jbrowse-plugin-msaview 3.9.0 → 4.0.0

package/dist/chunks/TreeNodeInfoDialog-BFF6JRCO.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../node_modules/.pnpm/react-msaview@8.4.1_35cd7d1fa06820f3dff395dec9803110/node_modules/react-msaview/src/components/tree/dialogs/TreeNodeInfoDialog.tsx"],
+  "sourcesContent": ["import React from 'react'\n\nimport { Dialog } from '@jbrowse/core/ui'\nimport { DialogContent, Typography } from '@mui/material'\nimport { observer } from 'mobx-react'\n\nimport MetadataTable from '../../MetadataTable.tsx'\nimport SequenceTextArea from '../../SequenceTextArea.tsx'\n\nimport type { MsaViewModel } from '../../../model.ts'\n\nconst TreeNodeInfoDialog = observer(function ({\n  info,\n  model,\n  nodeName,\n  onClose,\n}: {\n  info: Record<string, unknown>\n  model: MsaViewModel\n  nodeName: string\n  onClose: () => void\n}) {\n  const { rows } = model\n  const metadata = model.rowDataOf(nodeName)\n  const res = rows.find(f => f[0] === nodeName)\n  return (\n    <Dialog\n      onClose={() => {\n        onClose()\n      }}\n      open\n      title=\"Tree node info\"\n      maxWidth=\"xl\"\n    >\n      <DialogContent>\n        <Typography variant=\"h6\">Attributes</Typography>\n        <MetadataTable record={{ nodeName, ...info }} />\n        <Typography variant=\"h6\">Sequence</Typography>\n        {res ? (\n          <SequenceTextArea str={[res]} />\n        ) : (\n          <Typography>Sequence not found</Typography>\n        )}\n        {metadata ? (\n          <>\n            <Typography variant=\"h6\">Extra metadata</Typography>\n            <MetadataTable record={metadata} />\n          </>\n        ) : null}\n      </DialogContent>\n    </Dialog>\n  )\n})\n\nexport default TreeNodeInfoDialog\n"],
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+  "names": ["import_react", "import_ui", "import_material", "import_mobx_react", "TreeNodeInfoDialog", "info", "model", "nodeName", "onClose", "rows", "metadata", "res", "f", "React", "MetadataTable", "SequenceTextArea", "TreeNodeInfoDialog_default"]
+}

package/dist/chunks/chunk-2IWD4OO4.js

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+import{a as r}from"./chunk-FY3BTKY4.js";var e=r((s,o)=>{o.exports=JBrowseExports["@jbrowse/core/configuration"]});export{e as a};
+//# sourceMappingURL=chunk-2IWD4OO4.js.map

package/dist/chunks/chunk-2IWD4OO4.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["global-externals:@jbrowse/core/configuration"],
+  "sourcesContent": ["module.exports = JBrowseExports[\"@jbrowse/core/configuration\"];"],
+  "mappings": "wCAAA,IAAAA,EAAAC,EAAA,CAAAC,EAAAC,IAAA,CAAAA,EAAO,QAAU,eAAe,6BAA6B",
+  "names": ["require_configuration", "__commonJSMin", "exports", "module"]
+}

package/dist/chunks/chunk-5ORPTTMR.js

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+import{a}from"./chunk-FY3BTKY4.js";var i=a((p,c)=>{c.exports=JBrowseExports["@jbrowse/core/util/tss-react"]});function n(t){let o=navigator.clipboard;if(o?.writeText){o.writeText(t).catch(r=>{console.error("Failed to copy to clipboard:",r)});return}let e=document.createElement("textarea");e.value=t,e.style.position="fixed",e.style.opacity="0",document.body.append(e),e.select(),document.execCommand("copy"),e.remove()}export{i as a,n as b};
+//# sourceMappingURL=chunk-5ORPTTMR.js.map

package/dist/chunks/chunk-5ORPTTMR.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["global-externals:@jbrowse/core/util/tss-react", "../../node_modules/.pnpm/react-msaview@8.4.1_35cd7d1fa06820f3dff395dec9803110/node_modules/react-msaview/src/vendor/copyToClipboard.ts"],
+  "sourcesContent": ["module.exports = JBrowseExports[\"@jbrowse/core/util/tss-react\"];", "export default function copy(text: string) {\n  const clip = navigator.clipboard as Clipboard | undefined\n  if (clip?.writeText) {\n    clip.writeText(text).catch((e: unknown) => {\n      console.error('Failed to copy to clipboard:', e)\n    })\n    return\n  }\n  const textarea = document.createElement('textarea')\n  textarea.value = text\n  textarea.style.position = 'fixed'\n  textarea.style.opacity = '0'\n  document.body.append(textarea)\n  textarea.select()\n  document.execCommand('copy')\n  textarea.remove()\n}\n"],
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+  "names": ["require_tss_react", "__commonJSMin", "exports", "module", "copy", "text", "clip", "e", "textarea"]
+}

