length; regionIdx++){
+        const region = regions[regionIdx];
+        const n = region.binCount();
+        for(let binIdx = 0; binIdx < n; binIdx++){
+            const bin = region.bin(binIdx);
+            const size = bin.end - bin.start + 1;
+            if (acc + size > targetBase) return {
+                regionIdx: regionIdx,
+                binIdx: binIdx,
+                basesInBinUsedAlready: Math.max(0, targetBase - acc)
+            };
+            acc += size;
+        }
+    }
+    return null;
+}
+// Draw one genome's distribution into the visible [0, widthPx) strip at
+// vertical [y, y+height), under the shared { scale, leftFrac } transform. Only
+// the visible pixels are drawn (the cursor is fast-forwarded to the window's
+// left edge); consecutive equal-colour columns are batched into one fillRect,
+// which makes zoomed-in draws (where each bin spans many px) cheap. Ported from
+// drawGenome() in gramene-search-vis, generalised for pan/zoom.
+function $bfd29d54a0f0e853$var$drawGenomeRow(ctx, genome, y, widthPx, height, maxScore, scale, leftFrac) {
     const regions = genome && genome._regionsArray;
-    if (!regions || regions.length === 0 || !genome.fullGenomeSize) return;
-    const basesPerPx = genome.fullGenomeSize / width;
+    const full = genome && genome.fullGenomeSize;
+    if (!regions || regions.length === 0 || !full) return;
+    const virtualWidth = widthPx * scale; // full genome spans this many px when zoomed
+    const basesPerPx = full / virtualWidth;
     if (!(basesPerPx > 0)) return;
-    let binIdx = 0;
-    let basesInBinUsedAlready = 0;
-    let regionIdx = 0;
+    const cursor = $bfd29d54a0f0e853$var$seekCursor(regions, leftFrac * full);
+    if (!cursor) return;
+    let { regionIdx: regionIdx, binIdx: binIdx, basesInBinUsedAlready: basesInBinUsedAlready } = cursor;
     let region = regions[regionIdx];
     let regionUnanchored = region.name === 'UNANCHORED';
-    for(let px = 0; px < width; px++){
+    let runColor = null;
+    let runStart = 0;
+    const flush = (endExclusive)=>{
+        if (runColor !== null && endExclusive > runStart) {
+            ctx.fillStyle = runColor;
+            ctx.fillRect(runStart, y, endExclusive - runStart, height);
+        }
+    };
+    let px = 0;
+    for(; px < widthPx; px++){
         let baseCount = 0;
         let score;
-        let basesAvailableInBin = 0;
+        let ended = false;
         while(baseCount < basesPerPx){
             const basesNeededByThisPixel = basesPerPx - baseCount;
             const bin = region.bin(binIdx);
             const binSize = bin.end - bin.start + 1;
             const binScore = maxScore ? (bin.results ? bin.results.count : 0) / maxScore : 0;
-            basesAvailableInBin = binSize - basesInBinUsedAlready;
+            const basesAvailableInBin = binSize - basesInBinUsedAlready;
             let binBasesUsed;
             if (basesAvailableInBin <= basesNeededByThisPixel) {
                 binIdx++;
@@ -17003,14 +17062,30 @@ function $bfd29d54a0f0e853$var$drawGenomeRow(ctx, genome, x, y, width, height, m
             if (binIdx === region.binCount()) {
                 binIdx = 0;
                 regionIdx++;
-                if (regionIdx === regions.length) break;
+                if (regionIdx === regions.length) {
+                    ended = true;
+                    break;
+                }
                 region = regions[regionIdx];
                 regionUnanchored = region.name === 'UNANCHORED';
             }
         }
-        ctx.fillStyle = $bfd29d54a0f0e853$var$binColor(regionIdx, score || 0, regionUnanchored);
-        ctx.fillRect(x + px, y, 1, height);
+        const idxForColor = regionIdx >= regions.length ? regions.length - 1 : regionIdx;
+        const color = $bfd29d54a0f0e853$var$binColor(idxForColor, score || 0, regionUnanchored);
+        if (runColor === null) {
+            runColor = color;
+            runStart = px;
+        } else if (color !== runColor) {
+            flush(px);
+            runColor = color;
+            runStart = px;
+        }
+        if (ended) {
+            px++;
+            break;
+        }
     }
+    flush(px);
 }
 function $bfd29d54a0f0e853$export$390e10a52782f018(taxDist) {
     if (!taxDist || typeof taxDist.leafNodes !== 'function') return null;
@@ -17030,12 +17105,18 @@ function $bfd29d54a0f0e853$export$390e10a52782f018(taxDist) {
 }
 // ── interaction store (shared between Header and Body via hostData) ──────────
 // A tiny pub/sub kept OUT of the controlled tbrowse viewState so per-mousemove
-// hover/drag updates don't churn the whole tree. Holds the hovered chromosome,
-// the in-progress drag, and the committed drag-selections.
