react-msaview 3.1.10 → 3.1.12

package/dist/components/msa/renderMSABlock.js

@@ -1,6 +1,6 @@
 import { getClustalXColor, getPercentIdentityColor } from '../../colorSchemes';
 export function renderMSABlock({ model, offsetX, offsetY, contrastScheme, ctx, theme, highResScaleFactorOverride, blockSizeXOverride, blockSizeYOverride, }) {
-    const { hierarchy, colWidth, blockSize, rowHeight, fontSize, highResScaleFactor, featureMode, } = model;
+    const { hierarchy, colWidth, blockSize, rowHeight, fontSize, highResScaleFactor, showDomains, } = model;
     const k = highResScaleFactorOverride || highResScaleFactor;
     const bx = blockSizeXOverride || blockSize;
     const by = blockSizeYOverride || blockSize;
@@ -15,7 +15,7 @@ export function renderMSABlock({ model, offsetX, offsetY, contrastScheme, ctx, t
     const xStart = Math.max(0, Math.floor(offsetX / colWidth));
     const xEnd = Math.max(0, Math.ceil((offsetX + bx) / colWidth));
     const visibleLeaves = leaves.slice(yStart, yEnd);
-    if (!featureMode) {
+    if (!showDomains) {
         drawTiles({
             model,
             ctx,
@@ -61,7 +61,7 @@ function drawTiles({ model, offsetX, ctx, visibleLeaves, theme, xStart, xEnd, })
     }
 }
 function drawText({ model, offsetX, contrastScheme, ctx, visibleLeaves, xStart, xEnd, }) {
-    const { bgColor, featureMode, colorScheme, columns, colWidth, rowHeight } = model;
+    const { bgColor, showDomains, colorScheme, columns, colWidth, rowHeight } = model;
     if (rowHeight >= 5 && colWidth > rowHeight / 2) {
         for (const node of visibleLeaves) {
             const { data: { name }, } = node;
@@ -73,7 +73,7 @@ function drawText({ model, offsetX, contrastScheme, ctx, visibleLeaves, xStart,
                 const contrast = contrastScheme[letter.toUpperCase()] || 'black';
                 const x = i * colWidth + offsetX - (offsetX % colWidth);
                 // note: -rowHeight/4 matches +rowHeight/4 in tree
-                ctx.fillStyle = featureMode
+                ctx.fillStyle = showDomains
                     ? 'black'
                     : bgColor
                         ? contrast

package/dist/components/tree/TreeCanvas.js

@@ -1,5 +1,4 @@
 import React, { useEffect, useRef, useState } from 'react';
-import normalizeWheel from 'normalize-wheel';
 import { observer } from 'mobx-react';
 import TreeCanvasBlock from './TreeCanvasBlock';
 import { padding } from './renderTreeCanvas';
@@ -15,9 +14,8 @@ const TreeCanvas = observer(function ({ model }) {
         if (!curr) {
             return;
         }
-        function onWheel(origEvent) {
-            const event = normalizeWheel(origEvent);
-            deltaY.current += event.pixelY;
+        function onWheel(event) {
+            deltaY.current += event.deltaY;
             if (!scheduled.current) {
                 scheduled.current = true;
                 requestAnimationFrame(() => {
@@ -26,8 +24,8 @@ const TreeCanvas = observer(function ({ model }) {
                     scheduled.current = false;
                 });
             }
-            origEvent.preventDefault();
-            origEvent.stopPropagation();
+            event.preventDefault();
+            event.stopPropagation();
         }
         curr.addEventListener('wheel', onWheel);
         return () => {

