jbrowse-plugin-msaview 2.2.11 → 2.3.2

package/src/utils/msa.ts

@@ -2,93 +2,36 @@ import { textfetch, timeout } from './fetch'
 
 const base = `https://www.ebi.ac.uk/Tools/services/rest`
 
-async function runClustalOmega({
-  sequence,
-  onProgress,
-}: {
-  sequence: string
-  onProgress: (arg: string) => void
-}) {
-  const jobId = await textfetch(`${base}/clustalo/run`, {
-    method: 'POST',
-    body: new URLSearchParams({
-      email: 'colin.diesh@gmail.com',
-      sequence,
-    }),
-  })
-  await wait({ jobId, algorithm: 'clustalo', onProgress })
-  return {
-    msa: await textfetch(`${base}/clustalo/result/${jobId}/aln-clustal_num`),
-    tree: await textfetch(`${base}/clustalo/result/${jobId}/phylotree`),
-  }
-}
-
-async function runMuscle({
-  sequence,
-  onProgress,
-}: {
-  sequence: string
-  onProgress: (arg: string) => void
-}) {
-  const jobId = await textfetch(`${base}/muscle/run`, {
-    method: 'POST',
-    body: new URLSearchParams({
-      email: 'colin.diesh@gmail.com',
-      format: 'clw',
-      tree: 'tree1',
-      sequence,
-    }),
-  })
-  await wait({ jobId, algorithm: 'muscle', onProgress })
-  return {
-    msa: await textfetch(`${base}/muscle/result/${jobId}/fa`),
-    tree: await textfetch(`${base}/muscle/result/${jobId}/phylotree`),
+const algorithms: Record<
+  string,
+  {
+    params: Record<string, string>
+    msaResult: string
+    treeResult: string
   }
+> = {
+  clustalo: {
+    params: { email: 'colin.diesh@gmail.com' },
+    msaResult: 'aln-clustal_num',
+    treeResult: 'phylotree',
+  },
+  muscle: {
+    params: { email: 'colin.diesh@gmail.com', format: 'clw', tree: 'tree1' },
+    msaResult: 'fa',
+    treeResult: 'phylotree',
+  },
+  kalign: {
+    params: { email: 'colin.diesh@gmail.com', stype: 'protein' },
+    msaResult: 'fa',
+    treeResult: 'phylotree',
+  },
+  mafft: {
+    params: { email: 'colin.diesh@gmail.com', stype: 'protein' },
+    msaResult: 'fa',
+    treeResult: 'phylotree',
+  },
 }
 
-async function runKalign({
-  sequence,
-  onProgress,
-}: {
-  sequence: string
-  onProgress: (arg: string) => void
-}) {
-  const jobId = await textfetch(`${base}/kalign/run`, {
-    method: 'POST',
-    body: new URLSearchParams({
-      email: 'colin.diesh@gmail.com',
-      stype: 'protein',
-      sequence,
-    }),
-  })
-  await wait({ jobId, algorithm: 'kalign', onProgress })
-  return {
-    msa: await textfetch(`${base}/kalign/result/${jobId}/fa`),
-    tree: await textfetch(`${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,
@@ -123,22 +66,24 @@ export async function launchMSA({
   sequence: string
   onProgress: (arg: string) => void
 }) {
+  const config = algorithms[algorithm]
+  if (!config) {
+    throw new Error(`unknown algorithm: ${algorithm}`)
+  }
+
   onProgress(`Launching ${algorithm} MSA...`)
-  switch (algorithm) {
-    case 'clustalo': {
-      return runClustalOmega({ sequence, onProgress })
-    }
-    case 'muscle': {
-      return runMuscle({ sequence, onProgress })
-    }
-    case 'kalign': {
-      return runKalign({ sequence, onProgress })
-    }
-    case 'mafft': {
-      return runMafft({ sequence, onProgress })
-    }
-    default: {
-      throw new Error('unknown algorithm')
-    }
+
+  const jobId = await textfetch(`${base}/${algorithm}/run`, {
+    method: 'POST',
+    body: new URLSearchParams({ ...config.params, sequence }),
+  })
+  await wait({ jobId, algorithm, onProgress })
+  return {
+    msa: await textfetch(
+      `${base}/${algorithm}/result/${jobId}/${config.msaResult}`,
+    ),
+    tree: await textfetch(
+      `${base}/${algorithm}/result/${jobId}/${config.treeResult}`,
+    ),
   }
 }

