react-msaview 5.0.6 → 5.0.13

package/src/useWheelScroll.ts

@@ -0,0 +1,109 @@
+import { useEffect, useRef, useState } from 'react'
+
+export function useWheelScroll({
+  ref,
+  onScrollX,
+  onScrollY,
+}: {
+  ref: React.RefObject<HTMLDivElement | null>
+  onScrollX?: (delta: number) => void
+  onScrollY?: (delta: number) => void
+}) {
+  const scheduled = useRef(false)
+  const deltaX = useRef(0)
+  const deltaY = useRef(0)
+  const prevX = useRef(0)
+  const prevY = useRef(0)
+  const [mouseDragging, setMouseDragging] = useState(false)
+
+  useEffect(() => {
+    const curr = ref.current
+    if (!curr) {
+      return
+    }
+    function onWheel(event: WheelEvent) {
+      if (onScrollX) {
+        deltaX.current += event.deltaX
+      }
+      if (onScrollY) {
+        deltaY.current += event.deltaY
+      }
+
+      if (!scheduled.current) {
+        scheduled.current = true
+        requestAnimationFrame(() => {
+          if (onScrollX) {
+            onScrollX(-deltaX.current)
+            deltaX.current = 0
+          }
+          if (onScrollY) {
+            onScrollY(-deltaY.current)
+            deltaY.current = 0
+          }
+          scheduled.current = false
+        })
+      }
+      event.preventDefault()
+      event.stopPropagation()
+    }
+    curr.addEventListener('wheel', onWheel, { passive: false })
+    return () => {
+      curr.removeEventListener('wheel', onWheel)
+    }
+  }, [ref, onScrollX, onScrollY])
+
+  useEffect(() => {
+    if (!mouseDragging) {
+      return
+    }
+    function globalMouseMove(event: MouseEvent) {
+      event.preventDefault()
+      const distanceX = event.clientX - prevX.current
+      const distanceY = event.clientY - prevY.current
+      if ((distanceX && onScrollX) || (distanceY && onScrollY)) {
+        if (!scheduled.current) {
+          scheduled.current = true
+          requestAnimationFrame(() => {
+            onScrollX?.(distanceX)
+            onScrollY?.(distanceY)
+            scheduled.current = false
+            prevX.current = event.clientX
+            prevY.current = event.clientY
+          })
+        }
+      }
+    }
+
+    function globalMouseUp() {
+      prevX.current = 0
+      prevY.current = 0
+      setMouseDragging(false)
+    }
+
+    window.addEventListener('mousemove', globalMouseMove, true)
+    window.addEventListener('mouseup', globalMouseUp, true)
+    return () => {
+      window.removeEventListener('mousemove', globalMouseMove, true)
+      window.removeEventListener('mouseup', globalMouseUp, true)
+    }
+  }, [mouseDragging, onScrollX, onScrollY])
+
+  function onMouseDown(event: React.MouseEvent) {
+    const target = event.target as HTMLElement
+    if (target.draggable || target.dataset.resizer) {
+      return
+    }
+    if (event.button === 0) {
+      prevX.current = event.clientX
+      prevY.current = event.clientY
+      setMouseDragging(true)
+    }
+  }
+
+  function onMouseUp(event: React.MouseEvent) {
+    event.preventDefault()
+    setMouseDragging(false)
+  }
+
+  return { onMouseDown, onMouseUp }
+}

package/src/util.ts

@@ -1,10 +1,7 @@
 import { colord, extend } from 'colord'
 import namesPlugin from 'colord/plugins/names'
-import { max } from 'd3-array'
 
-import type { NodeWithIds } from './types.ts'
 import type { Theme } from '@mui/material'
-import type { HierarchyNode } from 'd3-hierarchy'
 
 extend([namesPlugin])
 
@@ -25,66 +22,24 @@ export function colorContrast(
   ])
 }
 
-export function skipBlanks(blanks: number[], arg: string | string[]) {
+export function skipBlanks(blanks: number[], str: string) {
   if (blanks.length === 0) {
-    return typeof arg === 'string' ? arg : arg.join('')
+    return str
   }
   const chunks = []
   let lastEnd = 0
   for (const blankIdx of blanks) {
     if (blankIdx > lastEnd) {
-      chunks.push(
-        typeof arg === 'string'
-          ? arg.slice(lastEnd, blankIdx)
-          : arg.slice(lastEnd, blankIdx).join(''),
-      )
+      chunks.push(str.slice(lastEnd, blankIdx))
     }
     lastEnd = blankIdx + 1
   }
-  if (lastEnd < arg.length) {
-    chunks.push(
-      typeof arg === 'string'
-        ? arg.slice(lastEnd)
-        : arg.slice(lastEnd).join(''),
-    )
+  if (lastEnd < str.length) {
+    chunks.push(str.slice(lastEnd))
   }
   return chunks.join('')
 }
 
