@apollo-annotation/jbrowse-plugin-apollo 0.3.4 → 0.3.5

package/src/LinearApolloDisplay/glyphs/BoxGlyph.ts

@@ -8,12 +8,7 @@ import {
   SessionWithWidgets,
 } from '@jbrowse/core/util'
 
-import {
-  AddChildFeature,
-  CopyFeature,
-  DeleteFeature,
-  ModifyFeatureAttribute,
-} from '../../components'
+import { AddChildFeature, CopyFeature, DeleteFeature } from '../../components'
 
 import { LinearApolloDisplay } from '../stateModel'
 import {
@@ -349,26 +344,6 @@ function getContextMenuItems(
         )
       },
     },
-    {
-      label: 'Modify feature attribute',
-      disabled: readOnly,
-      onClick: () => {
-        ;(session as unknown as AbstractSessionModel).queueDialog(
-          (doneCallback) => [
-            ModifyFeatureAttribute,
-            {
-              session,
-              handleClose: () => {
-                doneCallback()
-              },
-              changeManager,
-              sourceFeature,
-              sourceAssemblyId: currentAssemblyId,
-            },
-          ],
-        )
-      },
-    },
     {
       label: 'Edit feature details',
       onClick: () => {
@@ -394,7 +369,11 @@ function getContextMenuItems(
     throw new Error('featureTypeOntology is undefined')
   }
   if (
-    featureTypeOntology.isTypeOf(sourceFeature.type, 'transcript') &&
+    (featureTypeOntology.isTypeOf(sourceFeature.type, 'transcript') ||
+      featureTypeOntology.isTypeOf(
+        sourceFeature.type,
+        'pseudogenic_transcript',
+      )) &&
     isSessionModelWithWidgets(session)
   ) {
     menuItems.push({

package/src/LinearApolloDisplay/glyphs/GeneGlyph.ts

@@ -112,10 +112,9 @@ function draw(
   // Draw lines on different rows for each transcript
   let currentRow = 0
   for (const [, transcript] of children) {
-    const isTranscript = featureTypeOntology.isTypeOf(
-      transcript.type,
-      'transcript',
-    )
+    const isTranscript =
+      featureTypeOntology.isTypeOf(transcript.type, 'transcript') ||
+      featureTypeOntology.isTypeOf(transcript.type, 'pseudogenic_transcript')
     if (!isTranscript) {
       currentRow += 1
       continue
@@ -161,7 +160,12 @@ function draw(
   // Draw exon and CDS for each transcript
   currentRow = 0
   for (const [, child] of children) {
-    if (!featureTypeOntology.isTypeOf(child.type, 'transcript')) {
+    if (
+      !(
+        featureTypeOntology.isTypeOf(child.type, 'transcript') ||
+        featureTypeOntology.isTypeOf(child.type, 'pseudogenic_transcript')
+      )
+    ) {
       boxGlyph.draw(ctx, child, row, stateModel, displayedRegionIndex)
       currentRow += 1
       continue
@@ -455,7 +459,11 @@ function getFeatureFromLayout(
     if (
       featureTypeOntology.isTypeOf(featureObj.type, 'CDS') &&
       featureObj.parent &&
-      featureTypeOntology.isTypeOf(featureObj.parent.type, 'transcript')
+      (featureTypeOntology.isTypeOf(featureObj.parent.type, 'transcript') ||
+        featureTypeOntology.isTypeOf(
+          featureObj.parent.type,
+          'pseudogenic_transcript',
+        ))
     ) {
       const { cdsLocations } = featureObj.parent
       for (const cdsLoc of cdsLocations) {
@@ -483,7 +491,7 @@ function getCDSCount(
   if (!children) {
     return 0
   }
-  const isMrna = featureTypeOntology.isTypeOf(type, 'mRNA')
+  const isMrna = featureTypeOntology.isTypeOf(type, 'transcript')
   let cdsCount = 0
   if (isMrna) {
     for (const [, child] of children) {
@@ -504,7 +512,9 @@ function getRowCount(
   if (!children) {
     return 1
   }
-  const isTranscript = featureTypeOntology.isTypeOf(type, 'transcript')
+  const isTranscript =
+    featureTypeOntology.isTypeOf(type, 'transcript') ||
+    featureTypeOntology.isTypeOf(type, 'pseudogenic_transcript')
   let rowCount = 0
   if (isTranscript) {
     for (const [, child] of children) {
@@ -532,7 +542,9 @@ function featuresForRow(
   feature: AnnotationFeature,
   featureTypeOntology: OntologyRecord,
 ): AnnotationFeature[][] {
-  const isGene = featureTypeOntology.isTypeOf(feature.type, 'gene')
+  const isGene =
+    featureTypeOntology.isTypeOf(feature.type, 'gene') ||
+    featureTypeOntology.isTypeOf(feature.type, 'pseudogene')
   if (!isGene) {
     throw new Error('Top level feature for GeneGlyph must have type "gene"')
   }
@@ -542,7 +554,12 @@ function featuresForRow(
   }
   const features: AnnotationFeature[][] = []
   for (const [, child] of children) {
-    if (!featureTypeOntology.isTypeOf(child.type, 'transcript')) {
+    if (
+      !(
+        featureTypeOntology.isTypeOf(child.type, 'transcript') ||
+        featureTypeOntology.isTypeOf(child.type, 'pseudogenic_transcript')
+      )
+    ) {
       features.push([child, feature])
       continue
     }
@@ -651,8 +668,12 @@ function getDraggableFeatureInfo(
   if (!featureTypeOntology) {
     throw new Error('featureTypeOntology is undefined')
   }
-  const isGene = featureTypeOntology.isTypeOf(feature.type, 'gene')
-  const isTranscript = featureTypeOntology.isTypeOf(feature.type, 'transcript')
+  const isGene =
+    featureTypeOntology.isTypeOf(feature.type, 'gene') ||
+    featureTypeOntology.isTypeOf(feature.type, 'pseudogene')
+  const isTranscript =
+    featureTypeOntology.isTypeOf(feature.type, 'transcript') ||
+    featureTypeOntology.isTypeOf(feature.type, 'pseudogenic_transcript')
   const isCds = featureTypeOntology.isTypeOf(feature.type, 'CDS')
   if (isGene || isTranscript) {
     return
@@ -691,9 +712,10 @@ function getDraggableFeatureInfo(
     }
 
