react-msaview 5.1.1 → 5.2.1

package/dist/hierarchy.js

@@ -1,115 +1,149 @@
+// All traversals below are iterative (explicit stack / reversed-preorder) rather
+// than recursive: phylogenetic trees can be deeply unbalanced (a caterpillar tree
+// has depth ~= leaf count), which overflows the JS call stack on recursion.
+// Pre-order: every parent precedes all of its descendants. Iterating the result
+// in reverse therefore yields a valid post-order (children before parents), which
+// the accumulation helpers rely on.
+export function descendants(node) {
+    const result = [];
+    const stack = [node];
+    while (stack.length > 0) {
+        const n = stack.pop();
+        result.push(n);
+        if (n.children) {
+            for (let i = n.children.length - 1; i >= 0; i--) {
+                stack.push(n.children[i]);
+            }
+        }
+    }
+    return result;
+}
 function computeHeight(node) {
-    let h = 0;
-    if (node.children) {
-        for (const child of node.children) {
-            const ch = computeHeight(child) + 1;
-            if (ch > h) {
-                h = ch;
+    const nodes = descendants(node);
+    for (let i = nodes.length - 1; i >= 0; i--) {
+        const n = nodes[i];
+        let h = 0;
+        if (n.children) {
+            for (const child of n.children) {
+                if (child.height + 1 > h) {
+                    h = child.height + 1;
+                }
             }
         }
+        n.height = h;
     }
-    node.height = h;
-    return h;
 }
-function wrap(data, childrenAccessor, parent, depth) {
-    const kids = childrenAccessor(data);
-    const node = {
+export function hierarchy(data, childrenAccessor) {
+    const root = {
         data,
         children: null,
-        parent,
-        depth,
+        parent: null,
+        depth: 0,
         height: 0,
     };
-    if (kids?.length) {
-        node.children = kids.map(d => wrap(d, childrenAccessor, node, depth + 1));
+    const stack = [root];
+    while (stack.length > 0) {
+        const node = stack.pop();
+        const kids = childrenAccessor(node.data);
+        if (kids?.length) {
+            node.children = kids.map(d => ({
+                data: d,
+                children: null,
+                parent: node,
+                depth: node.depth + 1,
+                height: 0,
+            }));
+            for (const child of node.children) {
+                stack.push(child);
+            }
+        }
     }
-    return node;
-}
-export function hierarchy(data, childrenAccessor) {
-    const root = wrap(data, childrenAccessor, null, 0);
     computeHeight(root);
     return root;
 }
 export function sum(node, valueFn) {
-    function visit(n) {
+    const nodes = descendants(node);
+    for (let i = nodes.length - 1; i >= 0; i--) {
+        const n = nodes[i];
         let s = valueFn(n.data);
         if (n.children) {
             for (const child of n.children) {
-                s += visit(child);
+                s += child.value;
             }
         }
         n.value = s;
-        return s;
     }
-    visit(node);
     return node;
 }
 export function sort(node, compareFn) {
-    function visit(n) {
+    const stack = [node];
+    while (stack.length > 0) {
+        const n = stack.pop();
         if (n.children) {
             n.children.sort(compareFn);
             for (const child of n.children) {
-                visit(child);
+                stack.push(child);
             }
         }
     }
-    visit(node);
     return node;
 }
 export function find(node, predicate) {
-    if (predicate(node)) {
-        return node;
-    }
-    if (node.children) {
-        for (const child of node.children) {
-            const result = find(child, predicate);
-            if (result) {
-                return result;
+    const stack = [node];
+    let found;
+    while (stack.length > 0 && found === undefined) {
+        const n = stack.pop();
+        if (predicate(n)) {
+            found = n;
+        }
+        else if (n.children) {
+            for (let i = n.children.length - 1; i >= 0; i--) {
+                stack.push(n.children[i]);
             }
         }
     }
-    return undefined;
+    return found;
 }
 export function leaves(node) {
     const result = [];
-    function visit(n) {
+    const stack = [node];
+    while (stack.length > 0) {
+        const n = stack.pop();
         if (n.children) {
-            for (const child of n.children) {
-                visit(child);
+            for (let i = n.children.length - 1; i >= 0; i--) {
+                stack.push(n.children[i]);
             }
         }
         else {
             result.push(n);
         }
     }
-    visit(node);
     return result;
 }
-export function descendants(node) {
