react-msaview 5.0.7 → 5.0.16

package/dist/reparseTree.js

@@ -1,15 +0,0 @@
-// this reparse routine helps to allow the app to hide/collapse a single
-// leafnode
-export function reparseTree(tree) {
-    return {
-        ...tree,
-        children: tree.children.map(r => r.children.length
-            ? reparseTree(r)
-            : {
-                children: [r],
-                id: `${r.id}-leafnode`,
-                name: `${r.name}-hidden`,
-            }),
-    };
-}
-//# sourceMappingURL=reparseTree.js.map

package/dist/reparseTree.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"reparseTree.js","sourceRoot":"","sources":["../src/reparseTree.ts"],"names":[],"mappings":"AAEA,wEAAwE;AACxE,WAAW;AACX,MAAM,UAAU,WAAW,CAAC,IAAiB;IAC3C,OAAO;QACL,GAAG,IAAI;QACP,QAAQ,EAAE,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAC9B,CAAC,CAAC,QAAQ,CAAC,MAAM;YACf,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC;YAChB,CAAC,CAAC;gBACE,QAAQ,EAAE,CAAC,CAAC,CAAC;gBACb,EAAE,EAAE,GAAG,CAAC,CAAC,EAAE,WAAW;gBACtB,IAAI,EAAE,GAAG,CAAC,CAAC,IAAI,SAAS;aACzB,CACN;KACF,CAAA;AACH,CAAC"}

package/src/components/dialogs/AddTrackDialog.tsx

@@ -1,85 +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'
-
-import type { MsaViewModel } from '../../model.ts'
-import type { FileLocation } from '@jbrowse/core/util/types'
-
-const AddTrackDialog = observer(function ({
-  model,
-  onClose,
-  open,
-}: {
-  model: MsaViewModel
-  onClose: () => void
-  open: boolean
-}) {
-  const options = model.rows.map(r => r[0])
-  const [trackFile, setTrackFile] = useState<FileLocation>()
-  const [currentOption, setCurrentOption] = useState('')
-
-  return (
-    <Dialog
-      onClose={() => {
-        onClose()
-      }}
-      open={open}
-      title="Add track"
-    >
-      <DialogContent>
-        <Typography>
-          Open relevant per-alignment tracks e.g. protein domains
-        </Typography>
-        <TextField
-          select
-          helperText="Which row does this track apply to?"
-          value={currentOption}
-          onChange={event => {
-            setCurrentOption(event.target.value)
-          }}
-        >
-          {options.map((option, index) => (
-            <MenuItem key={`${option}-${index}`} value={option}>
-              {option}
-            </MenuItem>
-          ))}
-        </TextField>
-        <FileSelector location={trackFile} setLocation={setTrackFile} />
-        <DialogActions>
-          <Button
-            onClick={() => {
-              model.setError(undefined)
-              if (trackFile) {
-                model.setMSAFilehandle(trackFile)
-              }
-            }}
-            variant="contained"
-            color="primary"
-          >
-            Open
-          </Button>
-          <Button
-            color="secondary"
-            variant="contained"
-            onClick={() => {
-              onClose()
-            }}
-          >
-            Cancel
-          </Button>
-        </DialogActions>
-      </DialogContent>
-    </Dialog>
-  )
-})
-
-export default AddTrackDialog

package/src/components/dialogs/TabPanel.tsx

@@ -1,19 +0,0 @@
-import React from 'react'
-
-// this is from MUI example
-export default function TabPanel({
-  children,
-  value,
-  index,
-  ...other
-}: {
-  children?: React.ReactNode
-  index: number
-  value: number
-}) {
-  return (
-    <div role="tabpanel" hidden={value !== index} {...other}>
-      {value === index && <div>{children}</div>}
-    </div>
-  )
-}

