Misc

GMOD · Nov 4, 2024 · 3ab8c07 · 3ab8c07
1 parent b71c4a6
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diff --git a/eslint.config.mjs b/eslint.config.mjs
@@ -118,6 +118,7 @@ export default tseslint.config(
       'unicorn/prefer-at': 'off',
       'unicorn/prefer-string-replace-all': 'off',
       'unicorn/no-array-reduce': 'off',
+      'unicorn/prefer-global-this': 'off',
 
       '@typescript-eslint/no-explicit-any': 'off',
       '@typescript-eslint/explicit-module-boundary-types': 'off',
@@ -138,6 +139,7 @@ export default tseslint.config(
       '@typescript-eslint/no-extraneous-class': 'off',
       '@typescript-eslint/unbound-method': 'off',
       '@typescript-eslint/no-dynamic-delete': 'off',
+      '@typescript-eslint/no-deprecated': 'off',
       '@typescript-eslint/no-unused-vars': [
         'warn',
         {

diff --git a/lib/apidocs/MsaView.md b/lib/apidocs/MsaView.md
@@ -59,7 +59,7 @@ width of columns, px
 // type signature
 number
 // code
-colWidth: 16
+colWidth: 14
 ```
 
 #### property: contrastLettering
@@ -89,7 +89,11 @@ autorun
 // type signature
 IOptionalIType<IModelType<{ tree: IMaybe<ISimpleType<string>>; msa: IMaybe<ISimpleType<string>>; treeMetadata: IMaybe<ISimpleType<string>>; }, { ...; }, _NotCustomized, { ...; }>, [...]>
 // code
-data: types.optional(DataModelF(), { tree: '', msa: '' })
+data: types.optional(DataModelF(), {
+          tree: '',
+          msa: '',
+          treeMetadata: '',
+        })
 ```
 
 #### property: drawMsaLetters
@@ -134,9 +138,9 @@ height: types.optional(types.number, 550)
 
 ```js
 // type signature
-true
+false
 // code
-hideGaps: true
+hideGaps: false
 ```
 
 #### property: id
@@ -162,6 +166,15 @@ IMaybe<ISnapshotProcessor<ITypeUnion<ModelCreationType<ExtractCFromProps<{ locat
 msaFilehandle: types.maybe(FileLocation)
 ```
 
+#### property: relativeTo
+
+```js
+// type signature
+IMaybe<ISimpleType<string>>
+// code
+relativeTo: types.maybe(types.string)
+```
+
 #### property: rowHeight
 
 height of each row, px
@@ -170,7 +183,7 @@ height of each row, px
 // type signature
 number
 // code
-rowHeight: 20
+rowHeight: 18
 ```
 
 #### property: scrollX
@@ -437,7 +450,7 @@ number
 
 ```js
 // type
-any[]
+() => any[]
 ```
 
 #### getter: mouseOverRowName
@@ -451,7 +464,7 @@ any
 
 ```js
 // type
-;ClustalMSA | StockholmMSA | FastaMSA
+;ClustalMSA | EmfMSA | StockholmMSA | FastaMSA
 ```
 
 #### getter: msaAreaHeight
@@ -493,20 +506,41 @@ boolean
 number
 ```
 
+#### getter: realAllowedGappyness
+
+```js
+// type
+number
+```
+
 #### getter: root
 
 ```js
 // type
 HierarchyNode<any>
 ```
 
+#### getter: rowMap
+
+```js
+// type
+Map<unknown, unknown>
+```
+
 #### getter: rowNames
 
 ```js
 // type
 string[]
 ```
 
+#### getter: rowNamesSet
+
+```js
+// type
+Map<string, number>
+```
+
 #### getter: rows
 
 ```js
@@ -563,25 +597,25 @@ boolean
 { [k: string]: string; }
 ```
 
-#### getter: tidyInterProAnnotations
+#### getter: tidyFilteredGatheredInterProAnnotations
 
 ```js
 // type
-any[]
+Record<string, unknown[]>
 ```
 
-#### getter: tidyFilteredAnnotations
+#### getter: tidyFilteredInterProAnnotations
 
 ```js
 // type
 any
 ```
 
-#### getter: tidyFilteredGatheredAnnotations
+#### getter: tidyInterProAnnotations
 
 ```js
 // type
-Record<string, unknown[]>
+any[]
 ```
 
 #### getter: tidyInterProAnnotationTypes
@@ -685,17 +719,26 @@ extraViewMenuItems: () => any[]
 
 ```js
 // type signature
-getRowData: (name: string) => { data: any; }
+getRowData: (name: string) => { data: any; treeMetadata: any; }
 ```
 
-#### method: globalCoordToRowSpecificSeqCoord
+#### method: mouseOverCoordToGapRemovedRowCoord
 
-return a row-specific sequence coordinate, skipping gaps, given a global
-coordinate
+return a row-specific sequence coordinate, skipping gaps, given a
+global coordinate
 
 ```js
 // type signature
-globalCoordToRowSpecificSeqCoord: (rowName: string, position: number) => number
+mouseOverCoordToGapRemovedRowCoord: (rowName: string, position: number) => number
+```
+
+#### method: mouseOverCoordToRowLetter
+
+return a row-specific letter, or undefined if gap
+
+```js
+// type signature
+mouseOverCoordToRowLetter: (rowName: string, position: number) => any
 ```
 
 #### method: seqCoordToRowSpecificGlobalCoord
@@ -724,6 +767,13 @@ doScrollX: (deltaX: number) => void
 doScrollY: (deltaY: number) => void
 ```
 
+#### action: drawRelativeTo
+
+```js
+// type signature
+drawRelativeTo: (id: string) => void
+```
+
 #### action: exportSVG
 
 ```js
@@ -788,7 +838,7 @@ setCurrentAlignment: (n: number) => void
 
