jbrowse-plugin-mafviewer 1.3.1 → 1.4.0

package/README.md

@@ -9,7 +9,7 @@ JBrowse 2
 
 ## Demo
 
-https://jbrowse.org/code/jb2/main/?config=%2Fdemos%2Fmaf%2Fhg38%2Fdistconfig.json&session=share-jREsrEm0Q-&password=fRZjQ
+https://jbrowse.org/code/jb2/main/?config=%2Fdemos%2Fmaf%2Fhg38%2Fdistconfig.json&session=share-2v5qIkvufP&password=uYpiC
 
 ## GUI usage (e.g. in JBrowse Desktop)
 
@@ -92,36 +92,6 @@ can use nhLocation or samples array on adapter
 }
 ```
 
-### Example BgzipTaffyAdapter config
-
-Note: TAF files are actually significantly slower and has known bugs...will
-update once fixed
-
-This notice will be removed it it is improved
-
-As with other adapters, you can use nhLocation or samples array on adapter
-
-```json
-{
-  "type": "MafTrack",
-  "trackId": "bigMaf",
-  "name": "taffy",
-  "adapter": {
-    "type": "BgzipTaffyAdapter",
-    "nhLocation": {
-      "uri": "hg38.30way.nh"
-    },
-    "tafGzLocation": {
-      "uri": "30way.taf.gz"
-    },
-    "taiGzLocation": {
-      "uri": "30way.taf.gz.tai"
-    }
-  },
-  "assemblyNames": ["hg38"]
-}
-```
-
 ### Example with customized sample names and colors
 
 ```json
@@ -191,9 +161,6 @@ the case
 2. MAF tabix based format, based on a custom BED created via conversion tools in
    this repo (see maf2bed)
 
-3. TAF format (new!). Currently only supports bgzip'd TAF. This is pioneered by
-   https://github.com/ComparativeGenomicsToolkit/taffy
-
 _Note: All these formats generally start with a MAF as input. Note that your MAF
 file should contain the species name and chromosome name e.g. hg38.chr1 in the
 sequence identifiers._
@@ -229,17 +196,3 @@ separated by `:`.
 
 Note: If you can't use the `cargo install maf2bed` binary, there is a
 `bin/maf2bed.pl` perl version of it in this repo
-
-### Option 3. Preparing TAF
-
-Follow steps from https://github.com/ComparativeGenomicsToolkit/taffy
-
-```
-taffy view -i chr22.maf -o chr22.taf
-bgzip chr22.taf
-taffy index -i chr22.taf.gz
-```
-
-The above workflow requires that taffy is built with "htslib support"
-
-Note that the TAF support is beta, let me know if you run into any issues

package/dist/BigMafAdapter/BigMafAdapter.js

@@ -38,6 +38,8 @@ export default class BigMafAdapter extends BaseFeatureDataAdapter {
     }
     getFeatures(query, opts) {
         const { statusCallback = () => { } } = opts || {};
+        // Pre-compile regex for better performance
+        const WHITESPACE_REGEX = / +/;
         return ObservableCreate(async (observer) => {
             const { adapter } = await this.setup();
             const features = await updateStatus('Downloading alignments', statusCallback, () => firstValueFrom(adapter.getFeatures(query).pipe(toArray())));
@@ -45,46 +47,55 @@ export default class BigMafAdapter extends BaseFeatureDataAdapter {
                 for (const feature of features) {
                     const maf = feature.get('mafBlock');
                     const blocks = maf.split(';');
-                    let aln;
-                    const alns = [];
+                    // Count sequence blocks first to pre-size arrays
+                    let sequenceBlockCount = 0;
+                    for (const block of blocks) {
+                        if (block.startsWith('s')) {
+                            sequenceBlockCount++;
+                        }
+                    }
+                    // Pre-size arrays based on actual sequence block count
+                    const alns = new Array(sequenceBlockCount);
                     const alignments = {};
-                    const blocks2 = [];
+                    let sequenceIndex = 0;
+                    let referenceSeq;
+                    // Single-pass processing: combine both loops
                     for (const block of blocks) {
                         if (block.startsWith('s')) {
-                            if (aln) {
-                                alns.push(block.split(/ +/)[6]);
-                                blocks2.push(block);
-                            }
-                            else {
-                                aln = block.split(/ +/)[6];
-                                alns.push(aln);
-                                blocks2.push(block);
+                            // Split once and cache the result
+                            const parts = block.split(WHITESPACE_REGEX);
+                            const sequence = parts[6];
+                            const organismChr = parts[1];
+                            // Store sequence in pre-sized array
+                            alns[sequenceIndex] = sequence;
+                            // Set reference sequence from first block
+                            if (referenceSeq === undefined) {
+                                referenceSeq = sequence;
                             }
+                            // Parse organism and chromosome once
+                            const dotIndex = organismChr.indexOf('.');
+                            const org = organismChr.slice(0, Math.max(0, dotIndex));
+                            const chr = organismChr.slice(Math.max(0, dotIndex + 1));
+                            // Create alignment record directly
+                            alignments[org] = {
+                                chr,
+                                start: +parts[2],
+                                srcSize: +parts[3],
+                                strand: parts[4] === '+' ? 1 : -1,
+                                unknown: +parts[5],
+                                seq: sequence,
+                            };
+                            sequenceIndex++;
                         }
                     }
-                    for (let i = 0; i < blocks2.length; i++) {
-                        const elt = blocks2[i];
-                        const ad = elt.split(/ +/);
-                        const y = ad[1].split('.');
-                        const org = y[0];
-                        const chr = y[1];
-                        alignments[org] = {
-                            chr: chr,
-                            start: +ad[1],
-                            srcSize: +ad[2],
-                            strand: ad[3] === '+' ? 1 : -1,
-                            unknown: +ad[4],
-                            seq: alns[i],
-                        };
-                    }
                     observer.next(new SimpleFeature({
                         id: feature.id(),
                         data: {
                             start: feature.get('start'),
                             end: feature.get('end'),
                             refName: feature.get('refName'),
-                            seq: alns[0],
-                            alignments: alignments,
+                            seq: referenceSeq,
+                            alignments,
                         },
                     }));
                 }

