@jbrowse/plugin-alignments 2.6.1 → 2.6.3

package/src/LinearPileupDisplay/components/SetFeatureHeight.tsx

@@ -1,82 +0,0 @@
-import React, { useState } from 'react'
-import { observer } from 'mobx-react'
-import {
-  Button,
-  Checkbox,
-  DialogActions,
-  DialogContent,
-  FormControlLabel,
-  TextField,
-  Typography,
-} from '@mui/material'
-import { Dialog } from '@jbrowse/core/ui'
-
-function SetFeatureHeightDlg(props: {
-  model: {
-    setFeatureHeight: (arg?: number) => void
-    setNoSpacing: (arg?: boolean) => void
-    featureHeightSetting: number
-    noSpacing?: boolean
-  }
-  handleClose: () => void
-}) {
-  const { model, handleClose } = props
-  const { featureHeightSetting, noSpacing: noSpacingSetting } = model
-  const [height, setHeight] = useState(`${featureHeightSetting}`)
-  const [noSpacing, setNoSpacing] = useState(noSpacingSetting)
-
-  const ok = height !== '' && !Number.isNaN(+height)
-
-  return (
-    <Dialog open onClose={handleClose} title="Set feature height">
-      <DialogContent>
-        <Typography>
-          Adjust the feature height and whether there is any spacing between
-          features. Setting feature height to 1 and removing spacing makes the
-          display very compact.
-        </Typography>
-        <TextField
-          value={height}
-          helperText="Feature height"
-          onChange={event => setHeight(event.target.value)}
-        />
-        <FormControlLabel
-          control={
-            <Checkbox
-              checked={!!noSpacing}
-              onChange={() => setNoSpacing(val => !val)}
-            />
-          }
-          label="Remove spacing between features in y-direction?"
-        />
-        <DialogActions>
-          <Button
-            variant="contained"
-            color="primary"
-            type="submit"
-            autoFocus
-            disabled={!ok}
-            onClick={() => {
-              model.setFeatureHeight(
-                height !== '' && !Number.isNaN(+height) ? +height : undefined,
-              )
-              model.setNoSpacing(noSpacing)
-              handleClose()
-            }}
-          >
-            Submit
-          </Button>
-          <Button
-            variant="contained"
-            color="secondary"
-            onClick={() => handleClose()}
-          >
-            Cancel
-          </Button>
-        </DialogActions>
-      </DialogContent>
-    </Dialog>
-  )
-}
-
-export default observer(SetFeatureHeightDlg)

package/src/LinearPileupDisplay/components/SetMaxHeight.tsx

@@ -1,71 +0,0 @@
-import React, { useState } from 'react'
-import { observer } from 'mobx-react'
-import {
-  Button,
-  DialogActions,
-  DialogContent,
-  TextField,
-  Typography,
-} from '@mui/material'
-import { Dialog } from '@jbrowse/core/ui'
-import { makeStyles } from 'tss-react/mui'
-
-const useStyles = makeStyles()({
-  root: {
-    width: 500,
-  },
-})
-
-function SetMaxHeightDlg(props: {
-  model: {
-    maxHeight?: number
-    setMaxHeight: Function
-  }
-  handleClose: () => void
-}) {
-  const { model, handleClose } = props
-  const { classes } = useStyles()
-  const { maxHeight = '' } = model
-  const [max, setMax] = useState(`${maxHeight}`)
-
-  return (
-    <Dialog open onClose={handleClose} title="Filter options">
-      <DialogContent className={classes.root}>
-        <Typography>
-          Set max height for the track. For example, you can increase this if
-          the layout says &quot;Max height reached&quot;
-        </Typography>
-        <TextField
-          value={max}
-          onChange={event => setMax(event.target.value)}
-          placeholder="Enter max height for layout"
-        />
-        <DialogActions>
-          <Button
-            variant="contained"
-            color="primary"
-            type="submit"
-            autoFocus
-            onClick={() => {
-              model.setMaxHeight(
-                max !== '' && !Number.isNaN(+max) ? +max : undefined,
-              )
-              handleClose()
-            }}
-          >
-            Submit
-          </Button>
-          <Button
-            variant="contained"
-            color="secondary"
-            onClick={() => handleClose()}
-          >
-            Cancel
-          </Button>
-        </DialogActions>
-      </DialogContent>
-    </Dialog>
-  )
-}
-
-export default observer(SetMaxHeightDlg)

package/src/LinearPileupDisplay/components/SortByTag.tsx

@@ -1,64 +0,0 @@
-import React, { useState } from 'react'
-import { observer } from 'mobx-react'
-import {
-  Button,
-  DialogActions,
-  DialogContent,
-  TextField,
-  Typography,
-} from '@mui/material'
-import { Dialog } from '@jbrowse/core/ui'
-
-function SortByTagDlg(props: {
-  model: { setSortedBy: Function }
-  handleClose: () => void
-}) {
-  const { model, handleClose } = props
-  const [tag, setTag] = useState('')
-  const validTag = tag.match(/^[A-Za-z][A-Za-z0-9]$/)
-  return (
-    <Dialog open onClose={handleClose} title="Sort by tag">
-      <DialogContent>
-        <Typography>Set the tag to sort by</Typography>
-        <Typography color="textSecondary">
-          Examples: HP for haplotype, RG for read group, etc.
-        </Typography>
-        <TextField
-          value={tag}
-          onChange={event => setTag(event.target.value)}
-          placeholder="Enter tag name"
-          inputProps={{
-            maxLength: 2,
-            'data-testid': 'sort-tag-name-input',
-          }}
-          error={tag.length === 2 && !validTag}
-          helperText={tag.length === 2 && !validTag ? 'Not a valid tag' : ''}
-          autoComplete="off"
-          data-testid="sort-tag-name"
-        />
-        <DialogActions>
-          <Button
-            variant="contained"
-            color="primary"
-            type="submit"
-            autoFocus
-            onClick={() => {
-              model.setSortedBy('tag', tag)
-              handleClose()
-            }}
-          >
-            Submit
-          </Button>
-          <Button
-            variant="contained"
-            color="secondary"
-            onClick={() => handleClose()}
-          >
-            Cancel
-          </Button>
-        </DialogActions>
-      </DialogContent>
-    </Dialog>
-  )
-}
-export default observer(SortByTagDlg)

