jbrowse-plugin-msaview 2.0.1 → 2.0.3

package/dist/utils/msa.js

@@ -45,6 +45,21 @@ async function runKalign({ sequence, onProgress, }) {
         tree: await textfetch(`${base}/kalign/result/${jobId}/phylotree`),
     };
 }
+async function runMafft({ sequence, onProgress, }) {
+    const jobId = await textfetch(`${base}/mafft/run`, {
+        method: 'POST',
+        body: new URLSearchParams({
+            email: 'colin.diesh@gmail.com',
+            stype: 'protein',
+            sequence,
+        }),
+    });
+    await wait({ jobId, algorithm: 'mafft', onProgress });
+    return {
+        msa: await textfetch(`${base}/mafft/result/${jobId}/fa`),
+        tree: await textfetch(`${base}/mafft/result/${jobId}/phylotree`),
+    };
+}
 async function wait({ onProgress, jobId, algorithm, }) {
     while (true) {
         for (let i = 0; i < 10; i++) {
@@ -59,17 +74,22 @@ async function wait({ onProgress, jobId, algorithm, }) {
 }
 export async function launchMSA({ algorithm, sequence, onProgress, }) {
     onProgress(`Launching ${algorithm} MSA...`);
-    if (algorithm === 'clustalo') {
-        return runClustalOmega({ sequence, onProgress });
-    }
-    else if (algorithm === 'muscle') {
-        return runMuscle({ sequence, onProgress });
-    }
-    else if (algorithm === 'kalign') {
-        return runKalign({ sequence, onProgress });
-    }
-    else {
-        throw new Error('unknown algorithm');
+    switch (algorithm) {
+        case 'clustalo': {
+            return runClustalOmega({ sequence, onProgress });
+        }
+        case 'muscle': {
+            return runMuscle({ sequence, onProgress });
+        }
+        case 'kalign': {
+            return runKalign({ sequence, onProgress });
+        }
+        case 'mafft': {
+            return runMafft({ sequence, onProgress });
+        }
+        default: {
+            throw new Error('unknown algorithm');
+        }
     }
 }
 //# sourceMappingURL=msa.js.map