-// basically same as setRadius from https://observablehq.com/@d3/tree-of-life
-export function setBrLength(
-  d: HierarchyNode<NodeWithIds>,
-  y0: number,
-  k: number,
-) {
-  // @ts-expect-error
-  d.len = (y0 += Math.max(d.data.length || 0, 0)) * k
-
-  if (d.children) {
-    d.children.forEach(d => {
-      setBrLength(d, y0, k)
-    })
-  }
-}
-
-// basically same as maxLength from https://observablehq.com/@d3/tree-of-life
-export function maxLength(d: HierarchyNode<NodeWithIds>): number {
-  return (
-    (d.data.length || 0) + (d.children ? max(d.children, maxLength) || 0 : 0)
-  )
-}
-
-// Collapse the node and all it's children, from
-// https://bl.ocks.org/d3noob/43a860bc0024792f8803bba8ca0d5ecd
-export function collapse(d: HierarchyNode<NodeWithIds>) {
-  if (d.children) {
-    // @ts-expect-error
-    d._children = d.children
-    // @ts-expect-error
-    d.children = null
-  }
-}
-
 export function len(a: { end: number; start: number }) {
   return a.end - a.start
 }

package/src/vendor/copyToClipboard.ts

@@ -1,125 +1,17 @@
-/**
- * Copy text to clipboard utility.
- * Uses modern Clipboard API with fallback to execCommand.
- */
-
-function deselectCurrent() {
-  const selection = document.getSelection()
-  if (!selection?.rangeCount) {
-    return () => {}
-  }
-  const active = document.activeElement as HTMLElement | null
-
-  const ranges: Range[] = []
-  for (let i = 0; i < selection.rangeCount; i++) {
-    ranges.push(selection.getRangeAt(i))
-  }
-
-  const tagName = active?.tagName.toUpperCase()
-  if (tagName === 'INPUT' || tagName === 'TEXTAREA') {
-    active?.blur()
-  }
-
-  selection.removeAllRanges()
-  return () => {
-    if (selection.type === 'Caret') {
-      selection.removeAllRanges()
-    }
-    if (!selection.rangeCount) {
-      for (const range of ranges) {
-        selection.addRange(range)
-      }
-    }
-    active?.focus()
-  }
-}
-
-export interface CopyOptions {
-  debug?: boolean
-  format?: string
-  onCopy?: (clipboardData: DataTransfer) => void
-}
-
-export default function copy(text: string, options?: CopyOptions): boolean {
-  const debug = options?.debug || false
-  let success = false
-  let reselectPrevious: (() => void) | undefined
-  let range: Range | undefined
-  let selection: Selection | null = null
-  let mark: HTMLSpanElement | undefined
-
-  try {
-    reselectPrevious = deselectCurrent()
-    range = document.createRange()
-    selection = document.getSelection()
-
-    mark = document.createElement('span')
-    mark.textContent = text
-    mark.ariaHidden = 'true'
-    mark.style.all = 'unset'
-    mark.style.position = 'fixed'
-    mark.style.top = '0'
-    mark.style.clip = 'rect(0, 0, 0, 0)'
-    mark.style.whiteSpace = 'pre'
-    mark.style.webkitUserSelect = 'text'
-    ;(mark.style as unknown as Record<string, string>).MozUserSelect = 'text'
-    ;(mark.style as unknown as Record<string, string>).msUserSelect = 'text'
-    mark.style.userSelect = 'text'
-
-    mark.addEventListener('copy', e => {
-      e.stopPropagation()
-      if (options?.format) {
-        e.preventDefault()
-        if (e.clipboardData) {
-          e.clipboardData.clearData()
-          e.clipboardData.setData(options.format, text)
-        }
-      }
-      if (options?.onCopy && e.clipboardData) {
-        e.preventDefault()
-        options.onCopy(e.clipboardData)
-      }
+export default function copy(text: string) {
+  const clip = navigator.clipboard as Clipboard | undefined
+  if (clip?.writeText) {
+    clip.writeText(text).catch((e: unknown) => {
+      console.error('Failed to copy to clipboard:', e)
     })
-
-    document.body.append(mark)
-    range.selectNodeContents(mark)
-    selection?.addRange(range)
-
-    const successful = document.execCommand('copy')
-    if (!successful) {
-      throw new Error('copy command was unsuccessful')
-    }
-    success = true
-  } catch (err) {
-    if (debug) {
-      console.error('unable to copy using execCommand:', err)
-    }
-    try {
-      const clipboardData = (window as unknown as Record<string, DataTransfer>)
-        .clipboardData
-      if (clipboardData) {
-        clipboardData.setData(options?.format || 'text', text)
-        options?.onCopy?.(clipboardData)
-        success = true
-      }
-    } catch (err2) {
-      if (debug) {
-        console.error('unable to copy using clipboardData:', err2)
-      }
-    }
-  } finally {
-    if (selection) {
-      if (typeof selection.removeRange === 'function' && range) {
-        selection.removeRange(range)
-      } else {
-        selection.removeAllRanges()
-      }
-    }
-    if (mark) {
-      mark.remove()
-    }
-    reselectPrevious?.()
+    return
   }
-
-  return success
+  const textarea = document.createElement('textarea')
+  textarea.value = text
+  textarea.style.position = 'fixed'
+  textarea.style.opacity = '0'
+  document.body.append(textarea)
+  textarea.select()
+  document.execCommand('copy')
+  textarea.remove()
 }

