react-msaview 3.1.12 → 3.2.1

package/src/parseGFF.ts

@@ -8,23 +8,25 @@ export function parseGFF(str?: string) {
         f.split('\t')
 
       return {
-        seq_id,
-        source,
-        type,
-        start: +start,
-        end: +end,
-        score: +score,
-        strand,
-        phase,
+        seq_id: seq_id!,
+        source: source!,
+        type: type!,
+        start: +start!,
+        end: +end!,
+        score: +score!,
+        strand: strand!,
+        phase: phase!,
         ...Object.fromEntries(
-          col9
+          col9!
             .split(';')
             .map(f => f.trim())
             .filter(f => !!f)
             .map(f => f.split('='))
             .map(([key, val]) => [
-              key.trim(),
-              decodeURIComponent(val).trim().split(',').join(' '),
+              key!.trim(),
+              val
+                ? decodeURIComponent(val).trim().split(',').join(' ')
+                : undefined,
             ]),
         ),
       }

package/src/parseNewick.ts

@@ -59,11 +59,11 @@
  */
 export default function parse(s: string) {
   const ancestors = []
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
+
   let tree = {} as Record<string, any>
   const tokens = s.split(/\s*(;|\(|\)|,|:)\s*/)
   for (let i = 0; i < tokens.length; i++) {
-    const token = tokens[i]
+    const token = tokens[i]!
     const subtree = {}
     switch (token) {
       case '(': // new branchset
@@ -81,11 +81,11 @@ export default function parse(s: string) {
       case ':': // optional length next
         break
       default: {
-        const x = tokens[i - 1]
+        const x = tokens[i - 1]!
         if (x === ')' || x === '(' || x === ',') {
           tree.name = token
         } else if (x === ':') {
-          tree.length = parseFloat(token)
+          tree.length = Number.parseFloat(token)
         }
       }
     }

package/src/parsers/ClustalMSA.ts

@@ -1,5 +1,5 @@
 import { parse } from 'clustal-js'
-import { NodeWithIds } from '../util'
+import type { NodeWithIds } from '../util'
 export default class ClustalMSA {
   private MSA: ReturnType<typeof parse>
 
@@ -11,12 +11,12 @@ export default class ClustalMSA {
     return this.MSA
   }
 
-  getRow(name: string) {
+  getRow(name: string): string {
     return this.MSA.alns.find(aln => aln.id === name)?.seq || ''
   }
 
   getWidth() {
-    return this.MSA.alns[0].seq.length
+    return this.MSA.alns[0]!.seq.length
   }
 
   getRowData() {

package/src/parsers/FastaMSA.ts

@@ -1,4 +1,4 @@
-import { NodeWithIds } from '../util'
+import type { NodeWithIds } from '../util'
 
 function parseSmallFasta(text: string) {
   return text
@@ -6,7 +6,7 @@ function parseSmallFasta(text: string) {
     .filter(t => /\S/.test(t))
     .map(entryText => {
       const [defLine, ...seqLines] = entryText.split('\n')
-      const [id, ...description] = defLine.split(' ')
+      const [id, ...description] = defLine!.split(' ')
       const descriptionStr = description.join(' ')
       const seqLinesStr = seqLines.join('')
       const sequence = seqLinesStr.replaceAll(/\s/g, '')
@@ -18,7 +18,7 @@ export default class FastaMSA {
   constructor(text: string) {
     this.MSA = {
       seqdata: Object.fromEntries(
-        parseSmallFasta(text).map(m => [`${m.id}`, m.sequence]),
+        parseSmallFasta(text).map(m => [m.id, m.sequence]),
       ),
     }
   }
@@ -36,11 +36,11 @@ export default class FastaMSA {
   }
 
   getRow(name: string) {
-    return this.MSA?.seqdata[name] || ''
+    return this.MSA.seqdata[name] || ''
   }
 
   getWidth() {
-    const name = Object.keys(this.MSA?.seqdata)[0]
+    const name = Object.keys(this.MSA.seqdata)[0]!
     return this.getRow(name).length
   }
 

package/src/parsers/StockholmMSA.ts

@@ -1,15 +1,15 @@
 import Stockholm from 'stockholm-js'
 import parseNewick from '../parseNewick'
 
