react-msaview 3.1.10 → 3.1.12

package/src/components/msa/renderBoxFeatureCanvasBlock.ts

@@ -19,9 +19,9 @@ export function renderBoxFeatureCanvasBlock({
   highResScaleFactorOverride?: number
   blockSizeYOverride?: number
 }) {
-  const { hierarchy, blockSize, rowHeight, highResScaleFactor, featureMode } =
+  const { hierarchy, blockSize, rowHeight, highResScaleFactor, showDomains } =
     model
-  if (featureMode) {
+  if (showDomains) {
     const k = highResScaleFactorOverride || highResScaleFactor
     const by = blockSizeYOverride || blockSize
     ctx.resetTransform()

package/src/components/msa/renderMSABlock.ts

@@ -34,7 +34,7 @@ export function renderMSABlock({
     rowHeight,
     fontSize,
     highResScaleFactor,
-    featureMode,
+    showDomains,
   } = model
   const k = highResScaleFactorOverride || highResScaleFactor
   const bx = blockSizeXOverride || blockSize
@@ -53,7 +53,7 @@ export function renderMSABlock({
   const xEnd = Math.max(0, Math.ceil((offsetX + bx) / colWidth))
   const visibleLeaves = leaves.slice(yStart, yEnd)
 
-  if (!featureMode) {
+  if (!showDomains) {
     drawTiles({
       model,
       ctx,
@@ -152,7 +152,7 @@ function drawText({
   xStart: number
   xEnd: number
 }) {
-  const { bgColor, featureMode, colorScheme, columns, colWidth, rowHeight } =
+  const { bgColor, showDomains, colorScheme, columns, colWidth, rowHeight } =
     model
   if (rowHeight >= 5 && colWidth > rowHeight / 2) {
     for (const node of visibleLeaves) {
@@ -168,7 +168,7 @@ function drawText({
         const x = i * colWidth + offsetX - (offsetX % colWidth)
 
         // note: -rowHeight/4 matches +rowHeight/4 in tree
-        ctx.fillStyle = featureMode
+        ctx.fillStyle = showDomains
           ? 'black'
           : bgColor
             ? contrast

package/src/components/tree/TreeCanvas.tsx

@@ -1,5 +1,4 @@
 import React, { useEffect, useRef, useState } from 'react'
-import normalizeWheel from 'normalize-wheel'
 import { observer } from 'mobx-react'
 
 // locals
@@ -20,9 +19,8 @@ const TreeCanvas = observer(function ({ model }: { model: MsaViewModel }) {
     if (!curr) {
       return
     }
-    function onWheel(origEvent: WheelEvent) {
-      const event = normalizeWheel(origEvent)
-      deltaY.current += event.pixelY
+    function onWheel(event: WheelEvent) {
+      deltaY.current += event.deltaY
 
       if (!scheduled.current) {
         scheduled.current = true
@@ -32,8 +30,8 @@ const TreeCanvas = observer(function ({ model }: { model: MsaViewModel }) {
           scheduled.current = false
         })
       }
-      origEvent.preventDefault()
-      origEvent.stopPropagation()
+      event.preventDefault()
+      event.stopPropagation()
     }
     curr.addEventListener('wheel', onWheel)
     return () => {

package/src/fetchUtils.ts

@@ -15,9 +15,9 @@ export async function textfetch(url: string, args?: RequestInit) {
   return response.text()
 }
 
-export async function jsonfetch(url: string, args?: RequestInit) {
+export async function jsonfetch<T>(url: string, args?: RequestInit) {
   const response = await myfetch(url, args)
-  return response.json()
+  return response.json() as T
 }
 
 export async function arraybufferfetch(url: string) {

package/src/launchInterProScan.ts

@@ -1,4 +1,6 @@
+import { getSession } from '@jbrowse/core/util'
 import { jsonfetch, textfetch, timeout } from './fetchUtils'
+import { MsaViewModel } from './model'
 
 const base = `https://www.ebi.ac.uk/Tools/services/rest`
 
@@ -24,11 +26,13 @@ async function runInterProScan({
   onProgress,
   onJobId,
   programs,
+  model,
 }: {
   seq: string
   programs: string[]
   onProgress: (arg?: { msg: string; url?: string }) => void
-  onJobId: (arg: string) => void
+  onJobId?: (arg: string) => void
+  model: MsaViewModel
 }) {
   const jobId = await textfetch(`${base}/iprscan5/run`, {
     method: 'POST',
@@ -38,18 +42,18 @@ async function runInterProScan({
       programs: programs.join(','),
     }),
   })
-  onJobId(jobId)
+  onJobId?.(jobId)
   await wait({
     jobId,
     onProgress,
   })
-  return loadInterProScanResults(jobId)
+  return loadInterProScanResultsWithStatus({ jobId, model })
 }
 