+// hover/drag/pan/zoom updates don't churn the whole tree. Holds the hovered
+// chromosome, the in-progress select-drag, the committed drag-selections, and
+// the shared horizontal pan/zoom transform.
+const $bfd29d54a0f0e853$var$DEFAULT_TRANSFORM = {
+    scale: 1,
+    leftFrac: 0
+};
 const $bfd29d54a0f0e853$var$EMPTY_UI = {
     hovered: null,
     inProgress: null,
-    selections: []
+    selections: [],
+    transform: $bfd29d54a0f0e853$var$DEFAULT_TRANSFORM
 };
 const $bfd29d54a0f0e853$var$NOOP_SUB = ()=>()=>{};
 const $bfd29d54a0f0e853$var$NOOP_GET = ()=>$bfd29d54a0f0e853$var$EMPTY_UI;
@@ -17063,21 +17144,35 @@ function $bfd29d54a0f0e853$export$f06340802363875a() {
             };
             emit();
         },
+        setTransform: (t)=>{
+            state = {
+                ...state,
+                transform: t
+            };
+            emit();
+        },
+        resetTransform: ()=>{
+            state = {
+                ...state,
+                transform: $bfd29d54a0f0e853$var$DEFAULT_TRANSFORM
+            };
+            emit();
+        },
         // Add a selection, merging it with any existing selection on the SAME
-        // genome whose pixel range overlaps — so overlapping drags become one
+        // genome whose fraction range overlaps — so overlapping drags become one
         // region and shared bins aren't double-counted. Bins are unioned by their
         // global index.
         addSelection: (sel)=>{
             let merged = sel;
             const rest = [];
-            for (const s of state.selections)if (s.taxonId === merged.taxonId && s.x0 <= merged.x1 && s.x1 >= merged.x0) {
+            for (const s of state.selections)if (s.taxonId === merged.taxonId && s.f0 <= merged.f1 && s.f1 >= merged.f0) {
                 const byIdx = new Map();
                 for (const b of s.bins)byIdx.set(b.idx, b.count);
                 for (const b of merged.bins)byIdx.set(b.idx, b.count);
                 merged = {
                     taxonId: merged.taxonId,
-                    x0: Math.min(s.x0, merged.x0),
-                    x1: Math.max(s.x1, merged.x1),
+                    f0: Math.min(s.f0, merged.f0),
+                    f1: Math.max(s.f1, merged.f1),
                     bins: [
                         ...byIdx
                     ].map(([idx, count])=>({
@@ -17095,7 +17190,17 @@ function $bfd29d54a0f0e853$export$f06340802363875a() {
             };
             emit();
         },
+        // Clear hover/selections but keep the current zoom/pan transform — clearing
+        // selections shouldn't yank the user back out of their zoom.
         clear: ()=>{
+            state = {
+                ...$bfd29d54a0f0e853$var$EMPTY_UI,
+                transform: state.transform
+            };
+            emit();
+        },
+        // Full reset (new result set): drop everything including the transform.
+        reset: ()=>{
             state = $bfd29d54a0f0e853$var$EMPTY_UI;
             emit();
         }
@@ -17115,55 +17220,56 @@ function $bfd29d54a0f0e853$export$861100744513cc3(selections) {
         ...set
     ];
 }
-// Per-genome pixel layout across the [0,width) strip: region spans (for
+// Per-genome layout in genome-fraction space [0,1]: region spans (for
 // chromosome hit-testing) and bin spans with gene counts (for summing a
-// drag-selected range). Mirrors drawGenomeRow's region/bin walk.
-function $bfd29d54a0f0e853$var$buildGenomeLayout(genome, width) {
+// drag-selected range). Width/zoom-independent — the transform maps fractions
+// to screen pixels at render time.