package/dist/BigMafAdapter/BigMafAdapter.js.map

@@ -1 +1 @@
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+{"version":3,"file":"BigMafAdapter.js","sourceRoot":"","sources":["../../src/BigMafAdapter/BigMafAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,sBAAsB,EAAE,MAAM,yCAAyC,CAAA;AAChF,OAAO,EAAE,aAAa,EAAE,YAAY,EAAE,MAAM,oBAAoB,CAAA;AAChE,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,EAAE,WAAW,EAAE,MAAM,iBAAiB,CAAA;AAC7C,OAAO,EAAE,cAAc,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAE9C,OAAO,WAAW,MAAM,gBAAgB,CAAA;AACxC,OAAO,EAAE,SAAS,EAAE,MAAM,SAAS,CAAA;AAanC,MAAM,CAAC,OAAO,OAAO,aAAc,SAAQ,sBAAsB;IACxD,MAAM,CAA+C;IAE5D,KAAK,CAAC,KAAK;QACT,IAAI,CAAC,IAAI,CAAC,aAAa,EAAE,CAAC;YACxB,MAAM,IAAI,KAAK,CAAC,4BAA4B,CAAC,CAAA;QAC/C,CAAC;QACD,OAAO;YACL,OAAO,EAAE,CACP,MAAM,IAAI,CAAC,aAAa,CAAC;gBACvB,GAAG,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC;gBAC3B,IAAI,EAAE,eAAe;aACtB,CAAC,CACH,CAAC,WAAqC;SACxC,CAAA;IACH,CAAC;IACD,KAAK,CAAC,QAAQ;QACZ,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC;YACjB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,KAAK,EAAE,CAAC,KAAK,CAAC,CAAC,CAAU,EAAE,EAAE;gBAC9C,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;QACJ,CAAC;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAED,KAAK,CAAC,WAAW;QACf,MAAM,EAAE,OAAO,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACtC,OAAO,OAAO,CAAC,WAAW,EAAE,CAAA;IAC9B,CAAC;IAED,KAAK,CAAC,SAAS;QACb,MAAM,EAAE,OAAO,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACtC,OAAO,OAAO,CAAC,SAAS,EAAE,CAAA;IAC5B,CAAC;IAED,WAAW,CAAC,KAAa,EAAE,IAAkB;QAC3C,MAAM,EAAE,cAAc,GAAG,GAAG,EAAE,GAAE,CAAC,EAAE,GAAG,IAAI,IAAI,EAAE,CAAA;QAChD,2CAA2C;QAC3C,MAAM,gBAAgB,GAAG,IAAI,CAAA;QAE7B,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,OAAO,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;YACtC,MAAM,QAAQ,GAAG,MAAM,YAAY,CACjC,wBAAwB,EACxB,cAAc,EACd,GAAG,EAAE,CAAC,cAAc,CAAC,OAAO,CAAC,WAAW,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,OAAO,EAAE,CAAC,CAAC,CACjE,CAAA;YACD,MAAM,YAAY,CAAC,uBAAuB,EAAE,cAAc,EAAE,GAAG,EAAE;gBAC/D,KAAK,MAAM,OAAO,IAAI,QAAQ,EAAE,CAAC;oBAC/B,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,UAAU,CAAW,CAAA;oBAC7C,MAAM,MAAM,GAAG,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;oBAE7B,iDAAiD;oBACjD,IAAI,kBAAkB,GAAG,CAAC,CAAA;oBAC1B,KAAK,MAAM,KAAK,IAAI,MAAM,EAAE,CAAC;wBAC3B,IAAI,KAAK,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC;4BAC1B,kBAAkB,EAAE,CAAA;wBACtB,CAAC;oBACH,CAAC;oBAED,uDAAuD;oBACvD,MAAM,IAAI,GAAG,IAAI,KAAK,CAAS,kBAAkB,CAAC,CAAA;oBAClD,MAAM,UAAU,GAAG,EAAoC,CAAA;oBAEvD,IAAI,aAAa,GAAG,CAAC,CAAA;oBACrB,IAAI,YAAgC,CAAA;oBAEpC,6CAA6C;oBAC7C,KAAK,MAAM,KAAK,IAAI,MAAM,EAAE