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GMOD · Aug 22, 2024 · eb2f164 · eb2f164
1 parent a756359
commit eb2f164
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Showing 14 changed files with 455 additions and 446 deletions.
diff --git a/src/ProteinView/loadStructureFromData.ts → src/ProteinView/addStructureFromData.ts b/src/ProteinView/loadStructureFromData.ts → src/ProteinView/addStructureFromData.ts
@@ -7,7 +7,7 @@ export interface LoadStructureOptions {
 }
 
 // adapted from https://github.com/molstar/molstar/blob/ab4130d42d0ab2591f62460292ade0203207d4d2/src/apps/viewer/app.ts#L255C1-L259C6
-export async function loadStructureFromData({
+export async function addStructureFromData({
   data,
   format = 'pdb',
   options,
@@ -18,8 +18,6 @@ export async function loadStructureFromData({
   options?: LoadStructureOptions & { label?: string; dataLabel?: string }
   plugin: PluginContext
 }) {
-  await plugin.clear()
-
   const _data = await plugin.builders.data.rawData({
     data,
     label: options?.dataLabel,

diff --git a/src/ProteinView/loadStructureFromURL.ts → src/ProteinView/addStructureFromURL.ts b/src/ProteinView/loadStructureFromURL.ts → src/ProteinView/addStructureFromURL.ts
@@ -7,7 +7,7 @@ export interface LoadStructureOptions {
 }
 
 // adapted from https://github.com/molstar/molstar/blob/ab4130d42d0ab2591f62460292ade0203207d4d2/src/apps/viewer/app.ts#L230
-export async function loadStructureFromURL({
+export async function addStructureFromURL({
   url,
   format = 'mmcif',
   isBinary,
@@ -20,11 +20,16 @@ export async function loadStructureFromURL({
   options?: LoadStructureOptions & { label?: string }
   plugin: PluginContext
 }) {
-  await plugin.clear()
-
   const data = await plugin.builders.data.download(
-    { url, isBinary },
-    { state: { isGhost: true } },
+    {
+      url,
+      isBinary,
+    },
+    {
+      state: {
+        isGhost: true,
+      },
+    },
   )
 
   const trajectory = await plugin.builders.structure.parseTrajectory(

diff --git a/src/ProteinView/components/ProteinAlignment.tsx b/src/ProteinView/components/ProteinAlignment.tsx
@@ -3,7 +3,7 @@ import { observer } from 'mobx-react'
 import { Tooltip, Typography } from '@mui/material'
 
 // locals
-import { JBrowsePluginProteinViewModel } from '../model'
+import { JBrowsePluginProteinStructureModel } from '../model'
 import ProteinAlignmentHelpButton from './ProteinAlignmentHelpButton'
 import {
   clickProteinToGenome,
@@ -14,7 +14,7 @@ import SplitString from './SplitString'
 const ProteinAlignment = observer(function ({
   model,
 }: {
-  model: JBrowsePluginProteinViewModel
+  model: JBrowsePluginProteinStructureModel
 }) {
   const {
     structureSeqHoverPos,
@@ -26,8 +26,8 @@ const ProteinAlignment = observer(function ({
   if (!alignment) {
     return <div>No alignment</div>
   }
-  const a0 = alignment.alns[0]!.seq as string
-  const a1 = alignment.alns[1]!.seq as string
+  const a0 = alignment.alns[0].seq
+  const a1 = alignment.alns[1].seq
   const con = alignment.consensus
   const set = new Set<number>()
   // eslint-disable-next-line unicorn/no-for-loop

diff --git a/src/ProteinView/components/ProteinView.tsx b/src/ProteinView/components/ProteinView.tsx
@@ -29,88 +29,75 @@ const ProteinView = observer(function ({
 }: {
   model: JBrowsePluginProteinViewModel
 }) {
-  const { url, data, showControls } = model
-  const { plugin, seq, parentRef, error } = useProteinView({
-    url,
-    data,
+  const { showControls } = model
+  const { plugin, parentRef, error } = useProteinView({
     showControls,
   })
   return error ? (
     <ErrorMessage error={error} />
   ) : (
-    <ProteinViewContainer
-      model={model}
-      plugin={plugin}
-      seq={seq}
-      parentRef={parentRef}
-    />
+    <ProteinViewContainer model={model} plugin={plugin} parentRef={parentRef} />
   )
 })
 
 const ProteinViewContainer = observer(function ({
   model,
   plugin,
-  seq,
   parentRef,
 }: {
   model: JBrowsePluginProteinViewModel
   plugin?: PluginContext
-  seq?: string
   parentRef?: React.RefObject<HTMLDivElement>
 }) {
   const {
     width,
     height,
-    structureSeqToTranscriptSeqPosition,
-    seq2,
-    structureSeqHoverPos,
     showHighlight,
-    alignment,
+    // structureSeqToTranscriptSeqPosition,
+    // structureSeqHoverPos,
+    // alignment,
   } = model
 