package/dist/chunks/chunk-6YFCSBEE.js

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+import{c as o,d as l}from"./chunk-IBBQUV2I.js";import{a as c}from"./chunk-BX4Z274Q.js";import{a}from"./chunk-J6KYLXRD.js";import{b as r}from"./chunk-FY3BTKY4.js";var e=r(a());var t=r(l(),1),n=(0,o.createSvgIcon)((0,t.jsx)("path",{d:"M19 19H5V5h7V3H5c-1.11 0-2 .9-2 2v14c0 1.1.89 2 2 2h14c1.1 0 2-.9 2-2v-7h-2zM14 3v2h3.59l-9.83 9.83 1.41 1.41L19 6.41V10h2V3z"}),"OpenInNew");var i=r(c());function s(m){let{children:p,...f}=m;return e.default.createElement(i.Link,{...f,target:"_blank",rel:"noreferrer"},p," ",e.default.createElement(n,{fontSize:"small"}))}export{s as a};
+//# sourceMappingURL=chunk-6YFCSBEE.js.map

package/dist/chunks/chunk-6YFCSBEE.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/components/ExternalLink.tsx", "../../node_modules/.pnpm/@mui+icons-material@9.4.0_@mui+material@9.4.0_@emotion+react@11.14.0_@types+react@19.3._3766ec55733e6b150ee672ad270cc236/node_modules/@mui/icons-material/OpenInNew.mjs"],
+  "sourcesContent": ["import React from 'react'\n\nimport OpenInNewIcon from '@mui/icons-material/OpenInNew'\nimport { Link } from '@mui/material'\n\nimport type { LinkProps } from '@mui/material'\n\nexport default function ExternalLink(props: LinkProps) {\n  const { children, ...rest } = props\n  return (\n    <Link {...rest} target=\"_blank\" rel=\"noreferrer\">\n      {children} <OpenInNewIcon fontSize=\"small\" />\n    </Link>\n  )\n}\n", "\"use client\";\n\nimport createSvgIcon from \"./utils/createSvgIcon.mjs\";\nimport { jsx as _jsx } from \"react/jsx-runtime\";\nexport default createSvgIcon(/*#__PURE__*/_jsx(\"path\", {\n  d: \"M19 19H5V5h7V3H5c-1.11 0-2 .9-2 2v14c0 1.1.89 2 2 2h14c1.1 0 2-.9 2-2v-7h-2zM14 3v2h3.59l-9.83 9.83 1.41 1.41L19 6.41V10h2V3z\"\n}), 'OpenInNew');"],
+  "mappings": "kKAAA,IAAAA,EAAkB,OCGlB,IAAAC,EAA4B,SACrBC,KAAQ,oBAA2B,EAAAC,KAAK,OAAQ,CACrD,EAAG,+HACL,CAAC,EAAG,WAAW,EDHf,IAAAC,EAAqB,OAIN,SAARC,EAA8BC,EAAkB,CACrD,GAAM,CAAE,SAAAC,EAAU,GAAGC,CAAK,EAAIF,EAC9B,OACE,EAAAG,QAAA,cAAC,QAAM,GAAGD,EAAM,OAAO,SAAS,IAAI,cACjCD,EAAS,IAAC,EAAAE,QAAA,cAACC,EAAA,CAAc,SAAS,QAAQ,CAC7C,CAEJ",
+  "names": ["import_react", "import_jsx_runtime", "OpenInNew_default", "_jsx", "import_material", "ExternalLink", "props", "children", "rest", "React", "OpenInNew_default"]
+}

package/dist/chunks/chunk-73KAPCJ2.js

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package/dist/chunks/chunk-73KAPCJ2.js.map

