@apollo-annotation/jbrowse-plugin-apollo 0.3.12 → 1.0.0

package/src/LinearApolloDisplay/components/CheckResultWarnings.tsx

@@ -52,11 +52,7 @@ export const CheckResultWarnings = observer(function CheckResultWarnings({
       if (!feature) {
         return null
       }
-      let row = 0
-      const featureLayout = display.getFeatureLayoutPosition(feature)
-      if (featureLayout) {
-        row = featureLayout.layoutRow + featureLayout.featureRow
-      }
+      const row = display.getRowForFeature(feature) ?? 0
       const top = row * apolloRowHeight
       const height = apolloRowHeight
       return (

package/src/LinearApolloDisplay/components/LinearApolloDisplay.tsx

@@ -14,6 +14,7 @@ import { type Coord, useStyles } from '../../util/displayUtils'
 import type { LinearApolloDisplay as LinearApolloDisplayI } from '../stateModel'
 
 import { CheckResultWarnings } from './CheckResultWarnings'
+import { OverlayCanvas } from './OverlayCanvas'
 
 interface LinearApolloDisplayProps {
   model: LinearApolloDisplayI
@@ -29,18 +30,12 @@ export const LinearApolloDisplay = observer(function LinearApolloDisplay(
   const {
     loading,
     contextMenuItems: getContextMenuItems,
-    cursor,
-    featuresHeight,
+    featuresHeight: getFeaturesHeight,
     isShown,
-    onMouseDown,
-    onMouseLeave,
-    onMouseMove,
-    onMouseUp,
     regionCannotBeRendered,
     session,
     setCanvas,
     setCollaboratorCanvas,
-    setOverlayCanvas,
     setTheme,
   } = model
   const { classes } = useStyles()
@@ -55,115 +50,100 @@ export const LinearApolloDisplay = observer(function LinearApolloDisplay(
   if (!isShown) {
     return null
   }
+  const featuresHeight = getFeaturesHeight(lgv.assemblyNames[0])
   return (
-    <>
-      <div
-        className={classes.canvasContainer}
-        style={{
-          width: lgv.dynamicBlocks.totalWidthPx,
-          height: featuresHeight,
-        }}
-        onContextMenu={(event) => {
-          event.preventDefault()
-          if (contextMenuItems.length > 0) {
-            // There's already a context menu open, so close it
-            setContextMenuItems([])
-          } else {
-            const coord: [number, number] = [event.clientX, event.clientY]
-            setContextCoord(coord)
-            setContextMenuItems(getContextMenuItems(event))
-          }
-        }}
-      >
-        {session.isLocked ? (
-          <div className={classes.locked} data-testid="lock-icon">
-            <LockIcon />
-          </div>
-        ) : null}
-        {loading ? (
-          <div className={classes.loading}>
-            <CircularProgress size="18px" />
-          </div>
-        ) : null}
-        {/* This type is wrong in @jbrowse/core */}
-        {/* eslint-disable-next-line @typescript-eslint/no-unnecessary-condition */}
-        {message ? (
-          <Alert
-            severity="warning"
-            classes={{ message: classes.ellipses }}
-            slotProps={{ root: { className: classes.center } }}
-          >
-            <Tooltip title={message}>
-              <div>{message}</div>
-            </Tooltip>
-          </Alert>
-        ) : (
-          // Promise.resolve() in these 3 callbacks is to avoid infinite rendering loop
-          // https://github.com/mobxjs/mobx/issues/3728#issuecomment-1715400931
-          <>
-            <canvas
-              ref={async (node: HTMLCanvasElement) => {
-                await Promise.resolve()
-                setCollaboratorCanvas(node)
-              }}
-              width={lgv.dynamicBlocks.totalWidthPx}
-              height={featuresHeight}
-              className={classes.canvas}
-              data-testid="collaboratorCanvas"
-            />
-            <canvas
-              ref={async (node: HTMLCanvasElement) => {
-                await Promise.resolve()
-                setCanvas(node)
-              }}
-              width={lgv.dynamicBlocks.totalWidthPx}
-              height={featuresHeight}
-              className={classes.canvas}
-              data-testid="canvas"
-            />
-            <canvas
-              ref={async (node: HTMLCanvasElement) => {
-                await Promise.resolve()
-                setOverlayCanvas(node)
-              }}
-              width={lgv.dynamicBlocks.totalWidthPx}