package/src/components/header/ZoomStar.tsx

@@ -1,74 +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'
-
-import type { MsaViewModel } from '../../model.ts'
-
-const useStyles = makeStyles()(theme => ({
-  dpad: {
-    display: 'grid',
-    gridTemplateColumns: 'repeat(3, 1fr)',
-  },
-  icon: {
-    padding: theme.spacing(0.5),
-  },
-}))
-
-const ZoomStar = observer(function ({ model }: { model: MsaViewModel }) {
-  const { classes } = useStyles()
-  return (
-    <div className={classes.dpad}>
-      <div />
-      <IconButton
-        className={classes.icon}
-        onClick={() => {
-          model.zoomInVertical()
-        }}
-      >
-        Y+
-      </IconButton>
-      <div />
-
-      <IconButton
-        className={classes.icon}
-        onClick={() => {
-          model.zoomOutHorizontal()
-        }}
-      >
-        X-
-      </IconButton>
-      <IconButton
-        className={classes.icon}
-        onClick={() => {
-          model.resetZoom()
-        }}
-      >
-        <RestartAlt />
-      </IconButton>
-      <IconButton
-        className={classes.icon}
-        onClick={() => {
-          model.zoomInHorizontal()
-        }}
-      >
-        X+
-      </IconButton>
-
-      <div />
-      <IconButton
-        className={classes.icon}
-        onClick={() => {
-          model.zoomOutVertical()
-        }}
-      >
-        Y-
-      </IconButton>
-      <div />
-    </div>
-  )
-})
-
-export default ZoomStar

package/src/createPaletteMap.test.ts

@@ -1,57 +0,0 @@
-import { expect, test } from 'vitest'
-
-import { createPaletteMap } from './createPaletteMap.ts'
-import palettes from './ggplotPalettes.ts'
-
-// Original implementation for comparison
-function originalFillPalette(keys: string[]) {
-  let i = 0
-  const map = {} as Record<string, string>
-  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'])
-})

package/src/layout.ts

@@ -1,118 +0,0 @@
-import Flatbush from 'flatbush'
-
-export default class Layout {
-  public rectangles: Map<
-    string,
-    {
-      minY: number
-      maxY: number
-      minX: number
-      maxX: number
-      id: string
-      data: unknown
-    }
-  >
-
-  public maxHeightReached = false
-
-  private maxHeight: number
-
-  private flatbush: Flatbush | null = null
-
-  private indexToId: string[] = []
-
-  private pTotalHeight: number
-
-  constructor({
-    maxHeight = 10000,
-  }: {
-    maxHeight?: number
-  } = {}) {
-    this.rectangles = new Map()
-    this.maxHeight = Math.ceil(maxHeight)
-    this.pTotalHeight = 0 // total height, in units of bitmap squares (px/pitchY)
-  }
-
-  private rebuildIndex() {
-    // Rebuild the spatial index with current rectangles
-    const rects = Array.from(this.rectangles.values())
-    if (rects.length === 0) {
-      this.flatbush = null
-      this.indexToId = []
-      return
-    }
-
-    this.flatbush = new Flatbush(rects.length)
-    this.indexToId = []
-
-    for (const rect of rects) {
-      this.flatbush.add(rect.minX, rect.minY, rect.maxX, rect.maxY)
-      this.indexToId.push(rect.id)
-    }
-
-    this.flatbush.finish()
-  }
-
-  private collides(box: {
-    minX: number
-    minY: number
-    maxX: number
-    maxY: number
-  }): boolean {
-    if (!this.flatbush) {
-      return false
-    }
-
-    const results = this.flatbush.search(box.minX, box.minY, box.maxX, box.maxY)
-
-    return results.length > 0
-  }
-
-  /**
-   * @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 {
-    // add to flatbush
-    const existingRecord = this.rectangles.get(id)
-    if (existingRecord) {
-      return existingRecord.minY
-    }
-
-    let currHeight = 0
-    while (
-      this.collides({
-        minX: left,
-        minY: currHeight,
-        maxX: right,
-        maxY: currHeight + height,
-      }) &&
-      currHeight <= this.maxHeight
-    ) {
-      currHeight += 1
-    }
-
-    const record = {
-      minX: left,
-      minY: currHeight,
-      maxX: right,
-      maxY: currHeight + height,
-      id,
-      data,
-    }
-    this.rectangles.set(id, record)
-    this.rebuildIndex()
-    this.pTotalHeight = Math.max(this.pTotalHeight, currHeight)
-    return currHeight
-  }
-
-  get totalHeight() {
-    return this.pTotalHeight
-  }
-}

package/src/reparseTree.ts

@@ -1,18 +0,0 @@
-import type { NodeWithIds } from './types.ts'
-
-// this reparse routine helps to allow the app to hide/collapse a single
-// leafnode
-export function reparseTree(tree: NodeWithIds): NodeWithIds {
-  return {
-    ...tree,
-    children: tree.children.map(r =>
-      r.children.length
-        ? reparseTree(r)
-        : {
-            children: [r],
-            id: `${r.id}-leafnode`,
-            name: `${r.name}-hidden`,
-          },
-    ),
-  }
-}