package/dist/utils/msa.js.map

@@ -1 +1 @@
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+{"version":3,"file":"msa.js","sourceRoot":"","sources":["../../src/utils/msa.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,OAAO,EAAE,MAAM,SAAS,CAAA;AAE5C,MAAM,IAAI,GAAG,2CAA2C,CAAA;AAExD,KAAK,UAAU,eAAe,CAAC,EAC7B,QAAQ,EACR,UAAU,GAIX;IACC,MAAM,KAAK,GAAG,MAAM,SAAS,CAAC,GAAG,IAAI,eAAe,EAAE;QACpD,MAAM,EAAE,MAAM;QACd,IAAI,EAAE,IAAI,eAAe,CAAC;YACxB,KAAK,EAAE,uBAAuB;YAC9B,QAAQ;SACT,CAAC;KACH,CAAC,CAAA;IACF,MAAM,IAAI,CAAC,EAAE,KAAK,EAAE,SAAS,EAAE,UAAU,EAAE,UAAU,EAAE,CAAC,CAAA;IACxD,OAAO;QACL,GAAG,EAAE,MAAM,SAAS,CAAC,GAAG,IAAI,oBAAoB,KAAK,kBAAkB,CAAC;QACxE,IAAI,EAAE,MAAM,SAAS,CAAC,GAAG,IAAI,oBAAoB,KAAK,YAAY,CAAC;KACpE,CAAA;AACH,CAAC;AAED,KAAK,UAAU,SAAS,CAAC,EACvB,QAAQ,EACR,UAAU,GAIX;IACC,MAAM,KAAK,GAAG,MAAM,SAAS,CAAC,GAAG,IAAI,aAAa,EAAE;QAClD,MAAM,EAAE,MAAM;QACd,IAAI,EAAE,IAAI,eAAe,CAAC;YACxB,KAAK,EAAE,uBAAuB;YAC9B,MAAM,EAAE,KAAK;YACb,IAAI,EAAE,OAAO;YACb,QAAQ;SACT,CAAC;KACH,CAAC,CAAA;IACF,MAAM,IAAI,CAAC,EAAE,KAAK,EAAE,SAAS,EAAE,QAAQ,EAAE,UAAU,EAAE,CAAC,CAAA;IACtD,OAAO;QACL,GAAG,EAAE,MAAM,SAAS,CAAC,GAAG,IAAI,kBAAkB,KAAK,KAAK,CAAC;QACzD,IAAI,EAAE,MAAM,SAAS,CAAC,GAAG,IAAI,kBAAkB,KAAK,YAAY,CAAC;KAClE,CAAA;AACH,CAAC;AAED,KAAK,UAAU,SAAS,CAAC,EACvB,QAAQ,EACR,UAAU,GAIX;IACC,MAAM,KAAK,GAAG,MAAM,SAAS,CAAC,GAAG,IAAI,aAAa,EAAE;QAClD,MAAM,EAAE,MAAM;QACd,IAAI,EAAE,IAAI,eAAe,CAAC;YACxB,KAAK,EAAE,uBAAuB;YAC9B,KAAK,EAAE,SAAS;YAChB,QAAQ;SACT,CAAC;KACH,CAAC,CAAA;IACF,MAAM,IAAI,CAAC,EAAE,KAAK,EAAE,SAAS,EAAE,QAAQ,EAAE,UAAU,EAAE,CAAC,CAAA;IACtD,OAAO;QACL,GAAG,EAAE,MAAM,SAAS,CAAC,GAAG,IAAI,kBAAkB,KAAK,KAAK,CAAC;QACzD,IAAI,EAAE,MAAM,SAAS,CAAC,GAAG,IAAI,kBAAkB,KAAK,YAAY,CAAC;KAClE,CAAA;AACH,CAAC;AAED,KAAK,UAAU,QAAQ,CAAC,EACtB,QAAQ,EACR,UAAU,GAIX;IACC,MAAM,KAAK,GAAG,MAAM,SAAS,CAAC,GAAG,IAAI,YAAY,EAAE;QACjD,MAAM,EAAE,MAAM;QACd,IAAI,EAAE,IAAI,eAAe,CAAC;YACxB,KAAK,EAAE,uBAAuB;YAC9B,KAAK,EAAE,SAAS;YAChB,QAAQ;SACT,CAAC;KACH,CAAC,CAAA;IACF,MAAM,IAAI,CAAC,EAAE,KAAK,EAAE,SAAS,EAAE,OAAO,EAAE,UAAU,EAAE,CAAC,CAAA;IACrD,OAAO;QACL,GAAG,EAAE,MAAM,SAAS,CAAC,GAAG,IAAI,iBAAiB,KAAK,KAAK,CAAC;QACxD,IAAI,EAAE,MAAM,SAAS,CAAC,GAAG,IAAI,iBAAiB,KAAK,YAAY,CAAC;KACjE,CAAA;AACH,CAAC;AACD,KAAK,UAAU,IAAI,CAAC,EAClB,UAAU,EACV,KAAK,EACL,SAAS,GAKV;IACC,OAAO,IAAI,EAAE,CAAC;QACZ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC;YAC5B,MAAM,OAAO,CAAC,IAAI,CAAC,CAAA;YACnB,UAAU,CAAC,gCAAgC,EAAE,GAAG,CAAC,EAAE,CAAC,CAAA;QACtD,CAAC;QACD,MAAM,MAAM,GAAG,MAAM,SAAS,CAAC,GAAG,IAAI,IAAI,SAAS,WAAW,KAAK,EAAE,CAAC,CAAA;QAEtE,IAAI,MAAM,KAAK,UAAU,EAAE,CAAC;YAC1B,MAAK;QACP,CAAC;IACH,CAAC;AACH,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,SAAS,CAAC,EAC9B,SAAS,EACT,QAAQ,EACR,UAAU,GAKX;IACC,UAAU,CAAC,aAAa,SAAS,SAAS,CAAC,CAAA;IAC3C,QAAQ,SAAS,EAAE,CAAC;QAClB,KAAK,UAAU,CAAC,CAAC,CAAC;YAChB,OAAO,eAAe,CAAC,EAAE,QAAQ,EAAE,UAAU,EAAE,CAAC,CAAA;QAClD,CAAC;QACD,KAAK,QAAQ,CAAC,CAAC,CAAC;YACd,OAAO,SAAS,CAAC,EAAE,QAAQ,EAAE,UAAU,EAAE,CAAC,CAAA;QAC5C,CAAC;QACD,KAAK,QAAQ,CAAC,CAAC,CAAC;YACd,OAAO,SAAS,CAAC,EAAE,QAAQ,EAAE,UAAU,EAAE,CAAC,CAAA;QAC5C,CAAC;QACD,KAAK,OAAO,CAAC,CAAC,CAAC;YACb,OAAO,QAAQ,CAAC,EAAE,QAAQ,EAAE,UAAU,EAAE,CAAC,CAAA;QAC3C,CAAC;QACD,OAAO,CAAC,CAAC,CAAC;YACR,MAAM,IAAI,KAAK,CAAC,mBAAmB,CAAC,CAAA;QACtC,CAAC;IACH,CAAC;AACH,CAAC"}