     const overlappingExon = exonChildren.find((child) => {
-      const [start, end] = intersection2(bp, bp + 1, child.min, child.max)
+      const [start, end] = intersection2(bp - 1, bp, child.min, child.max)
       return start !== undefined && end !== undefined
     })
+
     if (!overlappingExon) {
       return
     }

package/src/LinearApolloDisplay/stateModel/layouts.ts

@@ -80,12 +80,17 @@ export function layoutsModelFactory(
         if (!children?.size) {
           return false
         }
-        const isGene = featureTypeOntology.isTypeOf(feature.type, 'gene')
+        const isGene =
+          featureTypeOntology.isTypeOf(feature.type, 'gene') ||
+          featureTypeOntology.isTypeOf(feature.type, 'pseudogene')
         if (!isGene) {
           return false
         }
         for (const [, child] of children) {
-          if (featureTypeOntology.isTypeOf(child.type, 'transcript')) {
+          if (
+            featureTypeOntology.isTypeOf(child.type, 'transcript') ||
+            featureTypeOntology.isTypeOf(child.type, 'pseudogenic_transcript')
+          ) {
             const { children: grandChildren } = child
             if (!grandChildren?.size) {
               return false

package/src/LinearApolloDisplay/stateModel/rendering.ts

@@ -155,6 +155,8 @@ function codonColorCode(letter: string) {
 }
 
 function reverseCodonSeq(seq: string): string {
+  // disable because sequence is all ascii
+  // eslint-disable-next-line @typescript-eslint/no-misused-spread
   return [...seq]
     .map((c) => revcom(c))
     .reverse()
@@ -272,6 +274,8 @@ export function sequenceRenderingModelFactory(
               if (!seq) {
                 return
               }
+              // disable because sequence is all ascii
+              // eslint-disable-next-line @typescript-eslint/no-misused-spread
               for (const [i, letter] of [...seq].entries()) {
                 const trnslXOffset =
                   (self.lgv.bpToPx({

package/src/OntologyManager/OntologyStore/fulltext-stopwords.ts

@@ -127,7 +127,16 @@ export const genericEnglishStopwords = new Set([
   'don',
   'should',
   'now',
-  ...'1234567890',
+  '0',
+  '1',
+  '2',
+  '3',
+  '4',
+  '5',
+  '6',
+  '7',
+  '8',
+  '9',
 ])
 