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+{
+  "version": 3,
+  "sources": ["../../node_modules/.pnpm/@gmod+newick@1.0.3/node_modules/@gmod/newick/src/hierarchy.ts", "../../node_modules/.pnpm/@gmod+newick@1.0.3/node_modules/@gmod/newick/src/newick.ts"],
+  "sourcesContent": ["/**\n * The d3-hierarchy traversals a tree viewer actually needs, without the\n * dependency.\n *\n * Every traversal here is iterative (an explicit stack, or a reversed pre-order\n * walk) rather than recursive. That is the whole point of the file: a\n * phylogenetic tree or a single-linkage dendrogram can be a caterpillar, whose\n * depth equals its leaf count, and the recursive form throws\n * `RangeError: Maximum call stack size exceeded` somewhere around 5000 tips.\n */\n\nexport interface HierarchyNode<T> {\n  data: T\n  children: HierarchyNode<T>[] | null\n  parent: HierarchyNode<T> | null\n  depth: number\n  height: number\n  /** set by `sum`, and otherwise absent */\n  value?: number\n}\n\nexport interface HierarchyLink<N> {\n  source: N\n  target: N\n}\n\n/**\n * What a traversal needs of a node, and the whole of it.\n *\n * The traversals are generic over the *node* type rather than over its data \u2014\n * `N extends TreeLike<N>` \u2014 so a caller that extends HierarchyNode with its own\n * layout fields gets its own type back instead of the base one, and a shape\n * that is not a HierarchyNode at all still walks.\n */\nexport interface TreeLike<N> {\n  children: N[] | null\n}\n\n/** A node `sum` can write to. */\ninterface Summable<N> extends TreeLike<N> {\n  data: unknown\n  value?: number\n}\n\nfunction pushChildren<N extends TreeLike<N>>(stack: N[], node: N) {\n  if (node.children) {\n    for (let i = node.children.length - 1; i >= 0; i--) {\n      stack.push(node.children[i]!)\n    }\n  }\n}\n\n/**\n * Pre-order: every parent precedes all of its descendants. Iterating the result\n * in reverse therefore yields a valid post-order (children before parents),\n * which the accumulation helpers rely on.\n */\nexport function descendants<N extends TreeLike<N>>(node: N): N[] {\n  const result: N[] = []\n  forEachDescendant(node, n => {\n    result.push(n)\n  })\n  return result\n}\n\nexport function forEachDescendant<N extends TreeLike<N>>(\n  node: N,\n  cb: (n: N) => void,\n) {\n  const stack = [node]\n  while (stack.length > 0) {\n    const n = stack.pop()!\n    cb(n)\n    pushChildren(stack, n)\n  }\n}\n\nexport function leaves<N extends TreeLike<N>>(node: N): N[] {\n  const result: N[] = []\n  forEachDescendant(node, n => {\n    if (!n.children) {\n      result.push(n)\n    }\n  })\n  return result\n}\n\n/**\n * Every parent->child edge, depth-first and left to right, so a link's whole\n * subtree is visited before its next sibling.\n *\n * The parent travels on the stack rather than being read back off the node, so\n * this works for a node type that carries no `parent` pointer.\n */\nexport function forEachLink<N extends TreeLike<N>>(\n  node: N,\n  cb: (source: N, target: N) => void,\n) {\n  const stack: { source: N | null; target: N }[] = [\n    { source: null, target: node },\n  ]\n  while (stack.length > 0) {\n    const { source, target } = stack.pop()!\n    if (source) {\n      cb(source, target)\n    }\n    if (target.children) {\n      for (let i = target.children.length - 1; i >= 0; i--) {\n        stack.push({ source: target, target: target.children[i]! })\n      }\n    }\n  }\n}\n\nexport function links<N extends TreeLike<N>>(node: N): HierarchyLink<N>[] {\n  const result: HierarchyLink<N>[] = []\n  forEachLink(node, (source, target) => {\n    result.push({ source, target })\n  })\n  return result\n}\n\n/**\n * Post-order: a node's children, left to right, then the node.\n *\n * Not `descendants().reverse()`, which also puts children before parents but\n * walks siblings right to left. Reversing a pre-order that pushes children\n * left-to-right (so the rightmost pops first) gives the real thing.\n */\nexport function eachAfter<N extends TreeLike<N>>(node: N, cb: (n: N) => void) {\n  const order: N[] = []\n  const stack = [node]\n  while (stack.length > 0) {\n    const n = stack.pop()!\n    order.push(n)\n    if (n.children) {\n      for (const child of n.children) {\n        stack.push(child)\n      }\n    }\n  }\n  for (let i = order.length - 1; i >= 0; i--) {\n    cb(order[i]!)\n  }\n}\n\nfunction computeHeight<T>(node: HierarchyNode<T>) {\n  eachAfter(node, n => {\n    let h = 0\n    if (n.children) {\n      for (const child of n.children) {\n        if (child.height + 1 > h) {\n          h = child.height + 1\n        }\n      }\n    }\n    n.height = h\n  })\n}\n\n/** Wrap plain data in hierarchy nodes, filling in depth, height and parent. */\nexport function hierarchy<T>(\n  data: T,\n  childrenAccessor: (d: T) => T[] | undefined | null,\n): HierarchyNode<T> {\n  const root: HierarchyNode<T> = {\n    data,\n    children: null,\n    parent: null,\n    depth: 0,\n    height: 0,\n  }\n  const stack = [root]\n  while (stack.length > 0) {\n    const node = stack.pop()!