package/dist/utils/ncbiBlast.js

@@ -32,8 +32,8 @@ async function initialQuery({ query, blastProgram, blastDatabase, }) {
     // the initial submission/query to the BLAST "REST API" does not return JSON
     // as a response (e.g. FORMAT_TYPE=JSON does not work), so the RID is
     // literally parsed from the text of the HTML that is returned
-    const rid = res.match(/^    RID = (.*$)/m)?.[1];
-    const rtoe = res.match(/^    RTOE = (.*$)/m)?.[1];
+    const rid = /^    RID = (.*$)/m.exec(res)?.[1];
+    const rtoe = /^    RTOE = (.*$)/m.exec(res)?.[1];
     if (!rid) {
         throw new Error('Failed to get RID from BLAST request');
     }
@@ -47,14 +47,14 @@ async function waitForRid({ rid, onProgress, }) {
             onProgress(`Re-checking BLAST status in... ${iter - i}`);
         }
         const res = await textfetch(`${BLAST_URL}?CMD=Get&FORMAT_OBJECT=SearchInfo&RID=${rid}`);
-        if (res.match(/\s+Status=WAITING/m)) {
+        if (/\s+Status=WAITING/m.test(res)) {
             continue;
         }
-        else if (res.match(/\s+Status=FAILED/m)) {
+        else if (/\s+Status=FAILED/m.test(res)) {
             throw new Error(`BLAST ${rid} failed; please report to blast-help@ncbi.nlm.nih.gov`);
         }
-        else if (res.match(/\s+Status=READY/m)) {
-            if (res.match(/\s+ThereAreHits=yes/m)) {
+        else if (/\s+Status=READY/m.test(res)) {
+            if (/\s+ThereAreHits=yes/m.test(res)) {
                 return true;
             }
             else {

package/dist/utils/ncbiBlast.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,5 +1,5 @@
 {
-  "version": "2.0.1",
+  "version": "2.0.3",
   "license": "MIT",
   "name": "jbrowse-plugin-msaview",
   "keywords": [
@@ -52,14 +52,15 @@
     "@types/node": "^20.8.6",
     "@types/pako": "^2.0.1",
     "@types/react": "^18.2.28",
-    "@typescript-eslint/eslint-plugin": "^7.0.1",
-    "@typescript-eslint/parser": "^7.0.1",
+    "@typescript-eslint/eslint-plugin": "^8.0.1",
+    "@typescript-eslint/parser": "^8.0.1",
     "esbuild": "^0.23.0",
     "eslint": "^9.0.0",
     "eslint-config-prettier": "^9.1.0",
     "eslint-plugin-prettier": "^5.1.0",
     "eslint-plugin-react": "^7.20.3",
     "eslint-plugin-react-hooks": "^4.6.0",
+    "eslint-plugin-unicorn": "^55.0.0",
     "mobx": "^6.10.2",
     "mobx-react": "^9.0.1",
     "mobx-state-tree": "^5.3.0",
@@ -67,7 +68,7 @@
     "pretty-bytes": "^6.1.1",
     "react": "^18.2.0",
     "react-dom": "^18.2.0",
-    "rimraf": "^5.0.5",
+    "rimraf": "^6.0.0",
     "rxjs": "^7.8.1",
     "tss-react": "^4.9.2",
     "typescript": "^5.2.2"

