jbrowse-plugin-mafviewer 1.0.6 → 1.1.1

package/src/MafAddTrackWorkflow/AddTrackWorkflow.tsx

@@ -1,4 +1,13 @@
 import React, { useState } from 'react'
+
+import { ErrorMessage, FileSelector } from '@jbrowse/core/ui'
+import {
+  FileLocation,
+  getSession,
+  isSessionModelWithWidgets,
+  isSessionWithAddTracks,
+} from '@jbrowse/core/util'
+import { AddTrackModel } from '@jbrowse/plugin-data-management'
 import {
   Button,
   FormControl,
@@ -9,16 +18,8 @@ import {
   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'
+import { makeStyles } from 'tss-react/mui'
 
 const useStyles = makeStyles()(theme => ({
   textbox: {
@@ -35,15 +36,25 @@ const useStyles = makeStyles()(theme => ({
   },
 }))
 
+type AdapterTypeOptions =
+  | 'BigMafAdapter'
+  | 'MafTabixAdapter'
+  | 'BgzipTaffyAdapter'
+type IndexTypeOptions = 'TBI' | 'CSI'
+
 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 [nhLoc, setNhLoc] = useState<FileLocation>()
   const [error, setError] = useState<unknown>()
   const [trackName, setTrackName] = useState('MAF track')
-  const [choice, setChoice] = useState('BigMafAdapter')
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
+  const [fileTypeChoice, setFileTypeChoice] =
+    useState<AdapterTypeOptions>('BigMafAdapter')
+  const [indexTypeChoice, setIndexTypeChoice] =
+    useState<IndexTypeOptions>('TBI')
+
   const rootModel = getRoot<any>(model)
   return (
     <Paper className={classes.paper}>
@@ -52,63 +63,121 @@ export default function MultiMAFWidget({ model }: { model: AddTrackModel }) {
         <FormControl>
           <FormLabel>File type</FormLabel>
           <RadioGroup
-            value={choice}
-            onChange={event => setChoice(event.target.value)}
+            value={fileTypeChoice}
+            onChange={event => {
+              setFileTypeChoice(event.target.value as AdapterTypeOptions)
+            }}
           >
-            <FormControlLabel
-              value="BigMafAdapter"
-              control={<Radio />}
-              checked={choice === 'BigMafAdapter'}
-              label="bigMaf"
-            />
-            <FormControlLabel
-              value="MafTabixAdapter"
-              control={<Radio />}
-              checked={choice === 'MafTabixAdapter'}
-              label="mafTabix"
-            />
+            {['BigMafAdapter', 'MafTabixAdapter', 'BgzipTaffyAdapter'].map(
+              r => (
+                <FormControlLabel
+                  value={r}
+                  control={<Radio />}
+                  checked={fileTypeChoice === r}
+                  label={r}
+                />
+              ),
+            )}
           </RadioGroup>
         </FormControl>
-        {choice === 'BigMafAdapter' ? (
+        {fileTypeChoice === 'BigMafAdapter' ? (
           <FileSelector
             location={loc}
             name="Path to bigMaf"
-            setLocation={arg => setLoc(arg)}
             rootModel={rootModel}
+            setLocation={arg => {
+              setLoc(arg)
+            }}
           />
-        ) : (
+        ) : fileTypeChoice === 'MafTabixAdapter' ? (
           <>
+            <FormControl>
+              <FormLabel>Index type</FormLabel>
+              <RadioGroup
+                value={fileTypeChoice}
+                onChange={event => {
+                  setIndexTypeChoice(event.target.value as IndexTypeOptions)
+                }}
+              >
+                {['TBI', 'CSI'].map(r => (
+                  <FormControlLabel
+                    value={r}
+                    control={<Radio />}
+                    checked={fileTypeChoice === r}
+                    label={r}
+                  />
+                ))}
+              </RadioGroup>
+            </FormControl>
             <FileSelector
               location={loc}
               name="Path to MAF tabix"
-              setLocation={arg => setLoc(arg)}
               rootModel={rootModel}
+              setLocation={arg => {
+                setLoc(arg)
+              }}
             />
             <FileSelector
               location={indexLoc}
               name="Path to MAF tabix index"
-              setLocation={arg => setIndexLoc(arg)}
               rootModel={rootModel}
+              setLocation={arg => {
+                setIndexLoc(arg)
+              }}
+            />
+          </>
+        ) : (
+          <>
+            <FileSelector
+              location={loc}
+              name="Path to TAF.gz (Bgzipped TAF)"
+              rootModel={rootModel}
+              setLocation={arg => {
+                setLoc(arg)
+              }}
+            />
+            <FileSelector
+              location={indexLoc}
+              name="Path to TAF.gz.tai (TAF index)"
+              rootModel={rootModel}
+              setLocation={arg => {
+                setIndexLoc(arg)
+              }}
             />
           </>
         )}
       </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
-      />
+      <div>
+        <FileSelector
+          location={nhLoc}
+          name="Path to newick tree (.nh)"
+          rootModel={rootModel}
+          setLocation={arg => {
+            setNhLoc(arg)
+          }}
+        />
+        <TextField
+          multiline
+          rows={10}
+          value={samples}
+          onChange={event => {
+            setSamples(event.target.value)
+          }}
+          helperText="Sample names (optional if .nh supplied, required if not)"
+          placeholder={
+            'Enter sample names from the MAF file, one per line, or JSON formatted array of samples'
+          }
+          variant="outlined"
+          fullWidth
+        />
+      </div>
 