-              height={featuresHeight}
-              onMouseMove={onMouseMove}
-              onMouseLeave={onMouseLeave}
-              onMouseDown={onMouseDown}
-              onMouseUp={onMouseUp}
-              className={classes.canvas}
-              style={{ cursor: cursor ?? 'default' }}
-              data-testid="overlayCanvas"
-            />
-            <CheckResultWarnings display={model} />
-            <Menu
-              open={contextMenuItems.length > 0}
-              onMenuItemClick={(_, callback) => {
-                callback()
-                setContextMenuItems([])
-              }}
-              onClose={() => {
-                setContextMenuItems([])
-              }}
-              slotProps={{
-                transition: {
-                  onExit: () => {
-                    setContextMenuItems([])
-                  },
+    <div
+      className={classes.canvasContainer}
+      style={{
+        width: lgv.dynamicBlocks.totalWidthPx,
+        height: featuresHeight,
+      }}
+      onContextMenu={(event) => {
+        event.preventDefault()
+        if (contextMenuItems.length > 0) {
+          // There's already a context menu open, so close it
+          setContextMenuItems([])
+        } else {
+          const coord: [number, number] = [event.clientX, event.clientY]
+          setContextCoord(coord)
+          setContextMenuItems(getContextMenuItems(event))
+        }
+      }}
+    >
+      {session.isLocked ? (
+        <div className={classes.locked} data-testid="lock-icon">
+          <LockIcon />
+        </div>
+      ) : null}
+      {loading ? (
+        <div className={classes.loading}>
+          <CircularProgress size="18px" />
+        </div>
+      ) : null}
+      {/* This type is wrong in @jbrowse/core */}
+      {/* eslint-disable-next-line @typescript-eslint/no-unnecessary-condition */}
+      {message ? (
+        <Alert
+          severity="warning"
+          classes={{ message: classes.ellipses }}
+          slotProps={{ root: { className: classes.center } }}
+        >
+          <Tooltip title={message}>
+            <div>{message}</div>
+          </Tooltip>
+        </Alert>
+      ) : (
+        // Promise.resolve() in these 2 callbacks is to avoid infinite rendering loop
+        // https://github.com/mobxjs/mobx/issues/3728#issuecomment-1715400931
+        <>
+          <canvas
+            ref={async (node: HTMLCanvasElement) => {
+              await Promise.resolve()
+              setCollaboratorCanvas(node)
+            }}
+            width={lgv.dynamicBlocks.totalWidthPx}
+            height={featuresHeight}
+            className={classes.canvas}
+            data-testid="collaboratorCanvas"
+          />
+          <canvas
+            ref={async (node: HTMLCanvasElement) => {
+              await Promise.resolve()
+              setCanvas(node)
+            }}
+            width={lgv.dynamicBlocks.totalWidthPx}
+            height={featuresHeight}
+            className={classes.canvas}
+            data-testid="canvas"
+          />
+          <OverlayCanvas model={model} />
+          <CheckResultWarnings display={model} />
+          <Menu
+            open={contextMenuItems.length > 0}
+            onMenuItemClick={(_, callback) => {
+              callback()
+              setContextMenuItems([])
+            }}
+            onClose={() => {
+              setContextMenuItems([])
+            }}
+            slotProps={{
+              transition: {
+                onExit: () => {
+                  setContextMenuItems([])
                 },
-              }}
-              anchorReference="anchorPosition"
-              anchorPosition={
-                contextCoord
-                  ? { top: contextCoord[1], left: contextCoord[0] }
-                  : undefined
-              }
-              menuItems={contextMenuItems}
-            />
-          </>
-        )}
-      </div>
-    </>
+              },
+            }}
+            anchorReference="anchorPosition"
+            anchorPosition={
+              contextCoord
+                ? { top: contextCoord[1], left: contextCoord[0] }
+                : undefined
+            }
+            menuItems={contextMenuItems}
+          />
+        </>
+      )}
+    </div>
   )
 })