package/dist/components/tree/TreeCanvas.js.map

@@ -1 +1 @@
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+{"version":3,"file":"TreeCanvas.js","sourceRoot":"","sources":["../../../src/components/tree/TreeCanvas.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,SAAS,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAC1D,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,OAAO,eAAe,MAAM,mBAAmB,CAAA;AAC/C,OAAO,EAAE,OAAO,EAAE,MAAM,oBAAoB,CAAA;AAE5C,MAAM,UAAU,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACtE,MAAM,GAAG,GAAG,MAAM,CAAiB,IAAI,CAAC,CAAA;IACxC,MAAM,SAAS,GAAG,MAAM,CAAC,KAAK,CAAC,CAAA;IAC/B,MAAM,MAAM,GAAG,MAAM,CAAC,CAAC,CAAC,CAAA;IACxB,MAAM,KAAK,GAAG,MAAM,CAAS,CAAC,CAAC,CAAA;IAC/B,MAAM,EAAE,SAAS,EAAE,MAAM,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;IAC5C,MAAM,CAAC,aAAa,EAAE,gBAAgB,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IAEzD,SAAS,CAAC,GAAG,EAAE;QACb,MAAM,IAAI,GAAG,GAAG,CAAC,OAAO,CAAA;QACxB,IAAI,CAAC,IAAI,EAAE,CAAC;YACV,OAAM;QACR,CAAC;QACD,SAAS,OAAO,CAAC,KAAiB;YAChC,MAAM,CAAC,OAAO,IAAI,KAAK,CAAC,MAAM,CAAA;YAE9B,IAAI,CAAC,SAAS,CAAC,OAAO,EAAE,CAAC;gBACvB,SAAS,CAAC,OAAO,GAAG,IAAI,CAAA;gBACxB,qBAAqB,CAAC,GAAG,EAAE;oBACzB,KAAK,CAAC,SAAS,CAAC,CAAC,MAAM,CAAC,OAAO,CAAC,CAAA;oBAChC,MAAM,CAAC,OAAO,GAAG,CAAC,CAAA;oBAClB,SAAS,CAAC,OAAO,GAAG,KAAK,CAAA;gBAC3B,CAAC,CAAC,CAAA;YACJ,CAAC;YACD,KAAK,CAAC,cAAc,EAAE,CAAA;YACtB,KAAK,CAAC,eAAe,EAAE,CAAA;QACzB,CAAC;QACD,IAAI,CAAC,gBAAgB,CAAC,OAAO,EAAE,OAAO,CAAC,CAAA;QACvC,OAAO,GAAG,EAAE;YACV,IAAI,CAAC,mBAAmB,CAAC,OAAO,EAAE,OAAO,CAAC,CAAA;QAC5C,CAAC,CAAA;IACH,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAAA;IAEX,SAAS,CAAC,GAAG,EAAE;QACb,IAAI,OAAO,GAAG,GAAG,EAAE,GAAE,CAAC,CAAA;QAEtB,SAAS,eAAe,CAAC,KAAiB;YACxC,KAAK,CAAC,cAAc,EAAE,CAAA;YACtB,MAAM,KAAK,GAAG,KAAK,CAAC,OAAO,CAAA;YAC3B,MAAM,SAAS,GAAG,KAAK,GAAG,KAAK,CAAC,OAAO,CAAA;YACvC,IAAI,SAAS,EAAE,CAAC;gBACd,uEAAuE;gBACvE,8EAA8E;gBAC9E,IAAI,CAAC,SAAS,CAAC,OAAO,EAAE,CAAC;oBACvB,SAAS,CAAC,OAAO,GAAG,IAAI,CAAA;oBACxB,MAAM,CAAC,qBAAqB,CAAC,GAAG,EAAE;wBAChC,KAAK,CAAC,SAAS,CAAC,SAAS,CAAC,CAAA;wBAC1B,SAAS,CAAC,OAAO,GAAG,KAAK,CAAA;wBACzB,KAAK,CAAC,OAAO,GAAG,KAAK,CAAC,OAAO,CAAA;oBAC/B,CAAC,CAAC,CAAA;gBACJ,CAAC;YACH,CAAC;QACH,CAAC;QAED,SAAS,aAAa;YACpB,KAAK,CAAC,OAAO,GAAG,CAAC,CAAA;YACjB,IAAI,aAAa,EAAE,CAAC;gBAClB,gBAAgB,CAAC,KAAK,CAAC,CAAA;YACzB,CAAC;QACH,CAAC;QAED,IAAI,aAAa,EAAE,CAAC;YAClB,MAAM,CAAC,gBAAgB,CAAC,WAAW,EAAE,eAAe,EAAE,IAAI,CAAC,CAAA;YAC3D,MAAM,CAAC,gBAAgB,CAAC,SAAS,EAAE,aAAa,EAAE,IAAI,CAAC,CAAA;YACvD,OAAO,GAAG,GAAG,EAAE;gBACb,MAAM,CAAC,mBAAmB,CAAC,WAAW,EAAE,eAAe,EAAE,IAAI,CAAC,CAAA;gBAC9D,MAAM,CAAC,mBAAmB,CAAC,SAAS,EAAE,aAAa,EAAE,IAAI,CAAC,CAAA;YAC5D,CAAC,CAAA;QACH,CAAC;QACD,OAAO,OAAO,CAAA;IAChB,CAAC,EAAE,CAAC,KAAK,EAAE,aAAa,CAAC,CAAC,CAAA;IAE1B,SAAS,SAAS,CAAC,KAAuB;QACxC,2DAA2D;QAC3D,MAAM,MAAM,GAAG,KAAK,CAAC,MAAqB,CAAA;QAC1C,IAAI,MAAM,CAAC,SAAS,IAAI,MAAM,CAAC,OAAO,CAAC,OAAO,EAAE,CAAC;YAC/C,OAAM;QACR,CAAC;QAED,qCAAqC;QACrC,IAAI,KAAK,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACvB,KAAK,CAAC,OAAO,GAAG,KAAK,CAAC,OAAO,CAAA;YAC7B,gBAAgB,CAAC,IAAI,CAAC,CAAA;QACxB,CAAC;IACH,CAAC;IAED,yEAAyE;IACzE,wEAAwE;IACxE,SAAS,OAAO,CAAC,KAAuB;QACtC,KAAK,CAAC,cAAc,EAAE,CAAA;QACtB,gBAAgB,CAAC,KAAK,CAAC,CAAA;IACzB,CAAC;IAED,SAAS,UAAU,CAAC,KAAuB;QACzC,KAAK,CAAC,cAAc,EAAE,CAAA;IACxB,CAAC;IAED,OAAO,CACL,6BACE,GAAG,EAAE,GAAG,EACR,WAAW,EAAE,SAAS,EACtB,SAAS,EAAE,OAAO,EAClB,YAAY,EAAE,UAAU,EACxB,KAAK,EAAE;YACL,MAAM;YACN,QAAQ,EAAE,UAAU;YACpB,KAAK,EAAE,SAAS,GAAG,OAAO;SAC3B,IAEA,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,CACpB,oBAAC,eAAe,IAAC,GAAG,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,OAAO,EAAE,KAAK,GAAI,CAC9D,CAAC,CACE,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,UAAU,CAAA"}

