From 5f757a2b348f8f8ffc7c72b29e722c2e3856fbc4 Mon Sep 17 00:00:00 2001
From: Colin <colin.diesh@gmail.com>
Date: Mon, 26 Aug 2024 17:51:55 -0400
Subject: [PATCH] Add ability to launch a protein view from any gene

---
 eslint.config.mjs                             |   1 +
 .../components/AlphaFoldDBSearch.tsx          | 125 +++++++++++++++++-
 src/LaunchProteinView/index.ts                |   8 +-
 3 files changed, 130 insertions(+), 4 deletions(-)

diff --git a/eslint.config.mjs b/eslint.config.mjs
index 5f9f9b2..c5ae967 100644
--- a/eslint.config.mjs
+++ b/eslint.config.mjs
@@ -71,6 +71,7 @@ export default tseslint.config(
       '@typescript-eslint/restrict-template-expressions': 'off',
       '@typescript-eslint/no-empty-function': 'off',
 
+      'unicorn/no-array-for-each': 'off',
       'unicorn/no-null': 'off',
       'unicorn/prefer-spread': 'off',
       'unicorn/no-nested-ternary': 'off',
diff --git a/src/LaunchProteinView/components/AlphaFoldDBSearch.tsx b/src/LaunchProteinView/components/AlphaFoldDBSearch.tsx
index 1e3c3d5..2aaa8b0 100644
--- a/src/LaunchProteinView/components/AlphaFoldDBSearch.tsx
+++ b/src/LaunchProteinView/components/AlphaFoldDBSearch.tsx
@@ -7,6 +7,7 @@ import {
   Feature,
   getContainingView,
   getSession,
+  isSessionWithAddTracks,
 } from '@jbrowse/core/util'
 import { ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui'
 import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
@@ -186,12 +187,132 @@ const AlphaFoldDBSearch = observer(function ({
                   connectedViewId: view.id,
                 },
               ],
-              displayName: `Protein view ${getGeneDisplayName(feature)} - ${getTranscriptDisplayName(selectedTranscript)}`,
+              displayName: `Protein view ${uniprotId} - ${getGeneDisplayName(feature)} - ${getTranscriptDisplayName(selectedTranscript)}`,
             })
             handleClose()
           }}
         >
-          Submit
+          Launch 3-D protein structure view
+        </Button>
+        <Button
+          variant="contained"
+          disabled={
+            !uniprotId || !userSelectedProteinSequence || !selectedTranscript
+          }
+          onClick={() => {
+            if (uniprotId && isSessionWithAddTracks(session)) {
+              session.addTemporaryAssembly?.({
+                name: uniprotId,
+                sequence: {
+                  type: 'ReferenceSequenceTrack',
+                  trackId: `${uniprotId}-ReferenceSequenceTrack`,
+                  sequenceType: 'pep',
+                  adapter: {
+                    type: 'UnindexedFastaAdapter',
+                    rewriteRefNames: "jexl:split(refName,'|')[1]",
+                    fastaLocation: {
+                      uri: `https://rest.uniprot.org/uniprotkb/${uniprotId}.fasta`,
+                    },
+                  },
+                },
+              })
+              ;[
+                'Alternative sequence',
+                'Beta strand',
+                'Binding site',
+                'Chain',
+                'Compositional bias',
+                'Cross-link',
+                'Disulfide bond',
+                'Domain',
+                'Glycosylation',
+                'Helix',
+                'Modified residue',
+                'Motif',
+                'Mutagenesis',
+                'Natural variant',
+                'Peptide',
+                'Region',
+                'Sequence conflict',
+                'Signal peptide',
+                'Site',
+                'Topological domain',
+                'Transmembrane',
+                'Turn',
+              ].forEach(type => {
+                const s = `${uniprotId}-${type}`
+                session.addTrackConf({
+                  type: 'FeatureTrack',
+                  trackId: s,
+                  name: type,
+                  adapter: {
+                    type: 'Gff3Adapter',
+                    gffLocation: {
+                      uri: `https://rest.uniprot.org/uniprotkb/${uniprotId}.gff`,
+                    },
+                  },
+                  assemblyNames: [uniprotId],
+                  displays: [
+                    {
+                      displayId: `${type}-LinearBasicDisplay`,
+                      type: 'LinearBasicDisplay',
+                      jexlFilters: [`get(feature,'type')=='${type}'`],
+                    },
+                  ],
+                })
+              })
+              session.addTrackConf({
+                type: 'QuantitativeTrack',
+                trackId: 'AlphaFold confidence',
+                name: 'AlphaFold confidence',
+                adapter: {
+                  type: 'AlphaFoldConfidenceAdapter',
+                  location: {
+                    uri: `https://alphafold.ebi.ac.uk/files/AF-${uniprotId}-F1-confidence_v4.json`,
+                    locationType: 'UriLocation',
+                  },
+                },
+                assemblyNames: [uniprotId],
+              })
+              session.addTrackConf({
+                type: 'MultiQuantitativeTrack',
+                trackId: 'AlphaMissense scores',
+                name: 'AlphaMissense scores',
+                assemblyNames: [uniprotId],
+                adapter: {
+                  type: 'AlphaMissensePathogenicityAdapter',
+                  location: {
+                    locationType: 'UriLocation',
+                    uri: `https://alphafold.ebi.ac.uk/files/AF-${uniprotId}-F1-aa-substitutions.csv`,
+                  },
+                },
+                displays: [
+                  {
+                    type: 'MultiLinearWiggleDisplay',
+                    displayId: 'AlphaMissense scores-MultiLinearWiggleDisplay',
+                    defaultRendering: 'multirowdensity',
+                    renderers: {
+                      MultiDensityRenderer: {
+                        type: 'MultiDensityRenderer',
+                        bicolorPivotValue: 0.5,
+                      },
+                    },
+                  },
+                ],
+              })
+              const view = session.addView('LinearGenomeView', {
+                type: 'LinearGenomeView',
+                displayName: `Protein view ${uniprotId} ${getGeneDisplayName(feature)} - ${getTranscriptDisplayName(selectedTranscript)}`,
+              }) as LinearGenomeViewModel
+              view.navToLocString(uniprotId, uniprotId).catch((e: unknown) => {
+                console.error(e)
+                session.notifyError(`${e}`, e)
+              })
+            }
+            handleClose()
+          }}
+        >
+          Launch linear protein annotation view
         </Button>
       </DialogActions>
     </>
diff --git a/src/LaunchProteinView/index.ts b/src/LaunchProteinView/index.ts
index ec1a692..64a54f0 100644
--- a/src/LaunchProteinView/index.ts
+++ b/src/LaunchProteinView/index.ts
@@ -31,12 +31,16 @@ function extendStateModel(stateModel: IAnyModelType) {
             ...(feature
               ? [
                   {
-                    label: 'Launch 3-D protein view',
+                    label: 'Launch protein view',
                     icon: AddIcon,
                     onClick: () => {
                       getSession(track).queueDialog(handleClose => [
                         LaunchProteinViewDialog,
-                        { model: track, handleClose, feature },
+                        {
+                          model: track,
+                          handleClose,
+                          feature,
+                        },
                       ])
                     },
                   },