package/src/vendor/fileSaver.ts

@@ -1,107 +1,10 @@
-/**
- * FileSaver.js
- * A saveAs() FileSaver implementation.
- *
- * By Eli Grey, http://eligrey.com
- * License: MIT
- * source: http://purl.eligrey.com/github/FileSaver.js
- *
- * Vendored and converted to ESM/TypeScript for pure ESM compatibility.
- */
-
-function click(node: HTMLAnchorElement) {
-  try {
-    node.dispatchEvent(new MouseEvent('click'))
-  } catch {
-    const evt = document.createEvent('MouseEvents')
-    evt.initMouseEvent(
-      'click',
-      true,
-      true,
-      window,
-      0,
-      0,
-      0,
-      80,
-      20,
-      false,
-      false,
-      false,
-      false,
-      0,
-      null,
-    )
-    node.dispatchEvent(evt)
-  }
-}
-
-// Detect WebView inside a native macOS app by ruling out all browsers
-const isMacOSWebView =
-  typeof navigator !== 'undefined' &&
-  navigator.userAgent.includes('Macintosh') &&
-  navigator.userAgent.includes('AppleWebKit') &&
-  !navigator.userAgent.includes('Safari')
-
-export function saveAs(blob: Blob | string, name?: string) {
-  if (typeof window === 'undefined') {
-    return
-  }
-
-  const URL = window.URL
+export function saveAs(blob: Blob, name: string) {
+  const url = URL.createObjectURL(blob)
   const a = document.createElement('a')
-  name = name || (blob instanceof Blob ? 'download' : 'download')
-
-  // Use download attribute if available and not macOS WebView
-  if ('download' in HTMLAnchorElement.prototype && !isMacOSWebView) {
-    a.download = name
-    a.rel = 'noopener'
-
-    if (typeof blob === 'string') {
-      a.href = blob
-      click(a)
-    } else {
-      a.href = URL.createObjectURL(blob)
-      setTimeout(() => {
-        URL.revokeObjectURL(a.href)
-      }, 40000)
-      setTimeout(() => {
-        click(a)
-      }, 0)
-    }
-    return
-  }
-
-  // Fallback for browsers without download attribute support
-  if (typeof blob === 'string') {
-    window.open(blob, '_blank')
-    return
-  }
-
-  const isSafari =
-    /constructor/i.test(
-      (window as unknown as { HTMLElement: unknown }).HTMLElement?.toString() ??
-        '',
-    ) || !!(window as unknown as { safari?: unknown }).safari
-  const isChromeIOS = /CriOS\/[\d]+/.test(navigator.userAgent)
-
-  if (
-    (isChromeIOS || isSafari || isMacOSWebView) &&
-    typeof FileReader !== 'undefined'
-  ) {
-    const reader = new FileReader()
-    reader.onloadend = () => {
-      let url = reader.result as string
-      url = isChromeIOS
-        ? url
-        : url.replace(/^data:[^;]*;/, 'data:attachment/file;')
-      window.open(url, '_blank')
-    }
-    reader.readAsDataURL(blob)
-  } else {
-    const url = URL.createObjectURL(blob)
-    window.open(url, '_blank')
-    setTimeout(() => {
-      URL.revokeObjectURL(url)
-    }, 40000)
-  }
+  a.href = url
+  a.download = name
+  a.click()
+  setTimeout(() => {
+    URL.revokeObjectURL(url)
+  }, 40_000)
 }

