XspecT 0.4.1__py3-none-any.whl → 0.5.0__py3-none-any.whl
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- xspect/classify.py +32 -0
- xspect/file_io.py +3 -9
- xspect/filter_sequences.py +56 -0
- xspect/main.py +13 -18
- xspect/mlst_feature/mlst_helper.py +102 -13
- xspect/mlst_feature/pub_mlst_handler.py +32 -6
- xspect/models/probabilistic_filter_mlst_model.py +160 -32
- xspect/models/probabilistic_filter_model.py +1 -0
- xspect/ncbi.py +8 -6
- xspect/train.py +13 -5
- xspect/web.py +173 -0
- xspect/xspect-web/.gitignore +24 -0
- xspect/xspect-web/README.md +54 -0
- xspect/xspect-web/components.json +21 -0
- xspect/xspect-web/dist/assets/index-CMG4V7fZ.js +290 -0
- xspect/xspect-web/dist/assets/index-jIKg1HIy.css +1 -0
- xspect/xspect-web/dist/index.html +14 -0
- xspect/xspect-web/dist/vite.svg +1 -0
- xspect/xspect-web/eslint.config.js +28 -0
- xspect/xspect-web/index.html +13 -0
- xspect/xspect-web/package-lock.json +6865 -0
- xspect/xspect-web/package.json +58 -0
- xspect/xspect-web/pnpm-lock.yaml +4317 -0
- xspect/xspect-web/public/vite.svg +1 -0
- xspect/xspect-web/src/App.tsx +29 -0
- xspect/xspect-web/src/api.tsx +62 -0
- xspect/xspect-web/src/assets/react.svg +1 -0
- xspect/xspect-web/src/components/classification-form.tsx +284 -0
- xspect/xspect-web/src/components/classify.tsx +18 -0
- xspect/xspect-web/src/components/data-table.tsx +78 -0
- xspect/xspect-web/src/components/dropdown-checkboxes.tsx +63 -0
- xspect/xspect-web/src/components/dropdown-slider.tsx +42 -0
- xspect/xspect-web/src/components/filter-form.tsx +423 -0
- xspect/xspect-web/src/components/filter.tsx +15 -0
- xspect/xspect-web/src/components/header.tsx +46 -0
- xspect/xspect-web/src/components/landing.tsx +7 -0
- xspect/xspect-web/src/components/models-details.tsx +138 -0
- xspect/xspect-web/src/components/models.tsx +53 -0
- xspect/xspect-web/src/components/result-chart.tsx +44 -0
- xspect/xspect-web/src/components/result.tsx +155 -0
- xspect/xspect-web/src/components/spinner.tsx +30 -0
- xspect/xspect-web/src/components/ui/accordion.tsx +64 -0
- xspect/xspect-web/src/components/ui/button.tsx +59 -0
- xspect/xspect-web/src/components/ui/card.tsx +92 -0
- xspect/xspect-web/src/components/ui/chart.tsx +351 -0
- xspect/xspect-web/src/components/ui/command.tsx +175 -0
- xspect/xspect-web/src/components/ui/dialog.tsx +135 -0
- xspect/xspect-web/src/components/ui/dropdown-menu.tsx +255 -0
- xspect/xspect-web/src/components/ui/file-upload.tsx +1459 -0
- xspect/xspect-web/src/components/ui/form.tsx +165 -0
- xspect/xspect-web/src/components/ui/input.tsx +21 -0
- xspect/xspect-web/src/components/ui/label.tsx +24 -0
- xspect/xspect-web/src/components/ui/navigation-menu.tsx +168 -0
- xspect/xspect-web/src/components/ui/popover.tsx +46 -0
- xspect/xspect-web/src/components/ui/select.tsx +183 -0
- xspect/xspect-web/src/components/ui/separator.tsx +26 -0
- xspect/xspect-web/src/components/ui/slider.tsx +61 -0
- xspect/xspect-web/src/components/ui/switch.tsx +29 -0
- xspect/xspect-web/src/components/ui/table.tsx +113 -0
- xspect/xspect-web/src/components/ui/tabs.tsx +64 -0
- xspect/xspect-web/src/index.css +120 -0
- xspect/xspect-web/src/lib/utils.ts +6 -0
- xspect/xspect-web/src/main.tsx +10 -0
- xspect/xspect-web/src/types.tsx +34 -0
- xspect/xspect-web/src/utils.tsx +6 -0
- xspect/xspect-web/src/vite-env.d.ts +1 -0
- xspect/xspect-web/tsconfig.app.json +32 -0
- xspect/xspect-web/tsconfig.json +13 -0
- xspect/xspect-web/tsconfig.node.json +24 -0
- xspect/xspect-web/vite.config.ts +24 -0
- {xspect-0.4.1.dist-info → xspect-0.5.0.dist-info}/METADATA +6 -8
- xspect-0.5.0.dist-info/RECORD +85 -0
- {xspect-0.4.1.dist-info → xspect-0.5.0.dist-info}/WHEEL +1 -1
- xspect/fastapi.py +0 -102
- xspect-0.4.1.dist-info/RECORD +0 -24
- {xspect-0.4.1.dist-info → xspect-0.5.0.dist-info}/entry_points.txt +0 -0
- {xspect-0.4.1.dist-info → xspect-0.5.0.dist-info}/licenses/LICENSE +0 -0
- {xspect-0.4.1.dist-info → xspect-0.5.0.dist-info}/top_level.txt +0 -0
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import * as React from "react"
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import * as DropdownMenuPrimitive from "@radix-ui/react-dropdown-menu"
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import { CheckIcon, ChevronRightIcon, CircleIcon } from "lucide-react"
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import { cn } from "@/lib/utils"
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function DropdownMenu({
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...props
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}: React.ComponentProps<typeof DropdownMenuPrimitive.Root>) {
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return <DropdownMenuPrimitive.Root data-slot="dropdown-menu" {...props} />
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}
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function DropdownMenuPortal({
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...props
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}: React.ComponentProps<typeof DropdownMenuPrimitive.Portal>) {
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return (
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<DropdownMenuPrimitive.Portal data-slot="dropdown-menu-portal" {...props} />
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)
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}
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function DropdownMenuTrigger({
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...props
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}: React.ComponentProps<typeof DropdownMenuPrimitive.Trigger>) {
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return (
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<DropdownMenuPrimitive.Trigger
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data-slot="dropdown-menu-trigger"
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{...props}
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/>
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)
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}
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function DropdownMenuContent({
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className,
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sideOffset = 4,
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...props
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}: React.ComponentProps<typeof DropdownMenuPrimitive.Content>) {
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return (
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<DropdownMenuPrimitive.Portal>
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<DropdownMenuPrimitive.Content
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data-slot="dropdown-menu-content"
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sideOffset={sideOffset}
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className={cn(
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"bg-popover text-popover-foreground data-[state=open]:animate-in data-[state=closed]:animate-out data-[state=closed]:fade-out-0 data-[state=open]:fade-in-0 data-[state=closed]:zoom-out-95 data-[state=open]:zoom-in-95 data-[side=bottom]:slide-in-from-top-2 data-[side=left]:slide-in-from-right-2 data-[side=right]:slide-in-from-left-2 data-[side=top]:slide-in-from-bottom-2 z-50 max-h-(--radix-dropdown-menu-content-available-height) min-w-[8rem] origin-(--radix-dropdown-menu-content-transform-origin) overflow-x-hidden overflow-y-auto rounded-md border p-1 shadow-md",