-export async function loadInterProScanResults(jobId: string) {
-  return (await jsonfetch(
+export function loadInterProScanResults(jobId: string) {
+  return jsonfetch<InterProScanResponse>(
     `${base}/iprscan5/result/${jobId}/json`,
-  )) as InterProScanResponse
+  )
 }
 
 async function wait({
@@ -60,17 +64,20 @@ async function wait({
   onProgress: (arg?: { msg: string; url?: string }) => void
 }) {
   const url = `${base}/iprscan5/status/${jobId}`
-  // eslint-disable-next-line no-constant-condition
-  while (true) {
-    for (let i = 0; i < 10; i++) {
-      await timeout(1000)
-      onProgress({ msg: `Checking status... ${10 - i}`, url })
-    }
-    const result = await textfetch(url)
-
-    if (result === 'FINISHED') {
-      break
+  try {
+    // eslint-disable-next-line no-constant-condition
+    while (true) {
+      for (let i = 0; i < 10; i++) {
+        await timeout(1000)
+        onProgress({ msg: `Checking status ${10 - i}`, url })
+      }
+      const result = await textfetch(url)
+      if (result.includes('FINISHED')) {
+        break
+      }
     }
+  } finally {
+    onProgress()
   }
 }
 
@@ -80,19 +87,59 @@ export async function launchInterProScan({
   programs,
   onJobId,
   onProgress,
+  model,
 }: {
   algorithm: string
   seq: string
   programs: string[]
   onProgress: (arg?: { msg: string; url?: string }) => void
-  onJobId: (arg: string) => void
+  onJobId?: (arg: string) => void
+  model: MsaViewModel
 }) {
-  onProgress({ msg: `Launching ${algorithm} MSA...` })
-  if (algorithm === 'interproscan') {
-    const result = await runInterProScan({ seq, onJobId, onProgress, programs })
+  try {
+    onProgress({ msg: `Launching ${algorithm} MSA` })
+    if (algorithm === 'interproscan') {
+      const result = await runInterProScan({
+        seq,
+        onJobId,
+        onProgress,
+        programs,
+        model,
+      })
+      return result
+    } else {
+      throw new Error('unknown algorithm')
+    }
+  } finally {
     onProgress()
-    return result
-  } else {
-    throw new Error('unknown algorithm')
+  }
+}
+
+export async function loadInterProScanResultsWithStatus({
+  jobId,
+  model,
+}: {
+  jobId: string
+  model: MsaViewModel
+}) {
+  try {
+    model.setStatus({
+      msg:
+        'Downloading results of ' +
+        jobId +
+        ' (for larger sequences this can be slow, click status to download and upload in the manual tab)',
+      url: `https://www.ebi.ac.uk/Tools/services/rest/iprscan5/result/${jobId}/json`,
+    })
+    const ret = await loadInterProScanResults(jobId)
+    model.setLoadedInterProAnnotations(
+      Object.fromEntries(ret.results.map(r => [r.xref[0].id, r])),
+    )
+    model.setShowDomains(true)
+    getSession(model).notify(`Loaded interproscan ${jobId} results`, 'success')
+  } catch (e) {
+    console.error(e)
+    getSession(model).notifyError(`${e}`, e)
+  } finally {
+    model.setStatus()
   }
 }

package/src/model.ts

@@ -52,11 +52,7 @@ import { DataModelF } from './model/DataModel'
 import { DialogQueueSessionMixin } from './model/DialogQueue'
 import { TreeF } from './model/treeModel'
 import { MSAModelF } from './model/msaModel'
-import {
-  InterProScanResults,
-  launchInterProScan,
-  loadInterProScanResults,
-} from './launchInterProScan'
+import { InterProScanResults } from './launchInterProScan'
 
 export interface Accession {
   accession: string
@@ -105,7 +101,7 @@ function stateModelFactory() {
         /**
          * #property
          */
-        featureMode: false,
+        showDomains: false,
         /**
          * #property
          */
@@ -296,12 +292,6 @@ function stateModelFactory() {
       loadedInterProAnnotations: undefined as
         | undefined
         | Record<string, InterProScanResults>,
-      /**
-       * #volatile
-       */
-      interProScanJobIds: JSON.parse(
-        localStorageGetItem('msaview-interproscanqueries') || '[]',
-      ) as { jobId: string; date: number }[],
     }))
     .actions(self => ({
       /**
@@ -349,8 +339,8 @@ function stateModelFactory() {
       /**
        * #action
        */
-      setFeatureMode(arg: boolean) {
-        self.featureMode = arg
+      setShowDomains(arg: boolean) {
+        self.showDomains = arg
       },
 
