Misc

GMOD · Oct 12, 2023 · abd1cbd · abd1cbd
1 parent d06a7e4
commit abd1cbd
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Showing 3 changed files with 20 additions and 4 deletions.
diff --git a/package.json b/package.json
@@ -46,6 +46,8 @@
     "name": "MsaView"
   },
   "dependencies": {
+    "@types/pako": "^2.0.1",
+    "pako": "^2.1.0",
     "react-msaview": "^2.0.0",
     "regenerator-runtime": "^0.14.0",
     "tslib": "^2.3.1"

diff --git a/src/LaunchMsaView/LaunchMsaViewDialog.tsx b/src/LaunchMsaView/LaunchMsaViewDialog.tsx
@@ -9,6 +9,7 @@ import {
 } from '@mui/material'
 import { Feature, getSession } from '@jbrowse/core/util'
 import { makeStyles } from 'tss-react/mui'
+import { ungzip } from 'pako'
 
 // locals
 
@@ -74,7 +75,6 @@ export default function LaunchProteinViewDialog({
   const options = getTranscriptFeatures(feature)
 
   const [userSelection, setUserSelection] = useState(getId(options[0]))
-  console.log({ options })
   return (
     <Dialog
       maxWidth="xl"
@@ -108,17 +108,21 @@ export default function LaunchProteinViewDialog({
             ;(async () => {
               try {
                 const res = await fetch(
-                  `https://jbrowse.org/demos/msaview/knownCanonical/${userSelection}.json`,
+                  `https://jbrowse.org/demos/msaview/knownCanonical/${userSelection}.mfa.gz`,
                 )
                 if (!res.ok) {
                   throw new Error(
                     `HTTP ${res.status} fetching ${await res.text()}`,
                   )
                 }
-                const data = await res.json()
-                console.log({ data })
+                const data = await res.arrayBuffer()
+                const d = new TextDecoder().decode(ungzip(data))
                 session.addView('MsaView', {
                   type: 'MsaView',
+                  data: {
+                    msa: d,
+                    tree: '',
+                  },
                 })
                 handleClose()
               } catch (e) {

diff --git a/yarn.lock b/yarn.lock
@@ -1818,6 +1818,11 @@
   dependencies:
     undici-types "~5.25.1"
 
+"@types/pako@^2.0.1":
+  version "2.0.1"
+  resolved "https://registry.yarnpkg.com/@types/pako/-/pako-2.0.1.tgz#99e4b7ae6a8560c5928d7f31e89a394e1e6fd169"
+  integrity sha512-fXhui1fHdLrUR0KEyQsBzqdi3Z+MitnRcpI2eeFJyzaRdqO2miX/BDz2Hh0VdkBbrWprgcQ+ItFmbdKYdbMjvg==
+
 "@types/parse-json@^4.0.0":
   version "4.0.0"
   resolved "https://registry.yarnpkg.com/@types/parse-json/-/parse-json-4.0.0.tgz#2f8bb441434d163b35fb8ffdccd7138927ffb8c0"
@@ -6545,6 +6550,11 @@ pako@^1.0.11:
   resolved "https://registry.yarnpkg.com/pako/-/pako-1.0.11.tgz#6c9599d340d54dfd3946380252a35705a6b992bf"
   integrity sha512-4hLB8Py4zZce5s4yd9XzopqwVv/yGNhV1Bl8NTmCq1763HeK2+EwVTv+leGeL13Dnh2wfbqowVPXCIO0z4taYw==
 
+pako@^2.1.0:
+  version "2.1.0"
+  resolved "https://registry.yarnpkg.com/pako/-/pako-2.1.0.tgz#266cc37f98c7d883545d11335c00fbd4062c9a86"
+  integrity sha512-w+eufiZ1WuJYgPXbV/PO3NCMEc3xqylkKHzp8bxp1uW4qaSNQUkwmLLEc3kKsfz8lpV1F8Ht3U1Cm+9Srog2ug==
+
 parent-module@^1.0.0:
   version "1.0.1"
   resolved "https://registry.yarnpkg.com/parent-module/-/parent-module-1.0.1.tgz#691d2709e78c79fae3a156622452d00762caaaa2"