\n    const kids = childrenAccessor(node.data)\n    if (kids?.length) {\n      node.children = kids.map(d => ({\n        data: d,\n        children: null,\n        parent: node,\n        depth: node.depth + 1,\n        height: 0,\n      }))\n      for (const child of node.children) {\n        stack.push(child)\n      }\n    }\n  }\n  computeHeight(root)\n  return root\n}\n\n/**\n * Accumulate a value up the tree, each node summing its children's.\n *\n * One type parameter, with the datum reached through `N['data']`: a second one\n * for the datum cannot be inferred from the arguments, so callers would have to\n * write both out or get `unknown` in the callback.\n */\nexport function sum<N extends Summable<N>>(\n  node: N,\n  valueFn: (d: N['data']) => number,\n): N {\n  eachAfter(node, n => {\n    let s = valueFn(n.data)\n    if (n.children) {\n      for (const child of n.children) {\n        s += child.value!\n      }\n    }\n    n.value = s\n  })\n  return node\n}\n\n/** Sort every node's children in place. */\nexport function sort<N extends TreeLike<N>>(\n  node: N,\n  compareFn: (a: N, b: N) => number,\n): N {\n  const stack = [node]\n  while (stack.length > 0) {\n    const n = stack.pop()!\n    if (n.children) {\n      n.children.sort(compareFn)\n      for (const child of n.children) {\n        stack.push(child)\n      }\n    }\n  }\n  return node\n}\n\n/** First node matching the predicate, in pre-order. */\nexport function find<N extends TreeLike<N>>(\n  node: N,\n  predicate: (n: N) => boolean,\n): N | undefined {\n  const stack = [node]\n  while (stack.length > 0) {\n    const n = stack.pop()!\n    if (predicate(n)) {\n      return n\n    }\n    pushChildren(stack, n)\n  }\n  return undefined\n}\n", "/**\n * Newick format parser.\n *\n * Originally based on Jason Davies' 2010 implementation (MIT). Rewritten around\n * a hand-rolled scanner so that single-quoted labels are read as labels rather\n * than as grammar.\n *\n * Supported forms:\n *\n *   (A:0.1,B:0.2)F        \u2014 name and `:` branch length (standard phylo Newick)\n *   (A:0.1,B:0.2)F:0.5    \u2014 internal node name + branch length to parent\n *   (A,B)Foo              \u2014 non-numeric post-paren stored as `name`\n *   (A,B)1.5              \u2014 numeric post-paren; see `postParenNumeric` below\n *   ('A (x)','B,y')1.5    \u2014 single-quoted labels, `''` for a literal quote\n *   (A:0.1[&&NHX:S=human]) \u2014 bracketed comments (NHX, BEAST), dropped\n *\n * The quoted form is not decoration: a leaf name is an arbitrary string out of\n * somebody's data file, and one holding a `(` or a `,` is grammar rather than a\n * label unless it is quoted. A comma inside an unquoted label splits one leaf\n * into two and hands every row below it its neighbour's name, so the tree comes\n * back the wrong shape rather than merely mislabelled.\n */\n\nexport interface NewickNode {\n  name?: string\n  length?: number\n  children?: NewickNode[]\n}\n\n/**\n * How to read a bare number sitting after a `)`.\n *\n * The Newick grammar puts the internal node's *label* there, so `95` in\n * `((A,B)95,(C,D)80);` is a bootstrap support value. `@gmod/hclust` reuses the\n * same slot for a cluster's absolute merge height (`(A,B)1.5`) and never emits a\n * `:`, so for that dialect the number is a length. Nothing in the string\n * distinguishes the two, which is why this is a parameter and not a guess.\n *\n *   'name'   \u2014 always a name. Standard Newick.\n *   'length' \u2014 always a length. `@gmod/hclust` output.\n *   'auto'   \u2014 length only when the tree contains no `:` branch length at all,\n *              which is the shape hclust writes. The default, since reading a\n *              real phylogeny's support values as lengths would sum 0-100 into\n *              the branch distances and flatten the real ones.\n *\n * A *quoted* post-paren token is always a name under every setting: quoting is\n * the writer saying \"this is a label\", and it is the only way to name a node\n * something that looks like a number.\n */\nexport type PostParenNumeric = 'name' | 'length' | 'auto'\n\nexport interface ParseNewickOptions {\n  postParenNumeric?: PostParenNumeric\n}\n\nconst NUMERIC_TOKEN = /^-?\\d+(\\.\\d+)?([eE][+-]?\\d+)?$/\n\ninterface Token {\n  text: string\n  // a bare grammar character, as opposed to label text that happens to equal one\n  delim: boolean\n  // arrived single-quoted, so it is a label whatever it looks like\n  quoted: boolean\n}\n\n/**\n * Split into grammar characters and labels.\n *\n * A scanner rather than a regex split on the grammar characters, because a\n * split cannot know it is inside a quoted label and so tears the label apart on\n * the very characters quoting exists to protect.\n *\n * Whitespace is consumed around the delimiters and not inside labels: phased\n * haplotype rows are named `NA18536 HP0`, and stripping globally welds them\n * shut. 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Without this the name is\n      // dropped, and a root leaf with no name matches no row.\n      prevDelim === undefined\n    ) {\n      tree.name = token.text\n    }\n  }\n  return tree\n}\n"],
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+}