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className
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)}
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{...props}
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/>
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</DropdownMenuPrimitive.Portal>
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)
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}
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function DropdownMenuGroup({
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...props
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}: React.ComponentProps<typeof DropdownMenuPrimitive.Group>) {
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return (
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<DropdownMenuPrimitive.Group data-slot="dropdown-menu-group" {...props} />
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)
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}
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function DropdownMenuItem({
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className,
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inset,
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variant = "default",
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...props
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}: React.ComponentProps<typeof DropdownMenuPrimitive.Item> & {
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inset?: boolean
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variant?: "default" | "destructive"
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}) {
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return (
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<DropdownMenuPrimitive.Item
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data-slot="dropdown-menu-item"
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data-inset={inset}
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data-variant={variant}
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className={cn(
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"focus:bg-accent focus:text-accent-foreground data-[variant=destructive]:text-destructive data-[variant=destructive]:focus:bg-destructive/10 dark:data-[variant=destructive]:focus:bg-destructive/20 data-[variant=destructive]:focus:text-destructive data-[variant=destructive]:*:[svg]:!text-destructive [&_svg:not([class*='text-'])]:text-muted-foreground relative flex cursor-default items-center gap-2 rounded-sm px-2 py-1.5 text-sm outline-hidden select-none data-[disabled]:pointer-events-none data-[disabled]:opacity-50 data-[inset]:pl-8 [&_svg]:pointer-events-none [&_svg]:shrink-0 [&_svg:not([class*='size-'])]:size-4",
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className
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)}
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{...props}
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/>
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)
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}
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function DropdownMenuCheckboxItem({
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className,
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children,
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checked,
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...props
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}: React.ComponentProps<typeof DropdownMenuPrimitive.CheckboxItem>) {
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return (
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<DropdownMenuPrimitive.CheckboxItem
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data-slot="dropdown-menu-checkbox-item"
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className={cn(
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"focus:bg-accent focus:text-accent-foreground relative flex cursor-default items-center gap-2 rounded-sm py-1.5 pr-2 pl-8 text-sm outline-hidden select-none data-[disabled]:pointer-events-none data-[disabled]:opacity-50 [&_svg]:pointer-events-none [&_svg]:shrink-0 [&_svg:not([class*='size-'])]:size-4",
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className
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)}
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checked={checked}
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{...props}
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>
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<span className="pointer-events-none absolute left-2 flex size-3.5 items-center justify-center">
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<DropdownMenuPrimitive.ItemIndicator>
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<CheckIcon className="size-4" />
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</DropdownMenuPrimitive.ItemIndicator>
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</span>
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{children}
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</DropdownMenuPrimitive.CheckboxItem>
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)
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}
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function DropdownMenuRadioGroup({
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...props
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}: React.ComponentProps<typeof DropdownMenuPrimitive.RadioGroup>) {
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return (
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<DropdownMenuPrimitive.RadioGroup
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data-slot="dropdown-menu-radio-group"
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{...props}
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/>
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)
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}
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function DropdownMenuRadioItem({
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className,
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children,
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...props
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}: React.ComponentProps<typeof DropdownMenuPrimitive.RadioItem>) {
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return (
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<DropdownMenuPrimitive.RadioItem
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data-slot="dropdown-menu-radio-item"
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className={cn(
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"focus:bg-accent focus:text-accent-foreground relative flex cursor-default items-center gap-2 rounded-sm py-1.5 pr-2 pl-8 text-sm outline-hidden select-none data-[disabled]:pointer-events-none data-[disabled]:opacity-50 [&_svg]:pointer-events-none [&_svg]:shrink-0 [&_svg:not([class*='size-'])]:size-4",
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className
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)}
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{...props}
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>