package/src/version.ts

@@ -1 +1 @@
-export const version = '5.0.6'
+export const version = '5.0.13'

package/dist/components/dialogs/AddTrackDialog.d.ts

@@ -1,8 +0,0 @@
-import React from 'react';
-import type { MsaViewModel } from '../../model.ts';
-declare const AddTrackDialog: ({ model, onClose, open, }: {
-    model: MsaViewModel;
-    onClose: () => void;
-    open: boolean;
-}) => React.JSX.Element;
-export default AddTrackDialog;

package/dist/components/dialogs/AddTrackDialog.js

@@ -1,30 +0,0 @@
-import React, { useState } from 'react';
-import { Dialog, FileSelector } from '@jbrowse/core/ui';
-import { Button, DialogActions, DialogContent, MenuItem, TextField, Typography, } from '@mui/material';
-import { observer } from 'mobx-react';
-const AddTrackDialog = observer(function ({ model, onClose, open, }) {
-    const options = model.rows.map(r => r[0]);
-    const [trackFile, setTrackFile] = useState();
-    const [currentOption, setCurrentOption] = useState('');
-    return (React.createElement(Dialog, { onClose: () => {
-            onClose();
-        }, open: open, title: "Add track" },
-        React.createElement(DialogContent, null,
-            React.createElement(Typography, null, "Open relevant per-alignment tracks e.g. protein domains"),
-            React.createElement(TextField, { select: true, helperText: "Which row does this track apply to?", value: currentOption, onChange: event => {
-                    setCurrentOption(event.target.value);
-                } }, options.map((option, index) => (React.createElement(MenuItem, { key: `${option}-${index}`, value: option }, option)))),
-            React.createElement(FileSelector, { location: trackFile, setLocation: setTrackFile }),
-            React.createElement(DialogActions, null,
-                React.createElement(Button, { onClick: () => {
-                        model.setError(undefined);
-                        if (trackFile) {
-                            model.setMSAFilehandle(trackFile);
-                        }
-                    }, variant: "contained", color: "primary" }, "Open"),
-                React.createElement(Button, { color: "secondary", variant: "contained", onClick: () => {
-                        onClose();
-                    } }, "Cancel")))));
-});
-export default AddTrackDialog;
-//# sourceMappingURL=AddTrackDialog.js.map

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

@@ -1 +0,0 @@
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package/dist/components/dialogs/TabPanel.d.ts

@@ -1,6 +0,0 @@
-import React from 'react';
-export default function TabPanel({ children, value, index, ...other }: {
-    children?: React.ReactNode;
-    index: number;
-    value: number;
-}): React.JSX.Element;

package/dist/components/dialogs/TabPanel.js

@@ -1,6 +0,0 @@
-import React from 'react';
-// this is from MUI example
-export default function TabPanel({ children, value, index, ...other }) {
-    return (React.createElement("div", { role: "tabpanel", hidden: value !== index, ...other }, value === index && React.createElement("div", null, children)));
-}
-//# sourceMappingURL=TabPanel.js.map

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

@@ -1 +0,0 @@
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package/dist/components/header/ZoomStar.js