+export function links(node) {
     const result = [];
-    function visit(n) {
-        result.push(n);
-        if (n.children) {
-            for (const child of n.children) {
-                visit(child);
-            }
-        }
-    }
-    visit(node);
+    forEachLink(node, (source, target) => {
+        result.push({ source, target });
+    });
     return result;
 }
-export function links(node) {
-    const result = [];
-    function visit(n) {
+export function forEachLink(node, cb) {
+    const stack = [node];
+    while (stack.length > 0) {
+        const n = stack.pop();
         if (n.children) {
-            for (const child of n.children) {
-                result.push({ source: n, target: child });
-                visit(child);
+            for (let i = n.children.length - 1; i >= 0; i--) {
+                const child = n.children[i];
+                cb(n, child);
+                stack.push(child);
             }
         }
     }
-    visit(node);
-    return result;
+}
+export function forEachDescendant(node, cb) {
+    for (const n of descendants(node)) {
+        cb(n);
+    }
 }
 export function clusterLayout(root, sizeX, sizeY) {
     const leafNodes = leaves(root);
@@ -118,30 +152,30 @@ export function clusterLayout(root, sizeX, sizeY) {
     for (let i = 0; i < n; i++) {
         leafNodes[i].x = (i + 0.5) * step;
     }
-    function assignX(node) {
-        if (!node.children) {
-            return;
-        }
-        for (const child of node.children) {
-            assignX(child);
-        }
-        let sum = 0;
-        for (const child of node.children) {
-            sum += child.x;
+    // x of an internal node is the mean of its children's x, so process in
+    // post-order (children before parents)
+    const nodes = descendants(root);
+    for (let i = nodes.length - 1; i >= 0; i--) {
+        const node = nodes[i];
+        if (node.children) {
+            let sum = 0;
+            for (const child of node.children) {
+                sum += child.x;
+            }
+            node.x = sum / node.children.length;
         }
-        node.x = sum / node.children.length;
     }
-    assignX(root);
     const rootHeight = root.height;
-    function assignY(node, depth) {
+    const stack = [{ node: root, depth: 0 }];
+    while (stack.length > 0) {
+        const { node, depth } = stack.pop();
         node.y = rootHeight === 0 ? sizeY : (depth / rootHeight) * sizeY;
         if (node.children) {
             for (const child of node.children) {
-                assignY(child, depth + 1);
+                stack.push({ node: child, depth: depth + 1 });
             }
         }
     }
-    assignY(root, 0);
 }
 export function collapse(node) {
     if (node.children) {
@@ -154,35 +188,54 @@ export function collapse(node) {
 // 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));
+    const nodes = descendants(node);
+    for (let i = nodes.length - 1; i >= 0; i--) {
+        const n = nodes[i];
+        if (n.depthToLeaf === undefined) {
+            let maxDepth = 0;
+            if (n.children) {
+                for (const child of n.children) {
+                    maxDepth = Math.max(maxDepth, 1 + child.depthToLeaf);
+                }
             }
+            n.depthToLeaf = maxDepth;
         }
-        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));
-        }
+    let maxLen = 0;
+    for (const n of descendants(node)) {
+        maxLen = Math.max(maxLen, n.len || 0);
     }
     return maxLen;
 }
+// Max root-to-leaf sum of branch lengths within the subtree at d
 export function maxLength(d) {
-    return ((d.data.length || 0) +
-        (d.children ? d.children.reduce((m, c) => Math.max(m, maxLength(c)), 0) : 0));
+    const nodes = descendants(d);
+    const pathLen = new Map();
+    for (let i = nodes.length - 1; i >= 0; i--) {
+        const n = nodes[i];
+        let childMax = 0;
+        if (n.children) {
+            for (const child of n.children) {
+                childMax = Math.max(childMax, pathLen.get(child));
+            }
+        }
+        pathLen.set(n, (n.data.length || 0) + childMax);
+    }
+    return pathLen.get(d);
 }
 export function setBrLength(d, y0, k) {
-    d.len = (y0 += Math.max(d.data.length || 0, 0)) * k;
-    if (d.children) {
-        for (const child of d.children) {
-            setBrLength(child, y0, k);
+    const stack = [{ node: d, y0 }];
+    while (stack.length > 0) {
+        const { node, y0: acc } = stack.pop();
+        const next = acc + Math.max(node.data.length || 0, 0);
+        node.len = next * k;
+        if (node.children) {
+            for (const child of node.children) {
+                stack.push({ node: child, y0: next });
+            }
         }
     }
 }