-  const { error } = useProteinViewClickBehavior({ plugin, model })
-  useProteinViewHoverBehavior({ plugin, model })
+  // const { error } = useProteinViewClickBehavior({ plugin, model })
+  // useProteinViewHoverBehavior({ plugin, model })
 
-  const structure =
-    plugin?.managers.structure.hierarchy.current.structures[0]?.cell.obj?.data
-
-  useEffect(() => {
-    model.setSeqs(seq, seq2)
-  }, [seq, model, seq2])
-
-  useEffect(() => {
-    if (!plugin || !structureSeqToTranscriptSeqPosition || !structure) {
-      return
-    }
-    if (showHighlight) {
-      for (const coord of Object.keys(structureSeqToTranscriptSeqPosition)) {
-        selectResidue({
-          structure,
-          plugin,
-          selectedResidue: +coord + 1,
-        })
-      }
-    } else {
-      clearSelection({ plugin })
-    }
-  }, [plugin, structure, showHighlight, structureSeqToTranscriptSeqPosition])
-
-  useEffect(() => {
-    if (!plugin || !structure) {
-      return
-    }
-
-    if (structureSeqHoverPos === undefined) {
-      console.warn('not found')
-    } else {
-      highlightResidue({
-        structure,
-        plugin,
-        selectedResidue: structureSeqHoverPos,
-      })
-    }
-  }, [plugin, structure, structureSeqHoverPos])
+  // const structure =
+  //   plugin?.managers.structure.hierarchy.current.structures[0]?.cell.obj?.data
 
+  // useEffect(() => {
+  //   if (!plugin || !structureSeqToTranscriptSeqPosition || !structure) {
+  //     return
+  //   }
+  //   if (showHighlight) {
+  //     for (const coord of Object.keys(structureSeqToTranscriptSeqPosition)) {
+  //       selectResidue({
+  //         structure,
+  //         plugin,
+  //         selectedResidue: +coord + 1,
+  //       })
+  //     }
+  //   } else {
+  //     clearSelection({ plugin })
+  //   }
+  // }, [plugin, structure, showHighlight, structureSeqToTranscriptSeqPosition])
+  //
+  // useEffect(() => {
+  //   if (!plugin || !structure) {
+  //     return
+  //   }
+  //
+  //   if (structureSeqHoverPos === undefined) {
+  //     console.warn('not found')
+  //   } else {
+  //     highlightResidue({
+  //       structure,
+  //       plugin,
+  //       selectedResidue: structureSeqHoverPos,
+  //     })
+  //   }
+  // }, [plugin, structure, structureSeqHoverPos])
+  const error = undefined
+  const alignment = undefined
   return (
     <div style={{ background: alignment ? undefined : '#ccc' }}>
       {error ? <ErrorMessage error={error} /> : null}

diff --git a/src/ProteinView/genomeToProtein.ts b/src/ProteinView/genomeToProtein.ts
@@ -1,21 +1,17 @@
 import { getSession } from '@jbrowse/core/util'
 import { checkHovered } from './util'
-import { JBrowsePluginProteinViewModel } from './model'
+import { JBrowsePluginProteinStructureModel } from './model'
 
 export function genomeToProtein({
   model,
 }: {
-  model: JBrowsePluginProteinViewModel
+  model: JBrowsePluginProteinStructureModel
 }): number | undefined {
   const { hovered } = getSession(model)
   const { genomeToTranscriptSeqMapping, connectedView } = model
-  if (
-    !connectedView?.initialized ||
+  return !connectedView?.initialized ||
     !genomeToTranscriptSeqMapping ||
     !checkHovered(hovered)
-  ) {
-    return undefined
-  }
-
-  return genomeToTranscriptSeqMapping.g2p[hovered.hoverPosition.coord]
+    ? undefined
+    : genomeToTranscriptSeqMapping.g2p[hovered.hoverPosition.coord]
 }