       <TextField
         value={trackName}
-        onChange={event => setTrackName(event.target.value)}
         helperText="Track name"
+        onChange={event => {
+          setTrackName(event.target.value)
+        }}
       />
       <Button
         variant="contained"
@@ -125,7 +194,7 @@ export default function MultiMAFWidget({ model }: { model: AddTrackModel }) {
 
             const trackId = [
               `${trackName.toLowerCase().replaceAll(' ', '_')}-${Date.now()}`,
-              `${session.adminMode ? '' : '-sessionTrack'}`,
+              session.adminMode ? '' : '-sessionTrack',
             ].join('')
 
             if (isSessionWithAddTracks(session)) {
@@ -135,18 +204,31 @@ export default function MultiMAFWidget({ model }: { model: AddTrackModel }) {
                 name: trackName,
                 assemblyNames: [model.assembly],
                 adapter:
-                  choice === 'BigMafAdapter'
+                  fileTypeChoice === 'BigMafAdapter'
                     ? {
-                        type: choice,
+                        type: fileTypeChoice,
                         bigBedLocation: loc,
                         samples: sampleNames,
+                        nhLocation: nhLoc,
                       }
-                    : {
-                        type: choice,
-                        bedGzLocation: loc,
-                        index: { location: indexLoc },
-                        samples: sampleNames,
-                      },
+                    : fileTypeChoice === 'MafTabixAdapter'
+                      ? {
+                          type: fileTypeChoice,
+                          bedGzLocation: loc,
+                          nhLocation: nhLoc,
+                          index: {
+                            indexType: indexTypeChoice,
+                            location: indexLoc,
+                          },
+                          samples: sampleNames,
+                        }
+                      : {
+                          type: fileTypeChoice,
+                          tafGzLocation: loc,
+                          taiLocation: indexLoc,
+                          nhLocation: nhLoc,
+                          samples: sampleNames,
+                        },
               })
 
               model.view?.showTrack(trackId)

package/src/MafRPC/index.ts

@@ -0,0 +1,39 @@
+import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache'
+import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions'
+
+import type PluginManager from '@jbrowse/core/PluginManager'
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration'
+import type { Region } from '@jbrowse/core/util'
+
+export class MafGetSamples extends RpcMethodTypeWithFiltersAndRenameRegions {
+  name = 'MafGetSamples'
+
+  async execute(
+    args: {
+      adapterConfig: AnyConfigurationModel
+      stopToken?: string
+      sessionId: string
+      headers?: Record<string, string>
+      regions: Region[]
+      bpPerPx: number
+    },
+    rpcDriverClassName: string,
+  ) {
+    const pm = this.pluginManager
+    const deserializedArgs = await this.deserializeArguments(
+      args,
+      rpcDriverClassName,
+    )
+    const { regions, adapterConfig, sessionId } = deserializedArgs
+    const { dataAdapter } = await getAdapter(pm, sessionId, adapterConfig)
+
+    // @ts-expect-error
+    return dataAdapter.getSamples(regions, deserializedArgs)
+  }
+}
+
+export default function MafRPCF(pluginManager: PluginManager) {
+  pluginManager.addRpcMethod(() => {
+    return new MafGetSamples(pluginManager)
+  })
+}

package/src/MafTabixAdapter/MafTabixAdapter.ts

@@ -1,9 +1,13 @@
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
-import { getSnapshot } from 'mobx-state-tree'
 import { Feature, Region, SimpleFeature } from '@jbrowse/core/util'
+import { openLocation } from '@jbrowse/core/util/io'
 import { ObservableCreate } from '@jbrowse/core/util/rxjs'
+import { getSnapshot } from 'mobx-state-tree'
 import { firstValueFrom, toArray } from 'rxjs'
 
