react-msaview 3.1.11 → 3.1.12

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
       },
 
       /**
@@ -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 = '3.1.11'
+export const version = '3.1.12'

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

@@ -1 +0,0 @@
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