package/dist/fetchUtils.d.ts

@@ -1,5 +1,5 @@
 export declare function myfetch(url: string, args?: RequestInit): Promise<Response>;
 export declare function textfetch(url: string, args?: RequestInit): Promise<string>;
-export declare function jsonfetch(url: string, args?: RequestInit): Promise<any>;
+export declare function jsonfetch<T>(url: string, args?: RequestInit): Promise<T>;
 export declare function arraybufferfetch(url: string): Promise<ArrayBuffer>;
 export declare function timeout(time: number): Promise<unknown>;

package/dist/fetchUtils.js.map

@@ -1 +1 @@
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+{"version":3,"file":"fetchUtils.js","sourceRoot":"","sources":["../src/fetchUtils.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,KAAK,UAAU,OAAO,CAAC,GAAW,EAAE,IAAkB;IAC3D,MAAM,QAAQ,GAAG,MAAM,KAAK,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;IAEvC,IAAI,CAAC,QAAQ,CAAC,EAAE,EAAE,CAAC;QACjB,MAAM,IAAI,KAAK,CACb,QAAQ,QAAQ,CAAC,MAAM,aAAa,GAAG,IAAI,MAAM,QAAQ,CAAC,IAAI,EAAE,EAAE,CACnE,CAAA;IACH,CAAC;IAED,OAAO,QAAQ,CAAA;AACjB,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,SAAS,CAAC,GAAW,EAAE,IAAkB;IAC7D,MAAM,QAAQ,GAAG,MAAM,OAAO,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;IACzC,OAAO,QAAQ,CAAC,IAAI,EAAE,CAAA;AACxB,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,SAAS,CAAI,GAAW,EAAE,IAAkB;IAChE,MAAM,QAAQ,GAAG,MAAM,OAAO,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;IACzC,OAAO,QAAQ,CAAC,IAAI,EAAO,CAAA;AAC7B,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,gBAAgB,CAAC,GAAW;IAChD,MAAM,GAAG,GAAG,MAAM,OAAO,CAAC,GAAG,CAAC,CAAA;IAC9B,OAAO,GAAG,CAAC,WAAW,EAAE,CAAA;AAC1B,CAAC;AAED,MAAM,UAAU,OAAO,CAAC,IAAY;IAClC,OAAO,IAAI,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC,UAAU,CAAC,GAAG,EAAE,IAAI,CAAC,CAAC,CAAA;AAClD,CAAC"}