package/dist/chunks/chunk-BX4Z274Q.js

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package/dist/chunks/chunk-BX4Z274Q.js.map

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+}

package/dist/chunks/chunk-CVLB4VFP.js

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package/dist/chunks/chunk-CVLB4VFP.js.map

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+}

package/dist/chunks/chunk-DNFD5II2.js

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+//# sourceMappingURL=chunk-DNFD5II2.js.map

package/dist/chunks/chunk-DNFD5II2.js.map

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+}

package/dist/chunks/chunk-ENTWPX2K.js

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+${t?o:S(o)}`}function G(e){return!/[^.-]/.test(e)}function O(e,o){let t=[],r=0;for(let c of e){if(t.length>=N||r>=$)break;let i=T(c,o);t.push(i),r+=i.length+1}return{text:t.join(`
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+`);return n.default.createElement(n.default.Fragment,null,n.default.createElement(x,{text:h}),n.default.createElement(f.Button,{onClick:()=>{b(new Blob([h()],{type:"text/plain"}),"sequences.fasta")}},"Download"),n.default.createElement(d,{label:"Show gaps",checked:t,onChange:()=>{r(!t)}}),n.default.createElement(d,{label:"Show empty",checked:c,onChange:()=>{i(!c)}}),n.default.createElement(f.TextField,{variant:"outlined",multiline:!0,className:o.dialogContent,minRows:5,maxRows:10,fullWidth:!0,value:R,helperText:u>0?`Showing ${m.length-u} of ${m.length.toLocaleString()} sequences. ${u.toLocaleString()} more are in the copy and the download.`:void 0,slotProps:{input:{readOnly:!0,className:o.textAreaFont}}}))}export{B as a,A as b,W as c};
+//# sourceMappingURL=chunk-ENTWPX2K.js.map