+function $bfd29d54a0f0e853$var$buildGenomeLayout(genome) {
     const out = {
         regions: []
     };
     const regions = genome && genome._regionsArray;
-    if (!regions || !genome.fullGenomeSize || !(width > 0)) return out;
-    const basesPerPx = genome.fullGenomeSize / width;
-    if (!(basesPerPx > 0)) return out;
-    let px = 0;
+    const full = genome && genome.fullGenomeSize;
+    if (!regions || !full) return out;
+    let base = 0;
     for (const region of regions){
-        const x0 = px;
+        const f0 = base / full;
         const binsArr = [];
         const n = region.binCount();
         for(let i = 0; i < n; i++){
             const bin = region.bin(i);
-            const bw = (bin.end - bin.start + 1) / basesPerPx;
+            const size = bin.end - bin.start + 1;
+            const bf0 = base / full;
+            base += size;
             binsArr.push({
-                x0: px,
-                x1: px + bw,
+                f0: bf0,
+                f1: base / full,
                 count: bin.results && bin.results.count || 0,
                 idx: bin.idx
             });
-            px += bw;
         }
         out.regions.push({
             name: region.name,
-            x0: x0,
-            x1: px,
+            f0: f0,
+            f1: base / full,
             bins: binsArr
         });
     }
     return out;
 }
-function $bfd29d54a0f0e853$var$regionAtPx(layout, mx) {
-    for (const r of layout.regions)if (mx >= r.x0 && mx < r.x1) return r;
+function $bfd29d54a0f0e853$var$regionAtFrac(layout, f) {
+    for (const r of layout.regions)if (f >= r.f0 && f < r.f1) return r;
     return null;
 }
-// Non-empty bins overlapping a pixel range, as {idx, count}. Empty bins are
+// Non-empty bins overlapping a fraction range, as {idx, count}. Empty bins are
 // excluded by design (the selection / filter only covers bins with genes).
-function $bfd29d54a0f0e853$var$selectedBinsInPxRange(layout, a, b) {
+function $bfd29d54a0f0e853$var$selectedBinsInFracRange(layout, a, b) {
     const lo = Math.min(a, b);
     const hi = Math.max(a, b);
     const bins = [];
     for (const r of layout.regions){
-        if (r.x1 < lo || r.x0 > hi) continue;
-        for (const bin of r.bins)if (bin.x1 > lo && bin.x0 < hi && bin.count > 0) bins.push({
+        if (r.f1 < lo || r.f0 > hi) continue;
+        for (const bin of r.bins)if (bin.f1 > lo && bin.f0 < hi && bin.count > 0) bins.push({
             idx: bin.idx,
             count: bin.count
         });
@@ -17177,11 +17283,46 @@ const $bfd29d54a0f0e853$var$HEADER_BTN = {
     padding: '1px 6px',
     cursor: 'pointer'
 };
+function $bfd29d54a0f0e853$var$ModeToggle({ mode: mode, setMode: setMode }) {
+    const seg = (id, label)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("button", {
+            type: "button",
+            onClick: ()=>setMode(id),
+            title: id === 'select' ? 'Drag to select a region' : 'Drag to pan, scroll to zoom',
+            style: {
+                fontSize: 11,
+                lineHeight: 1,
+                padding: '2px 7px',
+                cursor: 'pointer',
+                border: 'none',
+                background: mode === id ? 'var(--tbrowse-accent, #2878dc)' : 'transparent',
+                color: mode === id ? '#fff' : 'var(--tbrowse-text-muted)'
+            },
+            children: label
+        });
+    return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+        style: {
+            display: 'inline-flex',
+            border: '1px solid var(--tbrowse-border-soft)',
+            borderRadius: 4,
+            overflow: 'hidden'
+        },
+        children: [
+            seg('select', 'Select'),
+            seg('panzoom', 'Pan/Zoom')
+        ]
+    });
+}
 const $bfd29d54a0f0e853$var$BinsHeader = ({ data: data, zoneState: zoneState, setZoneState: setZoneState })=>{
     const store = data.hostData && data.hostData.binsUI;
     const snap = (0, $gXNCa$react.useSyncExternalStore)(store ? store.subscribe : $bfd29d54a0f0e853$var$NOOP_SUB, store ? store.getState : $bfd29d54a0f0e853$var$NOOP_GET);
     const total = $bfd29d54a0f0e853$export$cf7300886d7d9e1e(snap.selections);
     const hovered = snap.hovered;
+    const scale = snap.transform ? snap.transform.scale : 1;
+    const mode = zoneState && zoneState.mode || 'select';