package/src/LaunchMsaView/components/NewNCBIBlastQuery/NcbiBlastPanel.tsx

@@ -110,9 +110,9 @@ const NcbiBlastPanel = observer(function NcbiBlastPanel2({
         maxRows={10}
         fullWidth
         value={
-          !proteinSequence
-            ? 'Loading...'
-            : `>${getTranscriptDisplayName(selectedTranscript)}\n${proteinSequence}`
+          proteinSequence
+            ? `>${getTranscriptDisplayName(selectedTranscript)}\n${proteinSequence}`
+            : 'Loading...'
         }
         InputProps={{
           readOnly: true,

package/src/LaunchMsaView/components/NewNCBIBlastQuery/index.tsx

@@ -1,2 +1 @@
-import NcbiBlastPanel from './NcbiBlastPanel'
-export default NcbiBlastPanel
+export { default } from './NcbiBlastPanel'

package/src/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.tsx

@@ -23,6 +23,7 @@ import {
   getTranscriptDisplayName,
   getId,
   getTranscriptFeatures,
+  getGeneDisplayName,
 } from '../../util'
 import { fetchGeneList } from './fetchGeneList'
 import { preCalculatedLaunchView } from './preCalculatedLaunchView'
@@ -120,7 +121,7 @@ const PreLoadedMSA = observer(function PreLoadedMSA2({
                 await preCalculatedLaunchView({
                   userSelection,
                   session,
-                  newViewTitle: '',
+                  newViewTitle: getGeneDisplayName(ret),
                   view,
                   feature: ret,
                 })

package/src/MsaViewPanel/model.ts

@@ -1,7 +1,7 @@
 import { Instance, addDisposer, cast, types } from 'mobx-state-tree'
 import { autorun } from 'mobx'
 import { MSAModelF } from 'react-msaview'
-import { Feature, getSession, notEmpty } from '@jbrowse/core/util'
+import { Feature, getSession } from '@jbrowse/core/util'
 import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 import { BaseViewModel } from '@jbrowse/core/pluggableElementTypes'
 
@@ -101,7 +101,6 @@ export default function stateModelFactory() {
        * #getter
        */
       get transcriptToMsaMap() {
-        console.log(self.connectedFeature)
         return self.connectedFeature
           ? genomeToTranscriptSeqMapping(self.connectedFeature)
           : undefined
@@ -226,13 +225,20 @@ export default function stateModelFactory() {
           self,
           autorun(async () => {
             if (self.blastParams) {
-              self.setProgress('Submitting query')
-              const data = await doLaunchBlast({
-                self: self as JBrowsePluginMsaViewModel,
-              })
-              self.setData(data)
-              self.setBlastParams(undefined)
-              self.setProgress('')
+              try {
+                self.setProgress('Submitting query')
+                const data = await doLaunchBlast({
+                  self: self as JBrowsePluginMsaViewModel,
+                })
+                self.setData(data)
+                self.setBlastParams(undefined)
+                self.setProgress('')
+              } catch (e) {
+                self.setError(e)
+                console.error(e)
+              } finally {
+                self.setProgress('')
+              }
             }
           }),
         )
@@ -243,14 +249,14 @@ export default function stateModelFactory() {
           autorun(() => {
             const { mouseCol, mouseClickCol } = self
             const r1 =
-              mouseCol !== undefined
-                ? msaCoordToGenomeCoord({ model: self, coord: mouseCol })
-                : undefined
+              mouseCol === undefined
+                ? undefined
+                : msaCoordToGenomeCoord({ model: self, coord: mouseCol })
             const r2 =
-              mouseClickCol !== undefined
-                ? msaCoordToGenomeCoord({ model: self, coord: mouseClickCol })
-                : undefined
-            self.setConnectedHighlights([r1, r2].filter(notEmpty))
+              mouseClickCol === undefined
+                ? undefined
+                : msaCoordToGenomeCoord({ model: self, coord: mouseClickCol })
+            self.setConnectedHighlights([r1, r2].filter(f => !!f))
           }),
         )
 
