jbrowse-plugin-mafviewer 1.0.1

package/src/LinearMafRenderer/configSchema.ts

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+import { ConfigurationSchema } from '@jbrowse/core/configuration'
+
+/**
+ * #config LinearMafRenderer
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
+const configSchema = ConfigurationSchema(
+  'LinearMafRenderer',
+  {},
+  {
+    /**
+     * #baseConfiguration
+     */
+    explicitlyTyped: true,
+  },
+)
+
+export default configSchema

package/src/LinearMafRenderer/index.ts

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+import PluginManager from '@jbrowse/core/PluginManager'
+import configSchema from './configSchema'
+import LinearMafRenderer from './LinearMafRenderer'
+import ReactComponent from './components/ReactComponent'
+
+export default function LinearMafRendererF(pluginManager: PluginManager) {
+  pluginManager.addRendererType(
+    () =>
+      new LinearMafRenderer({
+        name: 'LinearMafRenderer',
+        ReactComponent,
+        configSchema,
+        pluginManager,
+      }),
+  )
+}

package/src/MafAddTrackWorkflow/AddTrackWorkflow.tsx

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+import React, { useState } from 'react'
+import {
+  Button,
+  FormControl,
+  FormControlLabel,
+  FormLabel,
+  Paper,
+  Radio,
+  RadioGroup,
+  TextField,
+} from '@mui/material'
+import { makeStyles } from 'tss-react/mui'
+import {
+  FileLocation,
+  getSession,
+  isSessionModelWithWidgets,
+  isSessionWithAddTracks,
+} from '@jbrowse/core/util'
+import { AddTrackModel } from '@jbrowse/plugin-data-management'
+import { ErrorMessage, FileSelector } from '@jbrowse/core/ui'
+import { getRoot } from 'mobx-state-tree'
+
+const useStyles = makeStyles()(theme => ({
+  textbox: {
+    width: '100%',
+  },
+  paper: {
+    margin: theme.spacing(),
+    padding: theme.spacing(),
+  },
+  submit: {
+    marginTop: 25,
+    marginBottom: 100,
+    display: 'block',
+  },
+}))
+
+export default function MultiMAFWidget({ model }: { model: AddTrackModel }) {
+  const { classes } = useStyles()
+  const [samples, setSamples] = useState('')
+  const [loc, setLoc] = useState<FileLocation>()
+  const [indexLoc, setIndexLoc] = useState<FileLocation>()
+  const [error, setError] = useState<unknown>()
+  const [trackName, setTrackName] = useState('MAF track')
+  const [choice, setChoice] = useState('BigMafAdapter')
+  const rootModel = getRoot<any>(model)
+  return (
+    <Paper className={classes.paper}>
+      <Paper>
+        {error ? <ErrorMessage error={error} /> : null}
+        <FormControl>
+          <FormLabel>File type</FormLabel>
+          <RadioGroup
+            value={choice}
+            onChange={event => setChoice(event.target.value)}
+          >
+            <FormControlLabel
+              value="BigMafAdapter"
+              control={<Radio />}
+              checked={choice === 'BigMafAdapter'}
+              label="bigMaf"
+            />
+            <FormControlLabel
+              value="MafTabixAdapter"
+              control={<Radio />}
+              checked={choice === 'MafTabixAdapter'}
+              label="mafTabix"
+            />
+          </RadioGroup>
+        </FormControl>
+        {choice === 'BigMafAdapter' ? (
+          <FileSelector
+            location={loc}
+            name="Path to bigMaf"
+            setLocation={arg => setLoc(arg)}
+            rootModel={rootModel}
+          />
+        ) : (
+          <>
+            <FileSelector
+              location={loc}
+              name="Path to MAF tabix"
+              setLocation={arg => setLoc(arg)}
+              rootModel={rootModel}
+            />
+            <FileSelector
+              location={indexLoc}
+              name="Path to MAF tabix index"
+              setLocation={arg => setIndexLoc(arg)}
+              rootModel={rootModel}
+            />
+          </>
+        )}
+      </Paper>
+      <TextField
+        multiline
+        rows={10}
+        value={samples}
+        onChange={event => setSamples(event.target.value)}
+        placeholder={
+          'Enter sample names from the MAF file, one per line, or JSON formatted array of samples'
+        }
+        variant="outlined"
+        fullWidth
+      />
+
+      <TextField
+        value={trackName}
+        onChange={event => setTrackName(event.target.value)}
+        helperText="Track name"
+      />
+      <Button
+        variant="contained"
+        className={classes.submit}
+        onClick={() => {
+          try {
+            const session = getSession(model)
+            let sampleNames = [] as string[]
+            try {
+              sampleNames = JSON.parse(samples)
+            } catch (e) {
+              sampleNames = samples.split(/\n|\r\n|\r/)
+            }
+
+            const trackId = [
+              `${trackName.toLowerCase().replaceAll(' ', '_')}-${Date.now()}`,
+              `${session.adminMode ? '' : '-sessionTrack'}`,
+            ].join('')
+
+            if (isSessionWithAddTracks(session)) {
+              session.addTrackConf({
+                trackId,
+                type: 'MafTrack',
+                name: trackName,
+                assemblyNames: [model.assembly],
+                adapter:
+                  choice === 'BigMafAdapter'
+                    ? {
+                        type: choice,
+                        bigBedLocation: loc,
+                        samples: sampleNames,
+                      }
+                    : {
+                        type: choice,
+                        bedGzLocation: loc,
+                        index: { location: indexLoc },
+                        samples: sampleNames,
+                      },
+              })
+
+              model.view?.showTrack(trackId)
+            }
+            model.clearData()
+            if (isSessionModelWithWidgets(session)) {
+              session.hideWidget(model)
+            }
+          } catch (e) {
+            setError(e)
+          }
+        }}
+      >
+        Submit
+      </Button>
+    </Paper>
+  )
+}