package/src/LinearPileupDisplay/configSchema.test.js

@@ -1,55 +0,0 @@
-import Plugin from '@jbrowse/core/Plugin'
-import PluginManager from '@jbrowse/core/PluginManager'
-import BoxRendererType from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType'
-import {
-  svgFeatureRendererConfigSchema,
-  SvgFeatureRendererReactComponent,
-} from '@jbrowse/plugin-svg'
-import PileupRenderer from '../PileupRenderer'
-import configSchemaFactory from './configSchema'
-
-// mock warnings to avoid unnecessary outputs
-beforeEach(() => {
-  jest.spyOn(console, 'warn').mockImplementation(() => {})
-})
-
-afterEach(() => {
-  console.warn.mockRestore()
-})
-
-class PileupRendererPlugin extends Plugin {
-  install(pluginManager) {
-    PileupRenderer(pluginManager)
-  }
-}
-
-class SvgFeatureRendererPlugin extends Plugin {
-  install(pluginManager) {
-    pluginManager.addRendererType(
-      () =>
-        new BoxRendererType({
-          name: 'SvgFeatureRenderer',
-          ReactComponent: SvgFeatureRendererReactComponent,
-          configSchema: svgFeatureRendererConfigSchema,
-          pluginManager,
-        }),
-    )
-  }
-}
-
-test('has a type attr', () => {
-  const configSchema = configSchemaFactory(
-    new PluginManager([
-      new PileupRendererPlugin(),
-      new SvgFeatureRendererPlugin(),
-    ])
-      .createPluggableElements()
-      .configure(),
-  )
-  const config = configSchema.create({
-    type: 'LinearPileupDisplay',
-    displayId: 'display0',
-    name: 'Zonker Display',
-  })
-  expect(config.type).toEqual('LinearPileupDisplay')
-})

package/src/LinearPileupDisplay/configSchema.ts

@@ -1,67 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-import { linearBasicDisplayConfigSchemaFactory } from '@jbrowse/plugin-linear-genome-view'
-import { types } from 'mobx-state-tree'
-import PluginManager from '@jbrowse/core/PluginManager'
-
-/**
- * #config LinearPileupDisplay
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-function configSchemaF(pluginManager: PluginManager) {
-  // modify config schema to take in a sub coverage display
-  return ConfigurationSchema(
-    'LinearPileupDisplay',
-    {
-      /**
-       * #slot
-       */
-      defaultRendering: {
-        type: 'stringEnum',
-        model: types.enumeration('Rendering', ['pileup']),
-        defaultValue: 'pileup',
-      },
-      /**
-       * #slot
-       */
-      renderers: ConfigurationSchema('RenderersConfiguration', {
-        PileupRenderer:
-          pluginManager.getRendererType('PileupRenderer').configSchema,
-      }),
-      /**
-       * #slot
-       */
-      maxFeatureScreenDensity: {
-        type: 'number',
-        description: 'maximum features per pixel that is displayed in the view',
-        defaultValue: 5,
-      },
-
-      /**
-       * #slot
-       */
-      colorScheme: {
-        type: 'stringEnum',
-        model: types.enumeration('colorScheme', [
-          'strand',
-          'normal',
-          'insertSize',
-          'insertSizeAndOrientation',
-          'mappingQuality',
-          'tag',
-        ]),
-        description: 'color scheme to use',
-        defaultValue: 'normal',
-      },
-    },
-    {
-      /**
-       * #baseConfiguration
-       */
-      baseConfiguration: linearBasicDisplayConfigSchemaFactory(pluginManager),
-      explicitlyTyped: true,
-    },
-  )
-}
-
-export default configSchemaF

package/src/LinearPileupDisplay/index.ts

@@ -1,24 +0,0 @@
-import configSchemaFactory from './configSchema'
-import modelFactory from './model'
-import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType'
-import PluginManager from '@jbrowse/core/PluginManager'
-import { BaseLinearDisplayComponent } from '@jbrowse/plugin-linear-genome-view'
-
-export default function register(pluginManager: PluginManager) {
-  pluginManager.addDisplayType(() => {
-    const configSchema = configSchemaFactory(pluginManager)
-    return new DisplayType({
-      name: 'LinearPileupDisplay',
-      displayName: 'Pileup display',
-      configSchema,
-      stateModel: modelFactory(configSchema),
-      subDisplay: { type: 'LinearAlignmentsDisplay', lowerPanel: true },
-      trackType: 'AlignmentsTrack',
-      viewType: 'LinearGenomeView',
-      ReactComponent: BaseLinearDisplayComponent,
-    })
-  })
-}
-
-export { default as linearPileupDisplayStateModelFactory } from './model'
-export { default as linearPileupDisplayConfigSchemaFactory } from './configSchema'