       /**
@@ -580,7 +570,7 @@ function stateModelFactory() {
        */
       get mouseOverRowName() {
         const { mouseRow } = self
-        return mouseRow !== undefined ? this.rowNames[mouseRow] : undefined
+        return mouseRow === undefined ? undefined : this.rowNames[mouseRow]
       },
 
       /**
@@ -835,15 +825,6 @@ function stateModelFactory() {
           self.turnedOffTracks.set(id, true)
         }
       },
-      /**
-       * #action
-       */
-      addInterProScanJobId(arg: string) {
-        self.interProScanJobIds = [
-          ...self.interProScanJobIds,
-          { jobId: arg, date: +Date.now() },
-        ]
-      },
       /**
        * #action
        */
@@ -1063,40 +1044,6 @@ function stateModelFactory() {
       },
     }))
     .actions(self => ({
-      /**
-       * #action
-       */
-      async loadInterProScanResults(jobId: string) {
-        self.setStatus({ msg: 'Loading ' + jobId })
-        const ret = await loadInterProScanResults(jobId)
-        self.setStatus()
-        self.setLoadedInterProAnnotations(
-          Object.fromEntries(ret.results.map(r => [r.xref[0].id, r])),
-        )
-      },
-      /**
-       * #action
-       */
-      async queryInterProScan(programs: string[]) {
-        const { rows } = self
-        if (rows.length > 140) {
-          throw new Error('Too many sequences, please run InterProScan offline')
-        }
-
-        const ret = await launchInterProScan({
-          algorithm: 'interproscan',
-          programs: programs,
-          seq: rows
-            .map(row => `>${row[0]}\n${row[1].replaceAll('-', '')}`)
-            .join('\n'),
-          onProgress: arg => self.setStatus(arg),
-          onJobId: jobId => self.addInterProScanJobId(jobId),
-        })
-
-        self.setLoadedInterProAnnotations(
-          Object.fromEntries(ret.results.map(r => [r.xref[0].id, r])),
-        )
-      },
       /**
        * #action
        */
@@ -1156,25 +1103,7 @@ function stateModelFactory() {
             }
           }),
         )
-        addDisposer(
-          self,
-          autorun(async () => {
-            // const res = Object.fromEntries(
-            //   await Promise.all(
-            //     self.annotationTracks.map(async f => {
-            //       const d = await jsonfetch(
-            //         `https://jbrowse.org/demos/interproscan/json/${encodeURIComponent(f)}`,
-            //       )
-            //       return [
-            //         decodeURIComponent(f).replace('.json', ''),
-            //         d.result.results[0],
-            //       ] as const
-            //     }),
-            //   ),
-            // )
-            // self.setLoadedInterProAnnotations(res)
-          }),
-        )
+
         // autorun opens treeFilehandle
         addDisposer(
           self,
@@ -1257,16 +1186,6 @@ function stateModelFactory() {
             }
           }),
         )
-
-        addDisposer(
-          self,
-          autorun(() => {
-            localStorageSetItem(
-              'msaview-interproscanqueries',
-              JSON.stringify(self.interProScanJobIds),
-            )
-          }),
-        )
       },
     }))
     .postProcessSnapshot(result => {

package/src/renderToSvg.tsx

@@ -84,30 +84,6 @@ async function render({
   )
 }
 
-// function renderMultiline({ model }: { model: MsaViewModel }) {
-//   const { treeAreaWidth, height } = model
-//   const clipId = 'tree'
-//   return (
-//     <Wrapper model={model}>
-//       <defs>
-//         <clipPath id={clipId}>
-//           <rect x={0} y={0} width={treeAreaWidth} height={height} />
-//         </clipPath>
-//       </defs>
-//       <g
-//         clipPath={`url(#${clipId})`}
-//         /* eslint-disable-next-line react/no-danger */
-//         dangerouslySetInnerHTML={{ __html: ctx1.getSvg().innerHTML }}
-//       />
-//       <g
-//         transform={`translate(${treeAreaWidth} 0)`}
-//         /* eslint-disable-next-line react/no-danger */
-//         dangerouslySetInnerHTML={{ __html: ctx2.getSvg().innerHTML }}
-//       />
-//     </Wrapper>
-//   )
-// }
-
 function CoreRendering({
   model,
   theme,

package/src/version.ts

@@ -1 +1 @@
-export const version = '3.1.10'
+export const version = '3.1.12'

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

@@ -1 +0,0 @@
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