diff --git a/viz/package.json b/viz/package.json index 12db81a..f522cfc 100644 --- a/viz/package.json +++ b/viz/package.json @@ -18,6 +18,7 @@ "@radix-ui/react-separator": "^1.1.0", "@radix-ui/react-slider": "^1.2.1", "@radix-ui/react-slot": "^1.1.0", + "@radix-ui/react-tabs": "^1.1.2", "@radix-ui/react-toggle": "^1.1.0", "@radix-ui/react-toggle-group": "^1.1.0", "@radix-ui/react-tooltip": "^1.1.3", diff --git a/viz/pnpm-lock.yaml b/viz/pnpm-lock.yaml index d4a7e35..593a1c9 100644 --- a/viz/pnpm-lock.yaml +++ b/viz/pnpm-lock.yaml @@ -32,6 +32,9 @@ importers: '@radix-ui/react-slot': specifier: ^1.1.0 version: 1.1.0(@types/react@18.3.3)(react@18.3.1) + '@radix-ui/react-tabs': + specifier: ^1.1.2 + version: 1.1.2(@types/react-dom@18.3.0)(@types/react@18.3.3)(react-dom@18.3.1(react@18.3.1))(react@18.3.1) '@radix-ui/react-toggle': specifier: ^1.1.0 version: 1.1.0(@types/react-dom@18.3.0)(@types/react@18.3.3)(react-dom@18.3.1(react@18.3.1))(react@18.3.1) @@ -443,6 +446,9 @@ packages: '@radix-ui/primitive@1.1.0': resolution: {integrity: sha512-4Z8dn6Upk0qk4P74xBhZ6Hd/w0mPEzOOLxy4xiPXOXqjF7jZS0VAKk7/x/H6FyY2zCkYJqePf1G5KmkmNJ4RBA==} + '@radix-ui/primitive@1.1.1': + resolution: {integrity: sha512-SJ31y+Q/zAyShtXJc8x83i9TYdbAfHZ++tUZnvjJJqFjzsdUnKsxPL6IEtBlxKkU7yzer//GQtZSV4GbldL3YA==} + '@radix-ui/react-accordion@1.2.1': resolution: {integrity: sha512-bg/l7l5QzUjgsh8kjwDFommzAshnUsuVMV5NM56QVCm+7ZckYdd9P/ExR8xG/Oup0OajVxNLaHJ1tb8mXk+nzQ==} peerDependencies: @@ -495,6 +501,19 @@ packages: '@types/react-dom': optional: true + '@radix-ui/react-collection@1.1.1': + resolution: {integrity: sha512-LwT3pSho9Dljg+wY2KN2mrrh6y3qELfftINERIzBUO9e0N+t0oMTyn3k9iv+ZqgrwGkRnLpNJrsMv9BZlt2yuA==} + peerDependencies: + '@types/react': '*' + '@types/react-dom': '*' + react: ^16.8 || ^17.0 || ^18.0 || ^19.0 || ^19.0.0-rc + react-dom: ^16.8 || ^17.0 || ^18.0 || ^19.0 || ^19.0.0-rc + peerDependenciesMeta: + '@types/react': + optional: true + '@types/react-dom': + optional: true + '@radix-ui/react-compose-refs@1.1.0': resolution: {integrity: sha512-b4inOtiaOnYf9KWyO3jAeeCG6FeyfY6ldiEPanbUjWd+xIk5wZeHa8yVwmrJ2vderhu/BQvzCrJI0lHd+wIiqw==} peerDependencies: @@ -504,6 +523,15 @@ packages: '@types/react': optional: true + '@radix-ui/react-compose-refs@1.1.1': + resolution: {integrity: sha512-Y9VzoRDSJtgFMUCoiZBDVo084VQ5hfpXxVE+NgkdNsjiDBByiImMZKKhxMwCbdHvhlENG6a833CbFkOQvTricw==} + peerDependencies: + '@types/react': '*' + react: ^16.8 || ^17.0 || ^18.0 || ^19.0 || ^19.0.0-rc + peerDependenciesMeta: + '@types/react': + optional: true + '@radix-ui/react-context@1.1.0': resolution: {integrity: sha512-OKrckBy+sMEgYM/sMmqmErVn0kZqrHPJze+Ql3DzYsDDp0hl0L62nx/2122/Bvps1qz645jlcu2tD9lrRSdf8A==} peerDependencies: @@ -658,6 +686,19 @@ packages: '@types/react-dom': optional: true + '@radix-ui/react-presence@1.1.2': + resolution: {integrity: sha512-18TFr80t5EVgL9x1SwF/YGtfG+l0BS0PRAlCWBDoBEiDQjeKgnNZRVJp/oVBl24sr3Gbfwc/Qpj4OcWTQMsAEg==} + peerDependencies: + '@types/react': '*' + '@types/react-dom': '*' + react: ^16.8 || ^17.0 || ^18.0 || ^19.0 || ^19.0.0-rc + react-dom: ^16.8 || ^17.0 || ^18.0 || ^19.0 || ^19.0.0-rc + peerDependenciesMeta: + '@types/react': + optional: true + '@types/react-dom': + optional: true + '@radix-ui/react-primitive@2.0.0': resolution: {integrity: sha512-ZSpFm0/uHa8zTvKBDjLFWLo8dkr4MBsiDLz0g3gMUwqgLHz9rTaRRGYDgvZPtBJgYCBKXkS9fzmoySgr8CO6Cw==} peerDependencies: @@ -671,6 +712,19 @@ packages: '@types/react-dom': optional: true + '@radix-ui/react-primitive@2.0.1': + resolution: {integrity: sha512-sHCWTtxwNn3L3fH8qAfnF3WbUZycW93SM1j3NFDzXBiz8D6F5UTTy8G1+WFEaiCdvCVRJWj6N2R4Xq6HdiHmDg==} + peerDependencies: + '@types/react': '*' + '@types/react-dom': '*' + react: ^16.8 || ^17.0 || ^18.0 || ^19.0 || ^19.0.0-rc + react-dom: ^16.8 || ^17.0 || ^18.0 || ^19.0 || ^19.0.0-rc + peerDependenciesMeta: + '@types/react': + optional: true + '@types/react-dom': + optional: true + '@radix-ui/react-roving-focus@1.1.0': resolution: {integrity: sha512-EA6AMGeq9AEeQDeSH0aZgG198qkfHSbvWTf1HvoDmOB5bBG/qTxjYMWUKMnYiV6J/iP/J8MEFSuB2zRU2n7ODA==} peerDependencies: @@ -684,6 +738,19 @@ packages: '@types/react-dom': optional: true + '@radix-ui/react-roving-focus@1.1.1': + resolution: {integrity: sha512-QE1RoxPGJ/Nm8Qmk0PxP8ojmoaS67i0s7hVssS7KuI2FQoc/uzVlZsqKfQvxPE6D8hICCPHJ4D88zNhT3OOmkw==} + peerDependencies: + '@types/react': '*' + '@types/react-dom': '*' + react: ^16.8 || ^17.0 || ^18.0 || ^19.0 || ^19.0.0-rc + react-dom: ^16.8 || ^17.0 || ^18.0 || ^19.0 || ^19.0.0-rc + peerDependenciesMeta: + '@types/react': + optional: true + '@types/react-dom': + optional: true + '@radix-ui/react-select@2.1.2': resolution: {integrity: sha512-rZJtWmorC7dFRi0owDmoijm6nSJH1tVw64QGiNIZ9PNLyBDtG+iAq+XGsya052At4BfarzY/Dhv9wrrUr6IMZA==} peerDependencies: @@ -732,6 +799,28 @@ packages: '@types/react': optional: true + '@radix-ui/react-slot@1.1.1': + resolution: {integrity: sha512-RApLLOcINYJA+dMVbOju7MYv1Mb2EBp2nH4HdDzXTSyaR5optlm6Otrz1euW3HbdOR8UmmFK06TD+A9frYWv+g==} + peerDependencies: + '@types/react': '*' + react: ^16.8 || ^17.0 || ^18.0 || ^19.0 || ^19.0.0-rc + peerDependenciesMeta: + '@types/react': + optional: true + + '@radix-ui/react-tabs@1.1.2': + resolution: {integrity: sha512-9u/tQJMcC2aGq7KXpGivMm1mgq7oRJKXphDwdypPd/j21j/2znamPU8WkXgnhUaTrSFNIt8XhOyCAupg8/GbwQ==} + peerDependencies: + '@types/react': '*' + '@types/react-dom': '*' + react: ^16.8 || ^17.0 || ^18.0 || ^19.0 || ^19.0.0-rc + react-dom: ^16.8 || ^17.0 || ^18.0 || ^19.0 || ^19.0.0-rc + peerDependenciesMeta: + '@types/react': + optional: true + '@types/react-dom': + optional: true + '@radix-ui/react-toggle-group@1.1.0': resolution: {integrity: sha512-PpTJV68dZU2oqqgq75Uzto5o/XfOVgkrJ9rulVmfTKxWp3HfUjHE6CP/WLRR4AzPX9HWxw7vFow2me85Yu+Naw==} peerDependencies: @@ -3115,6 +3204,8 @@ snapshots: '@radix-ui/primitive@1.1.0': {} + '@radix-ui/primitive@1.1.1': {} + '@radix-ui/react-accordion@1.2.1(@types/react-dom@18.3.0)(@types/react@18.3.3)(react-dom@18.3.1(react@18.3.1))(react@18.3.1)': dependencies: '@radix-ui/primitive': 1.1.0 @@ -3169,12 +3260,30 @@ snapshots: '@types/react': 18.3.3 '@types/react-dom': 18.3.0 + '@radix-ui/react-collection@1.1.1(@types/react-dom@18.3.0)(@types/react@18.3.3)(react-dom@18.3.1(react@18.3.1))(react@18.3.1)': + dependencies: + '@radix-ui/react-compose-refs': 1.1.1(@types/react@18.3.3)(react@18.3.1) + '@radix-ui/react-context': 