,CAAC;wBAC3B,IAAI,KAAK,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC;4BAC1B,kCAAkC;4BAClC,MAAM,KAAK,GAAG,KAAK,CAAC,KAAK,CAAC,gBAAgB,CAAC,CAAA;4BAC3C,MAAM,QAAQ,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;4BAC1B,MAAM,WAAW,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;4BAE7B,oCAAoC;4BACpC,IAAI,CAAC,aAAa,CAAC,GAAG,QAAQ,CAAA;4BAE9B,0CAA0C;4BAC1C,IAAI,YAAY,KAAK,SAAS,EAAE,CAAC;gCAC/B,YAAY,GAAG,QAAQ,CAAA;4BACzB,CAAC;4BAED,qCAAqC;4BACrC,MAAM,QAAQ,GAAG,WAAW,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;4BACzC,MAAM,GAAG,GAAG,WAAW,CAAC,KAAK,CAAC,CAAC,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,QAAQ,CAAC,CAAC,CAAA;4BACvD,MAAM,GAAG,GAAG,WAAW,CAAC,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,QAAQ,GAAG,CAAC,CAAC,CAAC,CAAA;4BAExD,mCAAmC;4BACnC,UAAU,CAAC,GAAG,CAAC,GAAG;gCAChB,GAAG;gCACH,KAAK,EAAE,CAAC,KAAK,CAAC,CAAC,CAAE;gCACjB,OAAO,EAAE,CAAC,KAAK,CAAC,CAAC,CAAE;gCACnB,MAAM,EAAE,KAAK,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;gCACjC,OAAO,EAAE,CAAC,KAAK,CAAC,CAAC,CAAE;gCACnB,GAAG,EAAE,QAAQ;6BACd,CAAA;4BAED,aAAa,EAAE,CAAA;wBACjB,CAAC;oBACH,CAAC;oBAED,QAAQ,CAAC,IAAI,CACX,IAAI,aAAa,CAAC;wBAChB,EAAE,EAAE,OAAO,CAAC,EAAE,EAAE;wBAChB,IAAI,EAAE;4BACJ,KAAK,EAAE,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC;4BAC3B,GAAG,EAAE,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC;4BACvB,OAAO,EAAE,OAAO,CAAC,GAAG,CAAC,SAAS,CAAC;4BAC/B,GAAG,EAAE,YAAY;4BACjB,UAAU;yBACX;qBACF,CAAC,CACH,CAAA;gBACH,CAAC;YACH,CAAC,CAAC,CAAA;YACF,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,CAAC,CAAA;IACJ,CAAC;IAED,KAAK,CAAC,UAAU,CAAC,MAAc;QAC7B,MAAM,KAAK,GAAG,IAAI,CAAC,OAAO,CAAC,YAAY,CAAC,CAAA;QACxC,MAAM,EAAE,GACN,KAAK,CAAC,GAAG,KAAK,gBAAgB;YAC5B,CAAC,CAAC,SAAS;YACX,CAAC,CAAC,MAAM,YAAY,CAAC,KAAK,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;QAEhD,2EAA2E;QAC3E,OAAO;QACP,OAAO;YACL,OAAO,EAAE,SAAS,CAAC,IAAI,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC;YAC3C,IAAI,EAAE,EAAE,CAAC,CAAC,CAAC,WAAW,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;SACvC,CAAA;IACH,CAAC;IAED,aAAa,KAAU,CAAC;CACzB"}

package/dist/LinearMafDisplay/components/Crosshairs.js

@@ -11,7 +11,7 @@ const Crosshairs = ({ width, height, scrollTop, mouseX, mouseY, }) => {
             position: 'absolute',
             top: scrollTop,
         } },
-        React.createElement("line", { x1: 0, x2: width, y1: mouseY - scrollTop, y2: mouseY - scrollTop, stroke: "black" }),
+        React.createElement("line", { x1: 0, x2: width, y1: mouseY, y2: mouseY, stroke: "black" }),
         React.createElement("line", { x1: mouseX, x2: mouseX, y1: 0, y2: height, stroke: "black" })));
 };
 export default Crosshairs;