package/dist/hierarchy.js.map

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

@@ -1,3 +1,4 @@
+export { renderToSvg } from './renderToSvg.tsx';
 export { default as MSAView } from './components/Loading.tsx';
 export { default as MSAViewer } from './components/MSAViewer.tsx';
 export { type MsaViewModel, default as MSAModelF } from './model.ts';

package/dist/index.js

@@ -1,3 +1,11 @@
+// PUBLIC API — consumed by external JBrowse 2 plugins. Changing or removing any
+// export here is a breaking change for downstream repos:
+//   - jbrowse-plugin-msaview   (wraps MSAModelF + MSAView into a JBrowse view)
+//   - jbrowse-plugin-protein3d (drives MSA<->structure hover/highlight sync)
+// Those plugins also reach into the MsaViewModel instance at runtime; the model
+// members they rely on (e.g. mouseCol/setMousePos, setHighlightedColumns,
+// seqPosToVisibleCol/visibleColToSeqPos) are flagged inline in model.ts.
+export { renderToSvg } from "./renderToSvg.js";
 export { default as MSAView } from "./components/Loading.js";
 export { default as MSAViewer } from "./components/MSAViewer.js";
 export { default as MSAModelF } from "./model.js";

package/dist/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,OAAO,EAAE,MAAM,yBAA0B,CAAA;AAC7D,OAAO,EAAE,OAAO,IAAI,SAAS,EAAE,MAAM,2BAA4B,CAAA;AACjE,OAAO,EAAqB,OAAO,IAAI,SAAS,EAAE,MAAM,YAAY,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,gFAAgF;AAChF,yDAAyD;AACzD,+EAA+E;AAC/E,6EAA6E;AAC7E,gFAAgF;AAChF,0EAA0E;AAC1E,yEAAyE;AACzE,OAAO,EAAE,WAAW,EAAE,MAAM,kBAAmB,CAAA;AAC/C,OAAO,EAAE,OAAO,IAAI,OAAO,EAAE,MAAM,yBAA0B,CAAA;AAC7D,OAAO,EAAE,OAAO,IAAI,SAAS,EAAE,MAAM,2BAA4B,CAAA;AACjE,OAAO,EAAqB,OAAO,IAAI,SAAS,EAAE,MAAM,YAAY,CAAA"}