package/dist/launchInterProScan.d.ts

@@ -1,3 +1,4 @@
+import { MsaViewModel } from './model';
 export interface InterProScanResults {
     matches: {
         signature: {
@@ -20,7 +21,7 @@ export interface InterProScanResponse {
     results: InterProScanResults[];
 }
 export declare function loadInterProScanResults(jobId: string): Promise<InterProScanResponse>;
-export declare function launchInterProScan({ algorithm, seq, programs, onJobId, onProgress, }: {
+export declare function launchInterProScan({ algorithm, seq, programs, onJobId, onProgress, model, }: {
     algorithm: string;
     seq: string;
     programs: string[];
@@ -28,5 +29,10 @@ export declare function launchInterProScan({ algorithm, seq, programs, onJobId,
         msg: string;
         url?: string;
     }) => void;
-    onJobId: (arg: string) => void;
-}): Promise<InterProScanResponse>;
+    onJobId?: (arg: string) => void;
+    model: MsaViewModel;
+}): Promise<void>;
+export declare function loadInterProScanResultsWithStatus({ jobId, model, }: {
+    jobId: string;
+    model: MsaViewModel;
+}): Promise<void>;

package/dist/launchInterProScan.js

@@ -1,6 +1,7 @@
+import { getSession } from '@jbrowse/core/util';
 import { jsonfetch, textfetch, timeout } from './fetchUtils';
 const base = `https://www.ebi.ac.uk/Tools/services/rest`;
-async function runInterProScan({ seq, onProgress, onJobId, programs, }) {
+async function runInterProScan({ seq, onProgress, onJobId, programs, model, }) {
     const jobId = await textfetch(`${base}/iprscan5/run`, {
         method: 'POST',
         body: new URLSearchParams({
@@ -9,39 +10,75 @@ async function runInterProScan({ seq, onProgress, onJobId, programs, }) {
             programs: programs.join(','),
         }),
     });
-    onJobId(jobId);
+    onJobId?.(jobId);
     await wait({
         jobId,
         onProgress,
     });
-    return loadInterProScanResults(jobId);
+    return loadInterProScanResultsWithStatus({ jobId, model });
 }
-export async function loadInterProScanResults(jobId) {
-    return (await jsonfetch(`${base}/iprscan5/result/${jobId}/json`));
+export function loadInterProScanResults(jobId) {
+    return jsonfetch(`${base}/iprscan5/result/${jobId}/json`);
 }
 async function wait({ onProgress, jobId, }) {
     const url = `${base}/iprscan5/status/${jobId}`;
-    // eslint-disable-next-line no-constant-condition
-    while (true) {
-        for (let i = 0; i < 10; i++) {
-            await timeout(1000);
-            onProgress({ msg: `Checking status... ${10 - i}`, url });
-        }
-        const result = await textfetch(url);
-        if (result === 'FINISHED') {
-            break;
+    try {
+        // eslint-disable-next-line no-constant-condition
+        while (true) {
+            for (let i = 0; i < 10; i++) {
+                await timeout(1000);
+                onProgress({ msg: `Checking status ${10 - i}`, url });
+            }
+            const result = await textfetch(url);
+            if (result.includes('FINISHED')) {
+                break;
+            }
         }
     }
+    finally {
+        onProgress();
+    }
 }
-export async function launchInterProScan({ algorithm, seq, programs, onJobId, onProgress, }) {
-    onProgress({ msg: `Launching ${algorithm} MSA...` });
-    if (algorithm === 'interproscan') {
-        const result = await runInterProScan({ seq, onJobId, onProgress, programs });
+export async function launchInterProScan({ algorithm, seq, programs, onJobId, onProgress, model, }) {
+    try {
+        onProgress({ msg: `Launching ${algorithm} MSA` });
+        if (algorithm === 'interproscan') {
+            const result = await runInterProScan({
+                seq,
+                onJobId,
+                onProgress,
+                programs,
+                model,
+            });
+            return result;
+        }
+        else {
+            throw new Error('unknown algorithm');
+        }
+    }
+    finally {
         onProgress();
-        return result;
     }
-    else {
-        throw new Error('unknown algorithm');
+}
+export async function loadInterProScanResultsWithStatus({ jobId, model, }) {
+    try {
+        model.setStatus({
+            msg: 'Downloading results of ' +
+                jobId +
+                ' (for larger sequences this can be slow, click status to download and upload in the manual tab)',
+            url: `https://www.ebi.ac.uk/Tools/services/rest/iprscan5/result/${jobId}/json`,
+        });
+        const ret = await loadInterProScanResults(jobId);
+        model.setLoadedInterProAnnotations(Object.fromEntries(ret.results.map(r => [r.xref[0].id, r])));
+        model.setShowDomains(true);
+        getSession(model).notify(`Loaded interproscan ${jobId} results`, 'success');
+    }
+    catch (e) {
+        console.error(e);
+        getSession(model).notifyError(`${e}`, e);
+    }
+    finally {
+        model.setStatus();
     }
 }
 //# sourceMappingURL=launchInterProScan.js.map