package/src/MafAddTrackWorkflow/index.ts

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+import PluginManager from '@jbrowse/core/PluginManager'
+import { AddTrackWorkflowType } from '@jbrowse/core/pluggableElementTypes'
+import { types } from 'mobx-state-tree'
+
+// locals
+import MultiMAFWidget from './AddTrackWorkflow'
+
+export default function MafAddTrackWorkflowF(pluginManager: PluginManager) {
+  pluginManager.addAddTrackWorkflowType(
+    () =>
+      new AddTrackWorkflowType({
+        name: 'MAF track',
+        ReactComponent: MultiMAFWidget,
+        stateModel: types.model({}),
+      }),
+  )
+}

package/src/MafTabixAdapter/MafTabixAdapter.ts

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+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
+import { getSnapshot } from 'mobx-state-tree'
+import { Feature, Region, SimpleFeature } from '@jbrowse/core/util'
+import { ObservableCreate } from '@jbrowse/core/util/rxjs'
+import { firstValueFrom, toArray } from 'rxjs'
+
+interface OrganismRecord {
+  chr: string
+  start: number
+  srcSize: number
+  strand: number
+  unknown: number
+  data: string
+}
+export default class BigMafAdapter extends BaseFeatureDataAdapter {
+  public setupP?: Promise<{ adapter: BaseFeatureDataAdapter }>
+
+  async setup() {
+    const config = this.config
+    if (!this.getSubAdapter) {
+      throw new Error('no getSubAdapter available')
+    }
+    const adapter = await this.getSubAdapter({
+      ...getSnapshot(config),
+      type: 'BedTabixAdapter',
+    })
+    return {
+      adapter: adapter.dataAdapter as BaseFeatureDataAdapter,
+    }
+  }
+  async setupPre() {
+    if (!this.setupP) {
+      this.setupP = this.setup().catch(e => {
+        this.setupP = undefined
+        throw e
+      })
+    }
+    return this.setupP
+  }
+
+  async getRefNames() {
+    const { adapter } = await this.setup()
+    return adapter.getRefNames()
+  }
+
+  getFeatures(query: Region) {
+    return ObservableCreate<Feature>(async observer => {
+      const { adapter } = await this.setup()
+      const features = await firstValueFrom(
+        adapter.getFeatures(query).pipe(toArray()),
+      )
+      for (const feature of features) {
+        const data = (feature.get('field5') as string).split(',')
+        const alignments = {} as Record<string, OrganismRecord>
+        const main = data[0]
+        const aln = main.split(':')[5]
+        const alns = data.map(elt => elt.split(':')[5])
+        const alns2 = data.map(() => '')
+        // remove extraneous data in other alignments
+        // reason being: cannot represent missing data in main species that are in others)
+        for (let i = 0, o = 0; i < aln.length; i++, o++) {
+          if (aln[i] !== '-') {
+            for (let j = 0; j < data.length; j++) {
+              alns2[j] += alns[j][i]
+            }
+          }
+        }
+        for (let j = 0; j < data.length; j++) {
+          const elt = data[j]
+
+          const ad = elt.split(':')
+          const org = ad[0].split('.')[0]
+          const chr = ad[0].split('.')[1]
+
+          alignments[org] = {
+            chr: chr,
+            start: +ad[1],
+            srcSize: +ad[2],
+            strand: ad[3] === '-' ? -1 : 1,
+            unknown: +ad[4],
+            data: alns2[j],
+          }
+        }
+
+        observer.next(
+          new SimpleFeature({
+            id: feature.id(),
+            data: {
+              start: feature.get('start'),
+              end: feature.get('end'),
+              refName: feature.get('refName'),
+              name: feature.get('name'),
+              score: feature.get('score'),
+              alignments: alignments,
+              seq: alns2[0],
+            },
+          }),
+        )
+      }
+      observer.complete()
+    })
+  }
+  freeResources(): void {}
+}

