react-msaview 5.0.13 → 5.1.0

package/dist/fetchUtils.js

@@ -13,7 +13,21 @@ export async function jsonfetch(url, args) {
     const response = await myfetch(url, args);
     return response.json();
 }
-export function timeout(time) {
-    return new Promise(res => setTimeout(res, time));
+export function timeout(time, signal) {
+    return new Promise((resolve, reject) => {
+        if (signal?.aborted) {
+            reject(new DOMException('Aborted', 'AbortError'));
+        }
+        else {
+            const id = setTimeout(resolve, time);
+            signal?.addEventListener('abort', () => {
+                clearTimeout(id);
+                reject(new DOMException('Aborted', 'AbortError'));
+            });
+        }
+    });
+}
+export function isAbortError(e) {
+    return e instanceof DOMException && e.name === 'AbortError';
 }
 //# sourceMappingURL=fetchUtils.js.map

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,UAAU,OAAO,CAAC,IAAY,EAAE,MAAoB;IACxD,OAAO,IAAI,OAAO,CAAO,CAAC,OAAO,EAAE,MAAM,EAAE,EAAE;QAC3C,IAAI,MAAM,EAAE,OAAO,EAAE,CAAC;YACpB,MAAM,CAAC,IAAI,YAAY,CAAC,SAAS,EAAE,YAAY,CAAC,CAAC,CAAA;QACnD,CAAC;aAAM,CAAC;YACN,MAAM,EAAE,GAAG,UAAU,CAAC,OAAO,EAAE,IAAI,CAAC,CAAA;YACpC,MAAM,EAAE,gBAAgB,CAAC,OAAO,EAAE,GAAG,EAAE;gBACrC,YAAY,CAAC,EAAE,CAAC,CAAA;gBAChB,MAAM,CAAC,IAAI,YAAY,CAAC,SAAS,EAAE,YAAY,CAAC,CAAC,CAAA;YACnD,CAAC,CAAC,CAAA;QACJ,CAAC;IACH,CAAC,CAAC,CAAA;AACJ,CAAC;AAED,MAAM,UAAU,YAAY,CAAC,CAAU;IACrC,OAAO,CAAC,YAAY,YAAY,IAAI,CAAC,CAAC,IAAI,KAAK,YAAY,CAAA;AAC7D,CAAC"}

package/dist/hierarchy.d.ts

@@ -9,6 +9,7 @@ export interface HierarchyNode<T = NodeWithIds> {
     x?: number;
     y?: number;
     len?: number;
+    depthToLeaf?: number;
     _children?: HierarchyNode<T>[] | null;
 }
 export interface HierarchyLink<T = NodeWithIds> {
@@ -24,5 +25,7 @@ export declare function descendants<T>(node: HierarchyNode<T>): HierarchyNode<T>
 export declare function links<T>(node: HierarchyNode<T>): HierarchyLink<T>[];
 export declare function clusterLayout<T>(root: HierarchyNode<T>, sizeX: number, sizeY: number): void;
 export declare function collapse<T>(node: HierarchyNode<T>): void;
+export declare function calcDepthToLeaf(node: HierarchyNode): number;
+export declare function findMaxBranchLen(node: HierarchyNode): number;
 export declare function maxLength(d: HierarchyNode): number;
 export declare function setBrLength(d: HierarchyNode, y0: number, k: number): void;

package/dist/hierarchy.js

@@ -149,6 +149,31 @@ export function collapse(node) {
         node.children = null;
     }
 }
+// Cladogram positioning based on ape's plot.phylo: uses topological depth (max
+// steps to a tip) instead of branch length so all leaves align at the rightmost
+// x. Memoizes onto node.depthToLeaf since the layout walks the tree repeatedly.
+// See https://github.com/emmanuelparadis/ape/blob/master/R/plot.phylo.R
+export function calcDepthToLeaf(node) {
+    if (node.depthToLeaf === undefined) {
+        let maxDepth = 0;
+        if (node.children) {
+            for (const child of node.children) {
+                maxDepth = Math.max(maxDepth, 1 + calcDepthToLeaf(child));
+            }
+        }
+        node.depthToLeaf = maxDepth;
+    }
+    return node.depthToLeaf;
+}
+export function findMaxBranchLen(node) {
+    let maxLen = node.len || 0;
+    if (node.children) {
+        for (const child of node.children) {
+            maxLen = Math.max(maxLen, findMaxBranchLen(child));
+        }
+    }
+    return maxLen;
+}
 export function maxLength(d) {
     return ((d.data.length || 0) +
         (d.children ? d.children.reduce((m, c) => Math.max(m, maxLength(c)), 0) : 0));

package/dist/hierarchy.js.map

@@ -1 +1 @@
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package/dist/launchInterProScan.d.ts