package/dist/LinearMafDisplay/components/Crosshairs.js.map

@@ -1 +1 @@
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+{"version":3,"file":"Crosshairs.js","sourceRoot":"","sources":["../../../src/LinearMafDisplay/components/Crosshairs.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,MAAM,EAAE;QACN,aAAa,EAAE,MAAM;KACtB;CACF,CAAC,CAAA;AAUF,MAAM,UAAU,GAAG,CAAC,EAClB,KAAK,EACL,MAAM,EACN,SAAS,EACT,MAAM,EACN,MAAM,GACU,EAAE,EAAE;IACpB,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAE/B,OAAO,CACL,6BACE,SAAS,EAAE,OAAO,CAAC,MAAM,EACzB,KAAK,EAAE,KAAK,EACZ,MAAM,EAAE,MAAM,EACd,KAAK,EAAE;YACL,QAAQ,EAAE,UAAU;YACpB,GAAG,EAAE,SAAS;SACf;QAED,8BAAM,EAAE,EAAE,CAAC,EAAE,EAAE,EAAE,KAAK,EAAE,EAAE,EAAE,MAAM,EAAE,EAAE,EAAE,MAAM,EAAE,MAAM,EAAC,OAAO,GAAG;QACjE,8BAAM,EAAE,EAAE,MAAM,EAAE,EAAE,EAAE,MAAM,EAAE,EAAE,EAAE,CAAC,EAAE,EAAE,EAAE,MAAM,EAAE,MAAM,EAAC,OAAO,GAAG,CAC9D,CACP,CAAA;AACH,CAAC,CAAA;AAED,eAAe,UAAU,CAAA"}

package/dist/LinearMafDisplay/components/MAFTooltip.d.ts

@@ -1,12 +1,11 @@
 import React from 'react';
 import type { LinearMafDisplayModel } from '../stateModel';
-interface MAFTooltipProps {
+declare const MAFTooltip: ({ model, mouseX, origMouseX, }: {
     mouseY: number;
     mouseX: number;
     rowHeight: number;
     sources: Record<string, any>[];
     model: LinearMafDisplayModel;
     origMouseX?: number;
-}
-declare const MAFTooltip: ({ model, mouseY, mouseX, origMouseX, rowHeight, sources, }: MAFTooltipProps) => React.JSX.Element | null;
+}) => React.JSX.Element | null;
 export default MAFTooltip;

package/dist/LinearMafDisplay/components/MAFTooltip.js

@@ -1,29 +1,16 @@
 import React from 'react';
 import { SanitizedHTML } from '@jbrowse/core/ui';
 import BaseTooltip from '@jbrowse/core/ui/BaseTooltip';
-import { getBpDisplayStr, getContainingView, toLocale, } from '@jbrowse/core/util';
+import { getContainingView } from '@jbrowse/core/util';
 import { observer } from 'mobx-react';
-const MAFTooltip = observer(function ({ model, mouseY, mouseX, origMouseX, rowHeight, sources, }) {
+import { generateTooltipContent } from '../util';
+const MAFTooltip = observer(function ({ model, mouseX, origMouseX, }) {
+    const { hoveredInfo } = model;
     const view = getContainingView(model);
-    const ret = Object.entries(sources[Math.floor(mouseY / rowHeight)] || {})
-        .filter(([key]) => key !== 'color' && key !== 'id')
-        .map(([key, value]) => `${key}:${value}`)
-        .join('\n');
     const p1 = origMouseX ? view.pxToBp(origMouseX) : undefined;
     const p2 = view.pxToBp(mouseX);
-    return ret ? (React.createElement(BaseTooltip, null,
-        React.createElement(SanitizedHTML, { html: [
-                ret,
-                ...(p1
-                    ? [
-                        `Start: ${p1.refName}:${toLocale(p1.coord)}`,
-                        `End: ${p2.refName}:${toLocale(p2.coord)}`,
-                        `Length: ${getBpDisplayStr(Math.abs(p1.coord - p2.coord))}`,
-                    ]
-                    : [`${p2.refName}:${toLocale(p2.coord)}`]),
-            ]
-                .filter(f => !!f)
-                .join('<br/>') }))) : null;
+    return hoveredInfo ? (React.createElement(BaseTooltip, null,
+        React.createElement(SanitizedHTML, { html: generateTooltipContent(hoveredInfo, p1, p2) }))) : null;
 });
 export default MAFTooltip;
 //# sourceMappingURL=MAFTooltip.js.map

