react-msaview 3.1.12 → 3.2.1

package/src/components/tree/renderTreeCanvas.ts

@@ -1,8 +1,8 @@
-import RBush from 'rbush'
-import { Theme } from '@mui/material'
+import type RBush from 'rbush'
+import type { Theme } from '@mui/material'
 
 // locals
-import { MsaViewModel } from '../../model'
+import type { MsaViewModel } from '../../model'
 
 export const padding = 600
 
@@ -38,6 +38,9 @@ export function renderTree({
   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
@@ -87,10 +90,9 @@ export function renderNodeBubbles({
     // @ts-expect-error
     const { [val]: x, data } = node
     const y = node.x!
-    const { branchset, id = '', name = '' } = data
+    const { id = '', name = '' } = data
     if (
-      !id.endsWith('-leafnode') &&
-      branchset.length &&
+      node.height > 1 &&
       y > offsetY - extendBounds &&
       y < offsetY + by + extendBounds
     ) {
@@ -134,13 +136,19 @@ export function renderTreeLabels({
     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) {
@@ -149,7 +157,7 @@ export function renderTreeLabels({
   } else {
     ctx.textAlign = 'start'
   }
-  for (const node of hierarchy.leaves()) {
+  for (const node of leaves) {
     const {
       data: { name, id },
       // @ts-expect-error
@@ -162,7 +170,18 @@ export function renderTreeLabels({
     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
@@ -223,13 +242,12 @@ export function renderTreeCanvas({
   const {
     noTree,
     drawTree,
-    drawLabels,
     drawNodeBubbles,
     treeWidth,
     highResScaleFactor,
     blockSize,
     fontSize,
-    rowHeight,
+    showTreeText,
     marginLeft,
     nref,
   } = model
@@ -243,7 +261,9 @@ export function renderTreeCanvas({
   // is updated and in order to convince bundlers like not to delete unused
   // usage with propertyReadSideEffects
   const k =
-    nref < 0 ? -Infinity : highResScaleFactorOverride || highResScaleFactor
+    nref < 0
+      ? Number.NEGATIVE_INFINITY
+      : highResScaleFactorOverride || highResScaleFactor
   ctx.scale(k, k)
   ctx.clearRect(0, 0, treeWidth + padding, by)
   ctx.translate(marginLeft, -offsetY)
@@ -272,7 +292,7 @@ export function renderTreeCanvas({
     }
   }
 
-  if (rowHeight >= 5 && drawLabels) {
+  if (showTreeText) {
     renderTreeLabels({
       ctx,
       offsetY,

package/src/components/util.ts

@@ -10,8 +10,8 @@ export function chooseGridPitch(
 ) {
   scale = Math.abs(scale)
   const minMajorPitchBp = minMajorPitchPx * scale
-  const majorMagnitude = parseInt(
-    Number(minMajorPitchBp).toExponential().split(/e/i)[1],
+  const majorMagnitude = Number.parseInt(
+    Number(minMajorPitchBp).toExponential().split(/e/i)[1]!,
     10,
   )
 
@@ -50,9 +50,6 @@ export function makeTicks(
 
   let minBase = start
   let maxBase = end
-  if (minBase === null || maxBase === null) {
-    return []
-  }
 
   if (bpPerPx < 0) {
     ;[minBase, maxBase] = [maxBase, minBase]

package/src/ggplotPalettes.ts

@@ -19,7 +19,7 @@ const palettes = [
 ]
 
 export function getPalette(l: number) {
-  return palettes[Math.min(l, palettes.length - 1)]
+  return palettes[Math.min(l, palettes.length - 1)]!
 }
 
 export default palettes

package/src/launchInterProScan.ts

@@ -1,8 +1,8 @@
 import { getSession } from '@jbrowse/core/util'
 import { jsonfetch, textfetch, timeout } from './fetchUtils'
-import { MsaViewModel } from './model'
+import type { MsaViewModel } from './model'
 
-const base = `https://www.ebi.ac.uk/Tools/services/rest`
+const base = 'https://www.ebi.ac.uk/Tools/services/rest'
 
 export interface InterProScanResults {
   matches: {
@@ -38,7 +38,7 @@ async function runInterProScan({
     method: 'POST',
     body: new URLSearchParams({
       email: 'colin.diesh@gmail.com',
-      sequence: `${seq}`,
+      sequence: seq,
       programs: programs.join(','),
     }),
   })
@@ -47,7 +47,7 @@ async function runInterProScan({
     jobId,
     onProgress,
   })
-  return loadInterProScanResultsWithStatus({ jobId, model })
+  await loadInterProScanResultsWithStatus({ jobId, model })
 }
 
 export function loadInterProScanResults(jobId: string) {
@@ -65,7 +65,7 @@ async function wait({
 }) {
   const url = `${base}/iprscan5/status/${jobId}`
   try {
-    // eslint-disable-next-line no-constant-condition
+    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
     while (true) {
       for (let i = 0; i < 10; i++) {
         await timeout(1000)
@@ -75,6 +75,9 @@ async function wait({
       if (result.includes('FINISHED')) {
         break
       }
+      if (result.includes('FAILURE')) {
+        throw new Error(`Failed to run: jobId ${jobId}`)
+      }
     }
   } finally {
     onProgress()
@@ -99,17 +102,15 @@ export async function launchInterProScan({
   try {
     onProgress({ msg: `Launching ${algorithm} MSA` })
     if (algorithm === 'interproscan') {
-      const result = await runInterProScan({
+      await runInterProScan({
         seq,
         onJobId,
         onProgress,
         programs,
         model,
       })
-      return result
-    } else {
-      throw new Error('unknown algorithm')
     }
+    throw new Error('unknown algorithm')
   } finally {
     onProgress()
   }
@@ -124,15 +125,12 @@ export async function loadInterProScanResultsWithStatus({
 }) {
   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)',
+      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.setLoadedInterProAnnotations(
-      Object.fromEntries(ret.results.map(r => [r.xref[0].id, r])),
+    model.setInterProAnnotations(
+      Object.fromEntries(ret.results.map(r => [r.xref[0]!.id, r])),
     )
     model.setShowDomains(true)
     getSession(model).notify(`Loaded interproscan ${jobId} results`, 'success')

package/src/model/DataModel.ts

@@ -43,4 +43,14 @@ export function DataModelF() {
         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,
+      }
+    })
 }

package/src/model/DialogQueue.ts

@@ -1,4 +1,4 @@
-import { DialogComponentType } from '@jbrowse/core/util'
+import type { DialogComponentType } from '@jbrowse/core/util'
 import { types } from 'mobx-state-tree'
 
 /**
@@ -8,7 +8,6 @@ export function DialogQueueSessionMixin() {
   return types
     .model('DialogQueueSessionMixin', {})
     .volatile(() => ({
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any
       queueOfDialogs: [] as [DialogComponentType, any][],
     }))
     .views(self => ({