 /**

package/src/OntologyManager/OntologyStore/index.test.ts

@@ -25,6 +25,7 @@ jest.mock('jsonpath', () => {
     // eslint-disable-next-line @typescript-eslint/no-explicit-any
     query: jest.fn((obj: any, pathExpression: string, count?: number) => {
       const newObj =
+        // eslint-disable-next-line unicorn/prefer-structured-clone
         obj instanceof Object ? obj : JSON.parse(JSON.stringify(obj))
       return original.query(newObj, pathExpression, count)
     }),

package/src/OntologyManager/index.ts

@@ -87,7 +87,9 @@ export const OntologyRecordType = types
           return
         }
         void self.loadEquivalentTypes('gene')
+        void self.loadEquivalentTypes('pseudogene')
         void self.loadEquivalentTypes('transcript')
+        void self.loadEquivalentTypes('pseudogenic_transcript')
         void self.loadEquivalentTypes('CDS')
         void self.loadEquivalentTypes('mRNA')
         reaction.dispose()

package/src/SixFrameFeatureDisplay/stateModel.ts

@@ -301,7 +301,11 @@ export function stateModelFactory(
           )) {
             for (const [, childFeature] of feature.children ?? new Map()) {
               if (
-                featureTypeOntology.isTypeOf(childFeature.type, 'transcript')
+                featureTypeOntology.isTypeOf(childFeature.type, 'transcript') ||
+                featureTypeOntology.isTypeOf(
+                  feature.type,
+                  'pseudogenic_transcript',
+                )
               ) {
                 for (const [, grandChildFeature] of childFeature.children ||
                   new Map()) {

package/src/TabularEditor/HybridGrid/Feature.tsx

@@ -1,4 +1,3 @@
-/* eslint-disable @typescript-eslint/use-unknown-in-catch-callback-variable */
 /* eslint-disable unicorn/no-nested-ternary */
 /* eslint-disable @typescript-eslint/unbound-method */
 

package/src/TabularEditor/HybridGrid/NumberCell.tsx

@@ -1,5 +1,4 @@
 /* eslint-disable @typescript-eslint/unbound-method */
-/* eslint-disable @typescript-eslint/use-unknown-in-catch-callback-variable */
 import { observer } from 'mobx-react'
 import React, { useEffect, useState } from 'react'
 import { makeStyles } from 'tss-react/mui'
@@ -37,6 +36,14 @@ export const NumberCell = observer(function NumberCell({
   const [blur, setBlur] = useState(false)
   const [inputNode, setInputNode] = useState<HTMLInputElement | null>(null)
   const { classes } = useStyles()
+
+  useEffect(() => {
+    if (initialValue !== value) {
+      setValue(initialValue)
+    }
+    // eslint-disable-next-line react-hooks/exhaustive-deps
+  }, [initialValue])
+
   useEffect(() => {
     if (blur) {
       inputNode?.blur()

package/src/TabularEditor/HybridGrid/ToolBar.tsx

@@ -47,18 +47,20 @@ export const ToolBar = observer(function ToolBar({
         onChange={(event) => {
           model.setFilterText(event.target.value)
         }}
-        InputProps={{
-          endAdornment: (
-            <InputAdornment position="end">
-              <IconButton
-                onClick={() => {
-                  model.clearFilterText()
-                }}
-              >
-                <ClearIcon />
-              </IconButton>
-            </InputAdornment>
-          ),
+        slotProps={{
+          input: {
+            endAdornment: (
+              <InputAdornment position="end">
+                <IconButton
+                  onClick={() => {
+                    model.clearFilterText()
+                  }}
+                >
+                  <ClearIcon />
+                </IconButton>
+              </InputAdornment>
+            ),
+          },
         }}
       />
     </div>

package/src/TabularEditor/HybridGrid/featureContextMenuItems.ts

@@ -7,12 +7,7 @@ import {
 } from '@jbrowse/core/util'
 
 import { ChangeManager } from '../../ChangeManager'
-import {
-  AddChildFeature,
-  CopyFeature,
-  DeleteFeature,
-  ModifyFeatureAttribute,
-} from '../../components'
+import { AddChildFeature, CopyFeature, DeleteFeature } from '../../components'
 import { ApolloSessionModel } from '../../session'
 import { getApolloInternetAccount } from '../../util'
 
@@ -116,33 +111,14 @@ export function featureContextMenuItems(
           )
         },
       },
-      {
-        label: 'Edit attributes',
-        disabled: readOnly,
-        onClick: () => {
-          ;(session as unknown as AbstractSessionModel).queueDialog(
-            (doneCallback) => [
-              ModifyFeatureAttribute,
-              {
-                session,
-                handleClose: () => {
-                  doneCallback()
-                },
-                changeManager,
-                sourceFeature: feature,
-                sourceAssemblyId: currentAssemblyId,
-              },
-            ],
-          )
-        },
-      },
     )
     const { featureTypeOntology } = session.apolloDataStore.ontologyManager
     if (!featureTypeOntology) {
       throw new Error('featureTypeOntology is undefined')
     }
     if (
-      featureTypeOntology.isTypeOf(feature.type, 'transcript') &&
+      (featureTypeOntology.isTypeOf(feature.type, 'transcript') ||
+        featureTypeOntology.isTypeOf(feature.type, 'pseudogenic_transcript')) &&
       isSessionModelWithWidgets(session)
     ) {
       menuItems.push({