package/dist/launchInterProScan.js.map

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+{"version":3,"file":"launchInterProScan.js","sourceRoot":"","sources":["../src/launchInterProScan.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC/C,OAAO,EAAE,SAAS,EAAE,SAAS,EAAE,OAAO,EAAE,MAAM,cAAc,CAAA;AAG5D,MAAM,IAAI,GAAG,2CAA2C,CAAA;AAmBxD,KAAK,UAAU,eAAe,CAAC,EAC7B,GAAG,EACH,UAAU,EACV,OAAO,EACP,QAAQ,EACR,KAAK,GAON;IACC,MAAM,KAAK,GAAG,MAAM,SAAS,CAAC,GAAG,IAAI,eAAe,EAAE;QACpD,MAAM,EAAE,MAAM;QACd,IAAI,EAAE,IAAI,eAAe,CAAC;YACxB,KAAK,EAAE,uBAAuB;YAC9B,QAAQ,EAAE,GAAG,GAAG,EAAE;YAClB,QAAQ,EAAE,QAAQ,CAAC,IAAI,CAAC,GAAG,CAAC;SAC7B,CAAC;KACH,CAAC,CAAA;IACF,OAAO,EAAE,CAAC,KAAK,CAAC,CAAA;IAChB,MAAM,IAAI,CAAC;QACT,KAAK;QACL,UAAU;KACX,CAAC,CAAA;IACF,OAAO,iCAAiC,CAAC,EAAE,KAAK,EAAE,KAAK,EAAE,CAAC,CAAA;AAC5D,CAAC;AAED,MAAM,UAAU,uBAAuB,CAAC,KAAa;IACnD,OAAO,SAAS,CACd,GAAG,IAAI,oBAAoB,KAAK,OAAO,CACxC,CAAA;AACH,CAAC;AAED,KAAK,UAAU,IAAI,CAAC,EAClB,UAAU,EACV,KAAK,GAIN;IACC,MAAM,GAAG,GAAG,GAAG,IAAI,oBAAoB,KAAK,EAAE,CAAA;IAC9C,IAAI,CAAC;QACH,iDAAiD;QACjD,OAAO,IAAI,EAAE,CAAC;YACZ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC;gBAC5B,MAAM,OAAO,CAAC,IAAI,CAAC,CAAA;gBACnB,UAAU,CAAC,EAAE,GAAG,EAAE,mBAAmB,EAAE,GAAG,CAAC,EAAE,EAAE,GAAG,EAAE,CAAC,CAAA;YACvD,CAAC;YACD,MAAM,MAAM,GAAG,MAAM,SAAS,CAAC,GAAG,CAAC,CAAA;YACnC,IAAI,MAAM,CAAC,QAAQ,CAAC,UAAU,CAAC,EAAE,CAAC;gBAChC,MAAK;YACP,CAAC;QACH,CAAC;IACH,CAAC;YAAS,CAAC;QACT,UAAU,EAAE,CAAA;IACd,CAAC;AACH,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,kBAAkB,CAAC,EACvC,SAAS,EACT,GAAG,EACH,QAAQ,EACR,OAAO,EACP,UAAU,EACV,KAAK,GAQN;IACC,IAAI,CAAC;QACH,UAAU,CAAC,EAAE,GAAG,EAAE,aAAa,SAAS,MAAM,EAAE,CAAC,CAAA;QACjD,IAAI,SAAS,KAAK,cAAc,EAAE,CAAC;YACjC,MAAM,MAAM,GAAG,MAAM,eAAe,CAAC;gBACnC,GAAG;gBACH,OAAO;gBACP,UAAU;gBACV,QAAQ;gBACR,KAAK;aACN,CAAC,CAAA;YACF,OAAO,MAAM,CAAA;QACf,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,KAAK,CAAC,mBAAmB,CAAC,CAAA;QACtC,CAAC;IACH,CAAC;YAAS,CAAC;QACT,UAAU,EAAE,CAAA;IACd,CAAC;AACH,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,iCAAiC,CAAC,EACtD,KAAK,EACL,KAAK,GAIN;IACC,IAAI,CAAC;QACH,KAAK,CAAC,SAAS,CAAC;YACd,GAAG,EACD,yBAAyB;gBACzB,KAAK;gBACL,iGAAiG;YACnG,GAAG,EAAE,6DAA6D,KAAK,OAAO;SAC/E,CAAC,CAAA;QACF,MAAM,GAAG,GAAG,MAAM,uBAAuB,CAAC,KAAK,CAAC,CAAA;QAChD,KAAK,CAAC,4BAA4B,CAChC,MAAM,CAAC,WAAW,CAAC,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,CAC5D,CAAA;QACD,KAAK,CAAC,cAAc,CAAC,IAAI,CAAC,CAAA;QAC1B,UAAU,CAAC,KAAK,CAAC,CAAC,MAAM,CAAC,uBAAuB,KAAK,UAAU,EAAE,SAAS,CAAC,CAAA;IAC7E,CAAC;IAAC,OAAO,CAAC,EAAE,CAAC;QACX,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;QAChB,UAAU,CAAC,KAAK,CAAC,CAAC,WAAW,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,CAAC,CAAA;IAC1C,CAAC;YAAS,CAAC;QACT,KAAK,CAAC,SAAS,EAAE,CAAA;IACnB,CAAC;AACH,CAAC"}