+import parseNewick from '../parseNewick'
+import { normalize } from '../util'
+
 interface OrganismRecord {
   chr: string
   start: number
@@ -13,7 +17,7 @@ interface OrganismRecord {
   data: string
 }
 
-export default class BigMafAdapter extends BaseFeatureDataAdapter {
+export default class MafTabixAdapter extends BaseFeatureDataAdapter {
   public setupP?: Promise<{ adapter: BaseFeatureDataAdapter }>
 
   async setup() {
@@ -31,7 +35,7 @@ export default class BigMafAdapter extends BaseFeatureDataAdapter {
   }
   async setupPre() {
     if (!this.setupP) {
-      this.setupP = this.setup().catch(e => {
+      this.setupP = this.setup().catch((e: unknown) => {
         this.setupP = undefined
         throw e
       })
@@ -55,13 +59,7 @@ export default class BigMafAdapter extends BaseFeatureDataAdapter {
       const features = await firstValueFrom(
         adapter.getFeatures(query).pipe(toArray()),
       )
-      const samples = this.getConf('samples') as string[] | { id: string }[]
-      const sampleStrings =
-        typeof samples[0] === 'string'
-          ? (samples as string[])
-          : (samples as { id: string }[]).map(s => s.id)
-      const sampleSet = new Set(sampleStrings)
-      let i = 0
+
       for (const feature of features) {
         const data = (feature.get('field5') as string).split(',')
         const alignments = {} as Record<string, OrganismRecord>
@@ -69,26 +67,18 @@ export default class BigMafAdapter extends BaseFeatureDataAdapter {
 
         for (const [j, elt] of data.entries()) {
           const ad = elt.split(':')
-          const idx = ad[0].lastIndexOf('.')
-          const org = ad[0].slice(0, idx)
-          const last = ad[0].slice(idx + 1)
-          const s = sampleSet.has(org)
-            ? org
-            : sampleStrings.find(f => ad[0].startsWith(f))
-          if (s) {
-            alignments[s] = {
+          const idx = ad[0]!.lastIndexOf('.')
+          const org = ad[0]!.slice(0, idx)
+          const last = ad[0]!.slice(idx + 1)
+          if (org) {
+            alignments[org] = {
               chr: last,
-              start: +ad[1],
-              srcSize: +ad[2],
+              start: +ad[1]!,
+              srcSize: +ad[2]!,
               strand: ad[3] === '-' ? -1 : 1,
-              unknown: +ad[4],
-              data: alns[j],
+              unknown: +ad[4]!,
+              data: alns[j]!,
             }
-          } else if (i < 100) {
-            console.error(`line not processed ${ad[0]}`)
-            i++
-          } else if (i > 100) {
-            console.error('too many errors, not printing any more')
           }
         }
 
@@ -110,5 +100,21 @@ export default class BigMafAdapter extends BaseFeatureDataAdapter {
       observer.complete()
     })
   }
+
+  async getSamples(_query: Region) {
+    const nhLoc = this.getConf('nhLocation')
+    const nh =
+      nhLoc.uri === '/path/to/my.nh'
+        ? undefined
+        : await openLocation(nhLoc).readFile('utf8')
+
+    // TODO: we may need to resolve the exact set of rows in the visible region
+    // here
+    return {
+      samples: normalize(this.getConf('samples')),
+      tree: nh ? parseNewick(nh) : undefined,
+    }
+  }
+
   freeResources(): void {}
 }

package/src/MafTabixAdapter/configSchema.ts

@@ -2,7 +2,6 @@ import { ConfigurationSchema } from '@jbrowse/core/configuration'
 
 /**
  * #config MafTabixAdapter
- * used to configure MafTabix adapter
  */
 function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
 
@@ -28,17 +27,34 @@ const configSchema = ConfigurationSchema(
       },
     },
     index: ConfigurationSchema('Index', {
+      /**
+       * #slot index.location
+       */
       location: {
         type: 'fileLocation',
         defaultValue: {
           uri: '/path/to/my.bed.gz.tbi',
         },
       },
+      /**
+       * #slot index.indexType
+       */
       indexType: {
         type: 'string',
         defaultValue: 'TBI',
       },
     }),
+    /**
+     * #slot
+     */
+    nhLocation: {
+      type: 'fileLocation',
+      description: 'newick tree',
+      defaultValue: {
+        uri: '/path/to/my.nh',
+        locationType: 'UriLocation',
+      },
+    },
   },
   { explicitlyTyped: true },
 )