+    const setMode = (m)=>setZoneState((s)=>({
+                ...s ?? {},
+                mode: m
+            }));
     return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
         style: {
             height: '100%',
@@ -17199,7 +17340,8 @@ const $bfd29d54a0f0e853$var$BinsHeader = ({ data: data, zoneState: zoneState, se
                     display: 'flex',
                     alignItems: 'center',
                     gap: 8,
-                    minHeight: 0
+                    minHeight: 0,
+                    flexWrap: 'wrap'
                 },
                 children: [
                     /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$tbrowse.EditableZoneName), {
@@ -17210,6 +17352,32 @@ const $bfd29d54a0f0e853$var$BinsHeader = ({ data: data, zoneState: zoneState, se
                                     name: next
                                 }))
                     }),
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($bfd29d54a0f0e853$var$ModeToggle, {
+                        mode: mode,
+                        setMode: setMode
+                    }),
+                    scale > 1.0001 && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactjsxruntime.Fragment), {
+                        children: [
+                            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("span", {
+                                style: {
+                                    color: 'var(--tbrowse-text-muted)',
+                                    fontSize: 11,
+                                    whiteSpace: 'nowrap'
+                                },
+                                children: [
+                                    scale.toFixed(scale < 10 ? 1 : 0),
+                                    "\xd7"
+                                ]
+                            }),
+                            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("button", {
+                                type: "button",
+                                style: $bfd29d54a0f0e853$var$HEADER_BTN,
+                                title: "Reset zoom",
+                                onClick: ()=>store && store.resetTransform(),
+                                children: "reset zoom"
+                            })
+                        ]
+                    }),
                     snap.selections.length > 0 && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactjsxruntime.Fragment), {
                         children: [
                             /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("span", {
@@ -17275,7 +17443,7 @@ function $bfd29d54a0f0e853$var$rowHighlight(isSelected, isExactHover, isInHovere
     return 'transparent';
 }
 const $bfd29d54a0f0e853$var$BinsBody = (props)=>{
-    const { visibleRows: visibleRows, rowRange: rowRange, width: width, data: data, hoveredNodeId: hoveredNodeId, hoveredSubtreeIds: hoveredSubtreeIds, selectedNodeId: selectedNodeId, onHoverNode: onHoverNode, onSelectNode: onSelectNode } = props;
+    const { visibleRows: visibleRows, rowRange: rowRange, width: width, data: data, zoneState: zoneState, hoveredNodeId: hoveredNodeId, hoveredSubtreeIds: hoveredSubtreeIds, selectedNodeId: selectedNodeId, onHoverNode: onHoverNode, onSelectNode: onSelectNode } = props;
     const canvasRef = (0, $gXNCa$react.useRef)(null);
     const containerRef = (0, $gXNCa$react.useRef)(null);
     const dragRef = (0, $gXNCa$react.useRef)(null);
@@ -17285,27 +17453,33 @@ const $bfd29d54a0f0e853$var$BinsBody = (props)=>{
     const suppressClickRef = (0, $gXNCa$react.useRef)(false);
     const store = data.hostData && data.hostData.binsUI;
     const snap = (0, $gXNCa$react.useSyncExternalStore)(store ? store.subscribe : $bfd29d54a0f0e853$var$NOOP_SUB, store ? store.getState : $bfd29d54a0f0e853$var$NOOP_GET);
+    const transform = snap.transform || $bfd29d54a0f0e853$var$DEFAULT_TRANSFORM;
+    const mode = zoneState && zoneState.mode || 'select';
     const totalHeight = visibleRows.length ? visibleRows[visibleRows.length - 1].y + visibleRows[visibleRows.length - 1].height : 0;
     const bins = data.hostData && data.hostData.bins;
     const rows = visibleRows.slice(rowRange.startIndex, rowRange.endIndex);
     const w = Math.max(1, Math.floor(width));
-    // Pixel layout per visible genome row (regions + bins), for hit-testing.