-import { NodeWithIds, generateNodeIds } from '../util'
+import { type NodeWithIds, generateNodeIds } from '../util'
 interface StockholmEntry {
   gf: {
     DE?: string[]
     NH?: string[]
   }
-  gs: {
+  gs?: {
     AC: Record<string, string>
-    DR: Record<string, string>
+    DR?: Record<string, string>
   }
   gc?: {
     SS_cons?: string
@@ -33,11 +33,11 @@ export default class StockholmMSA {
   }
 
   getRow(name: string) {
-    return this.MSA?.seqdata[name] || ''
+    return this.MSA.seqdata[name] || ''
   }
 
   getWidth() {
-    const name = Object.keys(this.MSA?.seqdata)[0]
+    const name = Object.keys(this.MSA.seqdata)[0]!
     return this.getRow(name).length
   }
 
@@ -56,7 +56,7 @@ export default class StockholmMSA {
   getRowData(rowName: string) {
     return {
       name: rowName,
-      accession: this.MSA.gs?.AC?.[rowName],
+      accession: this.MSA.gs?.AC[rowName],
       dbxref: this.MSA.gs?.DR?.[rowName],
     }
   }
@@ -74,10 +74,10 @@ export default class StockholmMSA {
       .map(([id, dr]) => [id, pdbRegex.exec(dr)] as const)
       .filter((item): item is [string, RegExpExecArray] => !!item[1])
       .map(([id, match]) => {
-        const pdb = match[1].toLowerCase()
-        const chain = match[2]
-        const startPos = +match[3]
-        const endPos = +match[4]
+        const pdb = match[1]!.toLowerCase()
+        const chain = match[2]!
+        const startPos = +match[3]!
+        const endPos = +match[4]!
         return { id, pdb, chain, startPos, endPos }
       })
 
@@ -93,7 +93,7 @@ export default class StockholmMSA {
   }
 
   getTree(): NodeWithIds {
-    const tree = this.MSA?.gf?.NH?.[0]
+    const tree = this.MSA.gf.NH?.[0]
     return tree
       ? generateNodeIds(parseNewick(tree))
       : {

package/src/renderToSvg.tsx

@@ -1,11 +1,12 @@
+/* eslint-disable react-refresh/only-export-components */
 import React from 'react'
 import { createRoot } from 'react-dom/client'
 import { when } from 'mobx'
 import { renderToStaticMarkup } from '@jbrowse/core/util'
-import { Theme } from '@mui/material'
+import type { Theme } from '@mui/material'
 
 // locals
-import { MsaViewModel } from './model'
+import type { MsaViewModel } from './model'
 import { renderTreeCanvas } from './components/tree/renderTreeCanvas'
 import { renderMSABlock } from './components/msa/renderMSABlock'
 import { colorContrast } from './util'
@@ -17,7 +18,7 @@ export async function renderToSvg(
   model: MsaViewModel,
   opts: { theme: Theme; includeMinimap?: boolean; exportType: string },
 ) {
-  await when(() => !!model.initialized)
+  await when(() => !!model.dataInitialized)
   const { width, height, scrollX, scrollY } = model
   const { exportType, theme, includeMinimap } = opts
 
@@ -31,7 +32,8 @@ export async function renderToSvg(
       offsetX: 0,
       includeMinimap,
     })
-  } else if (exportType === 'viewport') {
+  }
+  if (exportType === 'viewport') {
     return render({
       width,
       height,
@@ -41,9 +43,8 @@ export async function renderToSvg(
       offsetX: -scrollX,
       includeMinimap,
     })
-  } else {
-    throw new Error('unknown export type')
   }
+  throw new Error('unknown export type')
 }
 
 async function render({
@@ -153,13 +154,11 @@ function CoreRendering({
 
       <g
         clipPath={`url(#${clipId1})`}
-        /* eslint-disable-next-line react/no-danger */
         dangerouslySetInnerHTML={{ __html: ctx1.getSvg().innerHTML }}
       />
       <g
         clipPath={`url(#${clipId2})`}
         transform={`translate(${treeAreaWidth} 0)`}
-        /* eslint-disable-next-line react/no-danger */
         dangerouslySetInnerHTML={{ __html: ctx2.getSvg().innerHTML }}
       />
     </>

package/src/reparseTree.ts

@@ -1,4 +1,4 @@
-import { NodeWithIds } from './util'
+import type { NodeWithIds } from './util'
 
 export function reparseTree(tree: NodeWithIds): NodeWithIds {
   return {

package/src/rowCoordinateCalculations.test.ts

@@ -0,0 +1,19 @@
+import { expect, test } from 'vitest'
+import { mouseOverCoordToGlobalCoord } from './rowCoordinateCalculations'
+test('blanks3', () => {
+  const blanks = [2, 5, 8]
+  ;(
+    [
+      [0, 0],
+      [1, 1],
+      [2, 3],
+      [3, 4],
+      [4, 6],
+      [5, 7],
+      [6, 9],
+      [7, 10],
+    ] as const
+  ).forEach(r => {
+    expect(mouseOverCoordToGlobalCoord(blanks, r[0])).toBe(r[1])
+  })
+})