package/src/utils/ncbiBlast.ts

@@ -1,5 +1,6 @@
 import { jsonfetch, textfetch, timeout } from './fetch'
-import { BlastResults } from './types'
+
+import type { BlastResults } from './types'
 
 export async function queryBlastFromRid({
   rid,
@@ -48,18 +49,7 @@ export async function queryBlast({
     baseUrl,
   })
   onRid(rid)
-  await waitForRid({
-    rid,
-    onProgress,
-    baseUrl,
-  })
-  const ret = await jsonfetch<BlastResults>(
-    `${baseUrl}?CMD=Get&RID=${rid}&FORMAT_TYPE=JSON2_S&FORMAT_OBJECT=Alignment`,
-  )
-  return {
-    rid,
-    hits: ret.BlastOutput2[0]?.report.results.search.hits ?? [],
-  }
+  return queryBlastFromRid({ rid, baseUrl, onProgress })
 }
 
 async function initialQuery({

package/CHANGELOG.md

@@ -1,101 +0,0 @@
-# v1.0.18
-
-- Fix clicking on node labels
-
-# v1.0.17
-
-- Avoid Link redirection at react-msaview importform
-
-# v1.0.16
-
-- Update to latest react-msaview
-
-# v1.0.15
-
-- Change to add to 'Add' top level menu
-
-# v1.0.14
-
-- Fix session link loading from distconfig.json
-
-# v1.0.13
-
-- Factor out code into the react-msaview package on NPM, and make the plugin
-  more of a wrapper around this module
-
-# v1.0.12
-
-- Avoid scrolling too far right
-
-# v1.0.11
-
-- Add version number from package.json to about panel
-
-# v1.0.10
-
-- Fix scrolling for large MSA that loads after tree
-
-# v1.0.9
-
-- Fix for MSA loading bar when tree only is displayed
-
-# v1.0.8
-
-- Fix for side scrolling half rendered letters in MSA
-- drawNodeBubbles option
-
-# v1.0.7
-
-- Move yarn build script to prepare script in package.jsom
-
-# v1.0.6
-
-- Use postversion to run build so that the accurate version is encoded into the
-  release binary
-
-# v1.0.5
-
-- Add prebuild clean
-
-# v1.0.4
-
-- Fix running build before release
-
-# v1.0.3
-
-- Re-release
-
-# v1.0.2
-
-- Ensure clean build with prebuild rm -rf dist
-
-# v1.0.1
-
-- Fix for making demo config on unpkg
-
-# v1.0.0
-
-## Features
-
-- Vertical virtualized scrolling of phylogenetic tree
-- Vertical and horizontal virtualized scrolling of multiple sequence alignment
-  as a newick tree embedded in stockholm metadata
-- View metadata about alignment from MSA headers (e.g. stockholm)
-- Collapse subtrees with click action on branches
-- The collapse subtree action hides gaps that were introduced by that subtree in
-  the rest of the alignment
-- Allows "zooming out" by setting tiny rowHeight/colWidth settings
-- Allows changing color schemes, with jalview, clustal, and other color schemes
-- Allows toggling the branch length rendering for the phylogenetic tree
-- Can share sessions with other users which will send relevant settings and
-  links to files to automatically open your results
-- The tree or the MSA panel can be loaded separately from each other
-
-## File format supports
-
-- FASTA formatted for MSA (e.g. gaps already inserted)
-- Stockholm files (e.g. .stock file, with or without embedded newick tree, uses
-  stockholm-js parser. also supports "multi-stockholm" files with multiple
-  alignments embedded in a single file)
-- Clustal files (e.g. .aln file, uses clustal-js parser)
-- Newick (tree can be loaded separately as a .nh file)