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<span className="pointer-events-none absolute left-2 flex size-3.5 items-center justify-center">
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<DropdownMenuPrimitive.ItemIndicator>
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<CircleIcon className="size-2 fill-current" />
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</DropdownMenuPrimitive.ItemIndicator>
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</span>
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{children}
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</DropdownMenuPrimitive.RadioItem>
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)
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}
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function DropdownMenuLabel({
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...props
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}: React.ComponentProps<typeof DropdownMenuPrimitive.Label> & {
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inset?: boolean
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}) {
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return (
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<DropdownMenuPrimitive.Label
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data-slot="dropdown-menu-label"
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data-inset={inset}
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className={cn(
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"px-2 py-1.5 text-sm font-medium data-[inset]:pl-8",
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className
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)}
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{...props}
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/>
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)
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}
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function DropdownMenuSeparator({
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...props
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}: React.ComponentProps<typeof DropdownMenuPrimitive.Separator>) {
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return (
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<DropdownMenuPrimitive.Separator
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data-slot="dropdown-menu-separator"
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className={cn("bg-border -mx-1 my-1 h-px", className)}
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{...props}
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/>
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)
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}
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function DropdownMenuShortcut({
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...props
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}: React.ComponentProps<"span">) {
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return (
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<span
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data-slot="dropdown-menu-shortcut"
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className={cn(
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"text-muted-foreground ml-auto text-xs tracking-widest",
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)}
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{...props}
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/>
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)
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}
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function DropdownMenuSub({
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...props
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}: React.ComponentProps<typeof DropdownMenuPrimitive.Sub>) {
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return <DropdownMenuPrimitive.Sub data-slot="dropdown-menu-sub" {...props} />
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}
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function DropdownMenuSubTrigger({
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...props
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}: React.ComponentProps<typeof DropdownMenuPrimitive.SubTrigger> & {
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}) {
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return (
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data-slot="dropdown-menu-sub-trigger"
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data-inset={inset}
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className={cn(
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"focus:bg-accent focus:text-accent-foreground data-[state=open]:bg-accent data-[state=open]:text-accent-foreground flex cursor-default items-center rounded-sm px-2 py-1.5 text-sm outline-hidden select-none data-[inset]:pl-8",
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)}
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>
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</DropdownMenuPrimitive.SubTrigger>
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)
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}
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function DropdownMenuSubContent({
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}: React.ComponentProps<typeof DropdownMenuPrimitive.SubContent>) {
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return (
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<DropdownMenuPrimitive.SubContent
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data-slot="dropdown-menu-sub-content"
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className={cn(
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"bg-popover text-popover-foreground data-[state=open]:animate-in data-[state=closed]:animate-out data-[state=closed]:fade-out-0 data-[state=open]:fade-in-0 data-[state=closed]:zoom-out-95 data-[state=open]:zoom-in-95 data-[side=bottom]:slide-in-from-top-2 data-[side=left]:slide-in-from-right-2 data-[side=right]:slide-in-from-left-2 data-[side=top]:slide-in-from-bottom-2 z-50 min-w-[8rem] origin-(--radix-dropdown-menu-content-transform-origin) overflow-hidden rounded-md border p-1 shadow-lg",
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)}
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{...props}
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/>
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)
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}
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export {
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DropdownMenu,
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DropdownMenuPortal,
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DropdownMenuTrigger,
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DropdownMenuContent,
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|
+
DropdownMenuGroup,
|
|
245
|
+
DropdownMenuLabel,
|
|
246
|
+
DropdownMenuItem,
|
|
247
|
+
DropdownMenuCheckboxItem,
|
|
248
|
+
DropdownMenuRadioGroup,
|
|
249
|
+
DropdownMenuRadioItem,
|
|
250
|
+
DropdownMenuSeparator,
|
|
251
|
+
DropdownMenuShortcut,
|
|
252
|
+
DropdownMenuSub,
|
|
253
|
+
DropdownMenuSubTrigger,
|
|
254
|
+
DropdownMenuSubContent,
|
|
255
|
+
}
|