package/src/rowCoordinateCalculations.ts

@@ -0,0 +1,26 @@
+export function mouseOverCoordToGlobalCoord(blanks: number[], pos: number) {
+  let i = 0 // 'mouse over coord'
+  let j = 0 // 'position in blanks array'
+  let k = 0 // 'global coord'/return value
+
+  for (; i < pos; i++, k++) {
+    // skip multiple gaps in a row
+    while (j < blanks.length && blanks[j]! - 1 === k) {
+      j++
+      k++
+    }
+  }
+  return k
+}
+
+export function globalCoordToRowSpecificCoord(seq: string, pos: number) {
+  let k = 0
+  for (let i = 0; i < pos; i++) {
+    if (seq[i] !== '-') {
+      k++
+    } else if (k >= pos) {
+      break
+    }
+  }
+  return k
+}

package/src/util.ts

@@ -1,6 +1,6 @@
-import { HierarchyNode } from 'd3-hierarchy'
+import type { HierarchyNode } from 'd3-hierarchy'
 import { max } from 'd3-array'
-import { Theme } from '@mui/material'
+import type { Theme } from '@mui/material'
 import { colord, extend } from 'colord'
 import namesPlugin from 'colord/plugins/names'
 
@@ -106,8 +106,6 @@ export function collapse(d: HierarchyNode<NodeWithIds>) {
     // @ts-expect-error
     d._children = d.children
     // @ts-expect-error
-    d._children.forEach(collapse)
-    // @ts-expect-error
     d.children = null
   }
 }

package/src/version.ts

@@ -1 +1 @@
-export const version = '3.1.12'
+export const version = '3.2.1'

package/dist/components/dialogs/InterProScanPanel.js.map

@@ -1 +0,0 @@
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package/dist/components/dialogs/UserProvidedResultPanel.d.ts

@@ -1,7 +0,0 @@
-import React from 'react';
-import { MsaViewModel } from '../../model';
-declare const FeatureTypeDialog: ({ handleClose, model, }: {
-    handleClose: () => void;
-    model: MsaViewModel;
-}) => React.JSX.Element;
-export default FeatureTypeDialog;

package/dist/components/dialogs/UserProvidedResultPanel.js

@@ -1,56 +0,0 @@
-import React, { useState } from 'react';
-import { observer } from 'mobx-react';
-import { Button, DialogActions, DialogContent, FormControlLabel, FormControl, Radio, RadioGroup, TextField, Typography, } from '@mui/material';
-import { getSession } from '@jbrowse/core/util';
-import { jsonfetch } from '../../fetchUtils';
-const FeatureTypeDialog = observer(function ({ handleClose, model, }) {
-    const [file, setFile] = useState();
-    const [choice, setChoice] = useState('file');
-    const [interProURL, setInterProURL] = useState('');
-    return (React.createElement(React.Fragment, null,
-        React.createElement(DialogContent, null,
-            React.createElement("div", { style: { display: 'flex', margin: 30 } },
-                React.createElement(Typography, null, "Open a JSON file of InterProScan results that you run remotely on EBI servers or locally"),
-                React.createElement(FormControl, { component: "fieldset" },
-                    React.createElement(RadioGroup, { value: choice, onChange: event => setChoice(event.target.value) },
-                        React.createElement(FormControlLabel, { value: "url", control: React.createElement(Radio, null), label: "URL" }),
-                        React.createElement(FormControlLabel, { value: "file", control: React.createElement(Radio, null), label: "File" }))),
-                choice === 'url' ? (React.createElement("div", null,
-                    React.createElement(Typography, null, "Open a InterProScan JSON file remote URL"),
-                    React.createElement(TextField, { label: "URL", value: interProURL, onChange: event => setInterProURL(event.target.value) }))) : null,
-                choice === 'file' ? (React.createElement("div", { style: { paddingTop: 20 } },
-                    React.createElement(Typography, null, "Open a InterProScan JSON file file from your local drive"),
-                    React.createElement(Button, { variant: "outlined", component: "label" },
-                        "Choose File",
-                        React.createElement("input", { type: "file", hidden: true, onChange: ({ target }) => {
-                                const file = target?.files?.[0];
-                                if (file) {
-                                    setFile(file);
-                                }
-                            } })))) : null)),
-        React.createElement(DialogActions, null,
-            React.createElement(Button, { variant: "contained", color: "primary", onClick: () => {
-                    // eslint-disable-next-line @typescript-eslint/no-floating-promises
-                    ;
-                    (async () => {
-                        try {
-                            const ret = file
-                                ? JSON.parse(await file.text())
-                                : await jsonfetch(interProURL);
-                            model.setLoadedInterProAnnotations(Object.fromEntries(ret.results.map(r => [r.xref[0].id, r])));
-                            model.setShowDomains(true);
-                            getSession(model).notify('Loaded interproscan results', 'success');
-                        }
-                        catch (e) {
-                            console.error(e);
-                            getSession(model).notifyError(`${e}`, e);
-                        }
-                        finally {
-                            model.setStatus();
-                        }
-                    })();
-                    handleClose();
-                } }, "Open results"))));
-});
-export default FeatureTypeDialog;
-//# sourceMappingURL=UserProvidedResultPanel.js.map