package/dist/model.d.ts

@@ -49,7 +49,7 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
     colorSchemeName: import("mobx-state-tree").IType<string | undefined, string, string>;
 } & {
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    featureMode: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    showDomains: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     subFeatureRows: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     type: import("mobx-state-tree").ISimpleType<"MsaView">;
     height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
@@ -62,7 +62,9 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
         uri: import("mobx-state-tree").ISimpleType<string>;
         baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-        internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
+        internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree" /**
+         * #volatile
+         */).IModelType<{
             internetAccountType: import("mobx-state-tree").ISimpleType<string>;
             authInfo: import("mobx-state-tree").IType<any, any, any>;
         }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
@@ -99,15 +101,16 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
         locationType: "UriLocation";
         uri: string;
     } & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
-        locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
+        locationType: import("mobx-state-tree" /**
+         * #action
+         * set mouse position (row, column) in the MSA
+         */).ISimpleType<"UriLocation">;
         uri: import("mobx-state-tree").ISimpleType<string>;
         baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
             internetAccountType: import("mobx-state-tree").ISimpleType<string>;
-            authInfo: import("mobx-state-tree").IType<any, any, any>; /**
-             * #action
-             */
+            authInfo: import("mobx-state-tree").IType<any, any, any>;
         }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }>> & import("mobx-state-tree/dist/internal").NonEmptyObject)>, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     msaFilehandle: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISnapshotProcessor<import("mobx-state-tree").ITypeUnion<import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
@@ -158,9 +161,7 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
         internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
             internetAccountType: import("mobx-state-tree").ISimpleType<string>;
-            authInfo: import("mobx-state-tree").IType<any, any, any>; /**
-             * #action
-             */
+            authInfo: import("mobx-state-tree").IType<any, any, any>;
         }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }>> & import("mobx-state-tree/dist/internal").NonEmptyObject)>, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     treeMetadataFilehandle: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISnapshotProcessor<import("mobx-state-tree").ITypeUnion<import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
@@ -211,9 +212,7 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
         internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
             internetAccountType: import("mobx-state-tree").ISimpleType<string>;
-            authInfo: import("mobx-state-tree").IType<any, any, any>; /**
-             * #action
-             */
+            authInfo: import("mobx-state-tree").IType<any, any, any>;
         }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }>> & import("mobx-state-tree/dist/internal").NonEmptyObject)>, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     currentAlignment: import("mobx-state-tree").IType<number | undefined, number, number>;
@@ -226,9 +225,9 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
         msa: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         treeMetadata: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     }, {
-        setTree(tree?: string | undefined): void;
-        setMSA(msa?: string | undefined): void;
-        setTreeMetadata(treeMetadata?: string | undefined): void;
+        setTree(tree?: string): void;
+        setMSA(msa?: string): void;
+        setTreeMetadata(treeMetadata?: string): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
     featureFilters: import("mobx-state-tree").IMapType<import("mobx-state-tree").ISimpleType<boolean>>;
 }, {
@@ -254,7 +253,7 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
 } & {
     status: {
         msg: string;
-        url?: string | undefined;
+        url?: string;
     } | undefined;
     /**
      * #volatile
@@ -333,14 +332,7 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
      * #volatile
      *
      */
-    loadedInterProAnnotations: Record<string, InterProScanResults> | undefined;
-    /**
-     * #volatile
-     */
-    interProScanJobIds: {
-        jobId: string;
-        date: number;
-    }[];
+    loadedInterProAnnotations: undefined | Record<string, InterProScanResults>;
 } & {
     /**
      * #action
@@ -372,7 +364,7 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
     /**
      * #action
      */
-    setFeatureMode(arg: boolean): void;
+    setShowDomains(arg: boolean): void;
     /**
      * #action
      */
@@ -613,10 +605,6 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
      * #action
      */
     toggleTrack(id: string): void;
-    /**
-     * #action
-     */
-    addInterProScanJobId(arg: string): void;
     /**
      * #action
      */
@@ -711,14 +699,6 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
         [k: string]: string;
     };
 } & {
-    /**
-     * #action
-     */
-    loadInterProScanResults(jobId: string): Promise<void>;
-    /**
-     * #action
-     */
-    queryInterProScan(programs: string[]): Promise<void>;
     /**
      * #action
      */
@@ -758,7 +738,7 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
     bgColor: boolean;
     colorSchemeName: string;
     id: string;
-    featureMode: boolean;
+    showDomains: boolean;
     subFeatureRows: boolean;
     rowHeight: number;
     scrollY: number;