@@ -20,7 +20,7 @@ export interface InterProScanResults {
 export interface InterProScanResponse {
     results: InterProScanResults[];
 }
-export declare function launchInterProScan({ algorithm, seq, programs, onJobId, onProgress, model, }: {
+export declare function launchInterProScan({ algorithm, seq, programs, onJobId, onProgress, model, signal, }: {
     algorithm: string;
     seq: string;
     programs: string[];
@@ -30,4 +30,5 @@ export declare function launchInterProScan({ algorithm, seq, programs, onJobId,
     }) => void;
     onJobId?: (arg: string) => void;
     model: MsaViewModel;
+    signal?: AbortSignal;
 }): Promise<void>;

package/dist/launchInterProScan.js

@@ -1,7 +1,7 @@
 import { getSession } from '@jbrowse/core/util';
-import { jsonfetch, textfetch, timeout } from "./fetchUtils.js";
+import { isAbortError, jsonfetch, textfetch, timeout } from "./fetchUtils.js";
 const base = 'https://www.ebi.ac.uk/Tools/services/rest';
-async function runInterProScan({ seq, onProgress, onJobId, programs, model, }) {
+async function runInterProScan({ seq, onProgress, onJobId, programs, model, signal, }) {
     const jobId = await textfetch(`${base}/iprscan5/run`, {
         method: 'POST',
         body: new URLSearchParams({
@@ -9,27 +9,29 @@ async function runInterProScan({ seq, onProgress, onJobId, programs, model, }) {
             sequence: seq,
             programs: programs.join(','),
         }),
+        signal,
     });
     onJobId?.(jobId);
     await wait({
         jobId,
         onProgress,
+        signal,
     });
-    await loadInterProScanResultsWithStatus({ jobId, model });
+    await loadInterProScanResultsWithStatus({ jobId, model, onProgress, signal });
 }
-function loadInterProScanResults(jobId) {
-    return jsonfetch(`${base}/iprscan5/result/${jobId}/json`);
+function loadInterProScanResults(jobId, signal) {
+    return jsonfetch(`${base}/iprscan5/result/${jobId}/json`, { signal });
 }
-async function wait({ onProgress, jobId, }) {
+async function wait({ onProgress, jobId, signal, }) {
     const url = `${base}/iprscan5/status/${jobId}`;
     try {
         // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
         while (true) {
             for (let i = 0; i < 10; i++) {
-                await timeout(1000);
+                await timeout(1000, signal);
                 onProgress({ msg: `Checking status ${10 - i}`, url });
             }
-            const result = await textfetch(url);
+            const result = await textfetch(url, { signal });
             if (result.includes('FINISHED')) {
                 break;
             }
@@ -42,7 +44,7 @@ async function wait({ onProgress, jobId, }) {
         onProgress();
     }
 }
-export async function launchInterProScan({ algorithm, seq, programs, onJobId, onProgress, model, }) {
+export async function launchInterProScan({ algorithm, seq, programs, onJobId, onProgress, model, signal, }) {
     try {
         onProgress({ msg: `Launching ${algorithm} MSA` });
         if (algorithm === 'interproscan') {
@@ -52,33 +54,47 @@ export async function launchInterProScan({ algorithm, seq, programs, onJobId, on
                 onProgress,
                 programs,
                 model,
+                signal,
             });
         }
         else {
             throw new Error('unknown algorithm');
         }
     }
+    catch (e) {
+        if (isAbortError(e)) {
+            getSession(model).notify('Cancelled InterProScan query', 'info');
+        }
+        else {
+            throw e;
+        }
+    }
     finally {
         onProgress();
     }
 }
-async function loadInterProScanResultsWithStatus({ jobId, model, }) {
+async function loadInterProScanResultsWithStatus({ jobId, model, onProgress, signal, }) {
     try {
-        model.setStatus({
+        onProgress({
             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);
+        const ret = await loadInterProScanResults(jobId, signal);
         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);
+        if (isAbortError(e)) {
+            getSession(model).notify('Cancelled InterProScan query', 'info');
+        }
+        else {
+            console.error(e);
+            getSession(model).notifyError(`${e}`, e);
+        }
     }
     finally {
-        model.setStatus();
+        onProgress();
     }
 }
 //# sourceMappingURL=launchInterProScan.js.map

package/dist/launchInterProScan.js.map

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