+    // Fraction-space layout per visible genome row (regions + bins), for
+    // hit-testing. Independent of width/zoom, so it only rebuilds when the row
+    // set changes.
     const layouts = (0, $gXNCa$react.useMemo)(()=>{
         const m = {};
         if (bins) for (const r of rows){
             if (r.kind !== 'leaf') continue;
             const g = bins.genomesByTaxon[r.nodeId];
-            if (g) m[r.nodeId] = $bfd29d54a0f0e853$var$buildGenomeLayout(g, w);
+            if (g) m[r.nodeId] = $bfd29d54a0f0e853$var$buildGenomeLayout(g);
         }
         return m;
     // eslint-disable-next-line react-hooks/exhaustive-deps
     }, [
         bins,
-        w,
         rowRange.startIndex,
         rowRange.endIndex,
         visibleRows
     ]);
+    // Fraction <-> screen-pixel helpers under the current transform.
+    const fracToScreen = (f)=>(f - transform.leftFrac) * transform.scale * w;
+    const screenToFrac = (px)=>transform.leftFrac + px / w / transform.scale;
     (0, $gXNCa$react.useEffect)(()=>{
         const canvas = canvasRef.current;
         if (!canvas || !bins) return;
@@ -17321,7 +17495,7 @@ const $bfd29d54a0f0e853$var$BinsBody = (props)=>{
             const genome = bins.genomesByTaxon[r.nodeId];
             if (!genome) continue;
             const innerH = Math.max(1, r.height - 2 * $bfd29d54a0f0e853$var$ROW_PAD_Y);
-            $bfd29d54a0f0e853$var$drawGenomeRow(ctx, genome, 0, r.y + $bfd29d54a0f0e853$var$ROW_PAD_Y, w, innerH, bins.maxScore);
+            $bfd29d54a0f0e853$var$drawGenomeRow(ctx, genome, r.y + $bfd29d54a0f0e853$var$ROW_PAD_Y, w, innerH, bins.maxScore, transform.scale, transform.leftFrac);
         }
     }, [
         visibleRows,
@@ -17329,21 +17503,53 @@ const $bfd29d54a0f0e853$var$BinsBody = (props)=>{
         rowRange.endIndex,
         w,
         totalHeight,
-        bins
+        bins,
+        transform.scale,
+        transform.leftFrac
     ]);
     const pxFromEvent = (e)=>{
         const el = containerRef.current;
         if (!el) return 0;
         const rect = el.getBoundingClientRect();
-        return Math.max(0, Math.min(w, e.clientX - rect.left));
+        return $bfd29d54a0f0e853$var$clamp(e.clientX - rect.left, 0, w);
     };
+    // Wheel-to-zoom (panzoom mode only), centred on the cursor. Native non-passive
+    // listener so we can preventDefault the page scroll; re-attached when mode/
+    // width change. Transform is read live from the store to avoid stale closures.
+    (0, $gXNCa$react.useEffect)(()=>{
+        const el = containerRef.current;
+        if (!el || !store) return undefined;
+        const onWheel = (e)=>{
+            if (mode !== 'panzoom') return; // let the page scroll normally
+            e.preventDefault();
+            const t = store.getState().transform || $bfd29d54a0f0e853$var$DEFAULT_TRANSFORM;
+            const rect = el.getBoundingClientRect();
+            const cursorPx = $bfd29d54a0f0e853$var$clamp(e.clientX - rect.left, 0, w);
+            const fracAtCursor = t.leftFrac + cursorPx / w / t.scale;
+            const factor = Math.exp(-e.deltaY * 0.0015);
+            const newScale = $bfd29d54a0f0e853$var$clamp(t.scale * factor, 1, $bfd29d54a0f0e853$var$MAX_SCALE);
+            const newLeft = $bfd29d54a0f0e853$var$clamp(fracAtCursor - cursorPx / w / newScale, 0, 1 - 1 / newScale);
+            store.setTransform({
+                scale: newScale,
+                leftFrac: newLeft
+            });
+        };
+        el.addEventListener('wheel', onWheel, {
+            passive: false
+        });
+        return ()=>el.removeEventListener('wheel', onWheel);
+    }, [
+        store,
+        w,
+        mode
+    ]);
     const genomeName = (taxonId)=>{
         const tax = data.taxonomy && data.taxonomy[taxonId];
         return tax && (tax.commonName || tax.scientificName) || String(taxonId);
     };
     const onRowMouseMove = (e, r)=>{
         if (!store || dragRef.current || !layouts[r.nodeId]) return;
-        const reg = $bfd29d54a0f0e853$var$regionAtPx(layouts[r.nodeId], pxFromEvent(e));
+        const reg = $bfd29d54a0f0e853$var$regionAtFrac(layouts[r.nodeId], screenToFrac(pxFromEvent(e)));
         if (!reg) {
             store.setHovered(null);
             return;
@@ -17354,33 +17560,60 @@ const $bfd29d54a0f0e853$var$BinsBody = (props)=>{
             genomeName: genomeName(r.nodeId),
             regionName: reg.name,
             geneCount: geneCount,
-            x0: reg.x0,
-            x1: reg.x1
+            f0: reg.f0,
+            f1: reg.f1
         });
     };
-    const onRowPointerDown = (e, r)=>{
-        if (!store || !layouts[r.nodeId]) return;
+    // Pan drag (panzoom mode): translate leftFrac by the cursor delta, scaled by
+    // the current zoom. Shared transform → every genome row pans together.