package/dist/model.js

@@ -7,7 +7,7 @@ import { saveAs } from 'file-saver';
 // jbrowse
 import { FileLocation, ElementId } from '@jbrowse/core/util/types/mst';
 import { openLocation } from '@jbrowse/core/util/io';
-import { groupBy, localStorageGetItem, localStorageSetItem, notEmpty, sum, } from '@jbrowse/core/util';
+import { groupBy, notEmpty, sum, } from '@jbrowse/core/util';
 // locals
 import { clamp, collapse, generateNodeIds, maxLength, setBrLength, skipBlanks, len, } from './util';
 import { colord } from 'colord';
@@ -28,7 +28,6 @@ import { DataModelF } from './model/DataModel';
 import { DialogQueueSessionMixin } from './model/DialogQueue';
 import { TreeF } from './model/treeModel';
 import { MSAModelF } from './model/msaModel';
-import { launchInterProScan, loadInterProScanResults, } from './launchInterProScan';
 /**
  * #stateModel MsaView
  * extends
@@ -47,7 +46,7 @@ function stateModelFactory() {
         /**
          * #property
          */
-        featureMode: false,
+        showDomains: false,
         /**
          * #property
          */
@@ -211,10 +210,6 @@ function stateModelFactory() {
          *
          */
         loadedInterProAnnotations: undefined,
-        /**
-         * #volatile
-         */
-        interProScanJobIds: JSON.parse(localStorageGetItem('msaview-interproscanqueries') || '[]'),
     }))
         .actions(self => ({
         /**
@@ -260,8 +255,8 @@ function stateModelFactory() {
         /**
          * #action
          */
-        setFeatureMode(arg) {
-            self.featureMode = arg;
+        setShowDomains(arg) {
+            self.showDomains = arg;
         },
         /**
          * #action
@@ -477,7 +472,7 @@ function stateModelFactory() {
          */
         get mouseOverRowName() {
             const { mouseRow } = self;
-            return mouseRow !== undefined ? this.rowNames[mouseRow] : undefined;
+            return mouseRow === undefined ? undefined : this.rowNames[mouseRow];
         },
         /**
          * #getter
@@ -716,15 +711,6 @@ function stateModelFactory() {
                 self.turnedOffTracks.set(id, true);
             }
         },
-        /**
-         * #action
-         */
-        addInterProScanJobId(arg) {
-            self.interProScanJobIds = [
-                ...self.interProScanJobIds,
-                { jobId: arg, date: +Date.now() },
-            ];
-        },
         /**
          * #action
          */
@@ -923,34 +909,6 @@ function stateModelFactory() {
         },
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
-        async loadInterProScanResults(jobId) {
-            self.setStatus({ msg: 'Loading ' + jobId });
-            const ret = await loadInterProScanResults(jobId);
-            self.setStatus();
-            self.setLoadedInterProAnnotations(Object.fromEntries(ret.results.map(r => [r.xref[0].id, r])));
-        },
-        /**
-         * #action
-         */
-        async queryInterProScan(programs) {
-            const { rows } = self;
-            if (rows.length > 140) {
-                throw new Error('Too many sequences, please run InterProScan offline');
-            }
-            const ret = await launchInterProScan({
-                algorithm: 'interproscan',
-                programs: programs,
-                seq: rows
-                    .map(row => `>${row[0]}\n${row[1].replaceAll('-', '')}`)
-                    .join('\n'),
-                onProgress: arg => self.setStatus(arg),
-                onJobId: jobId => self.addInterProScanJobId(jobId),
-            });
-            self.setLoadedInterProAnnotations(Object.fromEntries(ret.results.map(r => [r.xref[0].id, r])));
-        },
         /**
          * #action
          */
@@ -1001,22 +959,6 @@ function stateModelFactory() {
                     this.initFilter(key);
                 }
             }));
-            addDisposer(self, autorun(async () => {
-                // const res = Object.fromEntries(
-                //   await Promise.all(
-                //     self.annotationTracks.map(async f => {
-                //       const d = await jsonfetch(
-                //         `https://jbrowse.org/demos/interproscan/json/${encodeURIComponent(f)}`,
-                //       )
-                //       return [
-                //         decodeURIComponent(f).replace('.json', ''),
-                //         d.result.results[0],
-                //       ] as const
-                //     }),
-                //   ),
-                // )
-                // self.setLoadedInterProAnnotations(res)
-            }));
             // autorun opens treeFilehandle
             addDisposer(self, autorun(async () => {
                 const { treeFilehandle } = self;
@@ -1081,9 +1023,6 @@ function stateModelFactory() {
                     self.setTreeWidth(Math.max(50, self.treeAreaWidth - self.labelsWidth - 10 - self.marginLeft));
                 }
             }));
-            addDisposer(self, autorun(() => {
-                localStorageSetItem('msaview-interproscanqueries', JSON.stringify(self.interProScanJobIds));
-            }));
         },
     }))
         .postProcessSnapshot(result => {

package/dist/model.js.map

@@ -1 +1 @@
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