package/src/MafTabixAdapter/configSchema.ts

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+import { ConfigurationSchema } from '@jbrowse/core/configuration'
+
+/**
+ * #config MafTabixAdapter
+ * used to configure MafTabix adapter
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
+const configSchema = ConfigurationSchema(
+  'MafTabixAdapter',
+  {
+    /**
+     * #slot
+     */
+    samples: {
+      type: 'stringArray',
+      defaultValue: [],
+    },
+    /**
+     * #slot
+     */
+    bedGzLocation: {
+      type: 'fileLocation',
+      defaultValue: {
+        uri: '/path/to/my.bed.gz.tbi',
+        locationType: 'UriLocation',
+      },
+    },
+    index: ConfigurationSchema('Index', {
+      location: {
+        type: 'fileLocation',
+        defaultValue: {
+          uri: '/path/to/my.bed.gz.tbi',
+        },
+      },
+      indexType: {
+        type: 'string',
+        defaultValue: 'TBI',
+      },
+    }),
+  },
+  { explicitlyTyped: true },
+)
+
+export default configSchema

package/src/MafTabixAdapter/index.ts

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+import PluginManager from '@jbrowse/core/PluginManager'
+import { AdapterType } from '@jbrowse/core/pluggableElementTypes'
+import configSchema from './configSchema'
+import MafTabixAdapter from './MafTabixAdapter'
+
+export default function MafTabixAdapterF(pluginManager: PluginManager) {
+  return pluginManager.addAdapterType(
+    () =>
+      new AdapterType({
+        name: 'MafTabixAdapter',
+        AdapterClass: MafTabixAdapter,
+        configSchema,
+      }),
+  )
+}

package/src/MafTrack/configSchema.ts

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+import PluginManager from '@jbrowse/core/PluginManager'
+import { ConfigurationSchema } from '@jbrowse/core/configuration'
+import { createBaseTrackConfig } from '@jbrowse/core/pluggableElementTypes'
+
+export default function configSchemaF(pluginManager: PluginManager) {
+  return ConfigurationSchema(
+    'MafTrack',
+    {},
+    {
+      /**
+       * #baseConfiguration
+       */
+      baseConfiguration: createBaseTrackConfig(pluginManager),
+      /**
+       * #identifier
+       */
+      explicitIdentifier: 'trackId',
+    },
+  )
+}

package/src/MafTrack/index.ts

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+import PluginManager from '@jbrowse/core/PluginManager'
+import {
+  TrackType,
+  createBaseTrackModel,
+} from '@jbrowse/core/pluggableElementTypes'
+import configSchemaF from './configSchema'
+
+export default function MafTrackF(pluginManager: PluginManager) {
+  return pluginManager.addTrackType(() => {
+    const configSchema = configSchemaF(pluginManager)
+    return new TrackType({
+      name: 'MafTrack',
+      configSchema,
+      displayName: 'MAF track',
+      stateModel: createBaseTrackModel(pluginManager, 'MafTrack', configSchema),
+    })
+  })
+}

package/src/declare.d.ts

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+declare module '*.json'

package/src/index.ts

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+import Plugin from '@jbrowse/core/Plugin'
+import PluginManager from '@jbrowse/core/PluginManager'
+
+import { version } from '../package.json'
+import BigMafAdapterF from './BigMafAdapter'
+import MafTrackF from './MafTrack'
+import LinearMafDisplayF from './LinearMafDisplay'
+import LinearMafRendererF from './LinearMafRenderer'
+import MafTabixAdapterF from './MafTabixAdapter'
+import MafAddTrackWorkflowF from './MafAddTrackWorkflow'
+
+export default class MafViewerPlugin extends Plugin {
+  name = 'MafViewerPlugin'
+  version = version
+
+  install(pluginManager: PluginManager) {
+    BigMafAdapterF(pluginManager)
+    MafTrackF(pluginManager)
+    LinearMafDisplayF(pluginManager)
+    LinearMafRendererF(pluginManager)
+    MafTabixAdapterF(pluginManager)
+    MafAddTrackWorkflowF(pluginManager)
+  }
+
+  configure(pluginManager: PluginManager) {}
+}