@@ -1,40 +0,0 @@
-import React from 'react';
-import RestartAlt from '@mui/icons-material/RestartAlt';
-import { IconButton } from '@mui/material';
-import { observer } from 'mobx-react';
-import { makeStyles } from 'tss-react/mui';
-const useStyles = makeStyles()(theme => ({
-    dpad: {
-        display: 'grid',
-        gridTemplateColumns: 'repeat(3, 1fr)',
-    },
-    icon: {
-        padding: theme.spacing(0.5),
-    },
-}));
-const ZoomStar = observer(function ({ model }) {
-    const { classes } = useStyles();
-    return (React.createElement("div", { className: classes.dpad },
-        React.createElement("div", null),
-        React.createElement(IconButton, { className: classes.icon, onClick: () => {
-                model.zoomInVertical();
-            } }, "Y+"),
-        React.createElement("div", null),
-        React.createElement(IconButton, { className: classes.icon, onClick: () => {
-                model.zoomOutHorizontal();
-            } }, "X-"),
-        React.createElement(IconButton, { className: classes.icon, onClick: () => {
-                model.resetZoom();
-            } },
-            React.createElement(RestartAlt, null)),
-        React.createElement(IconButton, { className: classes.icon, onClick: () => {
-                model.zoomInHorizontal();
-            } }, "X+"),
-        React.createElement("div", null),
-        React.createElement(IconButton, { className: classes.icon, onClick: () => {
-                model.zoomOutVertical();
-            } }, "Y-"),
-        React.createElement("div", null)));
-});
-export default ZoomStar;
-//# sourceMappingURL=ZoomStar.js.map

package/dist/components/header/ZoomStar.js.map

@@ -1 +0,0 @@
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package/dist/createPaletteMap.test.d.ts

@@ -1 +0,0 @@
-export {};

package/dist/createPaletteMap.test.js

@@ -1,49 +0,0 @@
-import { expect, test } from 'vitest';
-import { createPaletteMap } from "./createPaletteMap.js";
-import palettes from "./ggplotPalettes.js";
-// Original implementation for comparison
-function originalFillPalette(keys) {
-    let i = 0;
-    const map = {};
-    for (const key of keys) {
-        const k = Math.min(keys.length - 1, palettes.length - 1);
-        map[key] = palettes[k][i];
-        i++;
-    }
-    return map;
-}
-test('createPaletteMap matches original implementation with 1 key', () => {
-    const keys = ['IPR001234'];
-    expect(createPaletteMap(keys)).toEqual(originalFillPalette(keys));
-});
-test('createPaletteMap matches original implementation with 3 keys', () => {
-    const keys = ['IPR001234', 'IPR005678', 'IPR009012'];
-    expect(createPaletteMap(keys)).toEqual(originalFillPalette(keys));
-});
-test('createPaletteMap matches original implementation with 8 keys (max palette size)', () => {
-    const keys = ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H'];
-    expect(createPaletteMap(keys)).toEqual(originalFillPalette(keys));
-});
-test('createPaletteMap matches original implementation with more keys than palette colors', () => {
-    const keys = ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J'];
-    expect(createPaletteMap(keys)).toEqual(originalFillPalette(keys));
-});
-test('createPaletteMap returns correct colors for 3 keys', () => {
-    const keys = ['X', 'Y', 'Z'];
-    const result = createPaletteMap(keys);
-    // With 3 keys, uses palette index 2 (0-indexed)
-    expect(result).toEqual({
-        X: '#F8766D',
-        Y: '#00BA38',
-        Z: '#619CFF',
-    });
-});
-test('createPaletteMap returns empty object for empty keys', () => {
-    expect(createPaletteMap([])).toEqual({});
-});
-test('createPaletteMap preserves key order', () => {
-    const keys = ['Z', 'A', 'M'];
-    const result = createPaletteMap(keys);
-    expect(Object.keys(result)).toEqual(['Z', 'A', 'M']);
-});
-//# sourceMappingURL=createPaletteMap.test.js.map

package/dist/createPaletteMap.test.js.map

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package/dist/layout.d.ts

@@ -1,26 +0,0 @@
-export default class Layout {
-    rectangles: Map<string, {
-        minY: number;
-        maxY: number;
-        minX: number;
-        maxX: number;
-        id: string;
-        data: unknown;
-    }>;
-    maxHeightReached: boolean;
-    private maxHeight;
-    private flatbush;
-    private indexToId;
-    private pTotalHeight;
-    constructor({ maxHeight, }?: {
-        maxHeight?: number;
-    });
-    private rebuildIndex;
-    private collides;
-    /**
-     * @returns top position for the rect, or Null if laying
-     *  out the rect would exceed maxHeighe
-     */
-    addRect(id: string, left: number, right: number, height: number, data: unknown): number | null;
-    get totalHeight(): number;
-}