package/dist/components/dialogs/UserProvidedResultPanel.js.map

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package/src/components/dialogs/UserProvidedResultPanel.tsx

@@ -1,119 +0,0 @@
-import React, { useState } from 'react'
-import { observer } from 'mobx-react'
-import {
-  Button,
-  DialogActions,
-  DialogContent,
-  FormControlLabel,
-  FormControl,
-  Radio,
-  RadioGroup,
-  TextField,
-  Typography,
-} from '@mui/material'
-import { getSession } from '@jbrowse/core/util'
-
-// locals
-import { MsaViewModel } from '../../model'
-import { jsonfetch } from '../../fetchUtils'
-import { InterProScanResponse } from '../../launchInterProScan'
-
-const FeatureTypeDialog = observer(function ({
-  handleClose,
-  model,
-}: {
-  handleClose: () => void
-  model: MsaViewModel
-}) {
-  const [file, setFile] = useState<File>()
-  const [choice, setChoice] = useState('file')
-  const [interProURL, setInterProURL] = useState('')
-
-  return (
-    <>
-      <DialogContent>
-        <div style={{ display: 'flex', margin: 30 }}>
-          <Typography>
-            Open a JSON file of InterProScan results that you run remotely on
-            EBI servers or locally
-          </Typography>
-
-          <FormControl component="fieldset">
-            <RadioGroup
-              value={choice}
-              onChange={event => setChoice(event.target.value)}
-            >
-              <FormControlLabel value="url" control={<Radio />} label="URL" />
-              <FormControlLabel value="file" control={<Radio />} label="File" />
-            </RadioGroup>
-          </FormControl>
-          {choice === 'url' ? (
-            <div>
-              <Typography>Open a InterProScan JSON file remote URL</Typography>
-              <TextField
-                label="URL"
-                value={interProURL}
-                onChange={event => setInterProURL(event.target.value)}
-              />
-            </div>
-          ) : null}
-          {choice === 'file' ? (
-            <div style={{ paddingTop: 20 }}>
-              <Typography>
-                Open a InterProScan JSON file file from your local drive
-              </Typography>
-              <Button variant="outlined" component="label">
-                Choose File
-                <input
-                  type="file"
-                  hidden
-                  onChange={({ target }) => {
-                    const file = target?.files?.[0]
-                    if (file) {
-                      setFile(file)
-                    }
-                  }}
-                />
-              </Button>
-            </div>
-          ) : null}
-        </div>
-      </DialogContent>
-      <DialogActions>
-        <Button
-          variant="contained"
-          color="primary"
-          onClick={() => {
-            // eslint-disable-next-line @typescript-eslint/no-floating-promises
-            ;(async () => {
-              try {
-                const ret: InterProScanResponse = file
-                  ? JSON.parse(await file.text())
-                  : await jsonfetch(interProURL)
-
-                model.setLoadedInterProAnnotations(
-                  Object.fromEntries(ret.results.map(r => [r.xref[0].id, r])),
-                )
-                model.setShowDomains(true)
-                getSession(model).notify(
-                  'Loaded interproscan results',
-                  'success',
-                )
-              } catch (e) {
-                console.error(e)
-                getSession(model).notifyError(`${e}`, e)
-              } finally {
-                model.setStatus()
-              }
-            })()
-            handleClose()
-          }}
-        >
-          Open results
-        </Button>
-      </DialogActions>
-    </>
-  )
-})
-
-export default FeatureTypeDialog