package/src/LinearApolloDisplay/components/OverlayCanvas.tsx

@@ -0,0 +1,76 @@
+/* eslint-disable @typescript-eslint/unbound-method */
+
+/* eslint-disable @typescript-eslint/no-misused-promises */
+
+import { getContainingView } from '@jbrowse/core/util'
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
+import { observer } from 'mobx-react'
+import React, { useState } from 'react'
+
+import { type Coord, useStyles } from '../../util/displayUtils'
+import type { LinearApolloDisplay as LinearApolloDisplayI } from '../stateModel'
+
+import { Tooltip as LinearApolloDisplayTooltip } from './Tooltip'
+
+interface LinearApolloDisplayProps {
+  model: LinearApolloDisplayI
+}
+
+export const OverlayCanvas = observer(function OverlayCanvas(
+  props: LinearApolloDisplayProps,
+) {
+  const { model } = props
+  const {
+    apolloDragging,
+    cursor,
+    featuresHeight: getFeaturesHeight,
+    isShown,
+    onMouseDown,
+    onMouseLeave,
+    onMouseMove,
+    onMouseUp,
+    session,
+    setOverlayCanvas,
+  } = model
+  const { classes } = useStyles()
+  const lgv = getContainingView(model) as unknown as LinearGenomeViewModel
+
+  const [mouseCoord, setMouseCoord] = useState<Coord>()
+  if (!isShown) {
+    return null
+  }
+  const featuresHeight = getFeaturesHeight(lgv.assemblyNames[0])
+  // Promise.resolve() in this callback is to avoid infinite rendering loop
+  // https://github.com/mobxjs/mobx/issues/3728#issuecomment-1715400931
+  return (
+    <>
+      <canvas
+        ref={async (node: HTMLCanvasElement) => {
+          await Promise.resolve()
+          setOverlayCanvas(node)
+        }}
+        width={lgv.dynamicBlocks.totalWidthPx}
+        height={featuresHeight}
+        onMouseMove={(...args) => {
+          const [event] = args
+          setMouseCoord([event.clientX, event.clientY])
+          onMouseMove(...args)
+        }}
+        onMouseLeave={(...args) => {
+          setMouseCoord(undefined)
+          onMouseLeave(...args)
+        }}
+        onMouseDown={onMouseDown}
+        onMouseUp={onMouseUp}
+        className={classes.canvas}
+        style={{ cursor: cursor ?? 'default' }}
+        data-testid="overlayCanvas"
+      />
+      <LinearApolloDisplayTooltip
+        mouseCooordinate={mouseCoord}
+        session={session}
+        dragging={Boolean(apolloDragging)}
+      />
+    </>
+  )
+})

package/src/LinearApolloDisplay/components/Tooltip.tsx

@@ -0,0 +1,42 @@
+import { BaseTooltip } from '@jbrowse/core/ui'
+import { observer } from 'mobx-react'
+import React from 'react'
+
+import type { ApolloSessionModel } from '../../session'
+import type { Coord } from '../../util/displayUtils'
+
+interface LinearApolloDisplayProps {
+  mouseCooordinate: Coord | undefined
+  session: ApolloSessionModel
+  dragging: boolean
+}
+
+export const Tooltip = observer(function Tooltip(
+  props: LinearApolloDisplayProps,
+) {
+  const { mouseCooordinate, session, dragging } = props
+  const { apolloHoveredFeature } = session
+
+  if (!(mouseCooordinate && apolloHoveredFeature) || dragging) {
+    return
+  }
+  const [x, y] = mouseCooordinate
+  const { feature } = apolloHoveredFeature
+  const { attributes, min, max } = feature
+  const location = `Loc: ${min + 1}..${max}`
+  const featureType = `Type: ${feature.type}`
+  const featureName = attributes.get('gff_name')?.find((name) => name !== '')
+  return (
+    <BaseTooltip clientPoint={{ x, y }} placement="top-start">
+      {featureType}
+      <br />
+      {featureName ? (
+        <>
+          {featureName}
+          <br />
+        </>
+      ) : null}
+      {location}
+    </BaseTooltip>
+  )
+})