@@ -261,9 +267,9 @@ export default function stateModelFactory() {
             const { connectedView, zoomToBaseLevel, mouseClickCol } = self
             const { assemblyManager } = getSession(self)
             const r2 =
-              mouseClickCol !== undefined
-                ? msaCoordToGenomeCoord({ model: self, coord: mouseClickCol })
-                : undefined
+              mouseClickCol === undefined
+                ? undefined
+                : msaCoordToGenomeCoord({ model: self, coord: mouseClickCol })
 
             if (!r2 || !connectedView) {
               return

package/src/utils/msa.ts

@@ -67,6 +67,28 @@ async function runKalign({
     tree: await textfetch(`${base}/kalign/result/${jobId}/phylotree`),
   }
 }
+
+async function runMafft({
+  sequence,
+  onProgress,
+}: {
+  sequence: string
+  onProgress: (arg: string) => void
+}) {
+  const jobId = await textfetch(`${base}/mafft/run`, {
+    method: 'POST',
+    body: new URLSearchParams({
+      email: 'colin.diesh@gmail.com',
+      stype: 'protein',
+      sequence,
+    }),
+  })
+  await wait({ jobId, algorithm: 'mafft', onProgress })
+  return {
+    msa: await textfetch(`${base}/mafft/result/${jobId}/fa`),
+    tree: await textfetch(`${base}/mafft/result/${jobId}/phylotree`),
+  }
+}
 async function wait({
   onProgress,
   jobId,
@@ -99,13 +121,21 @@ export async function launchMSA({
   onProgress: (arg: string) => void
 }) {
   onProgress(`Launching ${algorithm} MSA...`)
-  if (algorithm === 'clustalo') {
-    return runClustalOmega({ sequence, onProgress })
-  } else if (algorithm === 'muscle') {
-    return runMuscle({ sequence, onProgress })
-  } else if (algorithm === 'kalign') {
-    return runKalign({ sequence, onProgress })
-  } else {
-    throw new Error('unknown algorithm')
+  switch (algorithm) {
+    case 'clustalo': {
+      return runClustalOmega({ sequence, onProgress })
+    }
+    case 'muscle': {
+      return runMuscle({ sequence, onProgress })
+    }
+    case 'kalign': {
+      return runKalign({ sequence, onProgress })
+    }
+    case 'mafft': {
+      return runMafft({ sequence, onProgress })
+    }
+    default: {
+      throw new Error('unknown algorithm')
+    }
   }
 }

package/src/utils/ncbiBlast.ts

@@ -62,8 +62,8 @@ async function initialQuery({
   // the initial submission/query to the BLAST "REST API" does not return JSON
   // as a response (e.g. FORMAT_TYPE=JSON does not work), so the RID is
   // literally parsed from the text of the HTML that is returned
-  const rid = res.match(/^    RID = (.*$)/m)?.[1]
-  const rtoe = res.match(/^    RTOE = (.*$)/m)?.[1]
+  const rid = /^    RID = (.*$)/m.exec(res)?.[1]
+  const rtoe = /^    RTOE = (.*$)/m.exec(res)?.[1]
 
   if (!rid) {
     throw new Error('Failed to get RID from BLAST request')
@@ -88,14 +88,14 @@ async function waitForRid({
     const res = await textfetch(
       `${BLAST_URL}?CMD=Get&FORMAT_OBJECT=SearchInfo&RID=${rid}`,
     )
-    if (res.match(/\s+Status=WAITING/m)) {
+    if (/\s+Status=WAITING/m.test(res)) {
       continue
-    } else if (res.match(/\s+Status=FAILED/m)) {
+    } else if (/\s+Status=FAILED/m.test(res)) {
       throw new Error(
         `BLAST ${rid} failed; please report to blast-help@ncbi.nlm.nih.gov`,
       )
-    } else if (res.match(/\s+Status=READY/m)) {
-      if (res.match(/\s+ThereAreHits=yes/m)) {
+    } else if (/\s+Status=READY/m.test(res)) {
+      if (/\s+ThereAreHits=yes/m.test(res)) {
         return true
       } else {
         throw new Error('No hits found')