+    const startPan = (e)=>{
         e.preventDefault();
         const startPx = pxFromEvent(e);
+        const t0 = store.getState().transform || $bfd29d54a0f0e853$var$DEFAULT_TRANSFORM;
+        let moved = false;
+        const onMove = (ev)=>{
+            const dx = pxFromEvent(ev) - startPx;
+            if (Math.abs(dx) > 2) moved = true;
+            const t = store.getState().transform || $bfd29d54a0f0e853$var$DEFAULT_TRANSFORM;
+            const newLeft = $bfd29d54a0f0e853$var$clamp(t0.leftFrac - dx / w / t.scale, 0, 1 - 1 / t.scale);
+            store.setTransform({
+                scale: t.scale,
+                leftFrac: newLeft
+            });
+        };
+        const onUp = ()=>{
+            document.removeEventListener('pointermove', onMove);
+            document.removeEventListener('pointerup', onUp);
+            if (moved) suppressClickRef.current = true;
+        };
+        document.addEventListener('pointermove', onMove);
+        document.addEventListener('pointerup', onUp);
+    };
+    // Select drag (select mode): brush a fraction range and add the non-empty
+    // bins under it as a committed selection.
+    const startSelect = (e, r)=>{
+        if (!layouts[r.nodeId]) return;
+        e.preventDefault();
+        const startFrac = screenToFrac(pxFromEvent(e));
         dragRef.current = {
             taxonId: r.nodeId,
-            startPx: startPx,
+            startFrac: startFrac,
             moved: false
         };
         store.setInProgress({
             taxonId: r.nodeId,
-            x0: startPx,
-            x1: startPx
+            f0: startFrac,
+            f1: startFrac
         });
         const onMove = (ev)=>{
             const d = dragRef.current;
             if (!d) return;
-            const cur = pxFromEvent(ev);
-            if (Math.abs(cur - d.startPx) > 2) d.moved = true;
+            const cur = screenToFrac(pxFromEvent(ev));
+            if (Math.abs(cur - d.startFrac) * w * transform.scale > 2) d.moved = true;
             store.setInProgress({
                 taxonId: d.taxonId,
-                x0: Math.min(d.startPx, cur),
-                x1: Math.max(d.startPx, cur)
+                f0: Math.min(d.startFrac, cur),
+                f1: Math.max(d.startFrac, cur)
             });
         };
         const onUp = (ev)=>{
@@ -17391,17 +17624,17 @@ const $bfd29d54a0f0e853$var$BinsBody = (props)=>{
             store.setInProgress(null);
             if (d && d.moved) {
                 suppressClickRef.current = true; // swallow the click that follows a drag
-                const cur = pxFromEvent(ev);
-                const x0 = Math.min(d.startPx, cur);
-                const x1 = Math.max(d.startPx, cur);
+                const cur = screenToFrac(pxFromEvent(ev));
+                const f0 = Math.min(d.startFrac, cur);
+                const f1 = Math.max(d.startFrac, cur);
                 const lay = layouts[d.taxonId];
                 if (lay) {
-                    const bins = $bfd29d54a0f0e853$var$selectedBinsInPxRange(lay, x0, x1);
-                    if (bins.length) store.addSelection({
+                    const selBins = $bfd29d54a0f0e853$var$selectedBinsInFracRange(lay, f0, f1);
+                    if (selBins.length) store.addSelection({
                         taxonId: d.taxonId,
-                        x0: x0,
-                        x1: x1,
-                        bins: bins
+                        f0: f0,
+                        f1: f1,
+                        bins: selBins
                     });
                 }
             }
@@ -17409,15 +17642,29 @@ const $bfd29d54a0f0e853$var$BinsBody = (props)=>{
         document.addEventListener('pointermove', onMove);
         document.addEventListener('pointerup', onUp);
     };
+    const onRowPointerDown = (e, r)=>{
+        if (!store) return;
+        if (mode === 'panzoom') {
+            startPan(e);
+            return;
+        }
+        startSelect(e, r);
+    };
     const rowByTaxon = new Map(rows.map((r)=>[
             r.nodeId,
             r
         ]));
-    // Outline rectangles (drawn above the canvas; pointer-events:none). The y
-    // comes from the current row so they track vertical scroll.