package/dist/launchInterProScan.js

@@ -24,21 +24,31 @@ function loadInterProScanResults(jobId, signal) {
 }
 async function wait({ onProgress, jobId, signal, }) {
     const url = `${base}/iprscan5/status/${jobId}`;
+    // EBI jobs run for minutes; cap polling so an unexpected/stuck status can't
+    // spin forever (the abort signal is the normal early exit). ~10s per check.
+    const maxChecks = 360;
     try {
-        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
-        while (true) {
+        let finished = false;
+        for (let check = 0; check < maxChecks && !finished; check++) {
             for (let i = 0; i < 10; i++) {
                 await timeout(1000, signal);
                 onProgress({ msg: `Checking status ${10 - i}`, url });
             }
-            const result = await textfetch(url, { signal });
-            if (result.includes('FINISHED')) {
-                break;
+            // status endpoint returns a bare status token; match exactly rather than
+            // substring so an error page mentioning "FINISHED" can't be a false hit
+            const status = (await textfetch(url, { signal })).trim();
+            if (status === 'FINISHED') {
+                finished = true;
             }
-            if (result.includes('FAILURE')) {
-                throw new Error(`Failed to run: jobId ${jobId}`);
+            else if (status === 'FAILURE' ||
+                status === 'ERROR' ||
+                status === 'NOT_FOUND') {
+                throw new Error(`InterProScan job ${jobId} ended with status: ${status}`);
             }
         }
+        if (!finished) {
+            throw new Error(`InterProScan job ${jobId} did not finish after ${maxChecks} status checks`);
+        }
     }
     finally {
         onProgress();
@@ -80,8 +90,11 @@ async function loadInterProScanResultsWithStatus({ jobId, model, onProgress, sig
             url: `https://www.ebi.ac.uk/Tools/services/rest/iprscan5/result/${jobId}/json`,
         });
         const ret = await loadInterProScanResults(jobId, signal);
-        model.setInterProAnnotations(Object.fromEntries(ret.results.map(r => [r.xref[0].id, r])));
-        model.setShowDomains(true);
+        // key each result by its xref id; skip any result lacking an xref entry
+        // rather than crashing the whole load on one malformed result
+        model.setDomains(Object.fromEntries(ret.results
+            .map(r => [r.xref[0]?.id, r])
+            .filter((e) => e[0] !== undefined)));
         getSession(model).notify(`Loaded interproscan ${jobId} results`, 'success');
     }
     catch (e) {

package/dist/launchInterProScan.js.map

@@ -1 +1 @@
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package/dist/measureTextCanvas.js

@@ -1,3 +1,4 @@
+import { setFontSize } from "./setFontSize.js";
 let canvasHandle;
 export function measureTextCanvas(text, fontSize) {
     if (!canvasHandle) {
@@ -7,7 +8,7 @@ export function measureTextCanvas(text, fontSize) {
     if (!ctx) {
         throw new Error('no canvas context');
     }
-    ctx.font = ctx.font.replace(/\d+px/, `${fontSize}px`);
+    setFontSize(ctx, fontSize);
     return ctx.measureText(text).width;
 }
 //# sourceMappingURL=measureTextCanvas.js.map

package/dist/measureTextCanvas.js.map

@@ -1 +1 @@
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+{"version":3,"file":"measureTextCanvas.js","sourceRoot":"","sources":["../src/measureTextCanvas.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,MAAM,kBAAkB,CAAA;AAE9C,IAAI,YAA2C,CAAA;AAE/C,MAAM,UAAU,iBAAiB,CAAC,IAAY,EAAE,QAAgB;IAC9D,IAAI,CAAC,YAAY,EAAE,CAAC;QAClB,YAAY,GAAG,QAAQ,CAAC,aAAa,CAAC,QAAQ,CAAC,CAAA;IACjD,CAAC;IAED,MAAM,GAAG,GAAG,YAAY,CAAC,UAAU,CAAC,IAAI,CAAC,CAAA;IACzC,IAAI,CAAC,GAAG,EAAE,CAAC;QACT,MAAM,IAAI,KAAK,CAAC,mBAAmB,CAAC,CAAA;IACtC,CAAC;IACD,WAAW,CAAC,GAAG,EAAE,QAAQ,CAAC,CAAA;IAC1B,OAAO,GAAG,CAAC,WAAW,CAAC,IAAI,CAAC,CAAC,KAAK,CAAA;AACpC,CAAC"}