package/dist/chunks/chunk-ENTWPX2K.js.map

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+{
+  "version": 3,
+  "sources": ["../../node_modules/.pnpm/react-msaview@8.4.1_35cd7d1fa06820f3dff395dec9803110/node_modules/react-msaview/src/components/MetadataTable.tsx", "../../node_modules/.pnpm/react-msaview@8.4.1_35cd7d1fa06820f3dff395dec9803110/node_modules/react-msaview/src/components/SequenceTextArea.tsx"],
+  "sourcesContent": ["import React from 'react'\n\nimport { makeStyles } from '@jbrowse/core/util/tss-react'\nimport { Table, TableBody, TableCell, TableRow } from '@mui/material'\n\nconst useStyles = makeStyles()({\n  key: {\n    fontWeight: 'bold',\n    verticalAlign: 'top',\n  },\n  value: {\n    whiteSpace: 'pre-wrap',\n    wordBreak: 'break-word',\n  },\n})\n\nfunction isRecord(value: unknown): value is Record<string, unknown> {\n  return typeof value === 'object' && value !== null && !Array.isArray(value)\n}\n\nexport function isEmpty(value: unknown) {\n  return isRecord(value) && Object.keys(value).length === 0\n}\n\nexport default function MetadataTable({\n  record,\n}: {\n  record: Record<string, unknown>\n}) {\n  const { classes } = useStyles()\n  return (\n    <Table size=\"small\">\n      <TableBody>\n        {Object.entries(record)\n          .filter(([, value]) => value != null && !isEmpty(value))\n          .map(([key, value]) => (\n            <TableRow key={key}>\n              <TableCell component=\"th\" className={classes.key}>\n                {key}\n              </TableCell>\n              <TableCell className={classes.value}>\n                {isRecord(value) ? (\n                  <MetadataTable record={value} />\n                ) : Array.isArray(value) ? (\n                  value.join('\\n')\n                ) : (\n                  String(value)\n                )}\n              </TableCell>\n            </TableRow>\n          ))}\n      </TableBody>\n    </Table>\n  )\n}\n", "import React, { useState } from 'react'\n\nimport { makeStyles } from '@jbrowse/core/util/tss-react'\nimport { Button, TextField } from '@mui/material'\nimport { getUngappedSequence } from 'msa-parsers'\n\nimport { saveAs } from '../vendor/fileSaver.ts'\nimport Checkbox2 from './Checkbox2.tsx'\nimport CopyButton from './CopyButton.tsx'\n\nconst useStyles = makeStyles()(theme => ({\n  textAreaFont: {\n    fontFamily: 'Courier New',\n    wordWrap: 'break-word',\n  },\n  dialogContent: {\n    background: theme.palette.action.selected,\n    margin: 4,\n  },\n}))\n\nexport const maxShownRecords = 100\nexport const maxShownChars = 200_000\n\nfunction fastaRecord([name, seq]: [string, string], showGaps: boolean) {\n  return `>${name}\\n${showGaps ? seq : getUngappedSequence(seq)}`\n}\n\nfunction isAllGaps(seq: string) {\n  return !/[^.-]/.test(seq)\n}\n\n/**\n * The first records of `rows` as FASTA, up to `maxShownRecords` records or\n * `maxShownChars` characters, whichever comes first. A textarea holding every\n * row of a large alignment freezes the page.\n */\nexport function fastaPreview(rows: [string, string][], showGaps: boolean) {\n  const shown: string[] = []\n  let chars = 0\n  for (const row of rows) {\n    if (shown.length >= maxShownRecords || chars >= maxShownChars) {\n      break\n    }\n    const record = fastaRecord(row, showGaps)\n    shown.push(record)\n    chars += record.length + 1\n  }\n  return { text: shown.join('\\n'), hidden: rows.length - shown.length }\n}\n\nexport default function SequenceTextArea({ str }: { str: [string, string][] }) {\n  const { classes } = useStyles()\n  const [showGaps, setShowGaps] = useState(false)\n  const [showEmpty, setShowEmpty] = useState(false)\n\n  const rows = showEmpty\n    ? str\n    : str.filter(([, seq]) => (showGaps ? !!seq : !isAllGaps(seq)))\n  const { text, hidden } = fastaPreview(rows, showGaps)\n  const fullText = () => rows.map(row => fastaRecord(row, showGaps)).join('\\n')\n  return (\n    <>\n      <CopyButton text={fullText} />\n      <Button\n        onClick={() => {\n          saveAs(\n            new Blob([fullText()], { type: 'text/plain' }),\n            'sequences.fasta',\n          )\n        }}\n      >\n        Download\n      </Button>\n      <Checkbox2\n        label=\"Show gaps\"\n        checked={showGaps}\n        onChange={() => {\n          setShowGaps(!showGaps)\n        }}\n      />\n      <Checkbox2\n        label=\"Show empty\"\n        checked={showEmpty}\n        onChange={() => {\n          setShowEmpty(!showEmpty)\n        }}\n      />\n      <TextField\n        variant=\"outlined\"\n        multiline\n        className={classes.dialogContent}\n        minRows={5}\n        maxRows={10}\n        fullWidth\n        value={text}\n        helperText={\n          hidden > 0\n            ? `Showing ${rows.length - hidden} of ${rows.length.toLocaleString()} sequences. ${hidden.toLocaleString()} more are in the copy and the download.`\n            : undefined\n        }\n        slotProps={{\n          input: {\n            readOnly: true,\n            className: classes.textAreaFont,\n          },\n        }}\n      />\n    </>\n  )\n}\n"],
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+  "names": ["import_react", "import_tss_react", "import_material", "useStyles", "isRecord", "value", "isEmpty", "MetadataTable", "record", "classes", "React", "key", "import_react", "import_tss_react", "import_material", "useStyles", "theme", "maxShownRecords", "maxShownChars", "fastaRecord", "name", "seq", "showGaps", "getUngappedSequence", "isAllGaps", "fastaPreview", "rows", "shown", "chars", "row", "record", "SequenceTextArea", "str", "classes", "setShowGaps", "showEmpty", "setShowEmpty", "text", "hidden", "fullText", "React", "CopyButton", "saveAs", "Checkbox2"]
+}