package/dist/LinearMafDisplay/components/MAFTooltip.js.map

@@ -1 +1 @@
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+{"version":3,"file":"MAFTooltip.js","sourceRoot":"","sources":["../../../src/LinearMafDisplay/components/MAFTooltip.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,aAAa,EAAE,MAAM,kBAAkB,CAAA;AAChD,OAAO,WAAW,MAAM,8BAA8B,CAAA;AACtD,OAAO,EAAE,iBAAiB,EAAE,MAAM,oBAAoB,CAAA;AACtD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,sBAAsB,EAAE,MAAM,SAAS,CAAA;AAMhD,MAAM,UAAU,GAAG,QAAQ,CAAC,UAAU,EACpC,KAAK,EACL,MAAM,EACN,UAAU,GAQX;IACC,MAAM,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IAC7B,MAAM,IAAI,GAAG,iBAAiB,CAAC,KAAK,CAA0B,CAAA;IAC9D,MAAM,EAAE,GAAG,UAAU,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;IAC3D,MAAM,EAAE,GAAG,IAAI,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;IAE9B,OAAO,WAAW,CAAC,CAAC,CAAC,CACnB,oBAAC,WAAW;QACV,oBAAC,aAAa,IACZ,IAAI,EAAE,sBAAsB,CAAC,WAA0B,EAAE,EAAE,EAAE,EAAE,CAAC,GAChE,CACU,CACf,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC,CAAC,CAAA;AAEF,eAAe,UAAU,CAAA"}

package/dist/LinearMafDisplay/stateModel.d.ts

@@ -222,6 +222,10 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/dist/BaseLinearDisplay").ExportSvgDisplayOptions): Promise<import("react/jsx-runtime").JSX.Element>;
     afterAttach(): void;
 } & {
+    /**
+     * #volatile
+     */
+    hoveredInfo: Record<string, unknown> | undefined;
     /**
      * #volatile
      */
@@ -235,6 +239,10 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
      */
     volatileTree: any;
 } & {
+    /**
+     * #action
+     */
+    setHoveredInfo(arg?: Record<string, unknown>): void;
     /**
      * #action
      */

package/dist/LinearMafDisplay/stateModel.js

@@ -57,6 +57,10 @@ export default function stateModelFactory(configSchema, pluginManager) {
         showAsUpperCase: true,
     }))
         .volatile(() => ({
+        /**
+         * #volatile
+         */
+        hoveredInfo: undefined,
         /**
          * #volatile
          */
@@ -71,6 +75,12 @@ export default function stateModelFactory(configSchema, pluginManager) {
         volatileTree: undefined,
     }))
         .actions(self => ({
+        /**
+         * #action
+         */
+        setHoveredInfo(arg) {
+            self.hoveredInfo = arg;
+        },
         /**
          * #action
          */

package/dist/LinearMafDisplay/stateModel.js.map

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package/dist/LinearMafDisplay/util.d.ts

@@ -1,4 +1,24 @@
 import type { NodeWithIds } from './types';
 import type { HierarchyNode } from 'd3-hierarchy';
+export interface HoveredInfo {
+    sampleId: string;
+    pos: number;
+    base: string;
+    chr: string;
+    [key: string]: unknown;
+}
+export interface GenomicPosition {
+    refName: string;
+    coord: number;
+}
+/**
+ * Generates tooltip HTML content for MAF alignments
+ * Truncates long sequences to 50 characters, with ellipses added if display exceeds 20 characters
+ * @param hoveredInfo - Information about the hovered base/position
+ * @param p1 - Start position (for range selections)
+ * @param p2 - End position (current mouse position)
+ * @returns HTML string for tooltip content
+ */
+export declare function generateTooltipContent(hoveredInfo: HoveredInfo | undefined, p1: GenomicPosition | undefined, p2: GenomicPosition): string;
 export declare function maxLength(d: HierarchyNode<NodeWithIds>): number;
 export declare function setBrLength(d: HierarchyNode<NodeWithIds>, y0: number, k: number): void;

package/dist/LinearMafDisplay/util.js

@@ -1,4 +1,33 @@
+import { getBpDisplayStr, toLocale } from '@jbrowse/core/util';
 import { max } from 'd3-array';
+/**
+ * Generates tooltip HTML content for MAF alignments
+ * Truncates long sequences to 50 characters, with ellipses added if display exceeds 20 characters
+ * @param hoveredInfo - Information about the hovered base/position
+ * @param p1 - Start position (for range selections)
+ * @param p2 - End position (current mouse position)
+ * @returns HTML string for tooltip content
+ */
+export function generateTooltipContent(hoveredInfo, p1, p2) {
+    const contentLines = [];
+    if (p1) {
+        // Range selection mode
+        contentLines.push(`Start: ${p1.refName}:${toLocale(p1.coord)}`, `End: ${p2.refName}:${toLocale(p2.coord)}`, `Length: ${getBpDisplayStr(Math.abs(p1.coord - p2.coord))}`);
+    }
+    else {
+        // Single position mode
+        contentLines.push(`Ref: ${p2.refName}:${toLocale(p2.coord)}`);
+        if (hoveredInfo) {
+            const { base, sampleId, pos, chr } = hoveredInfo;
+            const thresh = 20;
+            const len = base.length;
+            const lengthSuffix = len > 1 ? ` ${len}bp` : '';
+            const baseDisplay = base.length > thresh ? base.slice(0, thresh) + '...' : base;
+            contentLines.push(`Alt ${sampleId}: ${chr}:${pos.toLocaleString('en-US')} (${baseDisplay}${lengthSuffix})`);
+        }
+    }
+    return contentLines.filter(line => !!line).join('<br/>');
+}
 // basically same as maxLength from https://observablehq.com/@d3/tree-of-life
 export function maxLength(d) {
     return ((d.data.length || 0) + (d.children ? max(d.children, maxLength) || 0 : 0));

