Misc

Misc

Refactor base feature widget

M2

Worked

Misc

Allow changing default resolution and normalization in hic

packages/app-core/src/ui/App/ViewMenu.tsx

@@ -69,13 +69,17 @@ const ViewMenu = observer(function ({
                   label: 'View order',
                   type: 'subMenu' as const,
                   subMenu: [
-                    {
-                      label: 'Move view to top',
-                      icon: KeyboardDoubleArrowUpIcon,
-                      onClick: () => {
-                        session.moveViewToTop(model.id)
-                      },
-                    },
+                    ...(session.views.length > 2
+                      ? [
+                          {
+                            label: 'Move view to top',
+                            icon: KeyboardDoubleArrowUpIcon,
+                            onClick: () => {
+                              session.moveViewToTop(model.id)
+                            },
+                          },
+                        ]
+                      : []),
                     {
                       label: 'Move view up',
                       icon: KeyboardArrowUpIcon,
@@ -90,13 +94,17 @@ const ViewMenu = observer(function ({
                         session.moveViewDown(model.id)
                       },
                     },
-                    {
-                      label: 'Move view to bottom',
-                      icon: KeyboardDoubleArrowDownIcon,
-                      onClick: () => {
-                        session.moveViewToBottom(model.id)
-                      },
-                    },
+                    ...(session.views.length > 2
+                      ? [
+                          {
+                            label: 'Move view to bottom',
+                            icon: KeyboardDoubleArrowDownIcon,
+                            onClick: () => {
+                              session.moveViewToBottom(model.id)
+                            },
+                          },
+                        ]
+                      : []),
                   ],
                 },
               ]

packages/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard.tsx

@@ -0,0 +1,41 @@
+import React from 'react'
+import {
+  Accordion,
+  AccordionDetails,
+  AccordionSummary,
+  Typography,
+} from '@mui/material'
+import { makeStyles } from 'tss-react/mui'
+
+// icons
+import ExpandMore from '@mui/icons-material/ExpandMore'
+
+import { BaseCardProps } from '../types'
+
+const useStyles = makeStyles()(theme => ({
+  expansionPanelDetails: {
+    display: 'block',
+    padding: theme.spacing(1),
+  },
+  icon: {
+    color: theme.palette.tertiary.contrastText || '#fff',
+  },
+}))
+
+export default function BaseCard({
+  children,
+  title,
+  defaultExpanded = true,
+}: BaseCardProps) {
+  const { classes } = useStyles()
+  return (
+    <Accordion defaultExpanded={defaultExpanded}>
+      <AccordionSummary expandIcon={<ExpandMore className={classes.icon} />}>
+        <Typography variant="button">{title}</Typography>
+      </AccordionSummary>
+      <AccordionDetails className={classes.expansionPanelDetails}>
+        {children}
+      </AccordionDetails>
+    </Accordion>
+  )
+}

packages/core/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.tsx

@@ -0,0 +1,53 @@
+import React from 'react'
+// locals
+import { toLocale, SimpleFeatureSerialized } from '../../util'
+import { BaseProps } from '../types'
+import SimpleField from './SimpleField'
+import Position from './Position'
+
+export default function CoreDetails(props: BaseProps) {
+  const { feature } = props
+  const obj = feature as SimpleFeatureSerialized & {
+    start: number
+    end: number
+    assemblyName?: string
+    strand: number
+    refName: string
+    __jbrowsefmt: {
+      start?: number
+      assemblyName?: string
+      end?: number
+      refName?: string
+      name?: string
+    }
+  }
+
+  const formattedFeat = { ...obj, ...obj.__jbrowsefmt }
+  const { start, end } = formattedFeat
+
+  const displayedDetails: Record<string, any> = {
+    ...formattedFeat,
+    length: toLocale(end - start),
+  }
+
+  const coreRenderedDetails = {
+    description: 'Description',
+    name: 'Name',
+    length: 'Length',
+    type: 'Type',
+  }
+  return (
+    <>
+      <SimpleField
+        name="Position"
+        value={<Position {...props} feature={formattedFeat} />}
+      />
+      {Object.entries(coreRenderedDetails)
+        .map(([key, name]) => [name, displayedDetails[key]])
+        .filter(([, value]) => value != null)
+        .map(([name, value]) => (
+          <SimpleField key={name} name={name} value={value} />
+        ))}
+    </>
+  )
+}

