jbrowse-plugin-mafviewer 1.1.1 → 1.1.3

package/package.json

@@ -1,5 +1,5 @@
 {
-  "version": "1.1.1",
+  "version": "1.1.3",
   "license": "MIT",
   "name": "jbrowse-plugin-mafviewer",
   "keywords": [

package/src/BgzipTaffyAdapter/BgzipTaffyAdapter.ts

@@ -197,17 +197,25 @@ export default class BgzipTaffyAdapter extends BaseFeatureDataAdapter {
     if (records) {
       let firstEntry = records[0]
       let nextEntry
+      // two pass:
+      // first pass: find first block greater than query start, then -1 from
+      // that
       for (let i = 0; i < records.length; i++) {
         if (records[i]!.chrStart >= query.start) {
-          // we use i-1 for firstEntry because the current record is "greater
-          // than the query start", we go backwards one record to make sure to
-          // cover up until the query start. we use i+1 to ensure we get at
-          // least one block in the case that i=0
           firstEntry = records[Math.max(i - 1, 0)]
+          break
+        }
+      }
+      // second pass: find first block where query end less than record start,
+      // and +1 from that
+      for (let i = 0; i < records.length; i++) {
+        if (query.end <= records[i]!.chrStart) {
           nextEntry = records[i + 1]
           break
         }
       }
+
+      nextEntry = nextEntry ?? records.at(-1)
       if (firstEntry && nextEntry) {
         const response = await file.read(
           nextEntry.virtualOffset.blockPosition -

package/src/BigMafAdapter/BigMafAdapter.ts

@@ -1,9 +1,13 @@
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
 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
@@ -105,5 +109,21 @@ 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/LinearMafDisplay/components/Tree.tsx

@@ -3,7 +3,15 @@ import React from 'react'
 import { observer } from 'mobx-react'
 
 const Tree = observer(function ({ model }: { model: any }) {
-  const { hierarchy, showBranchLen } = model
+  const {
+    // this is needed for redrawing after zoom change, similar to react-msaview
+    // renderTreeCanvas
+    // eslint-disable-next-line  @typescript-eslint/no-unused-vars
+    rowHeight: _rowHeight,
+
+    hierarchy,
+    showBranchLen,
+  } = model
 
   return (
     <>

package/src/LinearMafDisplay/stateModel.ts

@@ -213,8 +213,9 @@ export default function stateModelFactory(
     }))
     .views(self => {
       const {
+        // eslint-disable-next-line @typescript-eslint/unbound-method
         trackMenuItems: superTrackMenuItems,
-
+        // eslint-disable-next-line @typescript-eslint/unbound-method
         renderProps: superRenderProps,
       } = self
       return {
@@ -316,6 +317,7 @@ export default function stateModelFactory(
       },
     }))
     .actions(self => {
+      // eslint-disable-next-line @typescript-eslint/unbound-method
       const { renderSvg: superRenderSvg } = self
       return {
         /**

package/src/MafAddTrackWorkflow/AddTrackWorkflow.tsx

@@ -71,6 +71,7 @@ export default function MultiMAFWidget({ model }: { model: AddTrackModel }) {
             {['BigMafAdapter', 'MafTabixAdapter', 'BgzipTaffyAdapter'].map(
               r => (
                 <FormControlLabel
+                  key={r}
                   value={r}
                   control={<Radio />}
                   checked={fileTypeChoice === r}
@@ -101,9 +102,10 @@ export default function MultiMAFWidget({ model }: { model: AddTrackModel }) {
               >
                 {['TBI', 'CSI'].map(r => (
                   <FormControlLabel
+                    key={r}
                     value={r}
                     control={<Radio />}
-                    checked={fileTypeChoice === r}
+                    checked={indexTypeChoice === r}
                     label={r}
                   />
                 ))}