react-msaview 3.1.11 → 3.2.0

package/dist/components/tree/renderTreeCanvas.js

@@ -8,6 +8,9 @@ export function renderTree({ offsetY, ctx, model, theme, blockSizeYOverride, })
     ctx.strokeStyle = theme.palette.text.primary;
     for (const link of hierarchy.links()) {
         const { source, target } = link;
+        if (target.height === 0 && !showBranchLen) {
+            continue;
+        }
         const sy = source.x;
         const ty = target.x;
         // @ts-expect-error
@@ -36,9 +39,8 @@ export function renderNodeBubbles({ ctx, clickMap, offsetY, model, blockSizeYOve
         // @ts-expect-error
         const { [val]: x, data } = node;
         const y = node.x;
-        const { branchset, id = '', name = '' } = data;
-        if (!id.endsWith('-leafnode') &&
-            branchset.length &&
+        const { id = '', name = '' } = data;
+        if (node.height > 1 &&
             y > offsetY - extendBounds &&
             y < offsetY + by + extendBounds) {
             ctx.strokeStyle = 'black';
@@ -60,7 +62,10 @@ export function renderNodeBubbles({ ctx, clickMap, offsetY, model, blockSizeYOve
     }
 }
 export function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, blockSizeYOverride, }) {
-    const { fontSize, showBranchLen, treeMetadata, hierarchy, blockSize, labelsAlignRight, drawTree, treeAreaWidth, treeAreaWidthMinusMargin, marginLeft, noTree, } = model;
+    const { fontSize, showBranchLen, treeMetadata, hierarchy, collapsed, collapsedLeaves, blockSize, labelsAlignRight, drawTree, treeAreaWidth, treeWidth, treeAreaWidthMinusMargin, marginLeft, leaves, noTree, 
+    // eslint-disable-next-line  @typescript-eslint/no-unused-vars
+    rowHeight: _rowHeight, // this is needed for redrawing after zoom change
+     } = model;
     const by = blockSizeYOverride || blockSize;
     if (labelsAlignRight) {
         ctx.textAlign = 'right';
@@ -69,7 +74,7 @@ export function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, blockSi
     else {
         ctx.textAlign = 'start';
     }
-    for (const node of hierarchy.leaves()) {
+    for (const node of leaves) {
         const { data: { name, id }, 
         // @ts-expect-error
         len, } = node;
@@ -79,7 +84,16 @@ export function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, blockSi
         if (y > offsetY - extendBounds && y < offsetY + by + extendBounds) {
             // note: +rowHeight/4 matches with -rowHeight/4 in msa
             const yp = y + fontSize / 4;
-            const xp = (showBranchLen ? len : x) || 0;
+            let xp = (showBranchLen ? len : x) || 0;
+            if (!showBranchLen &&
+                !collapsed.includes(id) &&
+                !collapsedLeaves.includes(id)) {
+                // this subtraction is a hack to compensate for the leafnode rendering
+                // glitch (issue #71). the context is that an extra leaf node is added
+                // so that 'collapsing/hiding leaf nodes is possible' but this causes
+                // weird workarounds
+                xp -= treeWidth / hierarchy.height;
+            }
             const { width } = ctx.measureText(displayName);
             const height = ctx.measureText('M').width; // use an 'em' for height
             ctx.fillStyle = theme.palette.text.primary;
@@ -119,7 +133,7 @@ export function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, blockSi
 }
 export function renderTreeCanvas({ model, clickMap, ctx, offsetY, theme, highResScaleFactorOverride, blockSizeYOverride, }) {
     clickMap?.clear();
-    const { noTree, drawTree, drawLabels, drawNodeBubbles, treeWidth, highResScaleFactor, blockSize, fontSize, rowHeight, marginLeft, nref, } = model;
+    const { noTree, drawTree, drawNodeBubbles, treeWidth, highResScaleFactor, blockSize, fontSize, showTreeText, marginLeft, nref, } = model;
     const by = blockSizeYOverride || blockSize;
     ctx.resetTransform();
     // this is a bogus use of nref, it is never less than 0. we just are using it
@@ -127,7 +141,9 @@ export function renderTreeCanvas({ model, clickMap, ctx, offsetY, theme, highRes
     // just need to use nref to indicate a redraw in an autorun when canvas ref
     // is updated and in order to convince bundlers like not to delete unused
     // usage with propertyReadSideEffects
-    const k = nref < 0 ? -Infinity : highResScaleFactorOverride || highResScaleFactor;
+    const k = nref < 0
+        ? Number.NEGATIVE_INFINITY
+        : highResScaleFactorOverride || highResScaleFactor;
     ctx.scale(k, k);
     ctx.clearRect(0, 0, treeWidth + padding, by);
     ctx.translate(marginLeft, -offsetY);
@@ -152,7 +168,7 @@ export function renderTreeCanvas({ model, clickMap, ctx, offsetY, theme, highRes
             });
         }
     }
-    if (rowHeight >= 5 && drawLabels) {
+    if (showTreeText) {
         renderTreeLabels({
             ctx,
             offsetY,