1.1.1(@types/react@18.3.3)(react@18.3.1) + '@radix-ui/react-primitive': 2.0.1(@types/react-dom@18.3.0)(@types/react@18.3.3)(react-dom@18.3.1(react@18.3.1))(react@18.3.1) + '@radix-ui/react-slot': 1.1.1(@types/react@18.3.3)(react@18.3.1) + react: 18.3.1 + react-dom: 18.3.1(react@18.3.1) + optionalDependencies: + '@types/react': 18.3.3 + '@types/react-dom': 18.3.0 + '@radix-ui/react-compose-refs@1.1.0(@types/react@18.3.3)(react@18.3.1)': dependencies: react: 18.3.1 optionalDependencies: '@types/react': 18.3.3 + '@radix-ui/react-compose-refs@1.1.1(@types/react@18.3.3)(react@18.3.1)': + dependencies: + react: 18.3.1 + optionalDependencies: + '@types/react': 18.3.3 + '@radix-ui/react-context@1.1.0(@types/react@18.3.3)(react@18.3.1)': dependencies: react: 18.3.1 @@ -3335,6 +3444,16 @@ snapshots: '@types/react': 18.3.3 '@types/react-dom': 18.3.0 + '@radix-ui/react-presence@1.1.2(@types/react-dom@18.3.0)(@types/react@18.3.3)(react-dom@18.3.1(react@18.3.1))(react@18.3.1)': + dependencies: + '@radix-ui/react-compose-refs': 1.1.1(@types/react@18.3.3)(react@18.3.1) + '@radix-ui/react-use-layout-effect': 1.1.0(@types/react@18.3.3)(react@18.3.1) + react: 18.3.1 + react-dom: 18.3.1(react@18.3.1) + optionalDependencies: + '@types/react': 18.3.3 + '@types/react-dom': 18.3.0 + '@radix-ui/react-primitive@2.0.0(@types/react-dom@18.3.0)(@types/react@18.3.3)(react-dom@18.3.1(react@18.3.1))(react@18.3.1)': dependencies: '@radix-ui/react-slot': 1.1.0(@types/react@18.3.3)(react@18.3.1) @@ -3344,6 +3463,15 @@ snapshots: '@types/react': 18.3.3 '@types/react-dom': 18.3.0 + '@radix-ui/react-primitive@2.0.1(@types/react-dom@18.3.0)(@types/react@18.3.3)(react-dom@18.3.1(react@18.3.1))(react@18.3.1)': + dependencies: + '@radix-ui/react-slot': 1.1.1(@types/react@18.3.3)(react@18.3.1) + react: 18.3.1 + react-dom: 18.3.1(react@18.3.1) + optionalDependencies: + '@types/react': 18.3.3 + '@types/react-dom': 18.3.0 + '@radix-ui/react-roving-focus@1.1.0(@types/react-dom@18.3.0)(@types/react@18.3.3)(react-dom@18.3.1(react@18.3.1))(react@18.3.1)': dependencies: '@radix-ui/primitive': 1.1.0 @@ -3361,6 +3489,23 @@ snapshots: '@types/react': 18.3.3 '@types/react-dom': 18.3.0 + '@radix-ui/react-roving-focus@1.1.1(@types/react-dom@18.3.0)(@types/react@18.3.3)(react-dom@18.3.1(react@18.3.1))(react@18.3.1)': + dependencies: + '@radix-ui/primitive': 1.1.1 + '@radix-ui/react-collection': 1.1.1(@types/react-dom@18.3.0)(@types/react@18.3.3)(react-dom@18.3.1(react@18.3.1))(react@18.3.1) + '@radix-ui/react-compose-refs': 1.1.1(@types/react@18.3.3)(react@18.3.1) + '@radix-ui/react-context': 1.1.1(@types/react@18.3.3)(react@18.3.1) + '@radix-ui/react-direction': 1.1.0(@types/react@18.3.3)(react@18.3.1) + '@radix-ui/react-id': 1.1.0(@types/react@18.3.3)(react@18.3.1) + '@radix-ui/react-primitive': 2.0.1(@types/react-dom@18.3.0)(@types/react@18.3.3)(react-dom@18.3.1(react@18.3.1))(react@18.3.1) + '@radix-ui/react-use-callback-ref': 1.1.0(@types/react@18.3.3)(react@18.3.1) + '@radix-ui/react-use-controllable-state': 1.1.0(@types/react@18.3.3)(react@18.3.1) + react: 18.3.1 + react-dom: 18.3.1(react@18.3.1) + optionalDependencies: + '@types/react': 18.3.3 + '@types/react-dom': 18.3.0 + '@radix-ui/react-select@2.1.2(@types/react-dom@18.3.0)(@types/react@18.3.3)(react-dom@18.3.1(react@18.3.1))(react@18.3.1)': dependencies: '@radix-ui/number': 1.1.0 @@ -3425,6 +3570,29 @@ snapshots: optionalDependencies: '@types/react': 18.3.3 + '@radix-ui/react-slot@1.1.1(@types/react@18.3.3)(react@18.3.1)': + dependencies: + '@radix-ui/react-compose-refs': 1.1.1(@types/react@18.3.3)(react@18.3.1) + react: 18.3.1 + optionalDependencies: + '@types/react': 18.3.3 + + '@radix-ui/react-tabs@1.1.2(@types/react-dom@18.3.0)(@types/react@18.3.3)(react-dom@18.3.1(react@18.3.1))(react@18.3.1)': + dependencies: + '@radix-ui/primitive': 1.1.1 + '@radix-ui/react-context': 1.1.1(@types/react@18.3.3)(react@18.3.1) + '@radix-ui/react-direction': 1.1.0(@types/react@18.3.3)(react@18.3.1) + '@radix-ui/react-id': 1.1.0(@types/react@18.3.3)(react@18.3.1) + '@radix-ui/react-presence': 1.1.2(@types/react-dom@18.3.0)(@types/react@18.3.3)(react-dom@18.3.1(react@18.3.1))(react@18.3.1) + '@radix-ui/react-primitive': 2.0.1(@types/react-dom@18.3.0)(@types/react@18.3.3)(react-dom@18.3.1(react@18.3.1))(react@18.3.1) + '@radix-ui/react-roving-focus': 1.1.1(@types/react-dom@18.3.0)(@types/react@18.3.3)(react-dom@18.3.1(react@18.3.1))(react@18.3.1) + '@radix-ui/react-use-controllable-state': 1.1.0(@types/react@18.3.3)(react@18.3.1) + react: 18.3.1 + react-dom: 18.3.1(react@18.3.1) + optionalDependencies: + '@types/react': 18.3.3 + '@types/react-dom': 18.3.0 + '@radix-ui/react-toggle-group@1.1.0(@types/react-dom@18.3.0)(@types/react@18.3.3)(react-dom@18.3.1(react@18.3.1))(react@18.3.1)': dependencies: '@radix-ui/primitive': 1.1.0 diff --git a/viz/src/components/Markdown.tsx b/viz/src/components/Markdown.tsx index 8b0689a..d994147 100644 --- a/viz/src/components/Markdown.tsx +++ b/viz/src/components/Markdown.tsx @@ -7,7 +7,7 @@ interface MarkdownProps { const Markdown: FC = ({ children }) => { return ( -
+ = ({ children }) => { > {children} -
+ ); }; diff --git a/viz/src/components/SeqsViewer.tsx b/viz/src/components/SeqsViewer.tsx index 06cd158..4d4bfcd 100644 --- a/viz/src/components/SeqsViewer.tsx +++ b/viz/src/components/SeqsViewer.tsx @@ -2,13 +2,16 @@ import { useEffect, useState, useRef, useCallback } from "react"; import { redColorMapHex } from "@/utils"; import { ToggleGroup, ToggleGroupItem } from "@/components/ui/toggle-group"; import { Tooltip, TooltipContent, TooltipProvider, TooltipTrigger } from "@/components/ui/tooltip"; -import { Copy, Check } from "lucide-react"; +import { Copy, Check, HelpCircle } from "lucide-react"; import { Skeleton } from "@/components/ui/skeleton"; +import { Tabs, TabsList, TabsTrigger } from "@/components/ui/tabs"; +import Markdown from "./Markdown"; // NOTE(liam): This component is written by Cursor pretty much entirely. export interface SeqWithSAEActs { sequence: string; + "3di_sequence"?: string; sae_acts: Array; alphafold_id: string; uniprot_id: string; @@ -26,6 +29,14 @@ export default function SeqsViewer({ seqs, title }: SeqsViewerProps) { const [isAligning, setIsAligning] = useState(false); const containerRef = useRef(null); const [copiedId, setCopiedId] = useState(null); + const [sequenceType, setSequenceType] = useState<"aa" | "3di">("aa"); + + const getSourceSequence = useCallback( + (seq: SeqWithSAEActs) => { + return sequenceType === "3di" && seq["3di_sequence"] ? seq["3di_sequence"] : seq.sequence; + }, + [sequenceType] + ); useEffect(() => { if (seqs.length === 0) return; @@ -52,7 +63,8 @@ export default function SeqsViewer({ seqs, title }: SeqsViewerProps) { const leftPadding = firstActIndex - firstNonzeroIdx; const rightPadding = maxLength - (leftPadding + seq.sequence.length); - const paddedSeq = "-".repeat(leftPadding) + seq.sequence + "-".repeat(rightPadding); + const paddedSeq = + "-".repeat(leftPadding) + getSourceSequence(seq) + "-".repeat(rightPadding); const paddedActs = Array(leftPadding) .fill(null) .concat(seq.sae_acts) @@ -88,7 +100,8 @@ export default function SeqsViewer({ seqs, title }: SeqsViewerProps) { const leftPadding = maxActIndex - maxLocalIdx; const rightPadding = maxLength - (leftPadding + seq.sequence.length); - const paddedSeq = "-".repeat(leftPadding) + seq.sequence + "-".repeat(rightPadding); + const paddedSeq = + "-".repeat(leftPadding) + getSourceSequence(seq) + "-".repeat(rightPadding); const paddedActs = Array(leftPadding) .fill(null) .concat(seq.sae_acts) @@ -106,8 +119,11 @@ export default function SeqsViewer({ seqs, title }: SeqsViewerProps) { setTimeout(() => scrollToPosition(maxActIndex - 30), 0); setIsAligning(false); } else if (alignmentMode === "msa") { + // Get the appropriate sequence type for each sequence + const sequencesToAlign = seqs.map(getSourceSequence); + // @ts-expect-error biomsa is loaded through a script tag in index.html - biomsa.align(seqs.map((seq) => seq.sequence)).then((result) => { + biomsa.align(sequencesToAlign).then((result) => { // Update sequences with aligned versions const newAlignedSeqs = seqs.map((seq, i) => { const alignedSeq = result[i]; @@ -138,7 +154,7 @@ export default function SeqsViewer({ seqs, title }: SeqsViewerProps) { }); } }, 0); - }, [seqs, alignmentMode]); + }, [seqs, alignmentMode, sequenceType, getSourceSequence]); const scrollToPosition = (index: number) => { if (!containerRef.current) return; @@ -168,7 +184,39 @@ export default function SeqsViewer({ seqs, title }: SeqsViewerProps) { <>
{title &&

{title}

} -
+
+
+ setSequenceType(value as "aa" | "3di")} + className="w-[120px]" + > + + AA + seq["3di_sequence"])}> + 3Di + + + + + + + + + +

+ AA: Amino acid tokens +
+ 3Di:{" "} + + Structural tokens describing geometric conformation, invented for + [Foldseek](https://www.nature.com/articles/s41587-023-01773-0) + +

+
+
+
+
, + React.ComponentPropsWithoutRef +>(({ className, ...props }, ref) => ( + +)); +TabsList.displayName = TabsPrimitive.List.displayName; + +const TabsTrigger = React.forwardRef< + React.ElementRef, + React.ComponentPropsWithoutRef +>(({ className, ...props }, ref) => ( + +)); +TabsTrigger.displayName = TabsPrimitive.Trigger.displayName; + +const TabsContent = React.forwardRef< + React.ElementRef, + React.ComponentPropsWithoutRef +>(({ className, ...props }, ref) => ( + +)); +TabsContent.displayName = TabsPrimitive.Content.displayName; + +export { Tabs, TabsList, TabsTrigger, TabsContent };