package/src/MafTabixAdapter/index.ts

@@ -1,7 +1,8 @@
 import PluginManager from '@jbrowse/core/PluginManager'
 import { AdapterType } from '@jbrowse/core/pluggableElementTypes'
-import configSchema from './configSchema'
+
 import MafTabixAdapter from './MafTabixAdapter'
+import configSchema from './configSchema'
 
 export default function MafTabixAdapterF(pluginManager: PluginManager) {
   return pluginManager.addAdapterType(

package/src/MafTrack/index.ts

@@ -3,6 +3,7 @@ import {
   TrackType,
   createBaseTrackModel,
 } from '@jbrowse/core/pluggableElementTypes'
+
 import configSchemaF from './configSchema'
 
 export default function MafTrackF(pluginManager: PluginManager) {

package/src/index.ts

@@ -2,12 +2,14 @@ import Plugin from '@jbrowse/core/Plugin'
 import PluginManager from '@jbrowse/core/PluginManager'
 
 import { version } from '../package.json'
+import BgzipTaffyAdapterF from './BgzipTaffyAdapter'
 import BigMafAdapterF from './BigMafAdapter'
-import MafTrackF from './MafTrack'
 import LinearMafDisplayF from './LinearMafDisplay'
 import LinearMafRendererF from './LinearMafRenderer'
-import MafTabixAdapterF from './MafTabixAdapter'
 import MafAddTrackWorkflowF from './MafAddTrackWorkflow'
+import MafRPCF from './MafRPC'
+import MafTabixAdapterF from './MafTabixAdapter'
+import MafTrackF from './MafTrack'
 
 export default class MafViewerPlugin extends Plugin {
   name = 'MafViewerPlugin'
@@ -19,7 +21,9 @@ export default class MafViewerPlugin extends Plugin {
     LinearMafDisplayF(pluginManager)
     LinearMafRendererF(pluginManager)
     MafTabixAdapterF(pluginManager)
+    BgzipTaffyAdapterF(pluginManager)
     MafAddTrackWorkflowF(pluginManager)
+    MafRPCF(pluginManager)
   }
 
   configure(_pluginManager: PluginManager) {}

package/src/parseNewick.ts

@@ -0,0 +1,94 @@
+/**
+ * Newick format parser in JavaScript.
+ *
+ * Copyright (c) Jason Davies 2010.
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ * THE SOFTWARE.
+ *
+ * Example tree (from http://en.wikipedia.org/wiki/Newick_format):
+ *
+ * +--0.1--A
+ * F-----0.2-----B            +-------0.3----C
+ * +------------------0.5-----E
+ *                            +---------0.4------D
+ *
+ * Newick format:
+ * (A:0.1,B:0.2,(C:0.3,D:0.4)E:0.5)F;
+ *
+ * Converted to JSON:
+ * {
+ *   name: "F",
+ *   children: [
+ *     {name: "A", length: 0.1},
+ *     {name: "B", length: 0.2},
+ *     {
+ *       name: "E",
+ *       length: 0.5,
+ *       children: [
+ *         {name: "C", length: 0.3},
+ *         {name: "D", length: 0.4}
+ *       ]
+ *     }
+ *   ]
+ * }
+ *
+ * Converted to JSON, but with no names or lengths:
+ * {
+ *   children: [
+ *     {}, {}, {
+ *       children: [{}, {}]
+ *     }
+ *   ]
+ * }
+ */
+export default function parseNewick(s: string) {
+  const ancestors = []
+
+  let tree = {} as Record<string, any>
+  const tokens = s.split(/\s*(;|\(|\)|,|:)\s*/)
+  for (let i = 0; i < tokens.length; i++) {
+    const token = tokens[i]!
+    const subtree = {}
+    switch (token) {
+      case '(': // new children
+        tree.children = [subtree]
+        ancestors.push(tree)
+        tree = subtree
+        break
+      case ',': // another branch
+        ancestors.at(-1)?.children.push(subtree)
+        tree = subtree
+        break
+      case ')': // optional name next
+        tree = ancestors.pop()!
+        break
+      case ':': // optional length next
+        break
+      default: {
+        const x = tokens[i - 1]!
+        if (x === ')' || x === '(' || x === ',') {
+          tree.name = token
+        } else if (x === ':') {
+          tree.length = Number.parseFloat(token)
+        }
+      }
+    }
+  }
+  return tree
+}

package/src/util.ts

@@ -0,0 +1,11 @@
+function isStrs(array: unknown[]): array is string[] {
+  return typeof array[0] === 'string'
+}
+
+export function normalize(
+  r: string[] | { id: string; label: string; color?: string }[],
+) {
+  return isStrs(r)
+    ? r.map(elt => ({ id: elt, label: elt, color: undefined }))
+    : r
+}