package/dist/LinearMafDisplay/util.js.map

@@ -1 +1 @@
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+{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/LinearMafDisplay/util.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,eAAe,EAAE,QAAQ,EAAE,MAAM,oBAAoB,CAAA;AAC9D,OAAO,EAAE,GAAG,EAAE,MAAM,UAAU,CAAA;AAkB9B;;;;;;;GAOG;AACH,MAAM,UAAU,sBAAsB,CACpC,WAAoC,EACpC,EAA+B,EAC/B,EAAmB;IAEnB,MAAM,YAAY,GAAa,EAAE,CAAA;IAEjC,IAAI,EAAE,EAAE,CAAC;QACP,uBAAuB;QACvB,YAAY,CAAC,IAAI,CACf,UAAU,EAAE,CAAC,OAAO,IAAI,QAAQ,CAAC,EAAE,CAAC,KAAK,CAAC,EAAE,EAC5C,QAAQ,EAAE,CAAC,OAAO,IAAI,QAAQ,CAAC,EAAE,CAAC,KAAK,CAAC,EAAE,EAC1C,WAAW,eAAe,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,KAAK,GAAG,EAAE,CAAC,KAAK,CAAC,CAAC,EAAE,CAC5D,CAAA;IACH,CAAC;SAAM,CAAC;QACN,uBAAuB;QACvB,YAAY,CAAC,IAAI,CAAC,QAAQ,EAAE,CAAC,OAAO,IAAI,QAAQ,CAAC,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAA;QAE7D,IAAI,WAAW,EAAE,CAAC;YAChB,MAAM,EAAE,IAAI,EAAE,QAAQ,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,WAAW,CAAA;YAChD,MAAM,MAAM,GAAG,EAAE,CAAA;YACjB,MAAM,GAAG,GAAG,IAAI,CAAC,MAAM,CAAA;YACvB,MAAM,YAAY,GAAG,GAAG,GAAG,CAAC,CAAC,CAAC,CAAC,IAAI,GAAG,IAAI,CAAC,CAAC,CAAC,EAAE,CAAA;YAC/C,MAAM,WAAW,GACf,IAAI,CAAC,MAAM,GAAG,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,MAAM,CAAC,GAAG,KAAK,CAAC,CAAC,CAAC,IAAI,CAAA;YAE7D,YAAY,CAAC,IAAI,CACf,OAAO,QAAQ,KAAK,GAAG,IAAI,GAAG,CAAC,cAAc,CAAC,OAAO,CAAC,KAAK,WAAW,GAAG,YAAY,GAAG,CACzF,CAAA;QACH,CAAC;IACH,CAAC;IAED,OAAO,YAAY,CAAC,MAAM,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;AAC1D,CAAC;AAED,6EAA6E;AAC7E,MAAM,UAAU,SAAS,CAAC,CAA6B;IACrD,OAAO,CACL,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAC1E,CAAA;AACH,CAAC;AAED,6EAA6E;AAC7E,MAAM,UAAU,WAAW,CACzB,CAA6B,EAC7B,EAAU,EACV,CAAS;IAET,mBAAmB;IACnB,CAAC,CAAC,GAAG,GAAG,CAAC,EAAE,IAAI,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,IAAI,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;IAEnD,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;QACf,CAAC,CAAC,QAAQ,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;YACrB,WAAW,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,CAAA;QACvB,CAAC,CAAC,CAAA;IACJ,CAAC;AACH,CAAC"}

package/dist/LinearMafRenderer/LinearMafRenderer.d.ts

@@ -27,6 +27,9 @@ export default class LinearMafRenderer extends FeatureRendererType {
         width: number;
         height: number;
         containsNoTransferables: boolean;
+        samples: import("./rendering").Sample[];
+        flatbush: ArrayBufferLike;
+        items: import("./rendering").RenderedBase[];
         canvasRecordedData: Record<string, unknown>;
         reactElement?: React.ReactElement;
         html?: string;
@@ -35,6 +38,9 @@ export default class LinearMafRenderer extends FeatureRendererType {
         width: number;
         height: number;
         containsNoTransferables: boolean;
+        samples: import("./rendering").Sample[];
+        flatbush: ArrayBufferLike;
+        items: import("./rendering").RenderedBase[];
         imageData: any;
         reactElement?: React.ReactElement;
         html?: string;
@@ -43,6 +49,9 @@ export default class LinearMafRenderer extends FeatureRendererType {
         width: number;
         height: number;
         containsNoTransferables: boolean;
+        samples: import("./rendering").Sample[];
+        flatbush: ArrayBufferLike;
+        items: import("./rendering").RenderedBase[];
         reactElement: React.ReactElement;
         html?: string;
     }>;