package/dist/chunks/chunk-EO7URJUB.js

@@ -0,0 +1,2 @@
+var l=["stack","splitRight","newTab"],a="splitRight",i="msaView-launchPlacement";function n(e,t){return t in e&&typeof e[t]=="function"}var r=!1;function w(e){return n(e,"setUseWorkspaces")&&n(e,"setPendingMove")}function p(e){let t=n(e,"setUseWorkspaces"),s=n(e,"setPendingMove");return t!==s&&!r&&(r=!0,console.warn(`jbrowse-plugin-msaview: this session supports workspaces but not ${s?"setUseWorkspaces":"setPendingMove"}, so the MSA view was stacked instead of tiled. Expected on releases through v4.3.0, which place views through @jbrowse/app-core instead; on a newer host it means the session API moved and the plugin needs updating to match.`)),t&&s}function c(e,t,s){s==="stack"||!p(e)||(e.setPendingMove({type:s,viewId:t}),e.setUseWorkspaces(!0))}function u(e){return l.includes(e)}function M(){try{let e=globalThis.localStorage.getItem(i);return u(e)?e:a}catch(e){return console.error(e),a}}function d(e){try{globalThis.localStorage.setItem(i,e)}catch(t){console.error(t)}}async function P(e,{placement:t="stack",...s}){let o=await e.launchView("MsaView",{type:"MsaView",...s});return c(e,o.id,t),o}export{w as a,M as b,d as c,P as d};
+//# sourceMappingURL=chunk-EO7URJUB.js.map