 ```js
 // type signature
-setData: (data: { msa?: string; tree?: string; }) => void
+setData: (data: { msa?: string; tree?: string; treeMetadata?: string; }) => void
 ```
 
 #### action: setDrawMsaLetters

diff --git a/lib/package.json b/lib/package.json
@@ -48,7 +48,6 @@
     "file-saver": "^2.0.5",
     "pako": "^2.1.0",
     "rbush": "^3.0.1",
-    "react-error-boundary": "^4.0.13",
     "stockholm-js": "^1.0.10",
     "svgcanvas": "^2.5.0"
   }

diff --git a/lib/src/components/Loading.tsx b/lib/src/components/Loading.tsx
@@ -1,7 +1,7 @@
 import React from 'react'
 import { observer } from 'mobx-react'
 import { Button, Typography } from '@mui/material'
-import { ErrorBoundary } from 'react-error-boundary'
+import { ErrorBoundary } from '@jbrowse/core/ui/ErrorBoundary'
 import { ErrorMessage } from '@jbrowse/core/ui'
 
 // locals
@@ -38,7 +38,7 @@ const Loading = observer(function ({ model }: { model: MsaViewModel }) {
   return (
     <div>
       <ErrorBoundary
-        fallbackRender={props => <Reset model={model} error={props.error} />}
+        FallbackComponent={e => <Reset model={model} error={e.error} />}
       >
         {dataInitialized ? (
           isLoading ? (

diff --git a/lib/src/components/dialogs/MetadataDialog.tsx b/lib/src/components/dialogs/MetadataDialog.tsx
@@ -2,10 +2,9 @@ import React from 'react'
 import { DialogContent } from '@mui/material'
 import { observer } from 'mobx-react'
 import { Dialog } from '@jbrowse/core/ui'
-import {
-  Attributes,
-  BaseCard,
-} from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail'
+
+import Attributes from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/Attributes'
+import BaseCard from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard'
 
 // locals
 import type { MsaViewModel } from '../../model'

diff --git a/lib/src/components/dialogs/SettingsDialog.tsx b/lib/src/components/dialogs/SettingsDialog.tsx
@@ -59,50 +59,50 @@ const TreeSettings = observer(function TreeSettings({
       <h1>Tree options</h1>
       <Checkbox2
         checked={showBranchLen}
+        label="Show branch length?"
         onChange={() => {
           model.setShowBranchLen(!showBranchLen)
         }}
-        label="Show branch length?"
       />
 
       <Checkbox2
         checked={drawNodeBubbles}
+        label="Draw clickable bubbles on tree branches?"
         onChange={() => {
           model.setDrawNodeBubbles(!drawNodeBubbles)
         }}
-        label="Draw clickable bubbles on tree branches?"
       />
       <Checkbox2
         checked={drawTree}
+        label="Show tree?"
         onChange={() => {
           model.setDrawTree(!drawTree)
         }}
-        label="Show tree?"
       />
 
       <Checkbox2
         checked={labelsAlignRight}
+        label="Tree labels align right?"
         onChange={() => {
           model.setLabelsAlignRight(!labelsAlignRight)
         }}
-        label="Tree labels align right?"
       />
 
       <Checkbox2
         checked={drawLabels}
+        label="Draw labels"
         onChange={() => {
           model.setDrawLabels(!drawLabels)
         }}
-        label="Draw labels"
       />
       {noTree ? null : (
         <div>
           <Checkbox2
             checked={treeWidthMatchesArea}
+            label="Make tree width fit to tree area?"
             onChange={() => {
               model.setTreeWidthMatchesArea(!treeWidthMatchesArea)
             }}
-            label="Make tree width fit to tree area?"
           />
           {treeWidthMatchesArea ? null : (
             <div className={classes.flex}>
@@ -146,35 +146,37 @@ const MSASettings = observer(function MSASettings({
       <h1>MSA options</h1>
       <Checkbox2
         checked={drawMsaLetters}
+        label="Draw letters"
         onChange={() => {
           model.setDrawMsaLetters(!drawMsaLetters)
         }}
-        label="Draw letters"
       />
       <Checkbox2
         checked={bgColor}
+        label="Color background tiles of MSA?"
         onChange={() => {
           model.setBgColor(!bgColor)
         }}
-        label="Color background tiles of MSA?"
       />
       <Checkbox2
         checked={contrastLettering}
+        label="Use contrast lettering"
         onChange={() => {
           model.setContrastLettering(!contrastLettering)
         }}
-        label="Use contrast lettering"
       />
       <Checkbox2
         checked={hideGaps}
+        label="Enable hiding gappy columns?"
         onChange={() => {
           model.setHideGaps(!hideGaps)
         }}
-        label={`Hide columns that are ${allowedGappyness}% gaps`}
       />
       {hideGaps ? (
         <div className={classes.flex}>
-          <Typography>Allowed gappyness ({100 - allowedGappyness}%)</Typography>
+          <Typography>
+            Hide columns with more than {allowedGappyness}% gaps
+          </Typography>
           <Slider
             className={classes.field}
             min={1}
@@ -240,21 +242,21 @@ const SettingsDialog = observer(function ({
   return (
     <Dialog
       open
+      title="Settings"
+      maxWidth="xl"
       onClose={() => {
         onClose()
       }}
-      title="Settings"
-      maxWidth="xl"
     >
       <DialogContent className={classes.minw}>
         <SettingsContent model={model} />
         <DialogActions>
           <Button
+            variant="contained"
+            color="primary"
             onClick={() => {
               onClose()
             }}
-            variant="contained"
-            color="primary"
           >
             Submit
           </Button>