package/dist/LinearMafRenderer/LinearMafRenderer.js

@@ -19,14 +19,13 @@ export default class LinearMafRenderer extends FeatureRendererType {
         const width = (region.end - region.start) / bpPerPx;
         const features = await this.getFeatures(renderProps);
         const res = await updateStatus('Rendering alignment', statusCallback, () => renderToAbstractCanvas(width, height, renderProps, ctx => {
-            makeImageData({
+            return makeImageData({
                 ctx,
                 renderArgs: {
                     ...renderProps,
                     features,
                 },
             });
-            return undefined;
         }));
         const results = await super.render({
             ...renderProps,

package/dist/LinearMafRenderer/LinearMafRenderer.js.map

@@ -1 +1 @@
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package/dist/LinearMafRenderer/components/LinearMafRendering.d.ts

@@ -0,0 +1,13 @@
+import React from 'react';
+import { RenderedBase } from '../rendering';
+import { Sample } from '../../LinearMafDisplay/types';
+type SerializedRBush = any;
+declare const LinearMafRendering: (props: {
+    width: number;
+    height: number;
+    displayModel: any;
+    flatbush: SerializedRBush;
+    items: RenderedBase[];
+    samples: Sample[];
+}) => React.JSX.Element;
+export default LinearMafRendering;

package/dist/LinearMafRenderer/components/LinearMafRendering.js

@@ -0,0 +1,46 @@
+import React, { useMemo, useRef } from 'react';
+import { PrerenderedCanvas } from '@jbrowse/core/ui';
+import Flatbush from 'flatbush';
+import { observer } from 'mobx-react';
+const LinearMafRendering = observer(function (props) {
+    const { items, displayModel, height, samples, flatbush } = props;
+    const ref = useRef(null);
+    const rbush2 = useMemo(() => Flatbush.from(flatbush), [flatbush]);
+    function getFeatureUnderMouse(eventClientX, eventClientY) {
+        let offsetX = 0;
+        let offsetY = 0;
+        if (ref.current) {
+            const r = ref.current.getBoundingClientRect();
+            offsetX = eventClientX - r.left;
+            offsetY = eventClientY - r.top;
+        }
+        const x = rbush2.search(offsetX, offsetY, offsetX + 1, offsetY + 1);
+        if (x.length) {
+            const elt = x.findIndex(idx => items[idx]?.isInsertion);
+            const r = elt !== -1 ? items[elt] : items[x[0]];
+            const s = samples[r.sampleId];
+            return {
+                ...r,
+                sampleId: s?.label || s?.id || 'unknown',
+            };
+        }
+        else {
+            return undefined;
+        }
+    }
+    return (React.createElement("div", { ref: ref, onMouseMove: e => displayModel.setHoveredInfo?.(getFeatureUnderMouse(e.clientX, e.clientY)), onMouseLeave: () => {
+            displayModel.setHoveredInfo?.(undefined);
+        }, onMouseOut: () => {
+            displayModel.setHoveredInfo?.(undefined);
+        }, style: {
+            overflow: 'visible',
+            position: 'relative',
+            height,
+        } },
+        React.createElement(PrerenderedCanvas, { ...props, style: {
+                position: 'absolute',
+                left: 0,
+            } })));
+});
+export default LinearMafRendering;
+//# sourceMappingURL=LinearMafRendering.js.map

package/dist/LinearMafRenderer/components/LinearMafRendering.js.map

@@ -0,0 +1 @@
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package/dist/LinearMafRenderer/components/ReactComponent.d.ts

@@ -1,6 +1,9 @@
 import React from 'react';
+type SerializedRBush = any;
 declare const LinearMafRendering: (props: {
     width: number;
     height: number;
+    displayModel: any;
+    rbush: SerializedRBush;
 }) => React.JSX.Element;
 export default LinearMafRendering;

package/dist/LinearMafRenderer/components/ReactComponent.js

@@ -1,8 +1,47 @@
-import React from 'react';
+import React, { useMemo, useRef } from 'react';
 import { PrerenderedCanvas } from '@jbrowse/core/ui';
 import { observer } from 'mobx-react';
+import RBush from 'rbush';
 const LinearMafRendering = observer(function (props) {
-    return React.createElement(PrerenderedCanvas, { ...props });
+    const { displayModel, height, rbush } = props;
+    const ref = useRef(null);
+    const rbush2 = useMemo(() => new RBush().fromJSON(rbush), [rbush]);
+    function getFeatureUnderMouse(eventClientX, eventClientY) {
+        let offsetX = 0;
+        let offsetY = 0;
+        if (ref.current) {
+            const r = ref.current.getBoundingClientRect();
+            offsetX = eventClientX - r.left;
+            offsetY = eventClientY - r.top;
+        }
+        const x = rbush2.search({
+            minX: offsetX,
+            maxX: offsetX + 1,
+            minY: offsetY,
+            maxY: offsetY + 1,
+        });
+        if (x.length) {
+            // prioritize insertions
+            const { minX, minY, maxX, maxY, ...rest } = x.find(f => f.isInsertion) || x[0];
+            return rest;
+        }
+        else {
+            return undefined;
+        }
+    }
+    return (React.createElement("div", { ref: ref, onMouseMove: e => displayModel.setHoveredInfo?.(getFeatureUnderMouse(e.clientX, e.clientY)), onMouseLeave: () => {
+            displayModel.setHoveredInfo?.(undefined);
+        }, onMouseOut: () => {
+            displayModel.setHoveredInfo?.(undefined);
+        }, style: {
+            overflow: 'visible',
+            position: 'relative',
+            height,
+        } },
+        React.createElement(PrerenderedCanvas, { ...props, style: {
+                position: 'absolute',
+                left: 0,
+            } })));
 });
 export default LinearMafRendering;
 //# sourceMappingURL=ReactComponent.js.map