package/dist/chunks/chunk-EO7URJUB.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/utils/workspaces.ts", "../../src/utils/launchMsaView.ts"],
+  "sourcesContent": ["import type { AbstractSessionModel } from '@jbrowse/core/util'\n\n/**\n * Where a launched MSA view lands. Every launch names one of these and stops\n * there, so a host that arranges views differently is one function to teach.\n *\n *   stack       append below whatever is on screen\n *   splitRight  its own cell to the right, beside the view it is connected to\n *   newTab      its own tab in the current cell\n */\nexport type MsaViewPlacement = 'stack' | 'splitRight' | 'newTab'\n\nconst PLACEMENTS: MsaViewPlacement[] = ['stack', 'splitRight', 'newTab']\n\n/**\n * What the dialog does unasked. Side-by-side, because a launch from a gene\n * feature sets `connectedViewId`: the pair shares a hover and a highlight, and\n * reads as a split. A session spec defaults to `stack` instead.\n */\nexport const DEFAULT_LAUNCH_PLACEMENT: MsaViewPlacement = 'splitRight'\n\nexport const LAUNCH_PLACEMENT_KEY = 'msaView-launchPlacement'\n\n/**\n * The session actions that place a view in a tiled workspace. Only jbrowse-web\n * and desktop have them, so feature-detect rather than import.\n */\ninterface SessionWithWorkspaces {\n  setUseWorkspaces: (useWorkspaces: boolean) => void\n  setPendingMove: (move: {\n    type: 'newTab' | 'splitRight'\n    viewId: string\n  }) => void\n}\n\nfunction hasAction(session: AbstractSessionModel, name: string) {\n  return (\n    name in session &&\n    typeof (session as unknown as Record<string, unknown>)[name] === 'function'\n  )\n}\n\n// Warned at most once. This is a property of the host, so the answer is the\n// same on every launch and a dialog the user reopens should not stack up noise.\nlet warnedPartial = false\n\nexport function resetWorkspacesWarning() {\n  warnedPartial = false\n}\n\n/**\n * Whether this host can honor anything other than `stack`. Silent: the dialog\n * asks on every render, and only a launch is worth warning about.\n */\nexport function sessionSupportsPlacement(session: AbstractSessionModel) {\n  return (\n    hasAction(session, 'setUseWorkspaces') &&\n    hasAction(session, 'setPendingMove')\n  )\n}\n\nfunction isSessionWithWorkspaces(\n  session: AbstractSessionModel,\n): session is AbstractSessionModel & SessionWithWorkspaces {\n  const canEnable = hasAction(session, 'setUseWorkspaces')\n  const canPlace = hasAction(session, 'setPendingMove')\n\n  // Missing BOTH is an embedded session: it has no workspaces, there is nothing\n  // to ask for, and silence is the right answer.\n  //\n  // Missing ONE is a host that has workspaces but places views some other way,\n  // and silence there is how the same feature broke in jbrowse-plugin-protein3d\n  // \u2014 jbrowse-web folded `setPendingMove` into its layout `init`, the guard went\n  // false, and the plugin simply stopped asking: no error, no missing feature,\n  // two views quietly stacking, nobody noticed for weeks. Feature detection\n  // cannot ask a host to announce a change, but it can tell \"not supported here\"\n  // from \"supported, and gone\".\n  //\n  // Two very different hosts produce this one shape and nothing on the session\n  // tells them apart, so the message carries both rather than a guess:\n  //\n  // - releases through v4.3.0, where placement is `setPendingMoveToSplitRight`,\n  //   a module function in @jbrowse/app-core rather than a session action.\n  //   Nothing is wrong and nothing needs fixing\n  // - a newer host that moved the action out from under us, which is the\n  //   regression this warning exists to catch\n  //\n  // Do not quiet the first case by sniffing the version. The alarm is only worth\n  // having if it fires on a shape it cannot explain, and these two are identical.\n  if (canEnable !== canPlace && !warnedPartial) {\n    warnedPartial = true\n    console.warn(\n      `jbrowse-plugin-msaview: this session supports workspaces but not ` +\n        `${canPlace ? 'setUseWorkspaces' : 'setPendingMove'}, so the MSA view ` +\n        `was stacked instead of tiled. Expected on releases through v4.3.0, ` +\n        `which place views through @jbrowse/app-core instead; on a newer host ` +\n        `it means the session API moved and the plugin needs updating to match.`,\n    )\n  }\n  return canEnable && canPlace\n}\n\n/**\n * Put a freshly added view where the launch said to. `stack` is a placement\n * rather than the absence of one, so no caller has to ask what host it is on.\n */\nexport function placeMsaView(\n  session: AbstractSessionModel,\n  viewId: string,\n  placement: MsaViewPlacement,\n) {\n  if (placement === 'stack' || !isSessionWithWorkspaces(session)) {\n    return\n  }\n  session.setPendingMove({ type: placement, viewId })\n  // Session-scoped: turning workspaces on for this session leaves the user's\n  // own default alone, which is what `setUseWorkspaces` (as against\n  // `setUseWorkspacesPreference`) is for.\n  session.setUseWorkspaces(true)\n}\n\nfunction isPlacement(value: unknown): value is MsaViewPlacement {\n  return PLACEMENTS.includes(value as MsaViewPlacement)\n}\n\n/**\n * The dialog's own remembered choice \u2014 not the host's preferences system, which\n * records whether the user likes workspaces and does not exist everywhere.\n */\nexport function readLaunchPlacement(): MsaViewPlacement {\n  try {\n    const stored = globalThis.localStorage.getItem(LAUNCH_PLACEMENT_KEY)\n    return isPlacement(stored) ? stored : DEFAULT_LAUNCH_PLACEMENT\n  } catch (error) {\n    console.error(error)\n    return DEFAULT_LAUNCH_PLACEMENT\n  }\n}\n\nexport function writeLaunchPlacement(placement: MsaViewPlacement) {\n  try {\n    globalThis.localStorage.setItem(LAUNCH_PLACEMENT_KEY, placement)\n  } catch (error) {\n    console.error(error)\n  }\n}\n", "import { placeMsaView } from './workspaces'\n\nimport type { MsaViewPlacement } from './workspaces'\nimport type { AbstractSessionModel } from '@jbrowse/core/util'\n\n/**\n * A launch, stated: what the view is, and where it goes. Everything but\n * `placement` is a react-msaview or plugin-model snapshot property, passed\n * through untouched so this never becomes a list that has to grow.\n */\nexport interface MsaViewLaunchSpec extends Record<string, unknown> {\n  /** default `stack`, the only thing an embedded session can do */\n  placement?: MsaViewPlacement\n}\n\n/**\n * The one place a launch adds an MSA view -- the dialog's four tabs, the Add\n * menu, and the `LaunchView-MsaView` extension point a session spec arrives on\n * all come through here. Each of them used to run its own `addView` and none\n * placed the result, which is how a launch from a gene feature landed stacked\n * under the very genome view it was connected to.\n */\nexport async function launchMsaView(\n  session: AbstractSessionModel,\n  { placement = 'stack', ...snapshot }: MsaViewLaunchSpec,\n) {\n  const view = await session.launchView('MsaView', {\n    type: 'MsaView',\n    ...snapshot,\n  })\n  placeMsaView(session, view.id, placement)\n  return view\n}\n"],
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+  "names": ["PLACEMENTS", "DEFAULT_LAUNCH_PLACEMENT", "LAUNCH_PLACEMENT_KEY", "hasAction", "session", "name", "warnedPartial", "sessionSupportsPlacement", "session", "hasAction", "isSessionWithWorkspaces", "canEnable", "canPlace", "warnedPartial", "placeMsaView", "viewId", "placement", "isPlacement", "value", "PLACEMENTS", "readLaunchPlacement", "stored", "LAUNCH_PLACEMENT_KEY", "DEFAULT_LAUNCH_PLACEMENT", "error", "writeLaunchPlacement", "launchMsaView", "session", "placement", "snapshot", "view", "placeMsaView"]
+}

package/dist/chunks/chunk-FCNT6B47.js

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