-    const outline = (key, taxonId, x0, x1, color, dashed)=>{
+    // Outline rectangles (drawn above the canvas; pointer-events:none). Stored in
+    // fraction space and projected to screen px under the transform, clipped to
+    // the visible strip. The y comes from the current row so they track scroll.
+    const outline = (key, taxonId, f0, f1, color, dashed)=>{
         const r = rowByTaxon.get(taxonId);
         if (!r) return null;
+        let x0 = fracToScreen(f0);
+        let x1 = fracToScreen(f1);
+        if (x1 <= 0 || x0 >= w) return null; // fully outside the visible window
+        x0 = Math.max(0, x0);
+        x1 = Math.min(w, x1);
         return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
             style: {
                 position: 'absolute',
@@ -17431,6 +17678,7 @@ const $bfd29d54a0f0e853$var$BinsBody = (props)=>{
             }
         }, key);
     };
+    const rowCursor = mode === 'panzoom' ? 'grab' : 'crosshair';
     return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
         ref: containerRef,
         style: {
@@ -17461,7 +17709,7 @@ const $bfd29d54a0f0e853$var$BinsBody = (props)=>{
                         right: 0,
                         height: r.height,
                         background: $bfd29d54a0f0e853$var$rowHighlight(selectedNodeId === r.nodeId, hoveredNodeId === r.nodeId, !!(hoveredSubtreeIds && hoveredSubtreeIds.has(r.nodeId))),
-                        cursor: 'crosshair',
+                        cursor: rowCursor,
                         opacity: r.opacity ?? 1
                     }
                 }, r.nodeId)),
@@ -17476,9 +17724,9 @@ const $bfd29d54a0f0e853$var$BinsBody = (props)=>{
                     pointerEvents: 'none'
                 }
             }),
-            snap.hovered && !snap.inProgress && outline('hover', snap.hovered.taxonId, snap.hovered.x0, snap.hovered.x1, 'var(--tbrowse-accent, #2878dc)', false),
-            snap.selections.map((s, i)=>outline(`sel-${i}`, s.taxonId, s.x0, s.x1, '#d62728', false)),
-            snap.inProgress && outline('drag', snap.inProgress.taxonId, snap.inProgress.x0, snap.inProgress.x1, '#d62728', true)
+            snap.hovered && !snap.inProgress && outline('hover', snap.hovered.taxonId, snap.hovered.f0, snap.hovered.f1, 'var(--tbrowse-accent, #2878dc)', false),
+            snap.selections.map((s, i)=>outline(`sel-${i}`, s.taxonId, s.f0, s.f1, '#d62728', false)),
+            snap.inProgress && outline('drag', snap.inProgress.taxonId, snap.inProgress.f0, snap.inProgress.f1, '#d62728', true)
         ]
     });
 };
@@ -17489,7 +17737,9 @@ const $bfd29d54a0f0e853$export$d85d069f2280460c = {
     Body: $bfd29d54a0f0e853$var$BinsBody,
     defaultWidth: 60,
     minWidth: 200,
-    defaultZoneState: {},
+    defaultZoneState: {
+        mode: 'select'
+    },
     isAvailable: (data)=>Boolean(data.hostData && data.hostData.bins && data.hostData.bins.genomesByTaxon && Object.keys(data.hostData.bins.genomesByTaxon).length > 0),
     defaultVisible: true
 };
@@ -17724,7 +17974,7 @@ const $15504f5eba8e73bd$var$TaxDistTbrowse = (props)=>{
     const binsUiRef = (0, $gXNCa$react.useRef)(null);
     if (!binsUiRef.current) binsUiRef.current = (0, $bfd29d54a0f0e853$export$f06340802363875a)();
     (0, $gXNCa$react.useEffect)(()=>{
-        binsUiRef.current.clear();
+        binsUiRef.current.reset();
     }, [
         grameneTaxDist
     ]);