package/dist/LinearMafRenderer/components/ReactComponent.js.map

@@ -1 +1 @@
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+{"version":3,"file":"ReactComponent.js","sourceRoot":"","sources":["../../../src/LinearMafRenderer/components/ReactComponent.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE,MAAM,OAAO,CAAA;AAE9C,OAAO,EAAE,iBAAiB,EAAE,MAAM,kBAAkB,CAAA;AACpD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,KAAK,MAAM,OAAO,CAAA;AAWzB,MAAM,kBAAkB,GAAG,QAAQ,CAAC,UAAU,KAK7C;IACC,MAAM,EAAE,YAAY,EAAE,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;IAC7C,MAAM,GAAG,GAAG,MAAM,CAAiB,IAAI,CAAC,CAAA;IACxC,MAAM,MAAM,GAAG,OAAO,CAAC,GAAG,EAAE,CAAC,IAAI,KAAK,EAAa,CAAC,QAAQ,CAAC,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAAA;IAE7E,SAAS,oBAAoB,CAAC,YAAoB,EAAE,YAAoB;QACtE,IAAI,OAAO,GAAG,CAAC,CAAA;QACf,IAAI,OAAO,GAAG,CAAC,CAAA;QACf,IAAI,GAAG,CAAC,OAAO,EAAE,CAAC;YAChB,MAAM,CAAC,GAAG,GAAG,CAAC,OAAO,CAAC,qBAAqB,EAAE,CAAA;YAC7C,OAAO,GAAG,YAAY,GAAG,CAAC,CAAC,IAAI,CAAA;YAC/B,OAAO,GAAG,YAAY,GAAG,CAAC,CAAC,GAAG,CAAA;QAChC,CAAC;QAED,MAAM,CAAC,GAAG,MAAM,CAAC,MAAM,CAAC;YACtB,IAAI,EAAE,OAAO;YACb,IAAI,EAAE,OAAO,GAAG,CAAC;YACjB,IAAI,EAAE,OAAO;YACb,IAAI,EAAE,OAAO,GAAG,CAAC;SAClB,CAAC,CAAA;QACF,IAAI,CAAC,CAAC,MAAM,EAAE,CAAC;YACb,wBAAwB;YACxB,MAAM,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,GAAG,IAAI,EAAE,GACvC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,WAAW,CAAC,IAAI,CAAC,CAAC,CAAC,CAAE,CAAA;YACrC,OAAO,IAAI,CAAA;QACb,CAAC;aAAM,CAAC;YACN,OAAO,SAAS,CAAA;QAClB,CAAC;IACH,CAAC;IACD,OAAO,CACL,6BACE,GAAG,EAAE,GAAG,EACR,WAAW,EAAE,CAAC,CAAC,EAAE,CACf,YAAY,CAAC,cAAc,EAAE,CAC3B,oBAAoB,CAAC,CAAC,CAAC,OAAO,EAAE,CAAC,CAAC,OAAO,CAAC,CAC3C,EAEH,YAAY,EAAE,GAAG,EAAE;YACjB,YAAY,CAAC,cAAc,EAAE,CAAC,SAAS,CAAC,CAAA;QAC1C,CAAC,EACD,UAAU,EAAE,GAAG,EAAE;YACf,YAAY,CAAC,cAAc,EAAE,CAAC,SAAS,CAAC,CAAA;QAC1C,CAAC,EACD,KAAK,EAAE;YACL,QAAQ,EAAE,SAAS;YACnB,QAAQ,EAAE,UAAU;YACpB,MAAM;SACP;QAED,oBAAC,iBAAiB,OACZ,KAAK,EACT,KAAK,EAAE;gBACL,QAAQ,EAAE,UAAU;gBACpB,IAAI,EAAE,CAAC;aACR,GACD,CACE,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,kBAAkB,CAAA"}

package/dist/LinearMafRenderer/components/util.d.ts

@@ -0,0 +1 @@
+export declare function minElt<T>(arr: Iterable<T>, cb: (arg: T) => number): T | undefined;