packages/core/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.tsx

@@ -0,0 +1,111 @@
+import React from 'react'
+import { ErrorBoundary } from '@jbrowse/core/ui/ErrorBoundary'
+import { Divider, Typography } from '@mui/material'
+import { IAnyStateTreeNode } from 'mobx-state-tree'
+
+// locals
+import { getEnv, getSession, SimpleFeatureSerialized } from '../../util'
+import { ErrorMessage } from '../../ui'
+import { generateTitle } from './util'
+import SequenceFeatureDetails from '../SequenceFeatureDetails'
+import Attributes from './Attributes'
+import BaseCard from './BaseCard'
+import CoreDetails from './CoreDetails'
+
+// coreDetails are omitted in some circumstances
+const coreDetails = [
+  'name',
+  'start',
+  'end',
+  'strand',
+  'refName',
+  'description',
+  'type',
+]
+
+interface PanelDescriptor {
+  name: string
+  Component: React.FC<any>
+}
+
+export default function FeatureDetails(props: {
+  model: IAnyStateTreeNode
+  feature: SimpleFeatureSerialized
+  depth?: number
+  omit?: string[]
+  descriptions?: Record<string, React.ReactNode>
+  formatter?: (val: unknown, key: string) => React.ReactNode
+}) {
+  const { omit = [], model, feature, depth = 0 } = props
+  const { maxDepth } = model
+  const { mate, name = '', id = '', type = '', subfeatures, uniqueId } = feature
+  const pm = getEnv(model).pluginManager
+  const session = getSession(model)
+
+  const ExtraPanel = pm.evaluateExtensionPoint('Core-extraFeaturePanel', null, {
+    session,
+    feature,
+    model,
+  }) as PanelDescriptor | undefined
+  const m = mate as { start: number; end: number; refName: string } | undefined
+  return (
+    <BaseCard title={generateTitle(name, id, type)}>
+      <Typography>Core details</Typography>
+      <CoreDetails {...props} />
+      {m ? (
+        <>
+          <Divider />
+          <Typography>Mate details</Typography>
+          <CoreDetails
+            {...props}
+            feature={{
+              ...m,
+              start: m.start,
+              end: m.end,
+              refName: m.refName,
+              uniqueId: `${uniqueId}-mate`,
+            }}
+          />
+        </>
+      ) : null}
+
+      <Divider />
+      <Typography>Attributes</Typography>
+      <Attributes
+        attributes={feature}
+        {...props}
+        omit={omit}
+        omitSingleLevel={coreDetails}
+      />
+
+      <ErrorBoundary FallbackComponent={e => <ErrorMessage error={e.error} />}>
+        <SequenceFeatureDetails {...props} />
+      </ErrorBoundary>
+
+      {ExtraPanel ? (
+        <>
+          <Divider />
+          <BaseCard title={ExtraPanel.name}>
+            <ExtraPanel.Component {...props} />
+          </BaseCard>
+        </>
+      ) : null}
+
+      {depth < maxDepth && subfeatures?.length ? (
+        <BaseCard title="Subfeatures" defaultExpanded={depth < 1}>
+          {subfeatures.map((sub, idx) => (
+            <FeatureDetails
+              key={JSON.stringify(sub)}
+              feature={{
+                ...sub,
+                uniqueId: `${uniqueId}_${idx}`,
+              }}
+              model={model}
+              depth={depth + 1}
+            />
+          ))}
+        </BaseCard>
+      ) : null}
+    </BaseCard>
+  )
+}

packages/core/BaseFeatureWidget/BaseFeatureDetail/Position.tsx

@@ -0,0 +1,16 @@
+import React from 'react'
+import { assembleLocString } from '../../util'
+import { BaseProps } from '../types'
+
+export default function Position(props: BaseProps) {
+  const { feature } = props
+  const strand = feature.strand as number
+  const strandMap: Record<string, string> = {
+    '-1': '-',
+    '0': '',
+    '1': '+',
+  }
+  const str = strandMap[strand] ? `(${strandMap[strand]})` : ''
+  const loc = assembleLocString(feature)
+  return <>{`${loc} ${str}`}</>
+}