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

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package/dist/components/util.js

@@ -6,7 +6,7 @@
 export function chooseGridPitch(scale, minMajorPitchPx, minMinorPitchPx) {
     scale = Math.abs(scale);
     const minMajorPitchBp = minMajorPitchPx * scale;
-    const majorMagnitude = parseInt(Number(minMajorPitchBp).toExponential().split(/e/i)[1], 10);
+    const majorMagnitude = Number.parseInt(Number(minMajorPitchBp).toExponential().split(/e/i)[1], 10);
     let majorPitch = 10 ** majorMagnitude;
     while (majorPitch < minMajorPitchBp) {
         majorPitch *= 2;

package/dist/components/util.js.map

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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 type { 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, }) {
+const base = 'https://www.ebi.ac.uk/Tools/services/rest';
+async function runInterProScan({ seq, onProgress, onJobId, programs, model, }) {
     const jobId = await textfetch(`${base}/iprscan5/run`, {
         method: 'POST',
         body: new URLSearchParams({
@@ -9,39 +10,73 @@ async function runInterProScan({ seq, onProgress, onJobId, programs, }) {
             programs: programs.join(','),
         }),
     });
-    onJobId(jobId);
+    onJobId?.(jobId);
     await wait({
         jobId,
         onProgress,
     });
-    return loadInterProScanResults(jobId);
+    return loadInterProScanResultsWithStatus({ jobId, model });
 }
-export async function loadInterProScanResults(jobId) {
-    return (await jsonfetch(`${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 {
+        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;
+            }
+            if (result.includes('FAILURE')) {
+                throw new Error(`Failed to run: jobId ${jobId}`);
+            }
         }
     }
-}
-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 });
+    finally {
         onProgress();
-        return result;
     }
-    else {
+}
+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;
+        }
         throw new Error('unknown algorithm');
     }
+    finally {
+        onProgress();
+    }
+}
+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.setInterProAnnotations(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

@@ -1 +1 @@
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package/dist/model/DataModel.d.ts

@@ -31,4 +31,8 @@ export declare function DataModelF(): import("mobx-state-tree").IModelType<{
      * #action
      */
     setTreeMetadata(treeMetadata?: string): void;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+}, import("mobx-state-tree")._NotCustomized, {
+    tree: string | undefined;
+    msa: string | undefined;
+    treeMetadata: string | undefined;
+}>;

package/dist/model/DataModel.js

@@ -41,6 +41,15 @@ export function DataModelF() {
         setTreeMetadata(treeMetadata) {
             self.treeMetadata = treeMetadata;
         },
-    }));
+    }))
+        .postProcessSnapshot(snap => {
+        const { tree, msa, treeMetadata } = snap;
+        const max = 50_000;
+        return {
+            tree: tree && tree.length > max ? undefined : tree,
+            msa: msa && msa.length > max ? undefined : msa,
+            treeMetadata: treeMetadata && treeMetadata.length > max ? undefined : treeMetadata,
+        };
+    });
 }
 //# sourceMappingURL=DataModel.js.map

package/dist/model/DataModel.js.map

@@ -1 +1 @@
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+{"version":3,"file":"DataModel.js","sourceRoot":"","sources":["../../src/model/DataModel.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAEvC;;;;;;GAMG;AACH,MAAM,UAAU,UAAU;IACxB,OAAO,KAAK;SACT,KAAK,CAAC;QACL;;WAEG;QACH,IAAI,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;QAC/B;;WAEG;QACH,GAAG,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;QAC9B;;WAEG;QACH,YAAY,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;KACxC,CAAC;SACD,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;WAEG;QACH,OAAO,CAAC,IAAa;YACnB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAClB,CAAC;QACD;;WAEG;QACH,MAAM,CAAC,GAAY;YACjB,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;QAChB,CAAC;QACD;;WAEG;QACH,eAAe,CAAC,YAAqB;YACnC,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA;QAClC,CAAC;KACF,CAAC,CAAC;SACF,mBAAmB,CAAC,IAAI,CAAC,EAAE;QAC1B,MAAM,EAAE,IAAI,EAAE,GAAG,EAAE,YAAY,EAAE,GAAG,IAAI,CAAA;QACxC,MAAM,GAAG,GAAG,MAAM,CAAA;QAClB,OAAO;YACL,IAAI,EAAE,IAAI,IAAI,IAAI,CAAC,MAAM,GAAG,GAAG,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI;YAClD,GAAG,EAAE,GAAG,IAAI,GAAG,CAAC,MAAM,GAAG,GAAG,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,GAAG;YAC9C,YAAY,EACV,YAAY,IAAI,YAAY,CAAC,MAAM,GAAG,GAAG,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,YAAY;SACvE,CAAA;IACH,CAAC,CAAC,CAAA;AACN,CAAC"}

package/dist/model/DialogQueue.d.ts

@@ -1,4 +1,4 @@
-import { DialogComponentType } from '@jbrowse/core/util';
+import type { DialogComponentType } from '@jbrowse/core/util';
 /**
  * #stateModel DialogQueueSessionMixin
  */